match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG0433	520	393	99.9	7.5E-26	[ ----------------------------------------]	YjgR	Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains
2	pfam12846	298	284	99.9	3.3E-20	[ ------------------------------- ]	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.
3	pfam01935	219	69	99.4	3.7E-12	[ ------ ]	DUF87	Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
4	pfam05872	504	276	99.4	2.3E-12	[ ------------------------------ ]	DUF853	Bacterial protein of unknown function (DUF853). This family consists of several bacterial proteins of unknown function. BMEI1370 is thought to be an ATPase.
5	cd01127	410	303	99.2	6.6E-09	[ -------------------------------- ]	TrwB	Bacterial conjugation protein TrwB, ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.
6	pfam01580	201	58	99.1	5.2E-10	[ ----- ]	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.
7	pfam10412	386	304	99.1	7.7E-09	[ ------------------------------- ]	TrwB_AAD_bind	Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
8	TIGR00929	785	123	99.1	4.5E-09	[ ----------- ]	VirB4_CagE	type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation).
9	TIGR03743	634	323	98.7	2.2E-06	[ ------------------------------- ]	SXT_TraD	conjugative coupling factor TraD, SXT/TOL subfamily. Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.
10	TIGR02746	797	282	98.7	8E-06	[ ------------------------------- ]	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.
11	COG1674	858	81	98.6	2.8E-07	[ ------- ]	FtsK	DNA segregation ATPase FtsK/SpoIIIE and related proteins
12	cd01120	165	98	98.6	7.8E-07	[ --------- ]	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.
13	COG3451	796	298	98.5	9.7E-06	[ --------------------------------- ]	VirB4	Type IV secretory pathway, VirB4 component
14	TIGR02759	566	381	97.8	0.002	[ --------------------------------------- ]	TraD_Ftype	type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).
15	cd00009	151	47	97.8	3.6E-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.
16	pfam13207	114	32	97.7	5E-05	[ ---- ]	AAA_17	AAA domain.
17	pfam00437	273	124	97.5	9.8E-05	[ ------------ ]	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.
18	PRK13873	811	91	97.1	0.00038	[ -------- ]	PRK13873	conjugal transfer ATPase TrbE; Provisional
19	TIGR03924	658	74	97.1	0.00072	[ ------ ]	T7SS_EccC_a	type VII secretion protein EccCa. This model represents the N-terminal domain or EccCa 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.
20	pfam13401	124	25	97.0	0.0021	[ -- ]	AAA_22	AAA domain.
21	TIGR03754	643	322	97.0	0.072	[ ------------------------------- ]	conj_TOL_TraD	conjugative coupling factor TraD, TOL family. Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.
22	pfam13238	128	22	97.0	0.00042	[ -- ]	AAA_18	AAA domain.
23	COG1132	567	133	96.9	0.0021	[ ------------ ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
24	TIGR02782	299	103	96.9	0.0015	[ ---------- ]	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.
25	PRK13894	319	172	96.8	0.0046	[ ---------------- ]	PRK13894	conjugal transfer ATPase TrbB; Provisional
26	cd02028	179	36	96.8	0.0012	[ --- ]	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).
27	pfam05707	183	57	96.7	0.0013	[ ----- ]	Zot	Zonular occludens toxin (Zot). This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers
28	cd01130	186	86	96.7	0.00084	[ -------- ]	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.
29	cd00267	157	37	96.7	0.0012	[ --- ]	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.
30	pfam03205	138	25	96.6	0.0023	[ -- ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
31	cd03214	180	56	96.6	0.0011	[ ----- ]	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.
32	TIGR00750	300	70	96.5	0.0022	[ ------ ]	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.
33	COG1703	323	89	96.5	0.0025	[ -------- ]	ArgK	Putative periplasmic protein kinase ArgK or related GTPase of G3E family
34	pfam00005	150	25	96.5	0.0017	[ -- ]	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.
35	COG1120	258	74	96.5	0.0016	[ ------ ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
36	cd03228	171	44	96.5	0.0025	[ ---- ]	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.
37	pfam13191	156	29	96.4	0.0065	[ --- ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
38	TIGR03925	566	102	96.4	0.0032	[ ----------- ]	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.
39	PRK13830	818	142	96.3	0.0035	[ ------------- ]	PRK13830	conjugal transfer protein TrbE; Provisional
40	cd03225	211	46	96.3	0.0023	[ ---- ]	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.
41	pfam03308	267	44	96.2	0.0047	[ ---- ]	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.
42	COG2804	500	32	96.2	0.0041	[ --- ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
43	TIGR03499	282	43	96.2	0.0052	[ --- ]	FlhF	flagellar biosynthetic protein FlhF.
44	PRK13768	253	40	96.1	0.0064	[ ---- ]	PRK13768	GTPase; Provisional
45	cd03230	173	28	96.1	0.0036	[ --- ]	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.
46	cd03235	213	42	96.1	0.0036	[ ---- ]	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.
47	pfam13304	144	58	96.1	0.0042	[ ------ ]	AAA_21	AAA domain.
48	cd02034	116	36	96.0	0.0085	[ ---- ]	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.
49	pfam13671	143	31	96.0	0.004	[ --- ]	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.
50	COG4555	245	56	96.0	0.0048	[ ---- ]	NatA	ABC-type Na+ transport system, ATPase component NatA
51	cd03116	159	32	95.9	0.011	[ --- ]	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.
52	cd01983	99	59	95.9	0.012	[ ----- ]	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.
53	cd03260	227	38	95.9	0.0065	[ --- ]	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).
54	cd03220	224	29	95.9	0.0054	[ --- ]	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.
55	COG1763	161	37	95.8	0.012	[ ---- ]	MobB	Molybdopterin-guanine dinucleotide biosynthesis protein
56	COG1136	226	44	95.8	0.0071	[ ---- ]	LolD	ABC-type lipoprotein export system, ATPase component
57	TIGR03819	340	82	95.8	0.0056	[ -------- ]	heli_sec_ATPase	helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.
58	pfam00448	195	56	95.8	0.013	[ ----- ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
59	cd03244	221	30	95.7	0.0067	[ --- ]	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.
60	COG0563	178	21	95.7	0.0066	[ -- ]	Adk	Adenylate kinase or related kinase
61	COG1131	293	39	95.7	0.0036	[ ---- ]	CcmA	ABC-type multidrug transport system, ATPase component
62	COG1122	235	47	95.7	0.0059	[ ---- ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
63	pfam00004	131	22	95.7	0.01	[ -- ]	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.
64	pfam00910	105	25	95.7	0.016	[ -- ]	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.
65	cd03221	144	42	95.6	0.0075	[ ---- ]	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.
66	PRK13548	258	77	95.6	0.0054	[ -------- ]	hmuV	hemin importer ATP-binding subunit; Provisional
67	COG2884	223	48	95.6	0.011	[ ----- ]	FtsE	ABC-type ATPase involved in cell division
68	COG1121	254	27	95.6	0.0076	[ --- ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
69	COG0467	260	37	95.5	0.02	[ --- ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
70	COG3839	338	69	95.5	0.0088	[ ------- ]	MalK	ABC-type sugar transport system, ATPase component
71	pfam13476	203	24	95.5	0.012	[ -- ]	AAA_23	AAA domain.
72	cd01131	198	41	95.4	0.019	[ ---- ]	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.
73	cd02023	198	34	95.4	0.014	[ --- ]	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.
74	TIGR02211	221	104	95.4	0.0073	[ ----------- ]	LolD_lipo_ex	lipoprotein releasing system, ATP-binding protein. This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.
75	cd03279	213	72	95.4	0.01	[ ------- ]	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.
76	cd03114	148	87	95.4	0.014	[ -------- ]	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.
77	PRK05342	412	38	95.4	0.013	[ ---- ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
78	pfam04665	241	28	95.3	0.014	[ --- ]	Pox_A32	Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging.
79	COG1119	257	26	95.3	0.01	[ -- ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
80	cd03229	178	56	95.3	0.012	[ ----- ]	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.
81	cd03255	218	46	95.2	0.013	[ ---- ]	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.
82	pfam13555	60	26	95.1	0.018	[ -- ]	AAA_29	P-loop containing region of AAA domain.
83	COG0378	202	39	95.1	0.024	[ ---- ]	HypB	Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase
84	PRK05703	424	68	95.1	0.028	[ ------ ]	flhF	flagellar biosynthesis regulator FlhF; Validated
85	cd03223	166	38	95.1	0.02	[ ---- ]	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).
86	PRK13539	207	28	95.0	0.014	[ --- ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
87	COG4559	259	121	95.0	0.011	[ -------------- ]	COG4559	ABC-type hemin transport system, ATPase component
88	cd03250	204	27	95.0	0.012	[ --- ]	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.
89	COG1219	408	38	95.0	0.017	[ ---- ]	ClpX	ATP-dependent protease Clp, ATPase subunit
90	PRK14490	369	46	94.9	0.013	[ ---- ]	PRK14490	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional
91	cd03254	229	44	94.9	0.018	[ ---- ]	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.
92	COG2805	353	54	94.9	0.018	[ ----- ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
93	COG1100	219	27	94.9	0.022	[ --- ]	Gem1	GTPase SAR1 family domain
94	cd03259	213	57	94.9	0.017	[ ----- ]	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.
95	COG0324	308	38	94.8	0.017	[ ---- ]	MiaA	tRNA A37 N6-isopentenylltransferase MiaA
96	PRK11701	258	27	94.8	0.015	[ --- ]	phnK	phosphonate C-P lyase system protein PhnK; Provisional
97	TIGR02788	308	70	94.8	0.017	[ ------- ]	VirB11	P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
98	COG1134	249	28	94.7	0.019	[ --- ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
99	TIGR04520	268	67	94.7	0.033	[ ------ ]	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.
100	cd02026	273	38	94.7	0.021	[ ---- ]	PRK	Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
101	cd03227	162	50	94.7	0.029	[ ----- ]	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.
102	cd03293	220	21	94.7	0.02	[ -- ]	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.
103	pfam02492	178	31	94.7	0.031	[ --- ]	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.
104	PRK11231	255	25	94.7	0.019	[ -- ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
105	COG4586	325	46	94.7	0.012	[ ---- ]	COG4586	ABC-type uncharacterized transport system, ATPase component
106	COG0572	218	34	94.7	0.028	[ --- ]	Udk	Uridine kinase
107	TIGR04521	277	142	94.7	0.019	[ ---------------- ]	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.
108	pfam01926	114	27	94.6	0.024	[ --- ]	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.
109	pfam05729	165	27	94.6	0.046	[ --- ]	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.
110	COG4962	355	106	94.6	0.018	[ ---------- ]	CpaF	Pilus assembly protein, ATPase of CpaF family
111	cd00882	161	23	94.6	0.018	[ -- ]	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.
112	COG1419	407	63	94.6	0.039	[ ----- ]	FlhF	Flagellar biosynthesis GTPase FlhF
113	COG3854	308	41	94.5	0.038	[ ---- ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
114	pfam13245	72	30	94.5	0.051	[ -- ]	AAA_19	Part of AAA domain.
115	PRK13891	852	136	94.5	0.036	[ ------------ ]	PRK13891	conjugal transfer protein TrbE; Provisional
116	COG0488	530	30	94.5	0.022	[ --- ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
117	cd03264	211	46	94.4	0.025	[ ----- ]	ABC_drug_resistance_like	ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
118	TIGR00382	413	38	94.4	0.024	[ ---- ]	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.
119	COG1116	248	20	94.4	0.025	[ -- ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
120	PRK00091	307	37	94.3	0.038	[ ---- ]	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
121	COG0419	908	30	94.3	0.027	[ --- ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
122	cd01673	193	21	94.3	0.032	[ -- ]	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.
123	pfam07724	168	36	94.3	0.043	[ ---- ]	AAA_2	AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
124	TIGR02868	530	27	94.2	0.028	[ -- ]	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.
125	COG1124	252	79	94.2	0.029	[ -------- ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
126	cd09639	353	237	94.2	1.3	[ --------------------------- ]	Cas3_I	CRISPR/Cas system-associated protein Cas3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
127	pfam08433	267	207	94.2	0.04	[ ------------------------ ]	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.
128	TIGR00176	155	33	94.2	0.059	[ --- ]	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.
129	TIGR02323	253	27	94.2	0.024	[ --- ]	CP_lyasePhnK	phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.
130	pfam13173	127	25	94.2	0.057	[ -- ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
131	COG3638	258	57	94.2	0.031	[ ---- ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
132	PRK06696	223	36	94.2	0.042	[ --- ]	PRK06696	uridine kinase; Validated
133	pfam12696	126	72	94.2	0.17	[ ------ ]	TraG-D_C	TraM recognition site of TraD and TraG. This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. This domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore.
134	pfam13521	162	20	94.2	0.035	[ -- ]	AAA_28	AAA domain.
135	COG1126	240	56	94.2	0.029	[ ----- ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
136	TIGR01420	343	44	94.2	0.033	[ ---- ]	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.
137	TIGR03744	893	86	94.1	0.057	[ -------- ]	traC_PFL_4706	conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.
138	PRK03695	248	18	94.1	0.027	[ - ]	PRK03695	vitamin B12-transporter ATPase; Provisional
139	cd03246	173	62	94.1	0.032	[ ------- ]	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.
140	cd02019	69	22	94.1	0.076	[ -- ]	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.
141	PRK05480	209	34	94.1	0.049	[ --- ]	PRK05480	uridine/cytidine kinase; Provisional
142	COG3842	352	20	94.1	0.032	[ -- ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
143	COG0542	786	39	94.1	0.04	[ ---- ]	ClpA	ATP-dependent Clp protease ATP-binding subunit ClpA
144	COG0488	530	30	94.0	0.03	[ --- ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
145	pfam03266	168	25	94.0	0.065	[ -- ]	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.
146	cd03257	228	73	94.0	0.035	[ -------- ]	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.
147	PRK10263	1355	114	94.0	0.13	[ ------------ ]	PRK10263	DNA translocase FtsK; Provisional
148	cd02020	147	127	94.0	0.18	[ --------------- ]	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.
149	cd03224	222	21	94.0	0.035	[ -- ]	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.
150	cd03261	235	28	93.9	0.029	[ --- ]	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.
151	COG4987	573	29	93.9	0.033	[ --- ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
152	COG4604	252	60	93.9	0.046	[ ----- ]	CeuD	ABC-type enterochelin transport system, ATPase component
153	TIGR02524	358	44	93.9	0.075	[ ---- ]	dot_icm_DotB	Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.
154	PRK07429	327	34	93.9	0.047	[ --- ]	PRK07429	phosphoribulokinase; Provisional
155	cd03262	213	40	93.9	0.036	[ ---- ]	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.
156	TIGR03928	1296	80	93.9	0.04	[ -------- ]	T7_EssCb_Firm	type VII secretion protein EssC, C-terminal domain. This model describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria.
157	TIGR03608	206	25	93.9	0.037	[ --- ]	L_ocin_972_ABC	putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.
158	TIGR01189	198	27	93.9	0.038	[ --- ]	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.
159	TIGR00174	287	36	93.9	0.044	[ ---- ]	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.
160	COG0410	237	24	93.8	0.038	[ -- ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
161	COG0630	312	39	93.8	0.036	[ ---- ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
162	pfam13481	192	25	93.8	0.12	[ -- ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
163	COG4988	559	44	93.7	0.071	[ ----- ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
164	COG4107	258	27	93.7	0.044	[ --- ]	PhnK	ABC-type phosphonate transport system, ATPase component
165	cd03213	194	23	93.7	0.044	[ -- ]	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.
166	cd01129	264	65	93.7	0.041	[ ------ ]	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.
167	PRK10789	569	22	93.7	0.038	[ -- ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
168	pfam00004	131	72	93.6	0.2	[ ------ ]	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.
169	pfam03029	235	35	93.6	0.052	[ --- ]	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.
170	cd03217	200	21	93.6	0.045	[ -- ]	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.
171	cd03231	201	62	93.6	0.047	[ ------- ]	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.
172	PRK14267	253	40	93.5	0.065	[ ---- ]	PRK14267	phosphate ABC transporter ATP-binding protein; Provisional
173	COG0470	325	30	93.5	0.06	[ --- ]	HolB	DNA polymerase III, delta prime subunit
174	cd03245	220	50	93.5	0.053	[ ----- ]	ABCC_bacteriocin_exporters	ATP-binding cassette domain of bacteriocin exporters, subfamily C. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
175	pfam10662	143	40	93.5	0.039	[ ---- ]	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.
176	cd03247	178	29	93.4	0.048	[ --- ]	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.
177	PRK06547	172	31	93.4	0.073	[ --- ]	PRK06547	hypothetical protein; Provisional
178	cd03253	236	92	93.4	0.08	[ ---------- ]	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.
179	TIGR00455	184	48	93.3	0.096	[ ---- ]	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.
180	COG0714	329	61	93.3	0.039	[ ----- ]	MoxR	MoxR-like ATPase
181	PRK09270	229	39	93.3	0.075	[ --- ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
182	cd00071	137	21	93.2	0.064	[ -- ]	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.
183	COG1618	179	27	93.2	0.11	[ -- ]	THEP1	Nucleoside-triphosphatase THEP1
184	COG2274	709	69	93.2	0.053	[ ------ ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
185	COG4088	261	142	93.2	0.062	[ --------------- ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
186	cd03298	211	27	93.2	0.052	[ --- ]	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.
187	PRK11160	574	78	93.1	0.059	[ -------- ]	PRK11160	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
188	PRK11819	556	21	93.1	0.056	[ -- ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
189	cd03301	213	43	93.1	0.054	[ ---- ]	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.
190	cd01850	275	26	93.1	0.059	[ --- ]	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.
191	cd03219	236	74	93.1	0.058	[ -------- ]	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).
192	cd03292	214	40	93.0	0.062	[ ---- ]	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.
193	cd00880	161	24	92.9	0.041	[ -- ]	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.
194	cd03299	235	29	92.9	0.062	[ --- ]	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.
195	cd01122	271	28	92.8	0.12	[ --- ]	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.
196	COG4133	209	22	92.8	0.07	[ -- ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
197	TIGR03719	552	21	92.8	0.066	[ -- ]	ABC_ABC_ChvD	ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.
198	COG1127	263	92	92.7	0.058	[ --------- ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
199	cd03297	214	68	92.7	0.096	[ ------- ]	ABC_ModC_molybdenum_transporter	ATP-binding cassette domain of the molybdenum transport system. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
200	COG3596	296	61	92.7	0.17	[ ------ ]	YeeP	Predicted GTPase
201	cd03256	241	53	92.7	0.071	[ ---- ]	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.
202	PRK13342	413	63	92.6	0.12	[ ------ ]	PRK13342	recombination factor protein RarA; Reviewed
203	COG0523	323	40	92.5	0.091	[ ---- ]	YejR	GTPase, G3E family
204	PRK13651	305	35	92.5	0.08	[ --- ]	PRK13651	cobalt transporter ATP-binding subunit; Provisional
205	cd03233	202	36	92.5	0.07	[ --- ]	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.
206	pfam04851	103	25	92.5	0.2	[ -- ]	ResIII	Type III restriction enzyme, res subunit.
207	cd03289	275	57	92.5	0.12	[ ------ ]	ABCC_CFTR2	ATP-binding cassette domain 2 of CFTR,subfamily C. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
208	PRK14246	257	38	92.5	0.11	[ ---- ]	PRK14246	phosphate ABC transporter ATP-binding protein; Provisional
209	TIGR02525	372	39	92.5	0.13	[ ---- ]	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).
210	cd01882	231	35	92.4	0.14	[ --- ]	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.
211	TIGR00972	247	35	92.3	0.099	[ --- ]	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.
212	cd01124	187	35	92.3	0.19	[ --- ]	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.
213	TIGR03873	256	27	92.3	0.074	[ --- ]	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.
214	TIGR00618	1042	48	92.3	0.087	[ ---- ]	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).
215	pfam08477	118	21	92.3	0.097	[ -- ]	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.
216	COG1117	253	36	92.3	0.11	[ --- ]	PstB	ABC-type phosphate transport system, ATPase component
217	pfam07728	135	43	92.3	0.16	[ ---- ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
218	COG1125	309	60	92.3	0.085	[ ------- ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
219	cd03267	236	34	92.2	0.073	[ --- ]	ABC_NatA_like	ATP-binding cassette domain of an uncharacterized transporter similar in sequence to NatA. NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single integral membrane protein.
220	COG4619	223	43	92.2	0.095	[ ---- ]	FetA	ABC-type iron transport system FetAB, ATPase component
221	PRK13695	174	25	92.2	0.18	[ -- ]	PRK13695	putative NTPase; Provisional
222	COG1123	539	55	92.2	0.088	[ ----- ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
223	PRK13634	290	44	92.2	0.095	[ ---- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
224	cd02021	150	22	92.1	0.12	[ -- ]	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.
225	TIGR03574	249	35	92.0	0.14	[ --- ]	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.
226	cd03216	163	72	92.0	0.1	[ -------- ]	ABC_Carb_Monos_I	First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
227	cd03268	208	23	92.0	0.1	[ -- ]	ABC_BcrA_bacitracin_resist	ATP-binding cassette domain of the bacitracin-resistance transporter. The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.
228	PRK09435	332	38	92.0	0.17	[ ---- ]	PRK09435	membrane ATPase/protein kinase; Provisional
229	cd02027	149	34	91.9	0.19	[ --- ]	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.
230	cd00046	144	26	91.9	0.27	[ -- ]	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.
231	cd03369	207	38	91.9	0.14	[ --- ]	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.
232	pfam02456	370	18	91.9	0.089	[ -- ]	Adeno_IVa2	Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter.
233	TIGR02324	224	27	91.9	0.1	[ --- ]	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.
234	PRK07667	193	36	91.9	0.19	[ --- ]	PRK07667	uridine kinase; Provisional
235	cd03226	205	42	91.9	0.11	[ ---- ]	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.
236	TIGR02315	243	63	91.8	0.1	[ ----- ]	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.
237	COG1341	398	35	91.8	0.2	[ --- ]	Grc3	Polynucleotide 5'-kinase, involved in rRNA processing
238	PRK09536	402	71	91.8	0.095	[ ------ ]	btuD	corrinoid ABC transporter ATPase; Reviewed
239	COG4608	268	21	91.7	0.11	[ -- ]	AppF	ABC-type oligopeptide transport system, ATPase component
240	COG0237	201	33	91.7	0.14	[ ---- ]	CoaE	Dephospho-CoA kinase
241	cd11383	140	23	91.7	0.076	[ -- ]	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.
242	PRK14489	366	76	91.6	0.15	[ -------- ]	PRK14489	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional
243	TIGR02673	214	89	91.6	0.12	[ ------------ ]	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.
244	COG1118	345	20	91.6	0.12	[ -- ]	CysA	ABC-type sulfate/molybdate transport systems, ATPase component
245	COG3840	231	45	91.6	0.12	[ ---- ]	ThiQ	ABC-type thiamine transport system, ATPase component
246	COG1474	366	40	91.5	0.22	[ ---- ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
247	COG0552	340	46	91.5	0.2	[ ---- ]	FtsY	Signal recognition particle GTPase
248	cd03258	233	54	91.4	0.12	[ ----- ]	ABC_MetN_methionine_transporter	ATP-binding cassette domain of methionine transporter. MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
249	COG0529	197	40	91.4	0.26	[ --- ]	CysC	Adenylylsulfate kinase or related kinase
250	TIGR00968	237	19	91.4	0.12	[ -- ]	3a0106s01	sulfate ABC transporter, ATP-binding protein.
251	pfam06414	194	39	91.3	0.17	[ ---- ]	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.
252	cd03251	234	106	91.3	0.13	[ ------------- ]	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.
253	cd03263	220	28	91.3	0.14	[ --- ]	ABC_subfamily_A	ATP-binding cassette domain of the lipid transporters, subfamily A. The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.
254	cd03265	220	40	91.2	0.79	[ ---- ]	ABC_DrrA	Daunorubicin/doxorubicin resistance ATP-binding protein. DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin. In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
255	PRK08118	167	31	91.2	0.19	[ --- ]	PRK08118	topology modulation protein; Reviewed
256	cd03115	173	56	91.2	0.29	[ ----- ]	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.
257	TIGR01978	243	44	91.1	0.11	[ ---- ]	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.
258	TIGR01166	190	40	91.1	0.17	[ ---- ]	cbiO	cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.
259	PRK05541	176	33	91.1	0.27	[ --- ]	PRK05541	adenylylsulfate kinase; Provisional
260	PRK13538	204	20	91.1	0.15	[ -- ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
261	cd04105	202	23	91.1	0.15	[ -- ]	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.
262	PRK09361	225	48	91.1	0.27	[ ---- ]	radB	DNA repair and recombination protein RadB; Provisional
263	COG0194	191	23	91.1	0.15	[ -- ]	Gmk	Guanylate kinase
264	COG4525	259	20	91.0	0.15	[ -- ]	TauB	ABC-type taurine transport system, ATPase component
265	cd03296	239	19	90.9	0.14	[ -- ]	ABC_CysA_sulfate_importer	ATP-binding cassette domain of the sulfate transporter. Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
266	PRK09493	240	18	90.9	0.14	[ -- ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
267	PRK13657	588	21	90.9	0.15	[ -- ]	PRK13657	cyclic beta-1,2-glucan ABC transporter; Provisional
268	COG4181	228	20	90.9	0.15	[ -- ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
269	COG4178	604	38	90.9	0.15	[ ---- ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
270	cd00464	154	22	90.9	0.2	[ -- ]	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.
271	COG1484	254	27	90.8	0.28	[ --- ]	DnaC	DNA replication protein DnaC
272	TIGR03928	1296	141	90.8	0.27	[ ------------ ]	T7_EssCb_Firm	type VII secretion protein EssC, C-terminal domain. This model describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria.
273	TIGR02857	529	119	90.7	0.53	[ ----------- ]	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
274	pfam12128	1198	24	90.7	0.11	[ -- ]	DUF3584	Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication.
275	TIGR02173	171	22	90.7	0.15	[ -- ]	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.
276	PRK13635	279	54	90.6	0.14	[ ----- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
277	COG0396	251	20	90.6	0.14	[ -- ]	SufC	Fe-S cluster assembly ATPase SufC
278	TIGR03269	520	44	90.6	0.15	[ ---- ]	met_CoM_red_A2	methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.
279	pfam01078	207	28	90.5	0.16	[ -- ]	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.
280	cd02042	104	59	90.5	0.11	[ ----- ]	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.
281	cd03283	199	27	90.5	0.25	[ --- ]	ABC_MutS-like	ATP-binding cassette domain of MutS-like homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
282	cd03252	237	27	90.5	0.19	[ --- ]	ABCC_Hemolysin	ATP-binding cassette domain of hemolysin B, subfamily C. The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.
283	PRK04182	180	22	90.5	0.21	[ -- ]	PRK04182	cytidylate kinase; Provisional
284	PRK10790	592	46	90.4	0.17	[ ---- ]	PRK10790	putative multidrug transporter membrane\ATP-binding components; Provisional
285	COG3911	183	48	90.3	0.2	[ ---- ]	COG3911	Predicted ATPase
286	TIGR02533	486	54	90.3	0.23	[ ----- ]	type_II_gspE	type II secretion system protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
287	PRK11784	345	20	90.3	0.18	[ -- ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
288	PRK11819	556	60	90.3	0.17	[ ------ ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
289	PRK15467	158	54	90.2	0.35	[ ----- ]	PRK15467	ethanolamine utilization protein EutP; Provisional
290	pfam06745	231	57	90.1	0.43	[ ----- ]	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.
291	PRK10247	225	27	90.1	0.18	[ --- ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
292	COG2255	332	27	90.1	0.23	[ -- ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
293	cd03237	246	22	90.0	0.2	[ -- ]	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.
294	COG1135	339	69	90.0	0.19	[ ------ ]	AbcC	ABC-type methionine transport system, ATPase component
295	TIGR03797	686	28	90.0	0.19	[ --- ]	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.
296	TIGR02639	730	35	90.0	0.28	[ ---- ]	ClpA	ATP-dependent Clp protease ATP-binding subunit clpA.
297	cd03269	210	28	89.9	0.21	[ --- ]	ABC_putative_ATPase	ATP-binding cassette domain of an uncharacterized transporter. This subgroup is related to the subfamily A transporters involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two integral membranes. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
298	cd03216	163	21	89.9	2.2	[ -- ]	ABC_Carb_Monos_I	First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
299	PRK13833	323	69	89.8	0.83	[ ------- ]	PRK13833	conjugal transfer protein TrbB; Provisional
300	cd01855	191	28	89.8	0.24	[ -- ]	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.
301	TIGR01271	1490	62	89.8	0.2	[ ------ ]	CFTR_protein	cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.
302	cd03266	218	38	89.8	0.2	[ ---- ]	ABC_NatA_sodium_exporter	ATP-binding cassette domain of the Na+ transporter. NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single integral membrane protein.
303	COG1157	441	33	89.8	0.33	[ --- ]	FliI	Flagellar biosynthesis/type III secretory pathway ATPase
304	PRK13851	344	26	89.8	0.13	[ -- ]	PRK13851	type IV secretion system protein VirB11; Provisional
305	PRK15064	530	32	89.7	0.18	[ --- ]	PRK15064	ABC transporter ATP-binding protein; Provisional
306	COG5635	824	49	89.6	0.2	[ ---- ]	COG5635	Predicted NTPase, NACHT family domain
307	TIGR02982	220	56	89.6	0.22	[ ----- ]	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.
308	TIGR03410	230	42	89.5	0.31	[ ---- ]	urea_trans_UrtE	urea ABC transporter, ATP-binding protein UrtE. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
309	TIGR00231	162	42	89.5	0.23	[ ---- ]	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
310	cd03240	204	66	89.5	0.22	[ ------- ]	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.
311	PRK11264	250	78	89.5	0.21	[ ------- ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
312	cd03238	176	34	89.4	0.28	[ --- ]	ABC_UvrA	ATP-binding cassette domain of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
313	TIGR03263	179	20	89.4	0.28	[ -- ]	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.
314	PRK00080	328	24	89.4	0.28	[ -- ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
315	TIGR03719	552	60	89.4	0.21	[ ------ ]	ABC_ABC_ChvD	ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.
316	TIGR03375	694	98	89.3	0.24	[ ---------- ]	type_I_sec_LssB	type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
317	COG0444	316	62	89.2	0.27	[ ------- ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
318	PRK11650	356	19	89.1	0.26	[ -- ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
319	cd03300	232	55	89.1	0.26	[ ----- ]	ABC_PotA_N	ATP-binding cassette domain of the polyamine transporter. PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
320	PRK09376	416	34	89.0	0.43	[ --- ]	rho	transcription termination factor Rho; Provisional
321	TIGR03864	236	34	89.0	0.28	[ --- ]	PQQ_ABC_ATP	ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.
322	TIGR01846	694	52	89.0	0.36	[ ----- ]	type_I_sec_HlyB	type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
323	PRK10851	353	20	89.0	0.19	[ -- ]	PRK10851	sulfate/thiosulfate transporter subunit; Provisional
324	cd01428	194	21	89.0	0.35	[ -- ]	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.
325	COG4618	580	89	89.0	0.25	[ ---------- ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
326	COG1101	263	62	89.0	0.23	[ ------ ]	PhnK	ABC-type uncharacterized transport system, ATPase component
327	COG3640	255	37	89.0	0.56	[ ---- ]	CooC	CO dehydrogenase nickel-insertion accessory protein CooC1
328	cd00881	183	23	88.9	0.48	[ -- ]	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.
329	pfam01443	227	20	88.9	0.27	[ -- ]	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.
330	cd03295	242	73	88.9	0.29	[ -------- ]	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.
331	COG2256	436	66	88.8	0.42	[ ------ ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
332	COG0703	172	23	88.8	0.33	[ -- ]	AroK	Shikimate kinase
333	COG4167	267	39	88.8	0.29	[ ---- ]	SapF	ABC-type antimicrobial peptide transport system, ATPase component
334	TIGR02858	270	86	88.7	0.37	[ -------- ]	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.
335	PRK10575	265	78	88.7	0.24	[ ------- ]	PRK10575	iron-hydroxamate transporter ATP-binding subunit; Provisional
336	PRK10246	1047	28	88.7	0.29	[ --- ]	PRK10246	exonuclease subunit SbcC; Provisional
337	COG4138	248	18	88.7	0.25	[ - ]	BtuD	ABC-type cobalamin transport system, ATPase component
338	PRK11147	635	28	88.7	0.29	[ --- ]	PRK11147	ABC transporter ATPase component; Reviewed
339	PRK10771	232	27	88.6	0.3	[ --- ]	thiQ	thiamine transporter ATP-binding subunit; Provisional
340	TIGR01192	585	21	88.6	0.3	[ -- ]	chvA	glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.
341	PRK12724	432	59	88.6	0.47	[ ----- ]	PRK12724	flagellar biosynthesis regulator FlhF; Provisional
342	TIGR03575	340	37	88.6	0.47	[ ---- ]	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.
343	cd04162	164	22	88.6	0.31	[ -- ]	Arl9_Arfrp2_like	Arf-like 9 (Arl9)/Arfrp2-like GTPase. Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.
344	COG5192	1077	34	88.5	0.45	[ --- ]	BMS1	GTP-binding protein required for 40S ribosome biogenesis
345	PRK10416	318	59	88.5	0.53	[ ----- ]	PRK10416	signal recognition particle-docking protein FtsY; Provisional
346	pfam01656	211	31	88.5	0.62	[ -- ]	CbiA	CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
347	COG5008	375	23	88.4	0.26	[ -- ]	PilU	Tfp pilus assembly protein, ATPase PilU
348	TIGR03498	418	40	88.4	0.47	[ ---- ]	FliI_clade3	flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
349	cd01128	249	33	88.3	0.53	[ --- ]	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.
350	cd03277	213	25	88.3	0.27	[ --- ]	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).
351	TIGR03925	566	85	88.3	2.1	[ ------- ]	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.
352	cd03234	226	54	88.3	0.33	[ ------ ]	ABCG_White	White pigment protein homolog of ABCG transporter subfamily. The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.
353	cd01878	204	84	88.3	0.33	[ --------- ]	HflX	HflX GTPase family. HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.
354	PRK00131	175	23	88.2	0.35	[ -- ]	aroK	shikimate kinase; Reviewed
355	COG4240	300	28	88.2	0.51	[ --- ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
356	PRK11174	588	61	88.2	0.31	[ ------ ]	PRK11174	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
357	COG1936	180	19	88.2	0.36	[ -- ]	Fap7	Broad-specificity NMP kinase
358	pfam02463	1162	29	88.1	0.29	[ --- ]	SMC_N	RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolizm and recombination.
359	cd02022	179	33	88.1	0.37	[ ---- ]	DPCK	Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
360	cd01136	326	36	88.1	0.49	[ ---- ]	ATPase_flagellum-secretory_path_III	Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
361	PRK11248	255	20	88.0	0.33	[ -- ]	tauB	taurine transporter ATP-binding subunit; Provisional
362	COG2019	189	38	88.0	0.42	[ ---- ]	AdkA	Archaeal adenylate kinase
363	TIGR03924	658	113	87.9	0.5	[ ----------- ]	T7SS_EccC_a	type VII secretion protein EccCa. This model represents the N-terminal domain or EccCa 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.
364	cd04170	268	20	87.8	0.41	[ -- ]	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.
365	TIGR01188	302	39	87.7	0.23	[ ---- ]	drrA	daunorubicin resistance ABC transporter ATP-binding subunit. This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.
366	pfam13401	124	39	87.7	1.8	[ --- ]	AAA_22	AAA domain.
367	PRK00300	205	21	87.6	0.37	[ -- ]	gmk	guanylate kinase; Provisional
368	cd01854	211	30	87.6	0.34	[ -- ]	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.
369	PRK12402	337	27	87.5	0.54	[ --- ]	PRK12402	replication factor C small subunit 2; Reviewed
370	PRK11247	257	20	87.5	0.41	[ -- ]	ssuB	aliphatic sulfonates transport ATP-binding subunit; Provisional
371	cd01898	170	20	87.4	0.32	[ -- ]	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.
372	COG0411	250	79	87.4	0.13	[ -------- ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
373	cd03225	211	34	87.4	0.73	[ --- ]	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.
374	pfam05673	248	58	87.3	0.73	[ ----- ]	DUF815	Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
375	cd03294	269	71	87.3	0.41	[ ------- ]	ABC_Pro_Gly_Betaine	ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system. This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
376	COG0802	149	22	87.2	0.46	[ -- ]	TsaE	tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE
377	cd03278	197	17	87.1	0.37	[ -- ]	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).
378	PRK06835	329	36	87.0	0.75	[ ---- ]	PRK06835	DNA replication protein DnaC; Validated
379	PRK10253	265	28	86.9	0.46	[ --- ]	PRK10253	iron-enterobactin transporter ATP-binding protein; Provisional
380	TIGR00101	199	35	86.9	0.73	[ --- ]	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.
381	TIGR00635	305	26	86.9	0.5	[ -- ]	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.
382	pfam00503	317	23	86.9	0.43	[ -- ]	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.
383	PRK13637	287	58	86.8	0.41	[ ----- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
384	pfam02367	123	26	86.8	0.43	[ --- ]	UPF0079	Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
385	cd02024	187	31	86.8	0.55	[ --- ]	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.
386	pfam01583	157	42	86.7	0.95	[ ---- ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
387	TIGR01187	325	17	86.7	0.32	[ - ]	potA	spermidine/putrescine ABC transporter ATP-binding subunit. This model describes spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Polyamines like spermidine and putrescine play vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).
388	COG1643	845	48	86.7	0.52	[ ---- ]	HrpA	HrpA-like RNA helicase
389	COG3910	233	53	86.7	0.43	[ ----- ]	COG3910	Predicted ATPase
390	cd01672	200	35	86.7	0.88	[ ---- ]	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).
391	pfam05496	234	24	86.6	0.54	[ -- ]	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.
392	PRK14271	276	18	86.6	0.29	[ - ]	PRK14271	phosphate ABC transporter ATP-binding protein; Provisional
393	TIGR02237	209	36	86.6	0.57	[ --- ]	recomb_radB	DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
394	TIGR02546	422	67	86.6	0.71	[ ------ ]	III_secr_ATP	type III secretion apparatus H+-transporting two-sector ATPase.
395	cd03249	238	59	86.5	0.77	[ ------- ]	ABC_MTABC3_MDL1_MDL2	ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins. MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
396	cd04164	159	28	86.5	0.4	[ --- ]	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.
397	TIGR03167	311	21	86.5	0.47	[ -- ]	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.
398	TIGR00064	277	43	86.4	0.73	[ ---- ]	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.
399	PRK13646	286	19	86.4	0.4	[ -- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
400	COG1129	500	24	86.3	0.45	[ -- ]	MglA	ABC-type sugar transport system, ATPase component
401	cd03112	158	17	86.3	0.56	[ -- ]	CobW_like	The function of this protein family is unkown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K.
402	pfam13604	195	33	86.2	1.1	[ --- ]	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.
403	TIGR01277	213	28	86.2	0.5	[ --- ]	thiQ	thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.
404	PRK00440	319	28	86.2	0.51	[ --- ]	rfc	replication factor C small subunit; Reviewed
405	cd03271	261	43	86.1	0.84	[ ---- ]	ABC_UvrA_II	ATP-binding cassette domain II of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.
406	COG1158	422	34	86.0	0.78	[ --- ]	Rho	Transcription termination factor Rho
407	PRK11147	635	27	85.9	0.36	[ --- ]	PRK11147	ABC transporter ATPase component; Reviewed
408	PRK14247	250	40	85.9	0.66	[ ---- ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
409	COG4136	213	27	85.9	0.47	[ --- ]	YnjD	ABC-type uncharacterized transport system YnjBCD, ATPase component
410	pfam00006	213	24	85.9	7.3	[ -- ]	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.
411	PRK15112	267	66	85.7	0.7	[ ------ ]	PRK15112	antimicrobial peptide ABC system ATP-binding protein SapF; Provisional
412	PRK14253	249	37	85.6	0.55	[ ---- ]	PRK14253	phosphate ABC transporter ATP-binding protein; Provisional
413	cd03272	243	46	85.6	0.48	[ ----- ]	ABC_SMC3_euk	ATP-binding cassette domain of eukaryotic SMC3 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).
414	PRK14240	250	37	85.5	0.5	[ ---- ]	PRK14240	phosphate transporter ATP-binding protein; Provisional
415	PRK13543	214	27	85.5	0.61	[ --- ]	PRK13543	cytochrome c biogenesis protein CcmA; Provisional
416	PRK11000	369	20	85.4	0.55	[ -- ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
417	COG0464	494	33	85.4	0.89	[ ---- ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
418	pfam03193	161	31	85.3	0.5	[ -- ]	DUF258	Protein of unknown function, DUF258.
419	cd03232	192	22	85.0	0.59	[ -- ]	ABCG_PDR_domain2	Second domain of the pleiotropic drug resistance-like (PDR) subfamily G of ATP-binding cassette transporters. The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
420	pfam00580	267	31	85.0	13	[ --- ]	UvrD-helicase	UvrD/REP helicase N-terminal domain. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Some members have large insertions near to the carboxy-terminus relative to other members of the family.
421	cd02038	139	31	84.8	1	[ -- ]	FleN-like	FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
422	COG5019	373	27	84.8	0.63	[ --- ]	CDC3	Septin family protein
423	PRK13409	590	26	84.8	0.58	[ --- ]	PRK13409	putative ATPase RIL; Provisional
424	TIGR00959	428	58	84.8	0.72	[ ----- ]	ffh	signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
425	TIGR03740	223	27	84.7	0.55	[ --- ]	galliderm_ABC	gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.
426	TIGR00955	617	27	84.7	0.6	[ --- ]	3a01204	The Eye Pigment Precursor Transporter (EPP) Family protein.
427	TIGR03015	269	23	84.7	0.68	[ -- ]	pepcterm_ATPase	putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
428	PRK11629	233	19	84.7	0.63	[ -- ]	lolD	lipoprotein transporter ATP-binding subunit; Provisional
429	PRK13547	272	29	84.7	0.5	[ -- ]	hmuV	hemin importer ATP-binding subunit; Provisional
430	TIGR03420	226	58	84.6	1.3	[ ----- ]	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.
431	PRK12608	380	33	84.6	0.99	[ --- ]	PRK12608	transcription termination factor Rho; Provisional
432	COG1428	216	23	84.6	0.76	[ -- ]	Dck	Deoxyadenosine/deoxycytidine kinase
433	COG4618	580	27	84.6	1.6	[ --- ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
434	COG0606	490	144	84.6	0.5	[ ------------- ]	YifB	Predicted ATPase with chaperone activity
435	cd03222	177	25	84.5	0.41	[ -- ]	ABC_RNaseL_inhibitor	ATP-binding cassette domain 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 more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
436	COG0645	170	22	84.5	0.66	[ -- ]	COG0645	Predicted kinase
437	pfam00270	167	27	84.5	0.57	[ -- ]	DEAD	DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
438	COG0283	222	38	84.4	0.55	[ ---- ]	Cmk	Cytidylate kinase
439	cd01851	224	21	84.4	0.7	[ -- ]	GBP	Guanylate-binding protein (GBP) family (N-terminal domain). Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.
440	PRK10938	490	37	84.3	0.31	[ --- ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
441	COG1196	1163	30	84.3	0.77	[ --- ]	Smc	Chromosome segregation ATPase
442	PRK14250	241	22	84.3	0.59	[ -- ]	PRK14250	phosphate ABC transporter ATP-binding protein; Provisional
443	PRK13641	287	70	84.3	0.83	[ ------ ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
444	TIGR01193	708	43	84.3	0.6	[ ----- ]	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.
445	PRK14491	597	44	84.2	1	[ ----- ]	PRK14491	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional
446	PRK11131	1294	103	84.0	0.65	[ ---------- ]	PRK11131	ATP-dependent RNA helicase HrpA; Provisional
447	COG4778	235	51	84.0	0.7	[ ----- ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
448	PRK14274	259	27	84.0	0.87	[ --- ]	PRK14274	phosphate ABC transporter ATP-binding protein; Provisional
449	TIGR03918	391	105	84.0	0.57	[ --------- ]	GTP_HydF
450	PRK10436	462	19	83.9	0.35	[ -- ]	PRK10436	hypothetical protein; Provisional
451	PRK07261	171	32	83.8	1.1	[ ---- ]	PRK07261	topology modulation protein; Provisional
452	COG0541	451	56	83.8	1.4	[ ----- ]	Ffh	Signal recognition particle GTPase
453	PRK10744	260	36	83.7	0.82	[ --- ]	pstB	phosphate transporter ATP-binding protein; Provisional
454	COG1123	539	73	83.6	0.71	[ -------- ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
455	COG4148	352	52	83.4	0.61	[ ------ ]	ModC	ABC-type molybdate transport system, ATPase component
456	PRK11153	343	19	83.4	0.75	[ -- ]	metN	DL-methionine transporter ATP-binding subunit; Provisional
457	cd01849	146	24	83.3	1.1	[ -- ]	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.
458	pfam13479	201	32	83.3	0.34	[ ---- ]	AAA_24	AAA domain. This AAA domain is found in a wide variety of presumed phage proteins.
459	PRK14239	252	29	82.9	0.78	[ --- ]	PRK14239	phosphate transporter ATP-binding protein; Provisional
460	TIGR02538	564	23	82.9	0.44	[ -- ]	type_IV_pilB	type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
461	cd04104	197	20	82.8	0.88	[ -- ]	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.
462	TIGR02142	354	101	82.7	0.81	[ --------- ]	modC_ABC	molybdenum ABC transporter, ATP-binding protein. This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.
463	cd03236	255	59	82.6	0.62	[ ----- ]	ABC_RNaseL_inhibitor_domain1	The ATP-binding cassette domain 1 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, RLIs 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 more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
464	TIGR01587	359	278	82.5	59	[ ---------------------------- ]	cas3_core	CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
465	cd01394	218	34	82.5	0.89	[ --- ]	radB	RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
466	COG1102	179	21	82.5	0.93	[ -- ]	CmkB	Cytidylate kinase
467	TIGR03348	1169	93	82.4	0.7	[ --------- ]	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.
468	TIGR03771	223	56	82.4	0.84	[ ------- ]	anch_rpt_ABC	anchored repeat-type ABC transporter, ATP-binding subunit. This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.
469	pfam00735	273	26	82.4	0.9	[ --- ]	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.
470	TIGR02168	1179	28	82.2	0.76	[ --- ]	SMC_prok_B	chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle.
471	cd00878	158	23	82.2	0.81	[ -- ]	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.
472	cd01918	149	25	82.1	1.4	[ -- ]	HprK_C	HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.
473	TIGR01842	544	46	82.1	0.86	[ ----- ]	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.
474	PRK09984	262	22	82.0	0.92	[ -- ]	PRK09984	phosphonate/organophosphate ester transporter subunit; Provisional
475	PRK13546	264	53	81.8	0.91	[ ----- ]	PRK13546	teichoic acids export protein ATP-binding subunit; Provisional
476	TIGR00150	133	22	81.6	1.1	[ -- ]	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.
477	COG0178	935	42	81.6	1.7	[ ---- ]	UvrA	Excinuclease UvrABC ATPase subunit
478	COG1162	301	75	81.5	0.9	[ ------ ]	RsgA	Putative ribosome biogenesis GTPase RsgA
479	cd04163	168	48	81.5	1.1	[ ---- ]	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.
480	PRK06793	432	90	81.5	2.1	[ ---------- ]	fliI	flagellum-specific ATP synthase; Validated
481	PRK13949	169	22	81.4	1.1	[ -- ]	PRK13949	shikimate kinase; Provisional
482	TIGR03265	353	19	81.4	1	[ -- ]	PhnT2	putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
483	PRK13764	602	85	81.4	1.3	[ -------- ]	PRK13764	ATPase; Provisional
484	PRK10867	433	57	81.2	2	[ ----- ]	PRK10867	signal recognition particle protein; Provisional
485	pfam13304	144	21	81.2	4.7	[ -- ]	AAA_21	AAA domain.
486	PRK00023	225	39	81.1	0.92	[ ---- ]	cmk	cytidylate kinase; Provisional
487	PRK10636	638	29	81.1	1.1	[ --- ]	PRK10636	putative ABC transporter ATP-binding protein; Provisional
488	PRK11124	242	74	80.9	1.3	[ -------- ]	artP	arginine transporter ATP-binding subunit; Provisional
489	PRK00889	175	38	80.9	2	[ ---- ]	PRK00889	adenylylsulfate kinase; Provisional
490	PRK00064	361	37	80.8	1.1	[ --- ]	recF	recombination protein F; Reviewed
491	PRK14974	336	125	80.7	2.1	[ ------------ ]	PRK14974	cell division protein FtsY; Provisional
492	TIGR02528	142	39	80.6	1.1	[ ---- ]	EutP	ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.
493	COG0464	494	90	80.5	5.7	[ -------- ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
494	PRK04040	188	72	80.4	1.8	[ -------- ]	PRK04040	adenylate kinase; Provisional
495	COG1159	298	20	80.4	1.2	[ -- ]	Era	GTPase Era, involved in 16S rRNA processing
496	PRK00411	394	37	80.3	2.4	[ --- ]	cdc6	cell division control protein 6; Reviewed
497	PRK08116	268	33	80.3	1.8	[ --- ]	PRK08116	hypothetical protein; Validated
498	PRK13898	800	107	80.3	1	[ ---------- ]	PRK13898	type IV secretion system ATPase VirB4; Provisional
499	PRK13721	844	110	80.2	2.5	[ ---------- ]	PRK13721	conjugal transfer ATP-binding protein TraC; Provisional
500	TIGR00017	217	39	80.2	0.93	[ ---- ]	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.