match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam13207	114	23	96.6	0.0012	[     --------                                    ]	AAA_17	AAA domain.
2	cd00009	151	80	96.5	0.0061	[     ------------------------------              ]	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.
3	cd02020	147	23	95.5	0.0078	[     --------                                    ]	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.
4	pfam13238	128	21	95.4	0.011	[     -------                                     ]	AAA_18	AAA domain.
5	pfam06414	194	40	95.0	0.014	[     --------------                              ]	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.
6	cd01120	165	38	94.9	0.073	[     --------------                              ]	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.
7	pfam13304	144	19	94.6	0.026	[     -------                                     ]	AAA_21	AAA domain.
8	pfam13245	72	38	94.6	0.055	[     -------------                               ]	AAA_19	Part of AAA domain.
9	PRK14526	211	25	94.6	0.018	[     ---------                                   ]	PRK14526	adenylate kinase; Provisional
10	cd03227	162	20	93.7	0.033	[     ------                                      ]	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.
11	pfam00004	131	70	93.5	0.052	[     --------------------------                  ]	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.
12	cd02019	69	22	93.5	0.056	[     --------                                    ]	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.
13	cd00071	137	24	93.4	0.047	[     --------                                    ]	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.
14	COG0572	218	84	93.3	0.05	[     -------------------------------             ]	Udk	Uridine kinase
15	COG0283	222	26	93.1	0.053	[     ---------                                   ]	Cmk	Cytidylate kinase
16	COG0563	178	23	92.9	0.068	[     --------                                    ]	Adk	Adenylate kinase or related kinase
17	pfam13191	156	51	92.7	0.29	[     ------------------                          ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
18	pfam13671	143	21	92.6	0.064	[     -------                                     ]	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.
19	cd01428	194	23	92.6	0.078	[     --------                                    ]	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.
20	cd03228	171	31	92.4	0.13	[     -----------                                 ]	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.
21	pfam13476	203	24	92.3	0.085	[     --------                                    ]	AAA_23	AAA domain.
22	pfam00005	150	32	92.2	0.17	[     -----------                                 ]	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.
23	TIGR02173	171	25	92.1	0.067	[     ---------                                   ]	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.
24	COG0593	408	68	92.1	0.36	[    ---------------------------                  ]	DnaA	Chromosomal replication initiation ATPase DnaA
25	PRK00023	225	26	92.0	0.09	[     ---------                                   ]	cmk	cytidylate kinase; Provisional
26	COG0470	325	52	91.9	0.44	[     -------------------                         ]	HolB	DNA polymerase III, delta prime subunit
27	cd00464	154	48	91.9	0.16	[     -------------------                         ]	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.
28	COG1136	226	23	91.8	0.11	[     --------                                    ]	LolD	ABC-type lipoprotein export system, ATPase component
29	PRK04182	180	25	91.5	0.11	[     ---------                                   ]	PRK04182	cytidylate kinase; Provisional
30	cd03255	218	21	91.4	0.13	[     -------                                     ]	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.
31	COG4088	261	106	91.2	0.7	[     --------------------------------------      ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
32	cd01673	193	20	91.2	0.14	[     -------                                     ]	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.
33	COG0703	172	48	91.1	0.16	[     -------------------                         ]	AroK	Shikimate kinase
34	cd00267	157	23	91.1	0.15	[     --------                                    ]	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.
35	COG1196	1163	52	90.9	0.19	[      ----------------------                     ]	Smc	Chromosome segregation ATPase
36	pfam07728	135	22	90.8	0.17	[     --------                                    ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
37	PRK13342	413	25	90.7	0.17	[     ---------                                   ]	PRK13342	recombination factor protein RarA; Reviewed
38	pfam13401	124	25	90.7	0.72	[     ---------                                   ]	AAA_22	AAA domain.
39	PRK06762	166	24	90.5	0.11	[     --------                                    ]	PRK06762	hypothetical protein; Provisional
40	COG3842	352	22	90.5	0.16	[     --------                                    ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
41	PRK00131	175	45	90.4	0.26	[     -----------------                           ]	aroK	shikimate kinase; Reviewed
42	COG1102	179	23	90.1	0.24	[     --------                                    ]	CmkB	Cytidylate kinase
43	COG0324	308	55	89.9	0.21	[     -------------------                         ]	MiaA	tRNA A37 N6-isopentenylltransferase MiaA
44	pfam00437	273	34	89.9	0.42	[    ------------                                 ]	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.
45	COG3839	338	20	89.7	0.2	[     -------                                     ]	MalK	ABC-type sugar transport system, ATPase component
46	COG0194	191	25	89.7	0.16	[     --------                                    ]	Gmk	Guanylate kinase
47	cd03293	220	22	89.6	0.23	[     --------                                    ]	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.
48	TIGR02237	209	34	89.4	0.42	[      -----------                                ]	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).
49	PRK00064	361	19	89.4	0.25	[     -------                                     ]	recF	recombination protein F; Reviewed
50	pfam12846	298	41	89.3	0.54	[     ---------------                             ]	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.
51	PRK13768	253	40	89.2	0.32	[     --------------                              ]	PRK13768	GTPase; Provisional
52	cd02028	179	21	89.1	0.21	[     -------                                     ]	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).
53	pfam03215	517	85	88.9	0.69	[     -------------------------------             ]	Rad17	Rad17 cell cycle checkpoint protein.
54	pfam13555	60	19	88.6	0.39	[     -------                                     ]	AAA_29	P-loop containing region of AAA domain.
55	PRK00300	205	23	88.5	0.2	[     -------                                     ]	gmk	guanylate kinase; Provisional
56	COG1132	567	26	88.4	0.45	[     ---------                                   ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
57	cd03296	239	21	88.4	0.22	[     -------                                     ]	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.
58	COG0714	329	49	88.3	0.64	[     ------------------                          ]	MoxR	MoxR-like ATPase
59	pfam02463	1162	40	88.3	0.29	[      -----------------                          ]	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.
60	PRK00091	307	17	88.1	0.33	[     -----                                       ]	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
61	COG4619	223	41	87.9	0.45	[     ---------------                             ]	FetA	ABC-type iron transport system FetAB, ATPase component
62	cd03278	197	18	87.8	0.35	[     ------                                      ]	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).
63	pfam04851	103	36	87.7	0.57	[     -------------                               ]	ResIII	Type III restriction enzyme, res subunit.
64	COG1100	219	24	87.7	0.47	[     ---------                                   ]	Gem1	GTPase SAR1 family domain
65	pfam05729	165	39	87.3	0.44	[     --------------                              ]	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.
66	cd03259	213	20	87.3	0.4	[     -------                                     ]	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.
67	PRK06547	172	20	87.2	0.38	[     -------                                     ]	PRK06547	hypothetical protein; Provisional
68	cd03229	178	21	87.1	0.43	[     -------                                     ]	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.
69	TIGR03263	179	22	86.6	0.32	[     -------                                     ]	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.
70	COG0542	786	76	86.5	0.46	[     -----------------------------               ]	ClpA	ATP-dependent Clp protease ATP-binding subunit ClpA
71	COG1116	248	20	86.4	0.46	[     -------                                     ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
72	COG1126	240	19	86.4	0.44	[     -------                                     ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
73	cd03225	211	20	85.9	0.5	[     -------                                     ]	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.
74	TIGR00235	207	82	85.9	0.62	[     -------------------------------             ]	udk	uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below
75	cd03253	236	23	85.6	0.53	[     --------                                    ]	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.
76	cd03251	234	37	85.2	0.58	[     -------------                               ]	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.
77	cd03300	232	19	85.1	0.56	[     -------                                     ]	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.
78	PRK05342	412	20	85.0	0.58	[     -------                                     ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
79	cd01130	186	75	84.9	1	[     --------------------------------            ]	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.
80	COG1118	345	22	84.9	0.41	[     -------                                     ]	CysA	ABC-type sulfate/molybdate transport systems, ATPase component
81	PRK07261	171	23	84.8	0.59	[     --------                                    ]	PRK07261	topology modulation protein; Provisional
82	PRK13539	207	20	84.7	0.61	[     -------                                     ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
83	TIGR02168	1179	19	84.6	0.54	[     -------                                     ]	SMC_prok_B	chromosome segregation protein SMC, common bacterial 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. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
84	PRK10247	225	29	84.6	0.93	[      ----------                                 ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
85	pfam01935	219	48	84.5	1.7	[   -----------------                             ]	DUF87	Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
86	COG1428	216	47	84.5	1.5	[     ------------------                          ]	Dck	Deoxyadenosine/deoxycytidine kinase
87	TIGR03005	252	20	84.5	0.57	[     -------                                     ]	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.
88	COG1125	309	23	84.4	0.59	[     --------                                    ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
89	TIGR00017	217	22	84.3	0.55	[     -------                                     ]	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.
90	TIGR03499	282	42	84.1	0.9	[     ---------------                             ]	FlhF	flagellar biosynthetic protein FlhF.
91	COG1484	254	78	84.0	5.1	[ -----------------------------                   ]	DnaC	DNA replication protein DnaC
92	PRK13538	204	23	83.9	0.57	[     --------                                    ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
93	cd03254	229	32	83.8	1.1	[     -----------                                 ]	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.
94	cd03257	228	53	83.8	0.73	[     ---------------------                       ]	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.
95	cd03240	204	19	83.7	0.82	[     -------                                     ]	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.
96	COG2256	436	34	83.7	2.3	[     ------------                                ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
97	PRK10851	353	19	83.4	0.49	[     -------                                     ]	PRK10851	sulfate/thiosulfate transporter subunit; Provisional
98	COG1195	363	19	83.2	0.83	[     -------                                     ]	RecF	Recombinational DNA repair ATPase RecF
99	TIGR02397	355	37	83.1	0.82	[     ---------------                             ]	dnaX_nterm	DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
100	cd03295	242	24	83.1	0.59	[     --------                                    ]	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.
101	PRK09361	225	31	83.0	1.3	[      -----------                                ]	radB	DNA repair and recombination protein RadB; Provisional
102	pfam07724	168	38	82.9	1.1	[     ---------------                             ]	AAA_2	AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
103	PRK11784	345	24	82.9	0.51	[    --------                                     ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
104	pfam01078	207	19	82.8	0.78	[     -------                                     ]	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.
105	PRK04195	482	25	82.7	0.83	[     --------                                    ]	PRK04195	replication factor C large subunit; Provisional
106	pfam02456	370	36	82.5	1.4	[      ------------                               ]	Adeno_IVa2	Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter.
107	PRK04040	188	28	82.4	1.6	[     ---------                                   ]	PRK04040	adenylate kinase; Provisional
108	TIGR02982	220	18	82.0	0.93	[     ------                                      ]	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.
109	cd02027	149	38	81.9	0.83	[     --------------                              ]	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.
110	COG1122	235	23	81.8	0.91	[     --------                                    ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
111	cd00046	144	59	81.8	5.8	[     ----------------------                      ]	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.
112	TIGR03796	710	25	81.8	0.89	[     ---------                                   ]	NHLM_micro_ABC1	NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes a multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHLM, Nitrile Hydratase Leader Microcin.
113	COG1124	252	19	81.7	0.95	[     -------                                     ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
114	TIGR01351	210	23	81.6	0.9	[     --------                                    ]	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.
115	cd03230	173	23	81.6	1.1	[     --------                                    ]	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.
116	cd03301	213	20	81.5	0.84	[     -------                                     ]	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.
117	PRK11650	356	19	81.4	0.91	[     -------                                     ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
118	TIGR03420	226	77	81.4	2	[     -------------------------------             ]	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.
119	cd02021	150	22	81.3	0.91	[     --------                                    ]	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.
120	pfam00910	105	23	81.2	1.2	[     --------                                    ]	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.
121	cd03260	227	22	81.2	1	[     --------                                    ]	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).
122	TIGR03608	206	20	81.2	0.72	[     -------                                     ]	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.
123	cd03249	238	23	80.8	1.8	[     --------                                    ]	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.
124	COG3950	440	23	80.8	0.9	[     --------                                    ]	COG3950	Predicted ATP-binding protein involved in virulence
125	TIGR03689	512	23	80.7	1.4	[     --------                                    ]	pup_AAA	proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
126	COG0529	197	23	80.5	1.1	[     --------                                    ]	CysC	Adenylylsulfate kinase or related kinase
127	PRK14964	491	77	80.5	1.5	[     ------------------------------------        ]	PRK14964	DNA polymerase III subunits gamma and tau; Provisional
128	PRK11176	582	64	80.4	2	[     -------------------------                   ]	PRK11176	lipid transporter ATP-binding/permease protein; Provisional
129	COG1123	539	22	80.4	1.1	[     --------                                    ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
130	PRK05480	209	22	80.4	1.3	[     --------                                    ]	PRK05480	uridine/cytidine kinase; Provisional
131	COG1219	408	49	80.3	1.1	[     --------------------                        ]	ClpX	ATP-dependent protease Clp, ATPase subunit
132	COG0378	202	19	80.0	1.2	[     ------                                      ]	HypB	Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase
133	pfam13173	127	32	79.9	5.3	[     -----------                                 ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
134	TIGR01189	198	20	79.8	1.2	[     -------                                     ]	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.
135	PRK05541	176	37	79.8	1.2	[     -------------                               ]	PRK05541	adenylylsulfate kinase; Provisional
136	PRK03992	389	25	79.8	1.6	[     ---------                                   ]	PRK03992	proteasome-activating nucleotidase; Provisional
137	cd03214	180	24	79.5	1.3	[     --------                                    ]	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.
138	COG4525	259	19	79.5	0.94	[     -------                                     ]	TauB	ABC-type taurine transport system, ATPase component
139	cd03231	201	20	79.5	1.2	[     -------                                     ]	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.
140	PRK05896	605	23	79.4	1.2	[     --------                                    ]	PRK05896	DNA polymerase III subunits gamma and tau; Validated
141	cd01672	200	24	79.3	0.98	[     --------                                    ]	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).
142	PRK09087	226	19	79.2	1.2	[     -------                                     ]	PRK09087	hypothetical protein; Validated
143	COG0237	201	21	79.1	1.4	[     -------                                     ]	CoaE	Dephospho-CoA kinase
144	COG1131	293	24	79.1	1.4	[     ---------                                   ]	CcmA	ABC-type multidrug transport system, ATPase component
145	COG0419	908	19	79.0	1.4	[     -------                                     ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
146	pfam02562	205	46	79.0	2.5	[-----------------                                ]	PhoH	PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
147	pfam02223	186	45	78.9	2.5	[      -----------------                          ]	Thymidylate_kin	Thymidylate kinase.
148	TIGR00174	287	16	78.6	0.83	[     -----                                       ]	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.
149	cd03221	144	31	78.6	1.6	[     -----------                                 ]	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.
150	COG1120	258	20	78.6	1.5	[     -------                                     ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
151	pfam01583	157	23	78.5	1.5	[     --------                                    ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
152	pfam08433	267	49	78.5	12	[                          -----------------      ]	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.
153	TIGR03922	557	25	78.1	1.2	[     ---------                                   ]	T7SS_EccA	type VII secretion AAA-ATPase EccA. This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc.
154	TIGR00455	184	21	78.1	1.5	[     -------                                     ]	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.
155	COG4133	209	20	77.9	1.4	[     -------                                     ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
156	PRK10078	186	21	77.9	1.2	[     -------                                     ]	PRK10078	ribose 1,5-bisphosphokinase; Provisional
157	COG0606	490	20	77.8	1.1	[     -------                                     ]	YifB	Predicted ATPase with chaperone activity
158	TIGR00968	237	21	77.8	1	[     -------                                     ]	3a0106s01	sulfate ABC transporter, ATP-binding protein.
159	cd14896	644	20	77.8	1.2	[     -------                                     ]	MYSc_Myo35	class XXXV myosin, motor domain. This class of metazoan myosins contains 2 IQ motifs, 2 MyTH4 domains, a single FERM domain, and an SH3 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.
160	COG0464	494	71	76.7	1.7	[     ---------------------------                 ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
161	COG1119	257	22	76.6	1.8	[      -------                                    ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
162	TIGR00611	365	17	76.4	1.8	[      -----                                      ]	recf	recF protein. All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
163	cd03262	213	19	76.3	1.7	[     -------                                     ]	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.
164	pfam01695	178	81	76.3	1.4	[     ---------------------------------           ]	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.
165	cd03116	159	22	76.2	1.4	[     -------                                     ]	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.
166	cd02022	179	20	76.0	1.9	[     -------                                     ]	DPCK	Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
167	TIGR04075	851	86	75.9	0.72	[     --------------------------------            ]	bacter_Pnkp	polynucleotide kinase-phosphatase. Members of this protein family are the bacterial polynucleotide kinase-phosphatase (Pnkp) whose genes occur paired with genes for the 3' terminal RNA ribose 2'-O-methyltransferase Hen1. All members of the seed alignment belong to a cassette with the Hen1. The pair acts in bacterial RNA repair. This enzyme performs end-healing reactions on broken RNA, preparing from the RNA ligase to close the break. The working hypothesis is that the combination of Pnkp (RNA repair) and Hen1 (RNA modification) serves to first repair RNA damage from ribotoxins and then perform a modification that prevents the damage from recurring.
168	PRK05201	443	21	75.8	1.8	[     -------                                     ]	hslU	ATP-dependent protease ATP-binding subunit HslU; Provisional
169	COG4148	352	20	75.6	1.7	[      ------                                     ]	ModC	ABC-type molybdate transport system, ATPase component
170	cd03268	208	22	75.6	1.9	[      -------                                    ]	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.
171	cd03261	235	23	75.6	1.9	[     --------                                    ]	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.
172	PRK13341	725	23	75.5	1.8	[     --------                                    ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
173	pfam03266	168	20	74.9	2.2	[     -------                                     ]	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.
174	cd02023	198	85	74.8	1.3	[     --------------------------------            ]	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.
175	cd03239	178	14	74.8	1.5	[      ----                                       ]	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.
176	TIGR01241	495	29	74.7	2.3	[  ----------                                     ]	FtsH_fam	ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
177	TIGR02673	214	31	74.7	2	[     -----------                                 ]	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.
178	PRK09452	375	20	74.6	1.9	[     -------                                     ]	potA	putrescine/spermidine ABC transporter ATPase protein; Reviewed
179	COG2884	223	30	74.3	2.1	[     -----------                                 ]	FtsE	ABC-type ATPase involved in cell division
180	PRK08118	167	23	74.3	2.2	[     --------                                    ]	PRK08118	topology modulation protein; Reviewed
181	pfam03029	235	34	74.3	2.1	[      ------------                               ]	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.
182	cd01393	226	16	74.2	1.8	[     ------                                      ]	recA_like	RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
183	cd04105	202	18	74.2	2.2	[     ------                                      ]	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.
184	pfam09439	181	56	74.2	5.1	[     ------------------------                    ]	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.
185	TIGR03265	353	20	74.0	1.7	[     -------                                     ]	PhnT2	putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
186	COG2804	500	34	74.0	2.2	[    ------------                                 ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
187	TIGR03167	311	23	74.0	1.5	[     -------                                     ]	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.
188	pfam10412	386	34	73.9	3.1	[     ------------                                ]	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.
189	pfam03193	161	23	73.8	1.6	[     -------                                     ]	DUF258	Protein of unknown function, DUF258.
190	PRK00080	328	23	73.8	2.2	[     --------                                    ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
191	cd03246	173	19	73.6	2.4	[     -------                                     ]	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.
192	PRK06761	282	22	73.6	1.6	[     -------                                     ]	PRK06761	hypothetical protein; Provisional
193	COG1222	406	30	73.5	2.9	[   ----------                                    ]	RPT1	ATP-dependent 26S proteasome regulatory subunit
194	COG2274	709	31	73.3	3.2	[     -----------                                 ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
195	TIGR02928	365	104	73.2	9.8	[     ----------------------------------------    ]	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.
196	COG1121	254	21	73.2	2.3	[     -------                                     ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
197	cd04170	268	60	73.2	2.2	[     -----------------------                     ]	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.
198	pfam00931	287	50	73.0	6.6	[     -------------------                         ]	NB-ARC	NB-ARC domain.
199	COG1127	263	76	72.7	2.4	[     -----------------------------               ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
200	cd03213	194	21	72.6	2.1	[     -------                                     ]	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.
201	TIGR00152	190	55	72.6	1.6	[     -------------------                         ]	TIGR00152	dephospho-CoA kinase. This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases.
202	cd03243	202	20	72.5	1.8	[     ------                                      ]	ABC_MutS_homologs	ATP-binding cassette domain of MutS homologs. 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 also possess 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.
203	TIGR03574	249	24	72.3	2.1	[     --------                                    ]	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.
204	PRK11831	269	78	72.2	6.3	[     ------------------------------              ]	PRK11831	putative ABC transporter ATP-binding protein YrbF; Provisional
205	TIGR02169	1164	18	72.2	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.
206	pfam13521	162	20	72.2	3	[     -------                                     ]	AAA_28	AAA domain.
207	COG0125	208	51	72.1	4.7	[     -------------------                         ]	Tmk	Thymidylate kinase
208	TIGR00390	441	23	72.1	4.7	[     --------                                    ]	hslU	ATP-dependent protease HslVU, ATPase subunit. This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment) is Ser in other members of the seed alignment.
209	COG1134	249	23	72.1	2.7	[     --------                                    ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
210	TIGR00382	413	20	72.1	2.5	[     -------                                     ]	clpX	endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
211	COG1474	366	78	72.0	2.6	[     -------------------------------             ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
212	PRK13648	269	17	72.0	2.4	[      -----                                      ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
213	COG2019	189	25	71.4	3.2	[    ---------                                    ]	AdkA	Archaeal adenylate kinase
214	TIGR00602	637	95	71.3	1.9	[     ---------------------------------------     ]	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).
215	COG0467	260	44	71.2	6.4	[     ---------------                             ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
216	cd03298	211	75	70.8	2.9	[      ----------------------------               ]	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.
217	cd03263	220	23	70.8	2.9	[     --------                                    ]	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.
218	cd03219	236	30	70.7	4	[     -----------                                 ]	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).
219	cd01122	271	36	70.6	2.4	[     -------------                               ]	GP4d_helicase	GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
220	cd03220	224	23	70.5	3.1	[     --------                                    ]	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.
221	cd03297	214	21	70.4	2.9	[     -------                                     ]	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.
222	PRK00279	215	23	70.1	3	[     --------                                    ]	adk	adenylate kinase; Reviewed
223	COG4608	268	23	70.0	2.9	[     --------                                    ]	AppF	ABC-type oligopeptide transport system, ATPase component
224	PRK13975	196	72	69.7	2.8	[     ------------------------------              ]	PRK13975	thymidylate kinase; Provisional
225	PRK05703	424	38	69.6	4.1	[     --------------                              ]	flhF	flagellar biosynthesis regulator FlhF; Validated
226	PRK12724	432	26	69.4	1.5	[    ---------                                    ]	PRK12724	flagellar biosynthesis regulator FlhF; Provisional
227	TIGR02322	179	17	69.2	2	[     -----                                       ]	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.
228	COG4778	235	31	69.2	4.9	[     -----------                                 ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
229	pfam14532	138	70	69.1	8.8	[     -----------------------------               ]	Sigma54_activ_2	Sigma-54 interaction domain.
230	pfam04670	229	23	69.0	2.2	[     --------                                    ]	Gtr1_RagA	Gtr1/RagA G protein conserved region. GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B.
231	TIGR02324	224	45	68.6	3.7	[     -----------------                           ]	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.
232	cd03274	212	23	68.5	2.5	[                      --------                   ]	ABC_SMC4_euk	ATP-binding cassette domain of eukaryotic SMC4 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).
233	COG1224	450	23	68.4	3.3	[     --------                                    ]	TIP49	DNA helicase TIP49, TBP-interacting protein
234	cd01854	211	24	68.3	3.3	[     --------                                    ]	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.
235	PRK09493	240	20	68.0	3.7	[     -------                                     ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
236	cd01123	235	33	67.9	3	[      -----------                                ]	Rad51_DMC1_radA	Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
237	cd00154	159	23	67.8	3.3	[     --------                                    ]	Rab	Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases). Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.
238	TIGR01184	230	20	67.6	3.5	[     -------                                     ]	ntrCD	nitrate transport ATP-binding subunits C and D. This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.
239	TIGR04520	268	21	67.5	3.9	[     -------                                     ]	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.
240	cd00882	161	20	67.4	4.7	[      -------                                    ]	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.
241	COG1220	444	23	67.4	3.8	[     --------                                    ]	HslU	ATP-dependent protease HslVU (ClpYQ), ATPase subunit
242	PRK11000	369	19	67.3	3.4	[     -------                                     ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
243	pfam04665	241	41	67.2	8.2	[     ---------------                             ]	Pox_A32	Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging.
244	cd01129	264	32	67.2	1.6	[     -----------                                 ]	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.
245	TIGR01243	733	73	67.0	8.7	[   ---------------------------                   ]	CDC48	AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
246	PRK13635	279	19	66.8	3.7	[     -------                                     ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
247	pfam03205	138	35	66.8	4	[     ------------                                ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
248	pfam06068	395	23	66.5	3.8	[     --------                                    ]	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.
249	cd01124	187	44	66.5	8.7	[     ----------------                            ]	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.
250	TIGR02203	571	42	66.4	3.4	[     ---------------                             ]	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.
251	cd03235	213	19	66.3	4.2	[     -------                                     ]	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.
252	PRK05416	288	21	66.0	3	[     -------                                     ]	PRK05416	glmZ(sRNA)-inactivating NTPase; Provisional
253	COG3709	192	17	65.8	2.6	[     -----                                       ]	PhnN	Ribose 1,5-bisphosphokinase PhnN
254	PRK00411	394	24	65.8	12	[     ---------                                   ]	cdc6	cell division control protein 6; Reviewed
255	PRK00698	205	24	65.6	3.2	[     --------                                    ]	tmk	thymidylate kinase; Validated
256	COG2255	332	23	65.6	4.2	[     --------                                    ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
257	pfam13481	192	53	65.5	17	[     -------------------                         ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
258	cd09639	353	92	65.3	12	[     -------------------------------------       ]	Cas3_I	CRISPR/Cas system-associated protein Cas3. 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; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
259	TIGR00958	711	23	65.3	4.3	[     --------                                    ]	3a01208	Conjugate Transporter-2 (CT2) Family protein.
260	TIGR01313	163	23	64.8	4.6	[     --------                                    ]	therm_gnt_kin	carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.
261	PRK14247	250	50	64.7	4.6	[      -------------------                        ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
262	PRK09183	259	84	64.6	3.6	[     ----------------------------------          ]	PRK09183	transposase/IS protein; Provisional
263	COG4170	330	18	64.4	4.1	[      ------                                     ]	SapD	ABC-type antimicrobial peptide transport system, ATPase component
264	cd01394	218	43	64.4	6.3	[      ---------------                            ]	radB	RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
265	PRK13640	282	18	64.3	4.1	[      ------                                     ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
266	PRK11248	255	20	64.1	3.7	[     -------                                     ]	tauB	taurine transporter ATP-binding subunit; Provisional
267	cd03275	247	18	63.9	4.1	[      ------                                     ]	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).
268	TIGR02072	240	90	63.8	15	[       ----------------------------------------- ]	BioC	malonyl-acyl carrier protein O-methyltransferase BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, carries out an enzymatic step prior to the formation of pimeloyl-CoA, namely O-methylation of the malonyl group preferentially while on acyl carrier protein. The enzyme is recognizable as a methyltransferase by homology.
269	pfam00006	213	48	63.8	18	[     ------------------                          ]	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.
270	PRK10938	490	50	63.6	6.4	[      -------------------                        ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
271	PRK11264	250	18	63.6	4.3	[     ------                                      ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
272	cd00124	633	20	63.5	4.5	[     -------                                     ]	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.
273	cd03234	226	23	63.2	4.4	[     --------                                    ]	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.
274	PRK13548	258	25	63.1	5.3	[     ---------                                   ]	hmuV	hemin importer ATP-binding subunit; Provisional
275	PRK14953	486	39	63.1	4.9	[     ----------------                            ]	PRK14953	DNA polymerase III subunits gamma and tau; Provisional
276	COG0468	279	35	62.7	4	[     ------------                                ]	RecA	RecA/RadA recombinase
277	cd03279	213	20	62.7	5.8	[     -------                                     ]	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.
278	cd03248	226	23	62.7	5.5	[     --------                                    ]	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.
279	TIGR01420	343	24	62.5	2.7	[  --------                                       ]	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.
280	pfam00625	183	26	62.4	5.8	[     ---------                                   ]	Guanylate_kin	Guanylate kinase.
281	pfam13604	195	26	62.2	6.2	[     ---------                                   ]	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.
282	pfam00485	196	82	61.9	13	[     ----------------------------------          ]	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.
283	PRK05563	559	23	61.7	5	[     --------                                    ]	PRK05563	DNA polymerase III subunits gamma and tau; Validated
284	COG3638	258	23	61.5	5.6	[     --------                                    ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
285	COG3840	231	30	61.4	5.5	[      ----------                                 ]	ThiQ	ABC-type thiamine transport system, ATPase component
286	cd03267	236	21	61.3	5.4	[     -------                                     ]	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.
287	pfam00503	317	23	61.2	5.7	[     --------                                    ]	G-alpha	G-protein alpha subunit. G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.
288	cd01131	198	16	61.0	3.2	[     -----                                       ]	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.
289	PRK09984	262	23	60.6	5.9	[     --------                                    ]	PRK09984	phosphonate/organophosphate ester transporter subunit; Provisional
290	cd03286	218	19	60.5	5.5	[     ------                                      ]	ABC_MSH6_euk	ATP-binding cassette domain of eukaryotic MutS6 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.
291	TIGR00041	195	47	60.5	7	[     -----------------                           ]	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.
292	PRK11432	351	20	60.3	4.9	[     -------                                     ]	fbpC	ferric transporter ATP-binding subunit; Provisional
293	PRK14490	369	38	60.0	5.4	[     --------------                              ]	PRK14490	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional
294	TIGR03797	686	18	59.8	5.6	[     ------                                      ]	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.
295	PRK01184	184	22	59.6	4.3	[     -------                                     ]	PRK01184	hypothetical protein; Provisional
296	COG1419	407	40	59.5	7.9	[     --------------                              ]	FlhF	Flagellar biosynthesis GTPase FlhF
297	COG2812	515	23	59.4	4.4	[     --------                                    ]	DnaX	DNA polymerase III, gamma/tau subunits
298	TIGR00763	775	76	59.4	5.2	[     ----------------------------                ]	lon	endopeptidase La. This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
299	PRK10436	462	16	59.3	3.1	[     -----                                       ]	PRK10436	hypothetical protein; Provisional
300	TIGR02142	354	21	59.3	6	[      -------                                    ]	modC_ABC	molybdenum ABC transporter, ATP-binding protein. This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.
301	TIGR02639	730	62	59.3	8.1	[     ------------------------                    ]	ClpA	ATP-dependent Clp protease ATP-binding subunit clpA.
302	cd01918	149	22	59.3	5.4	[     --------                                    ]	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.
303	PRK13951	488	23	59.3	5.1	[     --------                                    ]	PRK13951	bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
304	cd03223	166	37	59.2	6.8	[     -------------                               ]	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).
305	PRK15093	330	17	59.0	5.8	[      ------                                     ]	PRK15093	antimicrobial peptide ABC transporter ATP-binding protein; Provisional
306	COG0466	782	74	58.9	6	[     ----------------------------                ]	Lon	ATP-dependent Lon protease, bacterial type
307	TIGR02857	529	19	58.7	6.4	[     -------                                     ]	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
308	cd03242	270	19	58.6	7.1	[     -------                                     ]	ABC_RecF	ATP-binding cassette domain of RecF. RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters 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 with 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.
309	COG1117	253	18	58.6	6.7	[     ------                                      ]	PstB	ABC-type phosphate transport system, ATPase component
310	cd03292	214	21	58.5	6.9	[     -------                                     ]	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.
311	cd03299	235	23	58.4	6.7	[     --------                                    ]	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.
312	pfam01202	158	40	58.3	8.4	[       ----------------                          ]	SKI	Shikimate kinase.
313	pfam00448	195	73	58.1	8.7	[     -------------------------------             ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
314	PRK14528	186	24	58.1	5.9	[     --------                                    ]	PRK14528	adenylate kinase; Provisional
315	PRK13695	174	22	58.0	7.3	[     --------                                    ]	PRK13695	putative NTPase; Provisional
316	TIGR04435	555	19	57.8	7	[     -------                                     ]	restrict_AAA_1	restriction system-associated AAA family ATPase. Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements.
317	pfam02492	178	35	57.7	14	[     ------------                                ]	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.
318	pfam10662	143	27	57.6	6.7	[     ----------                                  ]	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.
319	cd03256	241	22	57.2	7.2	[     --------                                    ]	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.
320	pfam00488	235	19	57.2	5.5	[     ------                                      ]	MutS_V	MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.
321	PRK11701	258	36	56.7	7.5	[     -------------                               ]	phnK	phosphonate C-P lyase system protein PhnK; Provisional
322	COG5271	4600	70	56.4	12	[     -------------------------                   ]	MDN1	Midasin, AAA ATPase with vWA domain, involved in ribosome maturation
323	cd03264	211	22	56.2	8.2	[      -------                                    ]	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.
324	TIGR03873	256	22	56.2	7.4	[      -------                                    ]	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.
325	TIGR00368	499	20	56.1	6.2	[     -------                                     ]	TIGR00368	Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
326	COG0488	530	18	56.1	7.3	[     ------                                      ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
327	TIGR01242	364	30	56.0	10	[   ----------                                    ]	26Sp45	26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
328	COG2805	353	18	55.9	4.4	[    ------                                       ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
329	COG4107	258	31	55.8	7.7	[     -----------                                 ]	PhnK	ABC-type phosphonate transport system, ATPase component
330	COG1066	456	73	55.8	20	[     ----------------------------                ]	Sms	Predicted ATP-dependent serine protease
331	PRK00440	319	82	55.7	7	[     --------------------------------            ]	rfc	replication factor C small subunit; Reviewed
332	pfam07726	131	41	55.7	9.1	[     ---------------                             ]	AAA_3	ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
333	COG1936	180	23	55.7	7.1	[     --------                                    ]	Fap7	Broad-specificity NMP kinase
334	PRK14962	472	23	55.7	8	[     --------                                    ]	PRK14962	DNA polymerase III subunits gamma and tau; Provisional
335	cd03284	216	19	55.6	5	[     ------                                      ]	ABC_MutS1	ATP-binding cassette domain of MutS1 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.
336	COG4618	580	23	55.5	7.5	[     --------                                    ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
337	cd04107	201	26	55.5	10	[     ---------                                   ]	Rab32_Rab38	Rab GTPase families 18 (Rab18) and 32 (Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins.
338	PRK00081	194	20	55.2	8.9	[     -------                                     ]	coaE	dephospho-CoA kinase; Reviewed
339	cd03226	205	23	55.2	8.5	[     --------                                    ]	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.
340	COG1763	161	20	55.0	5.6	[     ------                                      ]	MobB	Molybdopterin-guanine dinucleotide biosynthesis protein
341	COG0444	316	78	54.6	8.5	[     -------------------------------             ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
342	cd03283	199	22	54.5	8.2	[     -------                                     ]	ABC_MutS-like	ATP-binding cassette domain of MutS-like 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.
343	TIGR03015	269	91	54.4	9.3	[  ------------------------------------           ]	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.
344	pfam00493	330	72	54.3	8.3	[     --------------------------                  ]	MCM	MCM2/3/5 family.
345	pfam07693	301	36	54.3	17	[     -------------                               ]	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.
346	COG4639	168	20	54.3	4.8	[    -------                                      ]	COG4639	Predicted kinase
347	cd02030	219	19	54.2	6.4	[     -------                                     ]	NDUO42	NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is a family of proteins that are highly similar to deoxyribonucleoside kinases (dNK). Members of this family have been identified as one of the subunits of NADH:Ubiquinone oxioreductase (complex I), a multi-protein complex located in the inner mitochondrial membrane. The main function of the complex is to transport electrons from NADH to ubiquinone, which is accompanied by the translocation of protons from the mitochondrial matrix to the inter membrane space.
348	PRK00098	298	21	54.1	8.6	[     -------                                     ]	PRK00098	GTPase RsgA; Reviewed
349	TIGR00972	247	20	53.9	8.9	[     -------                                     ]	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.
350	COG1618	179	19	53.7	9.2	[     -------                                     ]	THEP1	Nucleoside-triphosphatase THEP1
351	PRK14239	252	19	53.7	8.9	[      ------                                     ]	PRK14239	phosphate transporter ATP-binding protein; Provisional
352	cd03217	200	18	53.6	9.4	[      ------                                     ]	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.
353	cd03269	210	23	53.4	8.8	[     --------                                    ]	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.
354	COG2909	894	78	53.4	4.9	[    ------------------------------               ]	MalT	ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT
355	PRK14489	366	83	53.2	5.8	[     ------------------------------              ]	PRK14489	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
356	PRK14956	484	36	53.1	9.9	[     -------------                               ]	PRK14956	DNA polymerase III subunits gamma and tau; Provisional
357	COG4988	559	27	52.8	12	[     ---------                                   ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
358	COG0411	250	23	52.8	2.8	[     --------                                    ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
359	PRK00635	1809	40	52.6	12	[    --------------                               ]	PRK00635	excinuclease ABC subunit A; Provisional
360	cd14938	713	18	52.6	8.7	[     ------                                      ]	MYSc_Myo24B	class XXIV B myosin, motor domain. These myosins have a 1-2 IQ motifs in their neck and a coiled-coil region in their C-terminal tail. The functions of these myosins remain elusive. 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.
361	cd01868	165	25	52.3	11	[     ---------                                   ]	Rab11_like	Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
362	COG1204	766	35	52.0	12	[     ------------                                ]	BRR2	Replicative superfamily II helicase
363	PRK05057	172	23	51.9	10	[     --------                                    ]	aroK	shikimate kinase I; Reviewed
364	pfam00580	267	15	51.9	7.3	[     -----                                       ]	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.
365	pfam00158	168	19	51.8	24	[     -------                                     ]	Sigma54_activat	Sigma-54 interaction domain.
366	COG0465	596	24	51.8	6.3	[    --------                                     ]	HflB	ATP-dependent Zn proteases
367	TIGR02788	308	42	51.7	20	[ ---------------                                 ]	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.
368	PRK11174	588	19	51.7	9.3	[     -------                                     ]	PRK11174	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
369	TIGR01187	325	18	51.5	8	[      ------                                     ]	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).
370	PRK14529	223	23	51.4	6.7	[     --------                                    ]	PRK14529	adenylate kinase; Provisional
371	COG4181	228	18	51.3	8.5	[     ------                                      ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
372	PRK10744	260	27	50.8	9.5	[     ---------                                   ]	pstB	phosphate transporter ATP-binding protein; Provisional
373	cd03252	237	23	50.7	11	[     --------                                    ]	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.
374	COG0249	843	19	50.6	6.9	[     ------                                      ]	MutS	DNA mismatch repair ATPase MutS
375	COG1493	308	23	50.6	8.5	[     --------                                    ]	HprK	Serine kinase of the HPr protein, regulates carbohydrate metabolism
376	COG4178	604	23	50.3	10	[     --------                                    ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
377	cd00133	84	31	50.2	11	[     -----------                                 ]	PTS_IIB	PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby regulating their activity.
378	PRK06893	229	65	50.2	16	[      --------------------------                 ]	PRK06893	DNA replication initiation factor; Validated
379	TIGR00635	305	23	50.1	11	[     --------                                    ]	ruvB	Holliday junction DNA helicase, RuvB subunit. All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
380	TIGR03238	504	90	49.8	9	[     ----------------------------------          ]	dnd_assoc_3	DNA phosphorothioation-dependent restriction protein DptF. A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation.
381	pfam13175	344	20	49.7	10	[     ------                                      ]	AAA_15	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
382	cd03277	213	17	49.6	13	[      -----                                      ]	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).
383	PRK13851	344	31	49.4	9.8	[     -----------                                 ]	PRK13851	type IV secretion system protein VirB11; Provisional
384	COG0630	312	23	49.1	19	[     --------                                    ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
385	pfam00308	219	71	49.0	34	[     ---------------------------                 ]	Bac_DnaA	Bacterial dnaA protein.
386	TIGR02759	566	45	48.9	11	[     ----------------                            ]	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).
387	cd00876	160	54	48.8	11	[     -------------------                         ]	Ras	Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases). The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
388	pfam01443	227	20	48.8	11	[      ------                                     ]	Viral_helicase1	Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.
389	TIGR02315	243	20	48.7	9.9	[     -------                                     ]	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.
390	PRK08116	268	15	48.7	12	[     -----                                       ]	PRK08116	hypothetical protein; Validated
391	TIGR02528	142	27	48.6	10	[     ----------                                  ]	EutP	ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.
392	TIGR01485	249	57	48.3	43	[                 ---------------------           ]	SPP_plant-cyano	sucrose-6F-phosphate phosphohydrolase. This model describes the sucrose phosphate phosphohydrolase from plants and cyanobacteria (SPP). SPP is a member of the Class IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose, contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.
393	cd03233	202	22	48.1	13	[     --------                                    ]	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.
394	PRK03695	248	19	48.0	13	[     -------                                     ]	PRK03695	vitamin B12-transporter ATPase; Provisional
395	PRK14970	367	25	47.8	10	[     ---------                                   ]	PRK14970	DNA polymerase III subunits gamma and tau; Provisional
396	COG1223	368	60	47.7	12	[     ----------------------                      ]	COG1223	Predicted ATPase, AAA+ superfamily
397	PRK09473	330	15	47.5	9.1	[     -----                                       ]	oppD	oligopeptide transporter ATP-binding component; Provisional
398	TIGR01842	544	20	47.4	12	[     -------                                     ]	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.
399	cd03238	176	35	47.3	10	[     ------------                                ]	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.
400	TIGR03345	852	31	47.2	11	[     -----------                                 ]	VI_ClpV1	type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
401	cd04106	162	47	47.1	25	[      --------------------                       ]	Rab23_like	Rab GTPase family 23 (Rab23)-like. Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
402	pfam00270	167	56	46.8	11	[     ---------------------                       ]	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.
403	pfam05272	198	23	46.8	11	[     --------                                    ]	VirE	Virulence-associated protein E. This family contains several bacterial virulence-associated protein E like proteins. These proteins contain a P-loop motif.
404	PRK14243	264	57	46.6	12	[     ------------------------------              ]	PRK14243	phosphate transporter ATP-binding protein; Provisional
405	COG1162	301	20	46.5	13	[     -------                                     ]	RsgA	Putative ribosome biogenesis GTPase RsgA
406	cd01850	275	17	46.4	12	[     ------                                      ]	CDC_Septin	CDC/Septin GTPase family. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
407	TIGR02640	262	20	46.4	14	[     -------                                     ]	gas_vesic_GvpN	gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).
408	cd03250	204	21	46.0	9.7	[     -------                                     ]	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.
409	cd03282	204	16	45.7	15	[     ------                                      ]	ABC_MSH4_euk	ATP-binding cassette domain of eukaryotic MutS4 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.
410	TIGR03258	362	20	45.3	12	[     -------                                     ]	PhnT	2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT. This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.
411	COG4559	259	23	45.2	15	[     --------                                    ]	COG4559	ABC-type hemin transport system, ATPase component
412	pfam05496	234	23	45.1	15	[     --------                                    ]	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.
413	COG0396	251	23	44.9	15	[      --------                                   ]	SufC	Fe-S cluster assembly ATPase SufC
414	cd03247	178	24	44.9	15	[     ---------                                   ]	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.
415	COG3451	796	36	44.9	29	[      ------------                               ]	VirB4	Type IV secretory pathway, VirB4 component
416	PRK11147	635	21	44.7	14	[     -------                                     ]	PRK11147	ABC transporter ATPase component; Reviewed
417	COG4987	573	47	44.5	15	[     -----------------                           ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
418	COG4172	534	18	44.4	12	[     ------                                      ]	YejF	ABC-type microcin C transport system, duplicated ATPase component YejF
419	pfam06745	231	38	44.4	59	[     --------------                              ]	KaiC	KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria.
420	TIGR04521	277	17	44.2	16	[     ------                                      ]	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.
421	pfam07931	174	22	44.0	12	[     -------                                     ]	CPT	Chloramphenicol phosphotransferase-like protein. The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite.
422	TIGR01193	708	23	43.8	14	[     --------                                    ]	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.
423	PRK13632	271	22	43.6	15	[     --------                                    ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
424	pfam13477	139	53	43.6	68	[                   --------------------          ]	Glyco_trans_4_2	Glycosyl transferase 4-like.
425	TIGR02236	310	83	43.4	16	[      ------------------------------             ]	recomb_radA	DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
426	PRK09270	229	23	43.4	9.3	[     -------                                     ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
427	cd03276	198	66	43.4	17	[      -----------------------------              ]	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).
428	PRK12402	337	21	43.0	17	[     -------                                     ]	PRK12402	replication factor C small subunit 2; Reviewed
429	TIGR00176	155	51	42.9	16	[     ---------------------                       ]	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.
430	PRK14265	274	43	42.8	14	[    ----------------                             ]	PRK14265	phosphate ABC transporter ATP-binding protein; Provisional
431	COG0410	237	23	42.7	18	[     --------                                    ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
432	PRK13477	512	23	42.7	13	[     --------                                    ]	PRK13477	bifunctional pantoate ligase/cytidylate kinase; Provisional
433	cd03224	222	21	42.7	18	[     -------                                     ]	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.
434	TIGR01360	188	22	42.6	12	[     -------                                     ]	aden_kin_iso1	adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
435	COG1660	286	21	42.1	14	[     -------                                     ]	RapZ	RNase adaptor protein for sRNA GlmZ degradation, contains a P-loop ATPase domain
436	pfam01057	271	22	42.1	17	[     --------                                    ]	Parvo_NS1	Parvovirus non-structural protein NS1. This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity.
437	COG0488	530	25	42.0	17	[     ---------                                   ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
438	PRK12269	863	22	42.0	15	[     --------                                    ]	PRK12269	bifunctional cytidylate kinase/ribosomal protein S1; Provisional
439	PRK14734	200	24	41.8	13	[     --------                                    ]	coaE	dephospho-CoA kinase; Provisional
440	PRK06620	214	20	41.8	15	[     -------                                     ]	PRK06620	hypothetical protein; Validated
441	COG1061	442	34	41.7	25	[     -------------                               ]	SSL2	Superfamily II DNA or RNA helicase
442	COG5019	373	18	41.6	14	[     ------                                      ]	CDC3	Septin family protein
443	COG3854	308	35	41.4	27	[     ------------                                ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
444	COG2204	464	71	41.4	1.8E+02	[     -------------------------                   ]	AtoC	DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains
445	TIGR02903	615	27	41.1	29	[  ---------                                      ]	spore_lon_C	ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
446	PRK14250	241	32	40.9	27	[      -----------                                ]	PRK14250	phosphate ABC transporter ATP-binding protein; Provisional
447	PRK06073	124	26	40.9	20	[                             -----------         ]	PRK06073	NADH dehydrogenase subunit A; Validated
448	PRK05399	854	19	40.7	14	[     ------                                      ]	PRK05399	DNA mismatch repair protein MutS; Provisional
449	pfam08298	358	25	40.4	19	[     ---------                                   ]	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.
450	cd09914	161	23	40.2	20	[     --------                                    ]	RocCOR	Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family. RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease.
451	COG0542	786	31	40.0	18	[     -----------                                 ]	ClpA	ATP-dependent Clp protease ATP-binding subunit ClpA
452	pfam02302	96	19	40.0	21	[     -------                                     ]	PTS_IIB	PTS system, Lactose/Cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This family also contains the fructose specific IIB subunit.
453	TIGR01846	694	23	39.9	19	[     --------                                    ]	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.
454	pfam00071	162	25	39.9	20	[     ---------                                   ]	Ras	Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices.
455	cd03266	218	21	39.9	16	[      -------                                    ]	ABC_NatA_sodium_exporter	ATP-binding cassette domain of the Na+ transporter. 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 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 a single ATP-binding protein and a single integral membrane protein.
456	cd03232	192	21	39.8	20	[     -------                                     ]	ABCG_PDR_domain2	Second domain of the pleiotropic drug resistance-like (PDR) 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.
457	PRK10575	265	23	39.6	19	[     --------                                    ]	PRK10575	iron-hydroxamate transporter ATP-binding subunit; Provisional
458	COG0645	170	22	39.5	15	[     -------                                     ]	COG0645	Predicted kinase
459	pfam05970	362	71	39.0	88	[     -------------------------                   ]	PIF1	PIF1-like helicase. This family includes homologues of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.
460	TIGR00073	208	68	39.0	18	[     --------------------------                  ]	hypB	hydrogenase accessory protein HypB. A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs.
461	COG1123	539	20	38.7	21	[     -------                                     ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
462	pfam13166	713	67	38.6	23	[      ------------------------                   ]	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.
463	TIGR02538	564	16	38.5	10	[    ------                                       ]	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.
464	pfam15341	116	21	38.2	25	[                             -------             ]	SLX9	Ribosome biogenesis protein SLX9. SLX9 is present in pre-ribosomes from an early stage and is implicated in the processing events that remove the ITS1 spacer sequences. In eukaryotes, biogenesis of ribosomes starts in the nucleolus with transcription by RNA polymerase I of a large precursor RNA molecule, called 35S pre-rRNA in yeast, in which the 18S, 5.8S, and 25S mature rRNAs reside, while RNA polymerase III transcribes a 3'-extended pre-5S rRNA. The 35S precursor also contains external transcribed spacer elements (5' and 3'-ETS) at either end as well as internal transcribed spacers (ITS1 and ITS2) that separate the mature sequences.
465	COG5008	375	19	38.1	12	[    ------                                       ]	PilU	Tfp pilus assembly protein, ATPase PilU
466	TIGR00362	437	84	38.0	72	[     --------------------------------            ]	DnaA	chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
467	cd03216	163	58	37.8	24	[      --------------------                       ]	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.
468	cd00227	175	75	37.6	14	[     --------------------------------            ]	CPT	Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.
469	PRK11231	255	22	37.4	19	[     -------                                     ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
470	PRK08727	233	18	37.4	18	[     ------                                      ]	PRK08727	hypothetical protein; Validated
471	PRK07940	394	18	37.3	20	[     ------                                      ]	PRK07940	DNA polymerase III subunit delta'; Validated
472	COG4917	148	73	37.2	63	[     --------------------------                  ]	EutP	Ethanolamine utilization protein EutP, contains a P-loop NTPase domain
473	cd03273	251	52	36.8	41	[      ----------------------                     ]	ABC_SMC2_euk	ATP-binding cassette domain of eukaryotic SMC2 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).
474	cd01889	192	21	36.8	23	[      -------                                    ]	SelB_euk	SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea.
475	cd00878	158	63	36.7	25	[     -----------------------                     ]	Arf_Arl	ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.
476	pfam01926	114	19	36.6	27	[     -------                                     ]	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.
477	PRK04301	317	51	36.5	14	[      -------------------                        ]	radA	DNA repair and recombination protein RadA; Validated
478	PRK14237	267	20	36.4	21	[     ------                                      ]	PRK14237	phosphate transporter ATP-binding protein; Provisional
479	PRK09536	402	24	36.3	17	[     --------                                    ]	btuD	corrinoid ABC transporter ATPase; Reviewed
480	TIGR03771	223	20	36.1	21	[     -------                                     ]	anch_rpt_ABC	anchored repeat-type ABC transporter, ATP-binding subunit. This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.
481	COG3973	747	16	36.1	14	[     -----                                       ]	HelD	DNA helicase IV
482	cd03270	226	17	36.0	13	[     -----                                       ]	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.
483	cd11384	286	23	36.0	20	[     --------                                    ]	RagA_like	Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins A and B. RagA and RagB are closely related Rag GTPases (ras-related GTP-binding protein A and B) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr1. These domains function by forming heterodimers with RagC or RagD, and similarly, Gtr1 dimerizes with Gtr2, through the carboxy-terminal segments. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7.
484	TIGR02868	530	20	35.9	23	[     -------                                     ]	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.
485	TIGR00101	199	21	35.6	25	[     -------                                     ]	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.
486	TIGR02323	253	23	35.6	24	[     --------                                    ]	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.
487	COG0552	340	42	35.6	25	[     ---------------                             ]	FtsY	Signal recognition particle GTPase
488	TIGR02204	576	23	35.6	25	[     --------                                    ]	MsbA_rel	ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.
489	PRK10790	592	23	35.4	25	[     --------                                    ]	PRK10790	putative multidrug transporter membrane\ATP-binding components; Provisional
490	PRK06851	367	18	35.4	26	[      ------                                     ]	PRK06851	hypothetical protein; Provisional
491	TIGR00929	785	43	35.4	42	[      ---------------                            ]	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).
492	cd01863	161	23	35.3	20	[     --------                                    ]	Rab18	Rab GTPase family 18 (Rab18). Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
493	PRK14236	272	18	35.3	23	[     ------                                      ]	PRK14236	phosphate transporter ATP-binding protein; Provisional
494	PRK14249	251	18	35.1	38	[     ------                                      ]	PRK14249	phosphate ABC transporter ATP-binding protein; Provisional
495	TIGR02782	299	28	35.0	24	[   ----------                                    ]	TrbB_P	P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
496	cd01735	61	18	34.8	7.4	[     ------                                      ]	LSm12_N	Like-Sm protein 12, N-terminal domain. LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
497	PRK05506	632	23	34.8	25	[     --------                                    ]	PRK05506	bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
498	COG4962	355	31	34.4	38	[     -----------                                 ]	CpaF	Pilus assembly protein, ATPase of CpaF family
499	pfam01637	223	44	34.4	57	[     ----------------                            ]	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.
500	PRK05537	568	19	33.7	34	[     -------                                     ]	PRK05537	bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated