match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd09740	84	83	99.9	2.1E-22	[                                      -----------]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
2	pfam09620	80	78	99.9	5.1E-22	[                                       ----------]	Cas_csx3	CRISPR-associated protein (Cas_csx3). This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
3	cd09681	83	81	98.3	3.9E-07	[                                      -----------]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
4	TIGR02579	83	81	98.3	3.9E-07	[                                      -----------]	cas_csx3	CRISPR-associated protein, Csx3 family. Members of this family are found encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
5	pfam13238	128	98	97.7	0.00011	[---------------                                  ]	AAA_18	AAA domain.
6	pfam13207	114	22	97.4	9.7E-05	[---                                              ]	AAA_17	AAA domain.
7	pfam13191	156	40	97.4	0.0011	[-----                                            ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
8	cd00009	151	37	97.1	0.00066	[-----                                            ]	AAA	The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
9	pfam13671	143	20	97.1	0.0023	[---                                              ]	AAA_33	AAA domain. This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.
10	pfam12846	298	42	97.0	0.00055	[------                                           ]	AAA_10	AAA-like domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
11	pfam13401	124	104	96.9	0.0031	[-----------------                                ]	AAA_22	AAA domain.
12	cd02028	179	32	96.8	0.0011	[----                                             ]	UMPK_like	Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
13	PRK09270	229	28	96.7	0.0011	[----                                             ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
14	cd09681	83	50	96.5	0.001	[                            -------              ]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
15	TIGR02579	83	50	96.5	0.001	[                            -------              ]	cas_csx3	CRISPR-associated protein, Csx3 family. Members of this family are found encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
16	pfam06414	194	107	96.4	0.011	[---------------                                  ]	Zeta_toxin	Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.
17	pfam00004	131	38	96.4	0.0065	[------                                           ]	AAA	ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
18	PRK00091	307	146	96.4	0.0066	[----------------------                           ]	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
19	cd02019	69	32	96.3	0.0027	[----                                             ]	NK	Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
20	cd09740	84	32	96.2	0.0039	[                              -----              ]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
21	PRK04182	180	28	96.2	0.0028	[----                                             ]	PRK04182	cytidylate kinase; Provisional
22	pfam13476	203	24	96.1	0.0043	[---                                              ]	AAA_23	AAA domain.
23	pfam01583	157	145	96.1	0.0057	[--------------------------                       ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
24	COG0645	170	144	96.0	0.04	[------------------------                         ]	COG0645	Predicted kinase
25	TIGR02173	171	23	96.0	0.0043	[---                                              ]	cyt_kin_arch	cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.
26	COG0529	197	144	96.0	0.0068	[--------------------------                       ]	CysC	Adenylylsulfate kinase or related kinase
27	pfam03205	138	54	95.9	0.016	[-------                                          ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
28	TIGR00455	184	34	95.8	0.0095	[-----                                            ]	apsK	adenylyl-sulfate kinase. This protein, adenylylsulfate kinase, is often found as a fusion protein with sulfate adenylyltransferase. Important residue (active site in E.coli) is residue 100 of the seed alignment.
29	PRK06761	282	70	95.7	0.027	[---------                                        ]	PRK06761	hypothetical protein; Provisional
30	cd02020	147	22	95.7	0.007	[---                                              ]	CMPK	Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
31	COG0563	178	85	95.6	0.0085	[-------------                                    ]	Adk	Adenylate kinase or related kinase
32	pfam13481	192	23	95.6	0.067	[---                                              ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
33	pfam13245	72	26	95.5	0.017	[---                                              ]	AAA_19	Part of AAA domain.
34	PRK13768	253	89	95.4	0.018	[-------------                                    ]	PRK13768	GTPase; Provisional
35	COG0378	202	76	95.4	0.012	[-----------                                      ]	HypB	Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase
36	cd02027	149	128	95.4	0.016	[-----------------------                          ]	APSK	Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.
37	pfam00005	150	79	95.3	0.023	[----------                                       ]	ABC_tran	ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains.
38	pfam13173	127	33	95.2	0.022	[----                                             ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
39	pfam09620	80	34	95.2	0.017	[                              -----              ]	Cas_csx3	CRISPR-associated protein (Cas_csx3). This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
40	COG0324	308	118	95.2	0.058	[------------------                               ]	MiaA	tRNA A37 N6-isopentenylltransferase MiaA
41	pfam13555	60	25	95.1	0.012	[---                                              ]	AAA_29	P-loop containing region of AAA domain.
42	pfam03266	168	28	95.1	0.017	[----                                             ]	NTPase_1	NTPase. This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue.
43	cd00267	157	23	95.0	0.013	[---                                              ]	ABC_ATPase	ATP-binding cassette transporter nucleotide-binding domain. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
44	PRK13548	258	128	95.0	0.0073	[-----------------                                ]	hmuV	hemin importer ATP-binding subunit; Provisional
45	cd03114	148	35	95.0	0.021	[ ----                                            ]	ArgK-like	The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
46	cd00046	144	113	94.9	0.25	[-------------------                              ]	DEXDc	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
47	pfam00910	105	25	94.9	0.032	[----                                             ]	RNA_helicase	RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.
48	COG1428	216	29	94.9	0.02	[---                                              ]	Dck	Deoxyadenosine/deoxycytidine kinase
49	COG1102	179	27	94.9	0.019	[----                                             ]	CmkB	Cytidylate kinase
50	COG1136	226	25	94.9	0.015	[---                                              ]	LolD	ABC-type lipoprotein export system, ATPase component
51	cd03225	211	24	94.8	0.015	[---                                              ]	ABC_cobalt_CbiO_domain1	First domain of the ATP-binding cassette component of cobalt transport system. Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
52	COG1120	258	25	94.7	0.011	[----                                             ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
53	cd01672	200	34	94.6	0.035	[-----                                            ]	TMPK	Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
54	cd03214	180	106	94.6	0.012	[-----------------                                ]	ABC_Iron-Siderophores_B12_Hemin	ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins. ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
55	cd03228	171	24	94.5	0.02	[---                                              ]	ABCC_MRP_Like	ATP-binding cassette domain of multidrug resistance protein-like transporters. The MRP (Multidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
56	pfam00437	273	77	94.5	0.025	[------------                                     ]	T2SE	Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection.
57	COG1122	235	27	94.5	0.018	[----                                             ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
58	pfam02492	178	22	94.5	0.018	[---                                              ]	cobW	CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.
59	COG4088	261	32	94.3	0.038	[----                                             ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
60	cd04164	159	25	94.3	0.018	[---                                              ]	trmE	trmE is a tRNA modification GTPase. TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
61	COG0470	325	60	94.3	0.087	[--------                                         ]	HolB	DNA polymerase III, delta prime subunit
62	PRK06547	172	24	94.2	0.029	[---                                              ]	PRK06547	hypothetical protein; Provisional
63	COG0467	260	51	94.1	0.024	[--------                                         ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
64	cd03255	218	25	94.1	0.027	[---                                              ]	ABC_MJ0796_LolCDE_FtsE	ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.
65	pfam13304	144	25	94.1	0.038	[ ---                                             ]	AAA_21	AAA domain.
66	COG4559	259	89	94.0	0.02	[--------------                                   ]	COG4559	ABC-type hemin transport system, ATPase component
67	COG1703	323	38	94.0	0.058	[-----                                            ]	ArgK	Putative periplasmic protein kinase ArgK or related GTPase of G3E family
68	COG0283	222	29	94.0	0.044	[---                                              ]	Cmk	Cytidylate kinase
69	pfam03029	235	36	93.9	0.046	[ ----                                            ]	ATP_bind_1	Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.
70	COG0572	218	26	93.8	0.044	[----                                             ]	Udk	Uridine kinase
71	COG0593	408	138	93.8	0.44	[---------------------                            ]	DnaA	Chromosomal replication initiation ATPase DnaA
72	cd01983	99	33	93.7	0.19	[-----                                            ]	Fer4_NifH	The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
73	pfam01695	178	75	93.7	0.38	[------------                                     ]	IstB_IS21	IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
74	PRK11823	446	24	93.6	0.11	[---                                              ]	PRK11823	DNA repair protein RadA; Provisional
75	COG1618	179	27	93.5	0.058	[----                                             ]	THEP1	Nucleoside-triphosphatase THEP1
76	cd01428	194	101	93.3	0.064	[---------------                                  ]	ADK	Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
77	pfam13521	162	20	93.3	0.053	[---                                              ]	AAA_28	AAA domain.
78	cd01673	193	60	93.2	0.066	[---------                                        ]	dNK	Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
79	TIGR04352	280	26	93.1	0.053	[----                                             ]	HprK_rel_A	HprK-related kinase A. A number of protein families resemble HPr kinase (see TIGR00679) but do not belong to that system. They include this family, which appears instead to be the marker for a different type of gene neighborhood, in which one of the conserved neighboring proteins resembles (but is distinct from) PqqD.
80	cd00071	137	21	93.1	0.06	[---                                              ]	GMPK	Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
81	TIGR00174	287	143	93.0	0.12	[----------------------                           ]	miaA	tRNA dimethylallyltransferase. Alternate names include delta(2)-isopentenylpyrophosphate transferase, IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA modification enzyme. Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine. Understanding of substrate specificity has changed.
82	COG1066	456	106	93.0	0.3	[-----------------                                ]	Sms	Predicted ATP-dependent serine protease
83	cd03116	159	30	93.0	0.077	[----                                             ]	MobB	Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
84	PRK08118	167	47	93.0	0.066	[-------                                          ]	PRK08118	topology modulation protein; Reviewed
85	cd03277	213	37	92.9	0.034	[ ----                                            ]	ABC_SMC5_euk	ATP-binding cassette domain of eukaryotic SMC5 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
86	cd02021	150	101	92.9	0.11	[--------------                                   ]	GntK	Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
87	cd04105	202	105	92.9	0.059	[-------------------                              ]	SR_beta	Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP). Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer.
88	COG4240	300	76	92.9	0.3	[-----------                                      ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
89	COG1132	567	85	92.8	0.065	[-------------                                    ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
90	COG0396	251	45	92.8	0.053	[-------                                          ]	SufC	Fe-S cluster assembly ATPase SufC
91	PRK13539	207	26	92.8	0.064	[---                                              ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
92	pfam03308	267	37	92.6	0.12	[-----                                            ]	ArgK	ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
93	COG0125	208	37	92.5	0.17	[-----                                            ]	Tmk	Thymidylate kinase
94	COG0419	908	24	92.5	0.082	[---                                              ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
95	cd02024	187	120	92.5	0.051	[----------------                                 ]	NRK1	Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
96	pfam01926	114	20	92.5	0.077	[---                                              ]	MMR_HSR1	50S ribosome-binding GTPase. The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.
97	COG2884	223	29	92.5	0.069	[----                                             ]	FtsE	ABC-type ATPase involved in cell division
98	PRK00023	225	29	92.4	0.11	[---                                              ]	cmk	cytidylate kinase; Provisional
99	cd03262	213	20	92.2	0.077	[---                                              ]	ABC_HisP_GlnQ	ATP-binding cassette domain of the histidine and glutamine transporters. HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, respectively. Histidine permease is a multi-subunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryotic extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQMP system of S. typhimurium, where HisJ is the extracellular solute binding proteins and HisP is the ABC protein.
100	pfam08433	267	77	92.2	0.15	[-----------                                      ]	KTI12	Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity.
101	PRK13764	602	27	92.2	0.1	[----                                             ]	PRK13764	ATPase; Provisional
102	PRK13695	174	26	92.2	0.11	[----                                             ]	PRK13695	putative NTPase; Provisional
103	pfam13604	195	123	92.2	2.7	[------------------                               ]	AAA_30	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
104	cd03253	236	23	92.2	0.088	[---                                              ]	ABCC_ATM1_transporter	ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C. ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
105	COG1126	240	21	92.1	0.085	[---                                              ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
106	cd03217	200	46	92.0	0.084	[-------                                          ]	ABC_FeS_Assembly	ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multi-protein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.
107	TIGR00017	217	25	91.9	0.11	[---                                              ]	cmk	cytidylate kinase. This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.
108	COG2256	436	27	91.9	0.21	[---                                              ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
109	COG1119	257	57	91.9	0.14	[---------                                        ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
110	COG4604	252	121	91.7	0.13	[ ----------------                                ]	CeuD	ABC-type enterochelin transport system, ATPase component
111	TIGR03574	249	34	91.7	0.18	[-----                                            ]	selen_PSTK	L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
112	COG2804	500	77	91.7	0.11	[------------                                     ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
113	cd03219	236	24	91.6	0.057	[ ---                                             ]	ABC_Mj1267_LivG_branched	ATP-binding cassette component of branched chain amino acids transport system. The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).
114	COG1084	346	87	91.6	0.085	[-------------                                    ]	Nog1	GTP-binding protein, GTP1/Obg family
115	cd03231	201	24	91.6	0.11	[---                                              ]	ABC_CcmA_heme_exporter	Cytochrome c biogenesis ATP-binding export protein. CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperon that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.
116	COG1131	293	79	91.6	0.29	[-----------                                      ]	CcmA	ABC-type multidrug transport system, ATPase component
117	pfam09439	181	24	91.5	0.1	[---                                              ]	SRPRB	Signal recognition particle receptor beta subunit. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.
118	TIGR01978	243	47	91.5	0.097	[-------                                          ]	sufC	FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic () or associated with the membrane (). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.
119	cd01120	165	23	91.5	0.63	[---                                              ]	RecA-like_NTPases	RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
120	cd03261	235	53	91.4	0.15	[--------                                         ]	ABC_Org_Solvent_Resistant	ATP-binding cassette transport system involved in resistant to organic solvents. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
121	cd01129	264	78	91.3	0.16	[------------                                     ]	PulE-GspE	PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
122	PRK13477	512	28	91.2	0.16	[---                                              ]	PRK13477	bifunctional pantoate ligase/cytidylate kinase; Provisional
123	PRK07667	193	110	91.2	0.24	[----------------                                 ]	PRK07667	uridine kinase; Provisional
124	PRK03846	198	32	91.2	0.31	[ ----                                            ]	PRK03846	adenylylsulfate kinase; Provisional
125	COG1855	604	28	91.2	0.16	[----                                             ]	COG1855	Predicted ATPase, PilT family
126	TIGR03873	256	20	91.1	0.072	[ --                                              ]	F420-0_ABC_ATP	proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
127	COG4133	209	30	91.0	0.14	[----                                             ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
128	cd03279	213	24	90.9	0.18	[---                                              ]	ABC_sbcCD	ATP-binding cassette domain of sbcCD. SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.
129	PRK04195	482	211	90.9	0.15	[------------------------------                   ]	PRK04195	replication factor C large subunit; Provisional
130	COG1797	451	237	90.8	0.2	[-----------------------------------              ]	CobB	Cobyrinic acid a,c-diamide synthase
131	TIGR01846	694	21	90.8	0.13	[---                                              ]	type_I_sec_HlyB	type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
132	pfam00270	167	57	90.7	1.4	[          --------                               ]	DEAD	DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
133	COG1072	283	28	90.4	0.2	[----                                             ]	CoaA	Panthothenate kinase
134	pfam13086	183	39	90.4	0.76	[-----                                            ]	AAA_11	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
135	cd03254	229	76	90.3	0.16	[-------------                                    ]	ABCC_Glucan_exporter_like	ATP-binding cassette domain of glucan transporter and related proteins, subfamily C. Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virulence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
136	pfam01580	201	30	90.2	0.36	[----                                             ]	FtsK_SpoIIIE	FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from Escherichia coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
137	pfam07728	135	28	90.2	0.21	[----                                             ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
138	COG3840	231	23	90.2	0.16	[---                                              ]	ThiQ	ABC-type thiamine transport system, ATPase component
139	COG1121	254	24	90.1	0.16	[---                                              ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
140	TIGR01189	198	27	90.1	0.18	[---                                              ]	ccmA	heme ABC exporter, ATP-binding protein CcmA. This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.
141	cd03213	194	29	90.1	0.17	[----                                             ]	ABCG_EPDR	Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette superfamily. ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
142	PRK01077	451	237	90.0	0.27	[-----------------------------------              ]	PRK01077	cobyrinic acid a,c-diamide synthase; Validated
143	cd03235	213	23	89.8	0.19	[---                                              ]	ABC_Metallic_Cations	ATP-binding cassette domain of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.
144	cd01121	372	102	89.7	0.5	[-----------------                                ]	Sms	Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
145	cd03230	173	77	89.7	0.59	[ -----------                                     ]	ABC_DR_subfamily_A	ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A. This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
146	COG1224	450	24	89.7	0.23	[---                                              ]	TIP49	DNA helicase TIP49, TBP-interacting protein
147	COG1763	161	39	89.7	0.41	[-----                                            ]	MobB	Molybdopterin-guanine dinucleotide biosynthesis protein
148	COG4619	223	20	89.7	0.18	[---                                              ]	FetA	ABC-type iron transport system FetAB, ATPase component
149	cd03260	227	22	89.6	0.2	[---                                              ]	ABC_PstB_phosphate_transporter	ATP-binding cassette domain of the phosphate transport system. Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. PstA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).
150	COG2274	709	23	89.6	0.17	[---                                              ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
151	cd03298	211	20	89.6	0.2	[---                                              ]	ABC_ThiQ_thiamine_transporter	ATP-binding cassette domain of the thiamine transport system. Part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
152	cd03221	144	23	89.5	0.13	[---                                              ]	ABCF_EF-3	ATP-binding cassette domain of elongation factor 3, subfamily F. Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
153	COG1116	248	28	89.4	0.21	[----                                             ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
154	COG1484	254	72	89.3	1.7	[------------                                     ]	DnaC	DNA replication protein DnaC
155	TIGR00176	155	26	89.3	0.28	[----                                             ]	mobB	molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes.
156	COG4778	235	21	89.3	0.21	[---                                              ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
157	COG1100	219	26	89.1	0.21	[----                                             ]	Gem1	GTPase SAR1 family domain
158	TIGR03185	650	26	89.1	0.33	[---                                              ]	DNA_S_dndD	DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
159	cd03246	173	24	89.0	0.25	[---                                              ]	ABCC_Protease_Secretion	ATP-binding cassette domain of PrtD, subfamily C. This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substrates ranges from inorganic ions, nutrients such as amino acids, sugars, or peptides, hydrophobic drugs, to large polypeptides, such as HlyA.
160	cd00880	161	22	89.0	0.15	[ --                                              ]	Era_like	E. coli Ras-like protein (Era)-like GTPase. The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.
161	COG1341	398	54	88.9	0.5	[-------                                          ]	Grc3	Polynucleotide 5'-kinase, involved in rRNA processing
162	cd02034	116	36	88.9	0.53	[-----                                            ]	CooC	The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
163	TIGR04520	268	48	88.8	0.25	[--------                                         ]	ECF_ATPase_1	energy-coupling factor transporter ATPase. Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the upstream member of the pair of ECF ATPases in Firmicutes and Mollicutes.
164	PRK13538	204	22	88.7	0.25	[---                                              ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
165	pfam06068	395	24	88.7	0.3	[---                                              ]	TIP49	TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.
166	PRK13342	413	40	88.6	0.33	[-----                                            ]	PRK13342	recombination factor protein RarA; Reviewed
167	cd03293	220	24	88.6	0.26	[---                                              ]	ABC_NrtD_SsuB_transporters	ATP-binding cassette domain of the nitrate and sulfonate transporters. NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
168	TIGR00416	454	33	88.6	0.43	[----                                             ]	sms	DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
169	PRK00131	175	29	88.6	0.36	[---                                              ]	aroK	shikimate kinase; Reviewed
170	PRK09493	240	47	88.5	0.26	[--------                                         ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
171	PRK11784	345	25	88.5	0.3	[---                                              ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
172	PRK06696	223	55	88.4	0.51	[--------                                         ]	PRK06696	uridine kinase; Validated
173	cd01878	204	123	88.4	0.33	[----------------                                 ]	HflX	HflX GTPase family. HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.
174	COG4181	228	21	88.3	0.28	[---                                              ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
175	cd01131	198	82	88.3	0.43	[-------------                                    ]	PilT	Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
176	cd01897	167	86	88.2	0.23	[-------------                                    ]	NOG	Nucleolar GTP-binding protein (NOG). NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.
177	cd03229	178	28	88.2	0.28	[----                                             ]	ABC_Class3	ATP-binding cassette domain of the binding protein-dependent transport systems. This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
178	cd01882	231	29	88.2	0.39	[----                                             ]	BMS1	Bms1, an essential GTPase, promotes assembly of preribosomal RNA processing complexes. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
179	TIGR03797	686	19	88.1	0.26	[---                                              ]	NHLM_micro_ABC2	NHLM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal leader sequence cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, members of protein families related to nitrile hydratase alpha subunit or to nif11 have undergone paralogous family expansions, with members possessing a putative bacteriocin cleavage region ending with a classic Gly-Gly motif. Those sets of putative bacteriocins, members of this protein family and its partners TIGR03794 and TIGR03796, and cyclodehydratase/docking scaffold fusion proteins of thiazole/oxazole biosynthesis frequently show correlated species distribution and co-clustering within many of those genomes.
180	cd03220	224	23	88.0	0.32	[---                                              ]	ABC_KpsT_Wzt	ATP-binding cassette component of polysaccharide transport system. The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenza) and a cytoplasmic membrane protein MPA2.
181	TIGR02324	224	62	87.9	0.64	[---------                                        ]	CP_lyasePhnL	phosphonate C-P lyase system protein PhnL. Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.
182	cd03227	162	21	87.9	0.29	[---                                              ]	ABC_Class2	ATP-binding cassette domain of non-transporter proteins. ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.
183	PRK11231	255	116	87.7	0.28	[ ----------------                                ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
184	COG1127	263	32	87.4	0.23	[----                                             ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
185	COG0714	329	23	87.4	0.39	[---                                              ]	MoxR	MoxR-like ATPase
186	pfam05729	165	30	87.3	0.47	[----                                             ]	NACHT	NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.
187	TIGR02858	270	41	87.3	0.41	[-----                                            ]	spore_III_AA	stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.
188	TIGR02525	372	170	87.1	0.37	[ ----------------------------                    ]	plasmid_TraJ	plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
189	pfam08298	358	50	87.0	1	[ ------                                          ]	AAA_PrkA	PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
190	COG0486	454	80	87.0	0.3	[-------------                                    ]	MnmE	tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE
191	PRK09087	226	49	87.0	0.35	[                 ------                          ]	PRK09087	hypothetical protein; Validated
192	PRK05291	449	85	86.9	0.22	[-------------                                    ]	trmE	tRNA modification GTPase TrmE; Reviewed
193	cd03247	178	31	86.8	0.27	[----                                             ]	ABCC_cytochrome_bd	ATP-binding cassette domain of CydCD, subfamily C. The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilis, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
194	COG3911	183	108	86.8	2.3	[-----------------                                ]	COG3911	Predicted ATPase
195	pfam13614	145	102	86.7	6.1	[ -------------                                   ]	AAA_31	AAA domain. This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.
196	cd03223	166	20	86.4	0.4	[---                                              ]	ABCD_peroxisomal_ALDP	ATP-binding cassette domain of peroxisomal transporter, subfamily D. Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).
197	PRK12402	337	61	86.4	0.59	[--------                                         ]	PRK12402	replication factor C small subunit 2; Reviewed
198	COG3839	338	19	86.4	0.4	[---                                              ]	MalK	ABC-type sugar transport system, ATPase component
199	PRK11124	242	54	86.3	1.1	[--------                                         ]	artP	arginine transporter ATP-binding subunit; Provisional
200	PRK06067	234	36	86.3	0.85	[----                                             ]	PRK06067	flagellar accessory protein FlaH; Validated
201	cd03251	234	79	86.2	0.42	[-------------                                    ]	ABCC_MsbA	ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C. MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
202	cd00882	161	20	86.2	0.39	[ --                                              ]	Ras_like_GTPase	Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases). Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions.
203	cd04163	168	98	86.0	0.43	[-------------                                    ]	Era	E. coli Ras-like protein (Era) is a multifunctional GTPase. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
204	TIGR00750	300	37	85.9	0.96	[-----                                            ]	lao	LAO/AO transport system ATPase. In E. coli, mutation of this kinase blocks phosphorylation of two transporter system periplasmic binding proteins and consequently inhibits those transporters. This kinase is also found in Gram-positive bacteria, archaea, and the roundworm C. elegans. It may have a more general, but still unknown function. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.
205	TIGR03263	179	57	85.8	0.5	[--------                                         ]	guanyl_kin	guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.
206	COG2805	353	83	85.8	0.59	[-------------                                    ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
207	COG2074	299	65	85.6	0.54	[---------                                        ]	Pgk2	2-phosphoglycerate kinase
208	cd01130	186	23	85.5	0.48	[---                                              ]	VirB11-like_ATPase	Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
209	TIGR03864	236	22	85.5	0.43	[ ---                                             ]	PQQ_ABC_ATP	ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.
210	cd03252	237	22	85.4	0.51	[---                                              ]	ABCC_Hemolysin	ATP-binding cassette domain of hemolysin B, subfamily C. The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.
211	TIGR02673	214	25	85.4	0.38	[----                                             ]	FtsE	cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.
212	PRK14738	206	115	85.3	6.8	[----------------                                 ]	gmk	guanylate kinase; Provisional
213	cd03263	220	127	85.2	1.3	[ ----------------                                ]	ABC_subfamily_A	ATP-binding cassette domain of the lipid transporters, subfamily A. The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.
214	cd03250	204	61	85.2	0.36	[---------                                        ]	ABCC_MRP_domain1	ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C. This subfamily is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
215	PRK11160	574	42	85.2	0.49	[------                                           ]	PRK11160	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
216	TIGR01420	343	73	85.1	0.76	[-----------                                      ]	pilT_fam	pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.
217	COG0194	191	23	85.1	0.51	[---                                              ]	Gmk	Guanylate kinase
218	TIGR02211	221	20	84.7	0.53	[---                                              ]	LolD_lipo_ex	lipoprotein releasing system, ATP-binding protein. This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.
219	cd00464	154	22	84.6	0.72	[ --                                              ]	SK	Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.
220	COG1474	366	25	84.2	0.81	[----                                             ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
221	cd03240	204	23	84.1	0.75	[---                                              ]	ABC_Rad50	ATP-binding cassette domain of Rad50. The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
222	COG1134	249	24	84.1	0.64	[---                                              ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
223	PRK13830	818	24	83.8	0.74	[---                                              ]	PRK13830	conjugal transfer protein TrbE; Provisional
224	PRK00090	222	87	83.8	5.3	[------------                                     ]	bioD	dithiobiotin synthetase; Reviewed
225	cd04167	213	91	83.7	5	[-------------                                    ]	Snu114p	Snu114p, a spliceosome protein, is a GTPase. Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
226	TIGR03167	311	25	83.6	0.75	[---                                              ]	tRNA_sel_U_synt	tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene.
227	COG4618	580	68	83.5	0.66	[---------                                        ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
228	cd01574	264	81	83.5	0.93	[----------                                       ]	PBP1_LacI	Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
229	COG4987	573	23	83.3	0.59	[---                                              ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
230	COG3842	352	19	83.3	0.55	[---                                              ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
231	cd03264	211	73	83.0	1.5	[ ---------                                       ]	ABC_drug_resistance_like	ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
232	PRK10247	225	45	83.0	0.72	[-------                                          ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
233	COG2019	189	28	83.0	1.1	[---                                              ]	AdkA	Archaeal adenylate kinase
234	COG0703	172	98	82.9	0.84	[---------------                                  ]	AroK	Shikimate kinase
235	cd03256	241	24	82.8	0.65	[              ---                                ]	ABC_PhnC_transporter	ATP-binding cassette domain of the binding protein-dependent phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
236	COG1936	180	94	82.8	0.93	[----------------                                 ]	Fap7	Broad-specificity NMP kinase
237	cd02042	104	67	82.8	3.6	[ --------------                                  ]	ParA	ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
238	TIGR02203	571	22	82.5	0.69	[---                                              ]	MsbA_lipidA	lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.
239	PRK11701	258	119	82.4	0.64	[--------------------                             ]	phnK	phosphonate C-P lyase system protein PhnK; Provisional
240	PRK00698	205	36	82.4	1.5	[-----                                            ]	tmk	thymidylate kinase; Validated
241	COG1117	253	20	82.4	0.68	[ --                                              ]	PstB	ABC-type phosphate transport system, ATPase component
242	PRK03695	248	18	82.4	0.65	[ --                                              ]	PRK03695	vitamin B12-transporter ATPase; Provisional
243	PRK04040	188	25	81.9	1.4	[---                                              ]	PRK04040	adenylate kinase; Provisional
244	TIGR02323	253	77	81.8	0.98	[------------                                     ]	CP_lyasePhnK	phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.
245	TIGR03744	893	34	81.8	1.5	[-----                                            ]	traC_PFL_4706	conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.
246	COG3638	258	25	81.7	0.95	[---                                              ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
247	COG4185	187	14	81.6	0.51	[ -                                               ]	COG4185	Predicted ABC-type ATPase
248	cd03259	213	23	81.6	0.88	[---                                              ]	ABC_Carb_Solutes_like	ATP-binding cassette domain of the carbohydrate and solute transporters-like. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
249	TIGR00235	207	68	81.4	0.88	[----------                                       ]	udk	uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below
250	COG1160	444	115	81.4	0.84	[----------------                                 ]	Der	Predicted GTPases
251	TIGR00968	237	19	81.3	0.94	[---                                              ]	3a0106s01	sulfate ABC transporter, ATP-binding protein.
252	TIGR04521	277	66	81.2	0.86	[----------                                       ]	ECF_ATPase_2	energy-coupling factor transporter ATPase. Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the downstream member of the pair of ECF ATPases in Firmicutes and Mollicutes.
253	cd01879	159	18	81.1	0.79	[ --                                              ]	FeoB	Ferrous iron transport protein B (FeoB) family. Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
254	PRK13873	811	24	81.1	0.99	[ ---                                             ]	PRK13873	conjugal transfer ATPase TrbE; Provisional
255	TIGR00602	637	113	81.1	1.1	[---------------                                  ]	rad24	checkpoint protein rad24. All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
256	COG0411	250	46	81.1	0.35	[-------                                          ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
257	TIGR02868	530	63	81.1	0.77	[---------                                        ]	CydC	thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.
258	TIGR01842	544	68	81.0	0.97	[---------                                        ]	type_I_sec_PrtD	type I secretion system ABC transporter, PrtD family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
259	PRK10436	462	72	81.0	0.77	[-----------                                      ]	PRK10436	hypothetical protein; Provisional
260	COG3451	796	86	80.9	1.1	[--------------                                   ]	VirB4	Type IV secretory pathway, VirB4 component
261	cd03301	213	19	80.8	0.92	[---                                              ]	ABC_MalK_N	The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.
262	PRK07261	171	77	80.8	0.85	[--------------                                   ]	PRK07261	topology modulation protein; Provisional
263	TIGR02538	564	30	80.8	0.71	[----                                             ]	type_IV_pilB	type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
264	PRK00300	205	114	80.7	1.2	[----------------                                 ]	gmk	guanylate kinase; Provisional
265	COG2262	411	117	80.7	1	[----------------                                 ]	HflX	50S ribosomal subunit-associated GTPase HflX
266	pfam03215	517	23	80.6	1.2	[---                                              ]	Rad17	Rad17 cell cycle checkpoint protein.
267	TIGR00929	785	26	80.4	1.1	[----                                             ]	VirB4_CagE	type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).
268	PRK14247	250	21	80.3	1.1	[ --                                              ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
269	PRK14246	257	106	80.1	1.2	[ -----------------                               ]	PRK14246	phosphate ABC transporter ATP-binding protein; Provisional
270	COG0488	530	24	80.0	0.89	[---                                              ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
271	TIGR01351	210	99	80.0	1.4	[---------------                                  ]	adk	adenylate kinase. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is SP|Q9UIJ7, a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
272	COG4615	546	156	79.9	1	[-------------------------------                  ]	PvdE	ABC-type siderophore export system, fused ATPase and permease components
273	COG4107	258	141	79.8	1.1	[-----------------------                          ]	PhnK	ABC-type phosphonate transport system, ATPase component
274	PRK07940	394	24	79.8	1.5	[---                                              ]	PRK07940	DNA polymerase III subunit delta'; Validated
275	COG3910	233	54	79.7	1.1	[--------                                         ]	COG3910	Predicted ATPase
276	COG1159	298	85	79.7	1	[-------------                                    ]	Era	GTPase Era, involved in 16S rRNA processing
277	PRK05541	176	33	79.6	2.1	[----                                             ]	PRK05541	adenylylsulfate kinase; Provisional
278	PRK10789	569	72	79.5	0.99	[ ------------                                    ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
279	PRK00080	328	80	79.4	1.3	[------------                                     ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
280	cd01854	211	24	79.2	0.98	[---                                              ]	YjeQ_EngC	Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases. YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain.
281	PRK05506	632	33	79.0	2	[-----                                            ]	PRK05506	bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
282	TIGR02857	529	24	78.9	1.1	[---                                              ]	CydD	thiol reductant ABC exporter, CydD subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD
283	cd03257	228	21	78.8	1.2	[---                                              ]	ABC_NikE_OppD_transporters	ATP-binding cassette domain of nickel/oligopeptides specific transporters. The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
284	TIGR03420	226	30	78.6	1.9	[----                                             ]	DnaA_homol_Hda	DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
285	COG4962	355	22	78.4	1.2	[---                                              ]	CpaF	Pilus assembly protein, ATPase of CpaF family
286	TIGR01166	190	28	78.4	0.91	[----                                             ]	cbiO	cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.
287	PRK11819	556	53	78.4	1.1	[                         --------                ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
288	COG1921	395	89	78.4	10	[        -------------                            ]	SelA	Seryl-tRNA(Sec) selenium transferase
289	pfam03193	161	23	78.3	1.1	[---                                              ]	DUF258	Protein of unknown function, DUF258.
290	TIGR03608	206	19	78.1	1.2	[---                                              ]	L_ocin_972_ABC	putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.
291	cd03244	221	27	78.1	1.4	[---                                              ]	ABCC_MRP_domain2	ATP-binding cassette domain 2 of multidrug resistance-associated protein. The ABC subfamily C is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
292	cd03299	235	22	78.1	1.3	[---                                              ]	ABC_ModC_like	ATP-binding cassette domain similar to the molybdate transporter. Archaeal protein closely related to ModC. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
293	cd01918	149	21	78.0	1.5	[---                                              ]	HprK_C	HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.
294	cd01895	174	81	78.0	1.1	[-------------                                    ]	EngA2	EngA2 GTPase contains the second domain of EngA. This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
295	pfam10443	428	32	77.9	1.1	[----                                             ]	RNA12	RNA12 protein. This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.
296	TIGR03005	252	56	77.9	1.3	[--------                                         ]	ectoine_ehuA	ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.
297	TIGR02533	486	87	77.9	1.7	[-------------                                    ]	type_II_gspE	type II secretion system protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
298	TIGR03719	552	53	77.7	1.2	[                         --------                ]	ABC_ABC_ChvD	ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.
299	cd02023	198	52	77.6	2.2	[--------                                         ]	UMPK	Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
300	pfam02463	1162	28	77.6	1.2	[----                                             ]	SMC_N	RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolizm and recombination.
301	TIGR02982	220	24	77.5	1.6	[---                                              ]	heterocyst_DevA	ABC exporter ATP-binding subunit, DevA family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts.
302	pfam01078	207	19	77.5	1.3	[---                                              ]	Mg_chelatase	Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
303	PRK00089	292	97	77.4	1.3	[-------------                                    ]	era	GTPase Era; Reviewed
304	TIGR02928	365	40	77.1	2.3	[-----                                            ]	TIGR02928	orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
305	TIGR00101	199	25	77.1	2	[----                                             ]	ureG	urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.
306	PRK14239	252	17	77.0	1.3	[ --                                              ]	PRK14239	phosphate transporter ATP-binding protein; Provisional
307	TIGR00972	247	20	76.9	1.6	[ --                                              ]	3a0107s01c2	phosphate ABC transporter, ATP-binding protein. This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.
308	TIGR03740	223	72	76.8	1.1	[ ----------                                      ]	galliderm_ABC	gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.
309	PRK12337	475	29	76.6	1.7	[----                                             ]	PRK12337	2-phosphoglycerate kinase; Provisional
310	pfam02421	156	20	76.6	1.5	[---                                              ]	FeoB_N	Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
311	TIGR01277	213	24	76.3	1.6	[---                                              ]	thiQ	thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.
312	PRK13635	279	63	76.3	1.5	[----------                                       ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
313	PRK11650	356	19	76.2	1.5	[---                                              ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
314	cd03245	220	81	76.2	1.5	[-------------                                    ]	ABCC_bacteriocin_exporters	ATP-binding cassette domain of bacteriocin exporters, subfamily C. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
315	pfam01656	211	38	76.1	4.1	[-----                                            ]	CbiA	CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
316	TIGR01186	363	22	76.0	1.7	[---                                              ]	proV	glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature.
317	PRK09984	262	20	75.9	1.6	[---                                              ]	PRK09984	phosphonate/organophosphate ester transporter subunit; Provisional
318	pfam00485	196	28	75.9	2	[----                                             ]	PRK	Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
319	cd03276	198	22	75.7	1.9	[ --                                              ]	ABC_SMC6_euk	ATP-binding cassette domain of eukaryotic SM6 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
320	PRK05480	209	48	75.7	3.8	[-------                                          ]	PRK05480	uridine/cytidine kinase; Provisional
321	PRK11264	250	52	75.6	2.1	[--------                                         ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
322	PRK13341	725	22	75.3	1.5	[ --                                              ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
323	TIGR03783	829	31	75.2	2.8	[ ----                                            ]	Bac_Flav_CT_G	Bacteroides conjugation system ATPase, TraG family. Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4.
324	COG3172	187	39	74.9	1.4	[-----                                            ]	NadR3	Nicotinamide riboside kinase
325	PRK13657	588	23	74.7	1.8	[---                                              ]	PRK13657	cyclic beta-1,2-glucan ABC transporter; Provisional
326	cd11383	140	19	74.7	1.4	[ --                                              ]	YfjP	YfjP GTPase. The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.
327	COG1124	252	25	74.7	1.8	[----                                             ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
328	cd03216	163	73	74.5	1.5	[ -----------                                     ]	ABC_Carb_Monos_I	First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
329	COG1118	345	19	74.4	1.5	[---                                              ]	CysA	ABC-type sulfate/molybdate transport systems, ATPase component
330	cd03241	276	143	74.4	11	[ ----------------------                          ]	ABC_RecN	ATP-binding cassette domain of RecN. RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
331	cd03268	208	22	74.3	1.7	[ ---                                             ]	ABC_BcrA_bacitracin_resist	ATP-binding cassette domain of the bacitracin-resistance transporter. The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.
332	TIGR02524	358	30	74.1	2.7	[----                                             ]	dot_icm_DotB	Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.
333	pfam01637	223	32	74.0	3	[----                                             ]	Arch_ATPase	Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family.
334	PRK08233	182	91	74.0	7	[-------------                                    ]	PRK08233	hypothetical protein; Provisional
335	cd03278	197	33	74.0	2.4	[-----                                            ]	ABC_SMC_barmotin	ATP-binding cassette domain of barmotin, a member of the SMC protein family. Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
336	PRK10771	232	83	73.9	1.8	[-------------                                    ]	thiQ	thiamine transporter ATP-binding subunit; Provisional
337	COG0444	316	25	73.9	1.8	[---                                              ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
338	PRK06762	166	66	73.8	2.6	[                     ---------                   ]	PRK06762	hypothetical protein; Provisional
339	COG0464	494	45	73.7	1.6	[-------                                          ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
340	TIGR02315	243	25	73.6	1.9	[              ---                                ]	ABC_phnC	phosphonate ABC transporter, ATP-binding protein. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.
341	cd03296	239	19	73.5	2.1	[---                                              ]	ABC_CysA_sulfate_importer	ATP-binding cassette domain of the sulfate transporter. Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
342	PRK14489	366	40	73.4	4	[-----                                            ]	PRK14489	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
343	pfam07693	301	50	73.2	6.3	[-------                                          ]	KAP_NTPase	KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.
344	COG4988	559	28	73.2	2.3	[---                                              ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
345	cd03294	269	49	73.2	1.7	[ -------                                         ]	ABC_Pro_Gly_Betaine	ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system. This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
346	COG1674	858	43	73.1	2.9	[------                                           ]	FtsK	DNA segregation ATPase FtsK/SpoIIIE and related proteins
347	pfam00006	213	33	72.9	3.8	[-----                                            ]	ATP-synt_ab	ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.
348	COG5192	1077	25	72.9	3	[----                                             ]	BMS1	GTP-binding protein required for 40S ribosome biogenesis
349	cd01856	171	21	72.8	2.1	[---                                              ]	YlqF	Circularly permuted YlqF GTPase. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga).
350	TIGR00954	659	33	72.7	2	[            -----                                ]	3a01203	Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein.
351	TIGR00231	162	23	72.7	2.2	[---                                              ]	small_GTP	small GTP-binding protein domain. Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK
352	TIGR03156	351	117	72.6	2	[----------------                                 ]	GTP_HflX	GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).
353	pfam00580	267	29	72.3	3.6	[----                                             ]	UvrD-helicase	UvrD/REP helicase N-terminal domain. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Some members have large insertions near to the carboxy-terminus relative to other members of the family.
354	PRK00889	175	49	72.0	4.4	[--------                                         ]	PRK00889	adenylylsulfate kinase; Provisional
355	PRK13632	271	47	71.7	3	[--------                                         ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
356	TIGR00678	188	25	71.6	3.2	[---                                              ]	holB	DNA polymerase III, delta' subunit. This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
357	cd03297	214	25	71.4	2.7	[---                                              ]	ABC_ModC_molybdenum_transporter	ATP-binding cassette domain of the molybdenum transport system. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
358	PRK09580	248	26	71.3	1.7	[----                                             ]	sufC	cysteine desulfurase ATPase component; Reviewed
359	pfam13189	174	71	71.2	9.5	[                    ------------                 ]	Cytidylate_kin2	Cytidylate kinase-like family. This family includes enzymes related to cytidylate kinase.
360	COG4178	604	56	71.2	2.4	[---------                                        ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
361	cd03271	261	16	71.1	2.2	[--                                               ]	ABC_UvrA_II	ATP-binding cassette domain II of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.
362	PRK00411	394	77	70.9	3.9	[-----------                                      ]	cdc6	cell division control protein 6; Reviewed
363	pfam10412	386	32	70.9	3.4	[----                                             ]	TrwB_AAD_bind	Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
364	cd03226	205	24	70.8	2.7	[---                                              ]	ABC_cobalt_CbiO_domain2	Second domain of the ATP-binding cassette component of cobalt transport system. Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
365	PRK05416	288	118	70.8	3	[----------------------                           ]	PRK05416	glmZ(sRNA)-inactivating NTPase; Provisional
366	TIGR02746	797	33	70.6	4.3	[-----                                            ]	TraC-F-type	type-IV secretion system protein TraC. The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.
367	pfam02223	186	33	70.5	5.1	[ ----                                            ]	Thymidylate_kin	Thymidylate kinase.
368	cd01385	690	40	70.4	2.7	[-----                                            ]	MYSc_Myo9	class IX myosin, motor domain. Myosin IX is a processive single-headed motor, which might play a role in signalling. It has a N-terminal RA domain, an IQ domain, a C1_1 domain, and a RhoGAP domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy.
369	PRK10253	265	22	70.1	2.7	[ --                                              ]	PRK10253	iron-enterobactin transporter ATP-binding protein; Provisional
370	PRK15112	267	91	69.9	2.8	[-------------                                    ]	PRK15112	antimicrobial peptide ABC system ATP-binding protein SapF; Provisional
371	COG0630	312	30	69.9	3	[----                                             ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
372	COG1125	309	66	69.8	2.7	[---------                                        ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
373	TIGR03348	1169	41	69.8	2.4	[                      -----                      ]	VI_IcmF	type VI secretion protein IcmF. Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.
374	PRK09601	364	51	69.7	2.3	[-------                                          ]	PRK09601	GTP-binding protein YchF; Reviewed
375	TIGR01187	325	15	69.6	2.3	[ --                                              ]	potA	spermidine/putrescine ABC transporter ATP-binding subunit. This model describes spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Polyamines like spermidine and putrescine play vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).
376	cd03234	226	55	69.4	3	[--------                                         ]	ABCG_White	White pigment protein homolog of ABCG transporter subfamily. The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.
377	pfam10236	293	15	69.3	2.3	[--                                               ]	DAP3	Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
378	cd03267	236	25	69.3	2.5	[ ---                                             ]	ABC_NatA_like	ATP-binding cassette domain of an uncharacterized transporter similar in sequence to NatA. NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single integral membrane protein.
379	COG0488	530	103	69.1	2.6	[                      --------------             ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
380	cd01894	157	82	68.1	2.4	[ ------------                                    ]	EngA1	EngA1 GTPase contains the first domain of EngA. This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
381	cd03239	178	18	67.9	2.1	[---                                              ]	ABC_SMC_head	The SMC head domain belongs to the ATP-binding cassette superfamily. The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.
382	cd03249	238	23	67.4	3.7	[---                                              ]	ABC_MTABC3_MDL1_MDL2	ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins. MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
383	pfam05496	234	75	67.4	4	[-----------                                      ]	RuvB_N	Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
384	pfam13479	201	19	67.4	2.1	[---                                              ]	AAA_24	AAA domain. This AAA domain is found in a wide variety of presumed phage proteins.
385	cd03292	214	22	67.3	3.4	[---                                              ]	ABC_FtsE_transporter	ATP-binding cassette domain of the cell division transporter. FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.
386	COG0237	201	21	67.1	4.1	[---                                              ]	CoaE	Dephospho-CoA kinase
387	PRK00093	435	26	66.9	2.8	[---                                              ]	PRK00093	GTP-binding protein Der; Reviewed
388	cd01387	657	27	66.9	4.9	[----                                             ]	MYSc_Myo15	class XV mammal-like myosin, motor domain. The class XV myosins are monomeric. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. C-terminal to the head domain are 2 MyTH4 domain, a FERM domain, and a SH3 domain. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy.
389	COG4167	267	20	66.9	3.4	[---                                              ]	SapF	ABC-type antimicrobial peptide transport system, ATPase component
390	PRK06620	214	26	66.7	4.5	[---                                              ]	PRK06620	hypothetical protein; Validated
391	TIGR00618	1042	38	66.7	4.3	[-----                                            ]	sbcc	exonuclease SbcC. All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
392	pfam00519	432	51	66.6	3.5	[-------                                          ]	PPV_E1_C	Papillomavirus helicase. This protein is a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508.
393	PRK00440	319	27	66.6	4.8	[---                                              ]	rfc	replication factor C small subunit; Reviewed
394	PRK07429	327	33	66.6	3.9	[ ----                                            ]	PRK07429	phosphoribulokinase; Provisional
395	PRK00230	230	91	66.5	3.7	[               ------------                      ]	PRK00230	orotidine 5'-phosphate decarboxylase; Reviewed
396	cd03233	202	24	66.5	4	[---                                              ]	ABCG_PDR_domain1	First domain of the pleiotropic drug resistance-like subfamily G of ATP-binding cassette transporters. The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
397	PRK04220	301	23	66.3	4.2	[---                                              ]	PRK04220	2-phosphoglycerate kinase; Provisional
398	cd01124	187	66	66.3	3.6	[-----------                                      ]	KaiC	KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
399	COG4175	386	22	66.3	2.8	[---                                              ]	ProV	ABC-type proline/glycine betaine transport system, ATPase component
400	cd01881	167	22	66.2	3.2	[ --                                              ]	Obg_like	Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.
401	PRK10744	260	71	66.1	3.3	[ -------------                                   ]	pstB	phosphate transporter ATP-binding protein; Provisional
402	PRK11147	635	25	65.9	3	[----                                             ]	PRK11147	ABC transporter ATPase component; Reviewed
403	cd00124	633	27	65.8	4.6	[----                                             ]	MYSc	Myosin motor domain superfamily. Myosin motor domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy.
404	PRK06851	367	27	65.7	5.2	[ ---                                             ]	PRK06851	hypothetical protein; Provisional
405	TIGR02759	566	27	65.7	4.9	[----                                             ]	TraD_Ftype	type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).
406	cd03238	176	19	65.7	3.2	[---                                              ]	ABC_UvrA	ATP-binding cassette domain of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
407	cd03224	222	58	65.7	4.1	[--------                                         ]	ABC_TM1139_LivF_branched	ATP-binding cassette domain of branched-chain amino acid transporter. LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.
408	cd03300	232	17	65.5	3.2	[ --                                              ]	ABC_PotA_N	ATP-binding cassette domain of the polyamine transporter. PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
409	cd03295	242	21	65.4	4.4	[ --                                              ]	ABC_OpuCA_Osmoprotection	ATP-binding cassette domain of the osmoprotectant transporter. OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
410	PRK10522	547	29	65.4	3.7	[ ---                                             ]	PRK10522	multidrug transporter membrane component/ATP-binding component; Provisional
411	PRK10575	265	129	65.2	2.8	[-----------------                                ]	PRK10575	iron-hydroxamate transporter ATP-binding subunit; Provisional
412	cd01900	274	19	65.0	3.3	[ --                                              ]	YchF	YchF GTPase. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
413	TIGR02237	209	42	64.9	6.1	[ ------                                          ]	recomb_radB	DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
414	PRK13833	323	32	64.9	7	[----                                             ]	PRK13833	conjugal transfer protein TrbB; Provisional
415	COG4136	213	23	64.3	4.5	[---                                              ]	YnjD	ABC-type uncharacterized transport system YnjBCD, ATPase component
416	PRK14526	211	23	64.1	3.7	[---                                              ]	PRK14526	adenylate kinase; Provisional
417	cd00881	183	22	63.9	4.1	[---                                              ]	GTP_translation_factor	GTP translation factor family primarily contains translation initiation, elongation and release factors. The GTP translation factor family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
418	cd02026	273	34	63.9	5.1	[ ----                                            ]	PRK	Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
419	PRK10751	173	66	63.9	6.7	[---------                                        ]	PRK10751	molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
420	TIGR00041	195	33	63.9	8.6	[----                                             ]	DTMP_kinase	dTMP kinase. Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
421	COG4586	325	22	63.7	3.5	[ --                                              ]	COG4586	ABC-type uncharacterized transport system, ATPase component
422	COG4525	259	19	63.6	4.2	[---                                              ]	TauB	ABC-type taurine transport system, ATPase component
423	PRK11629	233	20	63.6	5	[---                                              ]	lolD	lipoprotein transporter ATP-binding subunit; Provisional
424	cd03111	106	89	63.6	63	[----------------                                 ]	CpaE_like	This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
425	PRK14236	272	19	63.5	3.9	[ --                                              ]	PRK14236	phosphate transporter ATP-binding protein; Provisional
426	pfam09848	348	24	63.5	5.4	[                                              ---]	DUF2075	Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
427	COG1373	398	26	63.5	4.9	[----                                             ]	COG1373	Predicted ATPase, AAA+ superfamily
428	COG1162	301	20	63.4	3.5	[---                                              ]	RsgA	Putative ribosome biogenesis GTPase RsgA
429	PRK00064	361	118	63.4	3.3	[-----------------                                ]	recF	recombination protein F; Reviewed
430	TIGR01193	708	23	63.4	3.9	[---                                              ]	bacteriocin_ABC	ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
431	COG0370	653	21	63.4	4.1	[---                                              ]	FeoB	Fe2+ transport system protein B
432	TIGR03575	340	25	63.3	5.7	[ ---                                             ]	selen_PSTK_euk	L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.
433	PRK14249	251	42	63.3	4.4	[------                                           ]	PRK14249	phosphate ABC transporter ATP-binding protein; Provisional
434	pfam10662	143	20	63.0	4.6	[---                                              ]	PduV-EutP	Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood.
435	pfam04665	241	101	63.0	6.2	[-------------                                    ]	Pox_A32	Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging.
436	PRK14237	267	16	62.9	4.2	[ --                                              ]	PRK14237	phosphate transporter ATP-binding protein; Provisional
437	COG1239	423	131	62.7	4.1	[-------------------                              ]	ChlI	Mg-chelatase subunit ChlI
438	COG3854	308	23	62.7	6.4	[---                                              ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
439	pfam02310	120	75	62.6	65	[  -----------                                    ]	B12-binding	B12 binding domain. This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.
440	TIGR02169	1164	29	62.1	5.2	[----                                             ]	SMC_prok_A	chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
441	PRK14250	241	20	62.0	4.7	[ --                                              ]	PRK14250	phosphate ABC transporter ATP-binding protein; Provisional
442	COG4608	268	63	61.7	5.7	[ --------                                        ]	AppF	ABC-type oligopeptide transport system, ATPase component
443	pfam04851	103	34	61.4	8.3	[-----                                            ]	ResIII	Type III restriction enzyme, res subunit.
444	PRK10938	490	37	61.3	2	[ ----                                            ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
445	TIGR01192	585	22	61.3	5.3	[---                                              ]	chvA	glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.
446	TIGR03375	694	82	61.3	4.9	[-------------                                    ]	type_I_sec_LssB	type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
447	PRK09518	712	26	61.1	6.1	[----                                             ]	PRK09518	bifunctional cytidylate kinase/GTPase Der; Reviewed
448	COG0410	237	25	61.1	5.2	[----                                             ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
449	pfam13166	713	83	60.9	5.1	[-------------                                    ]	AAA_13	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.
450	cd03248	226	20	60.8	4.9	[ --                                              ]	ABCC_TAP	ATP-binding cassette domain of the Transporter Associated with Antigen Processing, subfamily C. TAP (Transporter Associated with Antigen Processing) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
451	cd03269	210	18	60.8	4.3	[ --                                              ]	ABC_putative_ATPase	ATP-binding cassette domain of an uncharacterized transporter. This subgroup is related to the subfamily A transporters involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two integral membranes. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
452	TIGR03371	246	123	60.7	11	[ ----------------                                ]	cellulose_yhjQ	cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
453	cd03275	247	43	60.7	4.8	[              -----                              ]	ABC_SMC1_euk	ATP-binding cassette domain of eukaryotic SMC1 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
454	PRK07471	365	163	60.3	5.1	[-----------------------                          ]	PRK07471	DNA polymerase III subunit delta'; Validated
455	PRK04213	201	23	60.1	6.4	[---                                              ]	PRK04213	GTP-binding protein; Provisional
456	COG2255	332	110	60.1	6.4	[-----------------                                ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
457	PRK14490	369	46	60.1	8.4	[------                                           ]	PRK14490	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional
458	PRK14267	253	52	60.0	6.3	[ -------                                         ]	PRK14267	phosphate ABC transporter ATP-binding protein; Provisional
459	TIGR02788	308	22	60.0	6.2	[---                                              ]	VirB11	P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
460	PRK00093	435	80	59.9	5.4	[-------------                                    ]	PRK00093	GTP-binding protein Der; Reviewed
461	PRK00098	298	21	59.6	4.6	[ --                                              ]	PRK00098	GTPase RsgA; Reviewed
462	COG0606	490	75	59.5	4.7	[----------                                       ]	YifB	Predicted ATPase with chaperone activity
463	cd01383	647	27	59.1	8.5	[----                                             ]	MYSc_Myo8	class VIII myosin, motor domain. These plant-specific type VIII myosins has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. It also contains IQ domains Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy.
464	cd14879	647	26	59.1	7.5	[----                                             ]	MYSc_Myo17	class XVII myosin, motor domain. This fungal myosin which is also known as chitin synthase uses its motor domain to tether its vesicular cargo to peripheral actin. It works in opposition to dynein, contributing to the retention of Mcs1 vesicles at the site of cell growth and increasing vesicle fusion necessary for polarized growth. Class 17 myosins consist of a N-terminal myosin motor domain with Cyt-b5, chitin synthase 2, and a DEK_C domains at it C-terminus. The chitin synthase region contains several transmembrane domains by which myosin 17 is thought to bind secretory vesicles. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy.
465	COG3950	440	24	59.0	7.3	[---                                              ]	COG3950	Predicted ATP-binding protein involved in virulence
466	COG0012	372	22	59.0	4.8	[---                                              ]	GTP1	Ribosome-binding ATPase YchF, GTP1/OBG family
467	pfam02562	205	35	59.0	11	[-----                                            ]	PhoH	PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
468	COG4639	168	54	58.9	5.5	[             --------                            ]	COG4639	Predicted kinase
469	PRK11248	255	21	58.9	6	[---                                              ]	tauB	taurine transporter ATP-binding subunit; Provisional
470	pfam04735	1173	49	58.7	5.9	[--------                                         ]	Baculo_helicase	Baculovirus DNA helicase.
471	PRK10535	648	20	58.5	5.3	[---                                              ]	PRK10535	macrolide transporter ATP-binding /permease protein; Provisional
472	TIGR03015	269	27	58.5	6.5	[----                                             ]	pepcterm_ATPase	putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
473	PRK11000	369	19	58.4	5.9	[---                                              ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
474	PRK06921	266	29	58.4	9.6	[----                                             ]	PRK06921	hypothetical protein; Provisional
475	pfam05673	248	54	58.3	8.7	[--------                                         ]	DUF815	Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
476	COG1123	539	59	58.3	4.8	[                         --------                ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
477	TIGR00313	475	145	58.1	7.7	[ --------------------                            ]	cobQ	cobyric acid synthase CobQ.
478	COG1196	1163	33	58.0	5.5	[ ----                                            ]	Smc	Chromosome segregation ATPase
479	cd03281	213	28	57.9	6.1	[----                                             ]	ABC_MSH5_euk	ATP-binding cassette domain of eukaryotic MutS5 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
480	TIGR03594	428	80	57.8	6.2	[-------------                                    ]	GTPase_EngA	ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
481	cd03265	220	25	57.4	3.9	[ ---                                             ]	ABC_DrrA	Daunorubicin/doxorubicin resistance ATP-binding protein. DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin. In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
482	PRK08116	268	28	56.9	9.8	[----                                             ]	PRK08116	hypothetical protein; Validated
483	PRK10851	353	19	56.9	6.1	[---                                              ]	PRK10851	sulfate/thiosulfate transporter subunit; Provisional
484	PRK06851	367	26	56.8	9.5	[ ---                                             ]	PRK06851	hypothetical protein; Provisional
485	cd04170	268	20	56.6	6.4	[---                                              ]	EF-G_bact	Elongation factor G (EF-G) family. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members.
486	COG3640	255	38	56.6	15	[-----                                            ]	CooC	CO dehydrogenase nickel-insertion accessory protein CooC1
487	COG3596	296	20	56.6	6.8	[---                                              ]	YeeP	Predicted GTPase
488	cd01851	224	23	56.5	6.3	[---                                              ]	GBP	Guanylate-binding protein (GBP) family (N-terminal domain). Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.
489	cd03270	226	17	56.5	6.1	[--                                               ]	ABC_UvrA_I	ATP-binding cassette domain I of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
490	PRK11176	582	23	56.4	6.8	[---                                              ]	PRK11176	lipid transporter ATP-binding/permease protein; Provisional
491	COG3709	192	60	56.3	18	[--------                                         ]	PhnN	Ribose 1,5-bisphosphokinase PhnN
492	TIGR01188	302	19	56.3	3.7	[ --                                              ]	drrA	daunorubicin resistance ABC transporter ATP-binding subunit. This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.
493	PRK14253	249	18	56.2	6.2	[ --                                              ]	PRK14253	phosphate ABC transporter ATP-binding protein; Provisional
494	TIGR02322	179	98	56.2	13	[----------------                                 ]	phosphon_PhnN	phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN. Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see ), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.
495	TIGR00630	925	16	56.1	6	[--                                               ]	uvra	excinuclease ABC, A subunit. This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
496	TIGR01526	325	26	56.1	5.8	[----                                             ]	nadR_NMN_Atrans	nicotinamide-nucleotide adenylyltransferase, NadR type. The NadR protein of E. coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal to the region covered by this model, is a DNA-binding helix-turn-helix domain (pfam01381) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.
497	TIGR03522	301	23	56.0	2.2	[ ---                                             ]	GldA_ABC_ATP	gliding motility-associated ABC transporter ATP-binding subunit GldA. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
498	COG0802	149	24	56.0	8.1	[---                                              ]	TsaE	tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE
499	COG5008	375	64	55.8	7.2	[----------                                       ]	PilU	Tfp pilus assembly protein, ATPase PilU
500	pfam07724	168	110	55.8	9.1	[---------------                                  ]	AAA_2	AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.