match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	cd09740	84	69	99.9	2.6E-23	[     ------------                                ]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
2	pfam09620	80	69	99.9	2.1E-22	[     ------------                                ]	Cas_csx3	CRISPR-associated protein (Cas_csx3). This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
3	cd09681	83	67	99.9	4.4E-23	[     ------------                                ]	Csx3_III-U	CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains
4	TIGR02579	83	67	99.9	4.4E-23	[     ------------                                ]	cas_csx3	CRISPR-associated protein, Csx3 family. Members of this family are found encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
5	cd00009	151	77	98.0	2E-05	[                  ----------------               ]	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.
6	pfam13671	143	100	97.8	0.00038	[                   ----------------------        ]	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.
7	pfam13481	192	128	97.6	0.00085	[                  -----------------------        ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
8	pfam13207	114	22	97.5	0.00011	[                   ---                           ]	AAA_17	AAA domain.
9	PRK09270	229	41	97.3	0.00025	[                  -------                        ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
10	pfam01926	114	20	97.3	0.0019	[                   ---                           ]	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.
11	pfam13401	124	82	97.2	0.00089	[                   --------------                ]	AAA_22	AAA domain.
12	COG1100	219	100	97.2	0.00064	[                  -----------------              ]	Gem1	GTPase SAR1 family domain
13	pfam00004	131	45	97.2	0.001	[                   --------                      ]	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.
14	COG1084	346	117	97.1	0.00029	[                 ------------------------        ]	Nog1	GTP-binding protein, GTP1/Obg family
15	PRK00131	175	162	97.1	0.0016	[                  -------------------------------]	aroK	shikimate kinase; Reviewed
16	cd04163	168	101	97.0	0.0058	[                   -----------------             ]	Era	E. coli Ras-like protein (Era) is a multifunctional GTPase. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA.
17	cd00882	161	123	96.9	0.0047	[                   -------------------------     ]	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.
18	COG0563	178	32	96.8	0.0052	[                   -----                         ]	Adk	Adenylate kinase or related kinase
19	pfam08477	118	52	96.5	0.014	[                                ---------        ]	Miro	Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
20	cd01983	99	64	96.5	0.011	[                   ------------------            ]	Fer4_NifH	The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
21	pfam00910	105	25	96.5	0.0033	[                   ----                          ]	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.
22	pfam03266	168	89	96.5	0.0049	[                   ---------------               ]	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.
23	pfam13238	128	22	96.4	0.0022	[                   ---                           ]	AAA_18	AAA domain.
24	pfam13191	156	40	96.4	0.0044	[                  -------                        ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
25	cd01897	167	110	96.4	0.0018	[                   ---------------------         ]	NOG	Nucleolar GTP-binding protein (NOG). NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins.
26	cd00464	154	101	96.3	0.051	[                   -------------------           ]	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.
27	pfam07728	135	31	96.2	0.0047	[                   -----                         ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
28	PRK08116	268	92	96.2	0.0057	[               -------------------               ]	PRK08116	hypothetical protein; Validated
29	pfam13555	60	26	96.2	0.0071	[                   ----                          ]	AAA_29	P-loop containing region of AAA domain.
30	COG1484	254	71	96.1	0.017	[                   ---------------               ]	DnaC	DNA replication protein DnaC
31	COG4088	261	97	96.1	0.0046	[                   ------------------            ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
32	COG0470	325	27	96.0	0.0091	[                   ----                          ]	HolB	DNA polymerase III, delta prime subunit
33	cd04164	159	98	96.0	0.005	[                  -----------------              ]	trmE	trmE is a tRNA modification GTPase. TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
34	cd01893	168	94	96.0	0.041	[                  ---------------------          ]	Miro1	Mitochondrial Rho family 1 (Miro1), N-terminal. Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
35	pfam08433	267	33	95.9	0.0078	[                   -----                         ]	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.
36	cd01120	165	33	95.8	0.14	[                   -----                         ]	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.
37	pfam12846	298	42	95.8	0.013	[                  --------                       ]	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.
38	pfam13521	162	21	95.8	0.0068	[                   ---                           ]	AAA_28	AAA domain.
39	pfam13476	203	25	95.7	0.0094	[                   ---                           ]	AAA_23	AAA domain.
40	PRK13768	253	138	95.7	0.067	[                   ----------------------        ]	PRK13768	GTPase; Provisional
41	cd01898	170	30	95.6	0.0056	[                   -----                         ]	Obg	Obg GTPase. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.
42	pfam13604	195	146	95.5	0.071	[                  ----------------------------   ]	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.
43	pfam01695	178	78	95.4	0.017	[                  ----------------               ]	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.
44	pfam03205	138	51	95.4	0.021	[                  --------                       ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
45	pfam06414	194	107	95.4	0.033	[                  -------------------            ]	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.
46	cd02028	179	33	95.2	0.053	[                   -----                         ]	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).
47	pfam00448	195	155	95.2	0.24	[                   --------------------------    ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
48	pfam13304	144	22	95.1	0.015	[                   ---                           ]	AAA_21	AAA domain.
49	cd01881	167	29	94.8	0.015	[                   -----                         ]	Obg_like	Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified.
50	cd03262	213	34	94.5	0.026	[              --------                           ]	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.
51	cd00071	137	21	94.4	0.03	[                   ---                           ]	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.
52	COG1126	240	32	94.3	0.03	[                   -----                         ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
53	PRK08118	167	39	94.3	0.032	[                   ------                        ]	PRK08118	topology modulation protein; Reviewed
54	cd00881	183	113	94.2	0.083	[                   ----------------------        ]	GTP_translation_factor	GTP translation factor family primarily contains translation initiation, elongation and release factors. The GTP translation factor family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function.
55	cd01882	231	135	94.2	0.053	[                  -------------------------      ]	BMS1	Bms1, an essential GTPase, promotes assembly of preribosomal RNA processing complexes. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
56	cd04170	268	116	94.2	0.16	[                   ----------------------        ]	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.
57	cd03228	171	28	94.2	0.034	[                  -----                          ]	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.
58	cd02019	69	32	94.1	0.08	[                   -----                         ]	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.
59	PRK04195	482	31	94.1	0.034	[                 -----                           ]	PRK04195	replication factor C large subunit; Provisional
60	cd00267	157	38	94.1	0.035	[                  -------                        ]	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.
61	cd03227	162	120	94.1	0.11	[               -----------------------           ]	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.
62	TIGR03574	249	25	94.0	0.044	[                   ----                          ]	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.
63	pfam00519	432	84	94.0	0.04	[                  ---------------                ]	PPV_E1_C	Papillomavirus helicase. This protein is a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508.
64	cd01856	171	24	94.0	0.046	[                  ----                           ]	YlqF	Circularly permuted YlqF GTPase. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga).
65	COG0703	172	162	94.0	0.67	[                  ------------------------------ ]	AroK	Shikimate kinase
66	cd03225	211	22	93.7	0.048	[                  ----                           ]	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.
67	pfam13173	127	26	93.7	0.073	[                  ----                           ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
68	PRK09563	287	24	93.6	0.054	[                  ----                           ]	rbgA	GTPase YlqF; Reviewed
69	PRK09087	226	98	93.6	0.047	[              -----------------------            ]	PRK09087	hypothetical protein; Validated
70	PRK05800	170	36	93.6	0.095	[                   ------                        ]	cobU	adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated
71	pfam13614	145	107	93.6	1.3	[                   ------------------            ]	AAA_31	AAA domain. This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.
72	PRK00089	292	119	93.4	0.4	[                   --------------------          ]	era	GTPase Era; Reviewed
73	pfam08298	358	49	93.4	0.12	[                   --------                      ]	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.
74	TIGR02525	372	27	93.3	0.082	[                   ----                          ]	plasmid_TraJ	plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
75	cd00880	161	21	93.3	0.49	[                   ---                           ]	Era_like	E. coli Ras-like protein (Era)-like GTPase. The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.
76	TIGR03596	276	84	93.3	0.068	[                  --------------------           ]	GTPase_YlqF	ribosome biogenesis GTP-binding protein YlqF. Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members.
77	PRK05291	449	96	93.2	0.059	[                  -----------------              ]	trmE	tRNA modification GTPase TrmE; Reviewed
78	COG1341	398	112	93.2	0.55	[                  -------------------            ]	Grc3	Polynucleotide 5'-kinase, involved in rRNA processing
79	PRK04182	180	24	93.2	0.08	[                   ---                           ]	PRK04182	cytidylate kinase; Provisional
80	pfam13245	72	23	93.2	0.097	[                   ---                           ]	AAA_19	Part of AAA domain.
81	cd01855	191	68	93.2	0.088	[         -------------                           ]	YqeH	Circularly permuted YqeH GTPase. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH 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.
82	cd01895	174	101	93.2	0.071	[                  ------------------             ]	EngA2	EngA2 GTPase contains the second domain of EngA. This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
83	pfam05729	165	78	93.1	0.14	[                   --------------                ]	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.
84	cd02027	149	25	93.1	0.095	[                   ----                          ]	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.
85	pfam02421	156	32	93.0	0.1	[                  -------                        ]	FeoB_N	Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
86	COG0464	494	59	92.8	0.09	[                  -----------                    ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
87	PRK06620	214	54	92.7	0.062	[              ---------                          ]	PRK06620	hypothetical protein; Validated
88	COG0593	408	66	92.7	0.054	[              ----------                         ]	DnaA	Chromosomal replication initiation ATPase DnaA
89	COG0467	260	35	92.6	0.13	[                  ------                         ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
90	cd01428	194	108	92.6	0.094	[                   -----------------------       ]	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.
91	pfam01078	207	19	92.6	0.079	[                   --                            ]	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.
92	COG1072	283	38	92.6	0.14	[                  ------                         ]	CoaA	Panthothenate kinase
93	cd02042	104	63	92.5	1.7	[                    -----------------            ]	ParA	ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
94	pfam09848	348	124	92.5	0.62	[                   ----------------------        ]	DUF2075	Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
95	COG4639	168	20	92.4	0.063	[                   ---                           ]	COG4639	Predicted kinase
96	pfam02492	178	34	92.3	0.1	[                  ------                         ]	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.
97	pfam00005	150	25	92.2	0.11	[                  ----                           ]	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.
98	cd03240	204	29	92.2	0.13	[                  -----                          ]	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.
99	cd03253	236	32	92.1	0.14	[                  -----                          ]	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.
100	pfam02283	166	39	92.0	0.13	[                   -------                       ]	CobU	Cobinamide kinase / cobinamide phosphate guanyltransferase. This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.
101	cd03116	159	26	91.9	0.13	[                   ----                          ]	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.
102	PRK09376	416	57	91.9	0.17	[                  -----------                    ]	rho	transcription termination factor Rho; Provisional
103	PRK13342	413	26	91.9	0.12	[                  ----                           ]	PRK13342	recombination factor protein RarA; Reviewed
104	cd03221	144	28	91.9	0.097	[                  -----                          ]	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.
105	COG0125	208	75	91.8	0.78	[                   --------------                ]	Tmk	Thymidylate kinase
106	COG0378	202	27	91.8	0.15	[                  -----                          ]	HypB	Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase
107	TIGR00231	162	21	91.8	0.12	[                  ----                           ]	small_GTP	small GTP-binding protein domain. Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK
108	cd01859	157	24	91.8	0.12	[                  ----                           ]	MJ1464	An uncharacterized, circularly permuted subfamily of the Ras GTPases. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus.
109	COG1224	450	36	91.7	0.14	[                 ------                          ]	TIP49	DNA helicase TIP49, TBP-interacting protein
110	TIGR00176	155	26	91.7	0.14	[                   ----                          ]	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.
111	COG0486	454	96	91.7	0.12	[                  -----------------              ]	MnmE	tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE
112	COG0419	908	30	91.7	0.11	[                  -----                          ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
113	COG1618	179	92	91.6	0.18	[                  ----------------               ]	THEP1	Nucleoside-triphosphatase THEP1
114	TIGR02173	171	25	91.5	0.14	[                   ---                           ]	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.
115	cd04178	171	26	91.5	0.15	[                  ----                           ]	Nucleostemin_like	A circularly permuted subfamily of the Ras GTPases. Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the protein.
116	COG1161	322	26	91.5	0.13	[                  ----                           ]	RbgA	Ribosome biogenesis GTPase A
117	PRK12299	335	31	91.4	0.086	[                   -----                         ]	obgE	GTPase CgtA; Reviewed
118	COG1474	366	81	91.4	0.19	[                   --------------                ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
119	PRK00093	435	101	91.3	0.13	[                  ------------------             ]	PRK00093	GTP-binding protein Der; Reviewed
120	pfam03029	235	91	91.3	0.68	[                   ---------------               ]	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.
121	COG5192	1077	31	91.2	0.19	[                 -----                           ]	BMS1	GTP-binding protein required for 40S ribosome biogenesis
122	TIGR00455	184	40	91.2	0.27	[                  -------                        ]	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.
123	cd01849	146	27	91.2	0.31	[                  ----                           ]	YlqF_related_GTPase	Circularly permuted YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.
124	cd03214	180	38	91.1	0.13	[                                   ------        ]	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.
125	COG1763	161	25	91.1	0.18	[                   ----                          ]	MobB	Molybdopterin-guanine dinucleotide biosynthesis protein
126	COG0714	329	25	91.1	0.18	[                  ----                           ]	MoxR	MoxR-like ATPase
127	cd01672	200	37	91.0	1.6	[                   ------                        ]	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).
128	COG1122	235	31	91.0	0.15	[                  -----                          ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
129	PRK05541	176	35	90.8	0.2	[                  ------                         ]	PRK05541	adenylylsulfate kinase; Provisional
130	cd01894	157	104	90.8	0.27	[                   ------------------            ]	EngA1	EngA1 GTPase contains the first domain of EngA. This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability.
131	TIGR03594	428	110	90.8	0.2	[                  -------------------            ]	GTPase_EngA	ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
132	COG1136	226	43	90.8	0.17	[                                  -------        ]	LolD	ABC-type lipoprotein export system, ATPase component
133	pfam01580	201	52	90.7	0.44	[                   --------                      ]	FtsK_SpoIIIE	FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from Escherichia coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
134	COG0529	197	35	90.7	0.27	[                  ------                         ]	CysC	Adenylylsulfate kinase or related kinase
135	COG1163	365	34	90.7	0.16	[                  ------                         ]	Rbg1	Ribosome-interacting GTPase 1
136	COG1120	258	26	90.6	0.16	[                   ----                          ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
137	PRK13635	279	29	90.6	0.14	[                   ----                          ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
138	PRK06547	172	24	90.6	0.21	[                  ----                           ]	PRK06547	hypothetical protein; Provisional
139	cd03217	200	31	90.5	0.19	[                   -----                         ]	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.
140	TIGR02729	328	31	90.3	0.13	[                   -----                         ]	Obg_CgtA	Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.
141	cd02021	150	22	90.3	0.43	[                   ---                           ]	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.
142	TIGR04520	268	29	90.2	0.21	[                   ----                          ]	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.
143	COG0396	251	35	90.2	0.18	[                   ------                        ]	SufC	Fe-S cluster assembly ATPase SufC
144	cd01128	249	55	90.1	0.34	[                   ----------                    ]	rho_factor	Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
145	TIGR02858	270	151	90.0	0.19	[     ------------------------------              ]	spore_III_AA	stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.
146	COG0645	170	25	90.0	0.22	[                   ----                          ]	COG0645	Predicted kinase
147	cd03244	221	26	90.0	0.29	[                  ----                           ]	ABCC_MRP_domain2	ATP-binding cassette domain 2 of multidrug resistance-associated protein. The ABC subfamily C is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
148	PRK03992	389	30	90.0	0.18	[                   -----                         ]	PRK03992	proteasome-activating nucleotidase; Provisional
149	cd03279	213	28	89.8	0.26	[                  -----                          ]	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.
150	cd02020	147	30	89.7	0.29	[                   -----                         ]	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.
151	COG0194	191	130	89.6	0.28	[                   -----------------------       ]	Gmk	Guanylate kinase
152	cd00878	158	72	89.5	0.29	[                   ------------------            ]	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.
153	COG3910	233	63	89.5	0.36	[                  ------------                   ]	COG3910	Predicted ATPase
154	COG1160	444	109	89.4	0.41	[                  -------------------            ]	Der	Predicted GTPases
155	COG1159	298	54	89.4	0.24	[                               --------          ]	Era	GTPase Era, involved in 16S rRNA processing
156	cd03260	227	43	89.4	0.38	[                   -------                       ]	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).
157	PRK09493	240	25	89.2	0.27	[                   ----                          ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
158	PRK13548	258	25	89.2	0.22	[                   ----                          ]	hmuV	hemin importer ATP-binding subunit; Provisional
159	TIGR04352	280	22	89.1	0.28	[                  ----                           ]	HprK_rel_A	HprK-related kinase A. A number of protein families resemble HPr kinase (see TIGR00679) but do not belong to that system. They include this family, which appears instead to be the marker for a different type of gene neighborhood, in which one of the conserved neighboring proteins resembles (but is distinct from) PqqD.
160	pfam02367	123	28	89.1	0.3	[                  -----                          ]	UPF0079	Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
161	PRK00091	307	27	89.0	0.35	[                  -----                          ]	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
162	pfam06068	395	39	89.0	0.38	[                -------                          ]	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.
163	PRK00698	205	47	88.9	2.6	[                   --------                      ]	tmk	thymidylate kinase; Validated
164	COG1222	406	33	88.8	0.26	[                ------                           ]	RPT1	ATP-dependent 26S proteasome regulatory subunit
165	COG1936	180	21	88.8	0.34	[                  ----                           ]	Fap7	Broad-specificity NMP kinase
166	cd02024	187	22	88.8	0.37	[                   ---                           ]	NRK1	Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
167	TIGR03575	340	27	88.6	0.31	[                   ----                          ]	selen_PSTK_euk	L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.
168	TIGR01241	495	120	88.6	0.28	[                   -------------------------     ]	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.
169	COG2256	436	38	88.6	0.34	[                  -------                        ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
170	PRK07261	171	31	88.5	0.33	[                  ------                         ]	PRK07261	topology modulation protein; Provisional
171	PRK12298	390	31	88.5	0.23	[                   -----                         ]	obgE	GTPase CgtA; Reviewed
172	cd01124	187	32	88.5	0.5	[                   -----                         ]	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.
173	COG1132	567	34	88.5	0.35	[                  ------                         ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
174	PRK13539	207	139	88.4	0.35	[                  ------------------------       ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
175	cd01896	233	31	88.4	0.28	[                   -----                         ]	DRG	Developmentally Regulated GTP-binding protein (DRG). The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
176	cd03255	218	24	88.3	0.34	[                                     ----        ]	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.
177	TIGR01978	243	84	88.0	0.35	[                   --------------                ]	sufC	FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic () or associated with the membrane (). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA.
178	COG0536	369	31	87.8	0.26	[                   -----                         ]	Obg	GTPase involved in cell partioning and DNA repair
179	TIGR03263	179	129	87.8	0.43	[                   -----------------------       ]	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.
180	COG0802	149	55	87.8	0.55	[                  ---------                      ]	TsaE	tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE
181	cd03114	148	24	87.7	0.36	[                   ----                          ]	ArgK-like	The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
182	PRK13764	602	28	87.6	0.49	[                  -----                          ]	PRK13764	ATPase; Provisional
183	PRK12608	380	40	87.6	0.57	[                  -------                        ]	PRK12608	transcription termination factor Rho; Provisional
184	pfam03308	267	28	87.5	0.52	[                  -----                          ]	ArgK	ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
185	COG2087	175	35	87.4	0.71	[                   ------                        ]	CobU	Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase
186	cd04105	202	23	87.4	0.42	[                  ----                           ]	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.
187	COG1703	323	28	87.4	0.56	[                  -----                          ]	ArgK	Putative periplasmic protein kinase ArgK or related GTPase of G3E family
188	cd03213	194	20	87.3	0.43	[                   ---                           ]	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.
189	cd01879	159	28	87.3	0.29	[                   ------                        ]	FeoB	Ferrous iron transport protein B (FeoB) family. Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent.
190	cd03250	204	19	87.3	0.42	[                   --                            ]	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.
191	pfam01443	227	39	87.2	0.64	[                                ------           ]	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.
192	cd04106	162	106	87.2	2.9	[                  -----------------------        ]	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.
193	PRK13948	182	157	87.0	2.7	[                   ----------------------------- ]	PRK13948	shikimate kinase; Provisional
194	PRK14490	369	26	86.9	0.47	[                   ----                          ]	PRK14490	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional
195	PRK09518	712	117	86.8	2.1	[                  ---------------------          ]	PRK09518	bifunctional cytidylate kinase/GTPase Der; Reviewed
196	PRK03731	171	159	86.7	5.6	[                   ----------------------------- ]	aroL	shikimate kinase II; Reviewed
197	cd00544	169	39	86.6	0.69	[                   -------                       ]	CobU	Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.
198	cd03246	173	28	86.6	0.51	[                  -----                          ]	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.
199	TIGR02324	224	129	86.5	0.79	[                   ----------------------        ]	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.
200	pfam01583	157	37	86.5	0.67	[                   ------                        ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
201	COG1121	254	20	86.4	0.5	[                   ---                           ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
202	cd03111	106	30	86.3	2.6	[                                -----            ]	CpaE_like	This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome.
203	cd01673	193	126	86.3	1.3	[                   ----------------------        ]	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.
204	COG0324	308	84	86.2	0.61	[                  ----------------               ]	MiaA	tRNA A37 N6-isopentenylltransferase MiaA
205	cd03235	213	19	86.1	0.55	[                   ---                           ]	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.
206	cd01850	275	27	86.0	0.52	[                  -----                          ]	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.
207	TIGR00764	608	51	86.0	0.84	[                  --------                       ]	lon_rel	lon-related putative ATP-dependent protease. This model represents a set of proteins with extensive C-terminal homology to the ATP-dependent protease La, product of the lon gene of E. coli. The model is based on a seed alignment containing only archaeal members, but several bacterial proteins match the model well. Because several species, including Thermotoga maritima and Treponema pallidum, contain both a close homolog of the lon protease and nearly full-length homolog of the members of this family, we suggest there may also be a functional division between the two families. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
208	PRK00411	394	83	85.9	0.63	[                  ---------------                ]	cdc6	cell division control protein 6; Reviewed
209	TIGR03420	226	38	85.8	0.91	[                  ------                         ]	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.
210	COG1855	604	26	85.8	0.66	[                   ----                          ]	COG1855	Predicted ATPase, PilT family
211	pfam13479	201	117	85.8	0.3	[                  -----------------------        ]	AAA_24	AAA domain. This AAA domain is found in a wide variety of presumed phage proteins.
212	TIGR00767	415	39	85.7	0.88	[                  -------                        ]	rho	transcription termination factor Rho. This RNA helicase, the transcription termination factor Rho, occurs in nearly all bacteria but is missing from the Cyanobacteria, the Mollicutes (Mycoplasmas), and various Lactobacillales including Streptococcus. It is also missing, of course, from the Archaea, which also lack Nus factors. Members of this family from Micrococcus luteus, Mycobacterium tuberculosis, and related species have a related but highly variable long, highly charged insert near the amino end. Members of this family differ in the specificity of RNA binding.
213	cd03115	173	117	85.6	6.7	[                   ---------------------         ]	SRP	The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
214	pfam00071	162	114	85.5	3.4	[                   ---------------------         ]	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.
215	cd03257	228	37	85.5	0.6	[                                   ------        ]	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.
216	PRK12402	337	130	85.4	0.99	[                  ----------------------         ]	PRK12402	replication factor C small subunit 2; Reviewed
217	PRK13695	174	123	85.3	0.83	[                  ------------------------       ]	PRK13695	putative NTPase; Provisional
218	COG0606	490	21	85.1	0.47	[                  ---                            ]	YifB	Predicted ATPase with chaperone activity
219	COG1158	422	55	84.9	1	[                  ----------                     ]	Rho	Transcription termination factor Rho
220	COG3839	338	20	84.9	0.64	[                   ---                           ]	MalK	ABC-type sugar transport system, ATPase component
221	COG0283	222	66	84.8	0.94	[                  ------------                   ]	Cmk	Cytidylate kinase
222	COG1102	179	23	84.7	0.83	[                   ---                           ]	CmkB	Cytidylate kinase
223	COG2884	223	27	84.7	0.84	[                  -----                          ]	FtsE	ABC-type ATPase involved in cell division
224	cd03229	178	40	84.6	0.72	[                                   ------        ]	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.
225	PRK00080	328	28	84.5	0.8	[                  -----                          ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
226	COG5019	373	29	84.5	0.87	[                  -----                          ]	CDC3	Septin family protein
227	PRK03846	198	67	84.4	0.86	[                  --------------                 ]	PRK03846	adenylylsulfate kinase; Provisional
228	PRK06526	254	75	84.3	1.9	[                  ----------------               ]	PRK06526	transposase; Provisional
229	TIGR03903	1266	43	84.2	1.1	[                  -------                        ]	TOMM_kin_cyc	TOMM system kinase/cyclase fusion protein. This model represents proteins of 1350 in length, in multiple species of Burkholderia, in Acidovorax avenae subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1, and in multiple copies in Sorangium cellulosum, in genomic neighborhoods that include a cyclodehydratase/docking scaffold fusion protein (TIGR03882) and a member of the thiazole/oxazole modified metabolite (TOMM) precursor family TIGR03795. It has a kinase domain in the N-terminal 300 amino acids, followed by a cyclase homology domain, followed by regions without named domain definitions. It is a probable bacteriocin-like metabolite biosynthesis protein.
230	TIGR03925	566	70	84.1	0.84	[                  ------------                   ]	T7SS_EccC_b	type VII secretion protein EccCb. This model represents the C-terminal domain or EccCb subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes.
231	PRK12297	424	32	84.1	0.48	[                  ------                         ]	obgE	GTPase CgtA; Reviewed
232	cd03223	166	118	84.1	0.84	[                  -----------------------        ]	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).
233	PRK00300	205	132	84.0	0.81	[                  ------------------------       ]	gmk	guanylate kinase; Provisional
234	TIGR01242	364	30	84.0	0.7	[                   -----                         ]	26Sp45	26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
235	cd00154	159	21	83.9	0.9	[                  ----                           ]	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.
236	cd03277	213	24	83.9	0.82	[                   ----                          ]	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).
237	cd01130	186	25	83.8	0.85	[                  ----                           ]	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.
238	PRK13951	488	99	83.7	5.2	[                  --------------------           ]	PRK13951	bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
239	PRK00093	435	127	83.5	1.9	[                  ----------------------         ]	PRK00093	GTP-binding protein Der; Reviewed
240	PRK03003	472	129	83.3	2.3	[                  -----------------------        ]	PRK03003	GTP-binding protein Der; Reviewed
241	COG4240	300	28	83.1	0.98	[                  -----                          ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
242	COG3911	183	61	83.1	0.91	[                   ---------                     ]	COG3911	Predicted ATPase
243	PRK14974	336	133	83.1	9.5	[                  ------------------------       ]	PRK14974	cell division protein FtsY; Provisional
244	cd03369	207	47	83.0	1.1	[               --------                          ]	ABCC_NFT1	ATP-binding cassette domain 2 of NFT1, subfamily C. Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (multidrug resistance-associated protein) family of ABC transporters. 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.
245	cd03278	197	25	82.9	1.2	[                   ----                          ]	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).
246	COG3709	192	26	82.8	1.5	[                   ----                          ]	PhnN	Ribose 1,5-bisphosphokinase PhnN
247	pfam10662	143	21	82.7	0.87	[                   ---                           ]	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.
248	COG4133	209	35	82.7	1.2	[                  ------                         ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
249	pfam13654	509	80	82.6	4.2	[                  -------------                  ]	AAA_32	AAA domain. This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.
250	cd01918	149	40	82.4	1.3	[                  ------                         ]	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.
251	pfam00437	273	35	82.4	1.1	[                  ------                         ]	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.
252	COG0012	372	33	82.3	0.86	[                  ------                         ]	GTP1	Ribosome-binding ATPase YchF, GTP1/OBG family
253	cd01857	140	21	82.3	0.88	[                   ---                           ]	HSR1_MMR1	A circularly permuted subfamily of the Ras GTPases. Human HSR1 is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N-terminus.
254	PRK11784	345	75	82.1	0.81	[                  ----------------               ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
255	COG1428	216	27	82.0	1.3	[                  ----                           ]	Dck	Deoxyadenosine/deoxycytidine kinase
256	cd02023	198	45	81.8	1.7	[                   --------                      ]	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.
257	COG3854	308	97	81.8	1.3	[                  ------------------             ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
258	TIGR01243	733	34	81.6	0.64	[                ------                           ]	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.
259	COG4619	223	23	81.5	1.4	[                   ---                           ]	FetA	ABC-type iron transport system FetAB, ATPase component
260	COG1131	293	25	81.5	1.1	[                   ----                          ]	CcmA	ABC-type multidrug transport system, ATPase component
261	PRK00440	319	29	81.3	1.4	[                  -----                          ]	rfc	replication factor C small subunit; Reviewed
262	PRK13765	637	56	81.3	1.7	[                  ---------                      ]	PRK13765	ATP-dependent protease Lon; Provisional
263	COG1223	368	31	81.3	1	[                  ------                         ]	COG1223	Predicted ATPase, AAA+ superfamily
264	cd03243	202	95	81.2	1.7	[                   ----------------              ]	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.
265	PRK01184	184	80	81.1	5.1	[                   --------------                ]	PRK01184	hypothetical protein; Provisional
266	pfam13086	183	20	81.1	1.6	[                   ---                           ]	AAA_11	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
267	TIGR03922	557	54	81.1	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.
268	COG0466	782	81	81.0	1.3	[                  ----------------               ]	Lon	ATP-dependent Lon protease, bacterial type
269	PRK09601	364	25	81.0	0.99	[                  ----                           ]	PRK09601	GTP-binding protein YchF; Reviewed
270	cd03293	220	19	80.8	1.2	[                   ---                           ]	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.
271	PRK06696	223	39	80.7	1.9	[                  -------                        ]	PRK06696	uridine kinase; Validated
272	cd03233	202	23	80.6	1.2	[                   ---                           ]	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.
273	PRK12296	500	33	80.6	1.1	[                  ------                         ]	obgE	GTPase CgtA; Reviewed
274	cd00046	144	25	80.5	2.1	[                   ---                           ]	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.
275	COG1124	252	38	80.4	1.2	[                                   ------        ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
276	TIGR00618	1042	103	80.4	1.4	[                  --------------------           ]	sbcc	exonuclease SbcC. All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
277	cd03231	201	22	80.4	1.3	[                  ----                           ]	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.
278	pfam00158	168	86	80.3	1.9	[                  ----------------               ]	Sigma54_activat	Sigma-54 interaction domain.
279	COG3638	258	129	80.3	1.1	[                   ----------------------        ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
280	PRK05703	424	162	80.2	6.4	[                   ----------------------------  ]	flhF	flagellar biosynthesis regulator FlhF; Validated
281	PRK13341	725	22	80.1	1.2	[                   ---                           ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
282	COG2255	332	27	79.9	1.1	[                  -----                          ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
283	cd02034	116	103	79.9	4.6	[                   ------------------            ]	CooC	The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
284	TIGR03594	428	105	79.9	2.1	[                   ------------------            ]	GTPase_EngA	ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability.
285	TIGR03815	322	180	79.8	48	[                   ----------------------------- ]	CpaE_hom_Actino	helicase/secretion neighborhood CpaE-like protein. Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see ). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria.
286	COG0572	218	28	79.8	1.6	[                  -----                          ]	Udk	Uridine kinase
287	cd03256	241	28	79.7	1.1	[                   ----                          ]	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.
288	cd01878	204	88	79.5	1.6	[                  ----------------               ]	HflX	HflX GTPase family. HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.
289	COG4559	259	38	79.5	1.3	[                                   ------        ]	COG4559	ABC-type hemin transport system, ATPase component
290	cd03254	229	28	79.4	1.8	[                  -----                          ]	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.
291	PRK05537	568	52	79.4	2.3	[               ---------                         ]	PRK05537	bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
292	PRK03695	248	19	79.4	1.4	[                   ---                           ]	PRK03695	vitamin B12-transporter ATPase; Provisional
293	PRK07940	394	28	79.3	2.1	[                  -----                          ]	PRK07940	DNA polymerase III subunit delta'; Validated
294	COG2804	500	25	79.1	2.1	[                   ----                          ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
295	TIGR01189	198	23	79.1	1.5	[                  ----                           ]	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.
296	cd09912	180	31	78.9	1.5	[                   ----                          ]	DLP_2	Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins. The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.
297	COG4181	228	18	78.9	1.2	[                  ---                            ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
298	PRK00023	225	26	78.8	1.9	[                  ----                           ]	cmk	cytidylate kinase; Provisional
299	COG2229	187	134	78.7	16	[                  -------------------------      ]	Srp102	Signal recognition particle receptor subunit beta, a GTPase
300	TIGR01193	708	20	78.7	2.2	[                  ---                            ]	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.
301	COG0465	596	127	78.7	1.3	[                   -------------------------     ]	HflB	ATP-dependent Zn proteases
302	cd01858	157	88	78.6	0.58	[     -----------------                           ]	NGP_1	A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases. Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.
303	TIGR00968	237	19	78.6	1.5	[                   --                            ]	3a0106s01	sulfate ABC transporter, ATP-binding protein.
304	COG4618	580	30	78.5	1.5	[                  -----                          ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
305	cd03237	246	36	78.4	1.5	[                  ------                         ]	ABC_RNaseL_inhibitor_domain2	The ATP-binding cassette domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
306	PRK11650	356	19	78.3	1.4	[                   --                            ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
307	TIGR00368	499	21	78.3	1.3	[                  ---                            ]	TIGR00368	Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
308	COG4987	573	27	78.3	1.6	[                  ----                           ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
309	TIGR00101	199	27	78.0	2	[                  -----                          ]	ureG	urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel.
310	PRK12740	668	113	78.0	3.2	[                   ----------------------        ]	PRK12740	elongation factor G; Reviewed
311	PRK10078	186	63	78.0	2	[                   -------------                 ]	PRK10078	ribose 1,5-bisphosphokinase; Provisional
312	COG1116	248	19	77.8	1.7	[                   ---                           ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
313	pfam00006	213	48	77.8	3.1	[                   -------                       ]	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.
314	PRK05342	412	23	77.7	2	[                   ---                           ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
315	pfam03193	161	51	77.6	1.6	[                   --------                      ]	DUF258	Protein of unknown function, DUF258.
316	COG3596	296	51	77.4	2	[                  --------                       ]	YeeP	Predicted GTPase
317	pfam00735	273	159	77.3	1.7	[                  ---------------------------    ]	Septin	Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
318	cd01122	271	127	77.1	35	[                   ----------------------        ]	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.
319	COG4615	546	57	77.0	1.5	[                   ------------                  ]	PvdE	ABC-type siderophore export system, fused ATPase and permease components
320	TIGR02673	214	29	76.9	1.8	[                   ----                          ]	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.
321	PRK13632	271	33	76.8	1.9	[                   -----                         ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
322	pfam01057	271	122	76.7	1.9	[                  ---------------------          ]	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.
323	PRK08181	269	28	76.7	2.6	[                  -----                          ]	PRK08181	transposase; Validated
324	cd03298	211	37	76.5	1.5	[                                     -------     ]	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.
325	cd01900	274	28	76.5	1.3	[                   -----                         ]	YchF	YchF GTPase. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
326	TIGR03689	512	85	76.4	2.9	[         --------------                          ]	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.
327	COG1160	444	101	76.4	1.8	[                  ------------------             ]	Der	Predicted GTPases
328	cd05005	179	94	76.4	6.3	[    ---------------------                        ]	SIS_PHI	Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
329	COG3172	187	25	76.2	2.3	[                   ---                           ]	NadR3	Nicotinamide riboside kinase
330	COG1219	408	23	75.9	2.3	[                   ---                           ]	ClpX	ATP-dependent protease Clp, ATPase subunit
331	TIGR02782	299	35	75.8	3.7	[                  ------                         ]	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.
332	COG0630	312	26	75.8	2	[                  ----                           ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
333	PRK09518	712	150	75.8	3.5	[                  --------------------------     ]	PRK09518	bifunctional cytidylate kinase/GTPase Der; Reviewed
334	cd04114	169	27	75.7	1.1	[                  ----                           ]	Rab30	Rab GTPase family 30 (Rab30). Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. 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.
335	cd03261	235	40	75.7	2.1	[                   ------                        ]	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.
336	COG0370	653	120	75.7	1.9	[                  ------------------------       ]	FeoB	Fe2+ transport system protein B
337	TIGR01351	210	101	75.7	2.4	[                   ----------------------        ]	adk	adenylate kinase. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is SP|Q9UIJ7, a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
338	cd01854	211	46	75.7	1.8	[              --------                           ]	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.
339	TIGR00064	277	130	75.7	43	[                   ----------------------        ]	ftsY	signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
340	COG4778	235	83	75.6	2.1	[                  ---------------                ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
341	pfam07724	168	84	75.5	2.7	[                   -------------------           ]	AAA_2	AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
342	TIGR02868	530	29	75.4	2.4	[                  -----                          ]	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.
343	PRK11264	250	24	75.2	2	[                   ----                          ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
344	cd03230	173	26	75.2	2.3	[                   ----                          ]	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.
345	pfam00009	185	156	75.1	2.4	[                  ------------------------------ ]	GTP_EFTU	Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.
346	pfam09439	181	21	75.1	2.3	[                  ---                            ]	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.
347	COG5635	824	97	75.0	2.4	[                  ----------------               ]	COG5635	Predicted NTPase, NACHT family domain
348	PRK13833	323	33	74.9	3	[                  ------                         ]	PRK13833	conjugal transfer protein TrbB; Provisional
349	COG2274	709	21	74.8	2.2	[                   ---                           ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
350	TIGR00436	270	19	74.7	2.2	[                   --                            ]	era	GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
351	TIGR04521	277	28	74.7	2.1	[                   ----                          ]	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.
352	COG3950	440	26	74.6	2.4	[                   ----                          ]	COG3950	Predicted ATP-binding protein involved in virulence
353	TIGR01842	544	27	74.6	2.2	[                  ----                           ]	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.
354	PRK13851	344	25	74.6	1.5	[                  ----                           ]	PRK13851	type IV secretion system protein VirB11; Provisional
355	PRK09435	332	32	74.6	3.1	[                  -----                          ]	PRK09435	membrane ATPase/protein kinase; Provisional
356	TIGR00174	287	118	74.6	2.1	[                   ---------------------         ]	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.
357	cd04113	161	18	74.5	1.6	[                  ---                            ]	Rab4	Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. 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.
358	COG3840	231	37	74.4	1.9	[                                     -------     ]	ThiQ	ABC-type thiamine transport system, ATPase component
359	cd03301	213	48	74.3	2.2	[                   ---------                     ]	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.
360	pfam00625	183	105	74.3	8.2	[                   -----------------             ]	Guanylate_kin	Guanylate kinase.
361	pfam02463	1162	50	74.0	2.4	[                                  --------       ]	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.
362	COG4608	268	117	74.0	9.2	[                   ----------------------        ]	AppF	ABC-type oligopeptide transport system, ATPase component
363	cd03251	234	63	74.0	2.5	[                                ----------       ]	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.
364	COG5256	428	25	73.9	2.1	[                  ---                            ]	TEF1	Translation elongation factor EF-1alpha (GTPase)
365	COG0552	340	128	73.8	36	[                   ----------------------        ]	FtsY	Signal recognition particle GTPase
366	COG3267	269	26	73.7	2.5	[                   ----                          ]	ExeA	Type II secretory pathway, component ExeA (predicted ATPase)
367	TIGR00678	188	29	73.7	3.4	[                  ----                           ]	holB	DNA polymerase III, delta' subunit. This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
368	cd11383	140	51	73.7	1.8	[                   --------                      ]	YfjP	YfjP GTPase. The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.
369	PRK06762	166	22	73.5	3.2	[                   ---                           ]	PRK06762	hypothetical protein; Provisional
370	TIGR00972	247	36	73.5	2.8	[                                   ------        ]	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.
371	pfam05496	234	28	73.4	3	[                  -----                          ]	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.
372	PRK13549	506	37	73.4	2.2	[                   -------                       ]	PRK13549	xylose transporter ATP-binding subunit; Provisional
373	COG1134	249	118	73.2	2.4	[                  --------------------           ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
374	PRK06761	282	27	73.1	3.5	[                   ----                          ]	PRK06761	hypothetical protein; Provisional
375	cd01129	264	33	73.0	3.5	[                   -----                         ]	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.
376	PRK11231	255	36	72.7	3	[                                   ------        ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
377	pfam01637	223	19	72.7	15	[                  ---                            ]	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.
378	TIGR00954	659	35	72.7	2.5	[                                   ------        ]	3a01203	Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein.
379	TIGR03167	311	75	72.7	2.7	[                  ----------------               ]	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.
380	cd03220	224	26	72.5	2.5	[                   ----                          ]	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.
381	TIGR00750	300	28	72.3	3.1	[                  -----                          ]	lao	LAO/AO transport system ATPase. In E. coli, mutation of this kinase blocks phosphorylation of two transporter system periplasmic binding proteins and consequently inhibits those transporters. This kinase is also found in Gram-positive bacteria, archaea, and the roundworm C. elegans. It may have a more general, but still unknown function. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.
382	PRK04213	201	22	72.2	3.7	[                  ----                           ]	PRK04213	GTP-binding protein; Provisional
383	cd03299	235	26	72.1	2.7	[                   ----                          ]	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.
384	cd09914	161	60	72.0	3.2	[                                ----------       ]	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.
385	TIGR01447	582	114	72.0	5.1	[                   --------------------          ]	recD	exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
386	TIGR02857	529	81	72.0	3.2	[                  -------------                  ]	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
387	PRK10789	569	23	71.7	2.3	[                   ---                           ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
388	cd03288	257	24	71.6	2.1	[                  ----                           ]	ABCC_SUR2	ATP-binding cassette domain 2 of the sulfonylurea receptor SUR. The SUR domain 2. The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
389	cd04104	197	22	71.5	3.2	[                  ----                           ]	p47_IIGP_like	p47 GTPase family includes IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protein that participates in the organization of the cis-Golgi compartment.
390	TIGR01194	555	57	71.5	2.1	[                   ------------                  ]	cyc_pep_trnsptr	cyclic peptide transporter. This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.
391	TIGR02322	179	25	71.4	4.9	[                   ----                          ]	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.
392	cd03259	213	20	71.2	3.2	[                   ---                           ]	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.
393	PRK13894	319	36	71.2	4.8	[                   -----                         ]	PRK13894	conjugal transfer ATPase TrbB; Provisional
394	PRK14239	252	20	71.2	3.1	[                   ---                           ]	PRK14239	phosphate transporter ATP-binding protein; Provisional
395	cd03247	178	28	71.1	3.2	[                  -----                          ]	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.
396	COG0237	201	22	71.1	3.8	[                  ----                           ]	CoaE	Dephospho-CoA kinase
397	TIGR01243	733	114	71.1	2.8	[     ---------------------                       ]	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.
398	cd01876	170	98	71.1	3.1	[                   -----------------             ]	YihA_EngB	YihA (EngB) GTPase family. The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target.
399	PRK10733	644	44	71.1	2.8	[                --------                         ]	hflB	ATP-dependent metalloprotease; Reviewed
400	TIGR03156	351	27	71.1	2.8	[                  ----                           ]	GTP_HflX	GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like).
401	COG1117	253	26	71.0	3.1	[                   ----                          ]	PstB	ABC-type phosphate transport system, ATPase component
402	COG0542	786	83	70.9	3.1	[                 ----------------                ]	ClpA	ATP-dependent Clp protease ATP-binding subunit ClpA
403	COG1123	539	39	70.9	3	[                                   ------        ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
404	COG0488	530	43	70.8	3.1	[                                  -------        ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
405	TIGR00635	305	28	70.8	2.7	[                  -----                          ]	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.
406	COG1119	257	18	70.7	3.2	[                   --                            ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
407	TIGR02982	220	76	70.6	2.5	[                            -------------        ]	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.
408	cd01892	180	18	70.5	3.1	[                   --                            ]	Miro2	Mitochondrial Rho family 2 (Miro2), C-terminal. Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
409	pfam07693	301	40	70.4	13	[                  -------                        ]	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.
410	TIGR02746	797	52	70.4	2.6	[                  -----------                    ]	TraC-F-type	type-IV secretion system protein TraC. The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase.
411	cd01131	198	25	70.3	4.8	[                   ----                          ]	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.
412	PRK03003	472	107	70.3	21	[                  -------------------            ]	PRK03003	GTP-binding protein Der; Reviewed
413	PRK00098	298	20	70.2	2.5	[                   ---                           ]	PRK00098	GTPase RsgA; Reviewed
414	COG1196	1163	24	70.1	3.2	[                   ----                          ]	Smc	Chromosome segregation ATPase
415	TIGR03348	1169	18	70.1	2.5	[                  ---                            ]	VI_IcmF	type VI secretion protein IcmF. Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems.
416	COG1643	845	55	70.0	4.6	[                  -----------                    ]	HrpA	HrpA-like RNA helicase
417	TIGR03918	391	25	70.0	17	[                  ----                           ]	GTP_HydF
418	cd08070	128	35	69.9	6.5	[                                    ------       ]	MPN_like	Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
419	pfam01202	158	95	69.9	41	[                    ------------------           ]	SKI	Shikimate kinase.
420	TIGR00763	775	79	69.8	3.8	[                  ----------------               ]	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.
421	PRK09984	262	21	69.5	3.5	[                   ---                           ]	PRK09984	phosphonate/organophosphate ester transporter subunit; Provisional
422	COG4988	559	22	69.5	3.5	[                  ----                           ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
423	cd04167	213	121	69.5	18	[                   ----------------------        ]	Snu114p	Snu114p, a spliceosome protein, is a GTPase. Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs.
424	cd03275	247	145	69.4	5.9	[                   ------------------------------]	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).
425	PRK00625	173	81	69.3	6.7	[                   ---------------               ]	PRK00625	shikimate kinase; Provisional
426	pfam04670	229	26	69.0	2.3	[                   ----                          ]	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.
427	TIGR03797	686	84	68.9	3.5	[                  ----------------               ]	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.
428	PRK14247	250	26	68.9	4.2	[                  ----                           ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
429	cd01899	318	90	68.4	2.4	[                   ---------------               ]	Ygr210	Ygr210 GTPase. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi.
430	COG0444	316	37	68.4	3.5	[                   ------                        ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
431	TIGR04075	851	22	68.4	3	[                  ----                           ]	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.
432	COG1127	263	26	68.4	3.8	[                   ----                          ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
433	TIGR03881	229	38	68.3	3.6	[                  ------                         ]	KaiC_arch_4	KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
434	pfam04851	103	36	68.2	16	[                  ------                         ]	ResIII	Type III restriction enzyme, res subunit.
435	TIGR02315	243	27	68.1	3.8	[                   ----                          ]	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.
436	COG3842	352	18	68.0	3.9	[                   --                            ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
437	cd03239	178	25	68.0	2.5	[                   ---                           ]	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.
438	TIGR03005	252	43	67.9	3.7	[                  --------                       ]	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.
439	cd03295	242	28	67.7	4.6	[                   ----                          ]	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.
440	cd03219	236	23	67.7	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).
441	TIGR02768	744	108	67.7	26	[                  --------------------           ]	TraA_Ti	Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
442	PRK11147	635	52	67.6	8.2	[              ---------                          ]	PRK11147	ABC transporter ATPase component; Reviewed
443	COG2805	353	26	67.5	5.7	[                   ----                          ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
444	pfam02562	205	119	67.3	6.9	[                   -------------------           ]	PhoH	PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
445	cd04109	213	146	67.2	2.8	[                  -------------------------------]	Rab28	Rab GTPase family 28 (Rab28). Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. 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.
446	TIGR03873	256	32	67.2	3	[                  -----                          ]	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.
447	COG0468	279	88	66.7	3.5	[                  ----------------               ]	RecA	RecA/RadA recombinase
448	cd00876	160	23	66.7	5.1	[                   ---                           ]	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.
449	pfam06745	231	35	66.7	3.6	[                  ------                         ]	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.
450	cd03224	222	24	66.6	4.7	[                   ---                           ]	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.
451	cd01393	226	16	66.6	3.8	[                   --                            ]	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.
452	TIGR00382	413	23	66.6	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.
453	PRK06964	342	28	66.6	3.3	[                   ----                          ]	PRK06964	DNA polymerase III subunit delta'; Validated
454	cd03274	212	17	66.3	3.6	[                   --                            ]	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).
455	PRK09602	396	95	65.8	4.2	[                  -----------------              ]	PRK09602	translation-associated GTPase; Reviewed
456	TIGR00150	133	27	65.8	5.2	[                  ----                           ]	T6A_YjeE	tRNA threonylcarbamoyl adenosine modification protein YjeE. This protein family belongs to a four-gene system responsible for the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have (weak) ATPase activity.
457	COG3640	255	51	65.7	18	[                  ---------                      ]	CooC	CO dehydrogenase nickel-insertion accessory protein CooC1
458	PRK04040	188	84	65.5	6.1	[                  ----------------               ]	PRK04040	adenylate kinase; Provisional
459	PRK08903	227	44	65.5	6	[                  -------                        ]	PRK08903	DnaA regulatory inactivator Hda; Validated
460	COG0410	237	23	65.3	5.1	[                   ---                           ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
461	PRK09382	378	135	65.2	17	[       ----------------------------              ]	ispDF	bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional
462	PRK13657	588	29	65.1	5.4	[                  -----                          ]	PRK13657	cyclic beta-1,2-glucan ABC transporter; Provisional
463	cd03292	214	24	65.0	5.4	[                  ----                           ]	ABC_FtsE_transporter	ATP-binding cassette domain of the cell division transporter. FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.
464	PRK09862	506	71	64.9	4.8	[         -------------                           ]	PRK09862	putative ATP-dependent protease; Provisional
465	pfam00503	317	99	64.8	5.6	[                                -----------------]	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.
466	COG1106	371	19	64.7	4.7	[                   ---                           ]	AAA15	ATPase/GTPase, AAA15 family
467	pfam02223	186	46	64.6	29	[                   ----------                    ]	Thymidylate_kin	Thymidylate kinase.
468	pfam13166	713	22	64.5	6.5	[                   ---                           ]	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.
469	pfam10236	293	128	64.5	4.2	[                  -----------------------        ]	DAP3	Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
470	cd03226	205	125	64.4	5.3	[                   --------------------          ]	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.
471	PRK14526	211	52	64.4	4.1	[                  -----------                    ]	PRK14526	adenylate kinase; Provisional
472	PRK06921	266	39	64.3	7.3	[                 -------                         ]	PRK06921	hypothetical protein; Provisional
473	pfam00350	168	20	64.3	4.5	[                   ---                           ]	Dynamin_N	Dynamin family.
474	COG2019	189	24	64.2	6.9	[                  ----                           ]	AdkA	Archaeal adenylate kinase
475	PRK13651	305	27	64.2	4.5	[                   ----                          ]	PRK13651	cobalt transporter ATP-binding subunit; Provisional
476	TIGR01420	343	116	64.1	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.
477	PRK11124	242	22	64.1	5.2	[                  ----                           ]	artP	arginine transporter ATP-binding subunit; Provisional
478	PRK11819	556	55	64.0	10	[            -----------                          ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
479	pfam00931	287	27	64.0	5.1	[                  ----                           ]	NB-ARC	NB-ARC domain.
480	TIGR00611	365	19	63.7	5.1	[                   ---                           ]	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).
481	cd01483	143	66	63.6	32	[                              -----------        ]	E1_enzyme_family	Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS.
482	TIGR02633	500	37	63.6	5.2	[                   -------                       ]	xylG	D-xylose ABC transporter, ATP-binding protein. Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).
483	TIGR00602	637	23	63.5	5.8	[                   ---                           ]	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).
484	TIGR00017	217	24	63.4	6.7	[                   ---                           ]	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.
485	COG1221	403	74	63.4	8.2	[                  --------------                 ]	PspF	Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain
486	PRK13633	280	39	63.4	4.1	[                                   ------        ]	PRK13633	cobalt transporter ATP-binding subunit; Provisional
487	PRK10790	592	154	63.2	5	[               --------------------------        ]	PRK10790	putative multidrug transporter membrane\ATP-binding components; Provisional
488	COG0218	200	102	63.0	7.7	[                  ------------------             ]	EngB	GTP-binding protein EngB required for normal cell division
489	PRK11000	369	19	62.9	5.5	[                   --                            ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
490	COG1239	423	25	62.9	7	[                   ----                          ]	ChlI	Mg-chelatase subunit ChlI
491	COG3451	796	33	62.8	7.6	[                   -----                         ]	VirB4	Type IV secretory pathway, VirB4 component
492	PRK14237	267	25	62.7	5.7	[                   ----                          ]	PRK14237	phosphate transporter ATP-binding protein; Provisional
493	cd08771	278	24	62.7	5.8	[                  ----                           ]	DLP_1	Dynamin_like protein family includes dynamins and Mx proteins. The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes interferon-induced Mx proteins that inhibit a wide range of viruses by blocking an early stage of the replication cycle. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner.
494	PRK00454	196	101	62.6	7.4	[                  ------------------             ]	engB	GTP-binding protein YsxC; Reviewed
495	PRK10938	490	33	62.6	4.3	[                   -----                         ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
496	pfam07726	131	25	62.4	5.1	[                   ----                          ]	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.
497	COG4178	604	119	62.4	5.4	[                  -----------------------        ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
498	TIGR02928	365	141	62.4	9.2	[                  ------------------------       ]	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.
499	cd04107	201	22	62.3	5.7	[                  ----                           ]	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.
500	PRK02224	880	25	62.2	6	[                   ----                          ]	PRK02224	chromosome segregation protein; Provisional