match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG4637	373	96	99.7	2.2E-17	[                               ----------------  ]	COG4637	Predicted ATPase
2	COG4938	374	65	99.6	1.2E-14	[                                 ----------      ]	COG4938	Predicted ATPase
3	COG1106	371	67	99.3	1.2E-11	[                                -----------      ]	AAA15	ATPase/GTPase, AAA15 family
4	COG3950	440	45	99.3	3.5E-11	[------                                           ]	COG3950	Predicted ATP-binding protein involved in virulence
5	pfam13304	144	55	99.2	1.5E-10	[                                   --------      ]	AAA_21	AAA domain.
6	COG3593	581	79	99.2	1.3E-10	[                                 ------------    ]	YbjD	Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains
7	pfam13175	344	72	99.2	3.1E-10	[                                -----------      ]	AAA_15	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
8	COG1120	258	74	99.2	1.5E-10	[                                 -------------   ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
9	cd03225	211	72	99.1	6.9E-10	[                                 ------------    ]	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.
10	cd03214	180	74	99.0	4.3E-09	[                                 -------------   ]	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.
11	COG1131	293	77	99.0	9.1E-09	[                                 -------------   ]	CcmA	ABC-type multidrug transport system, ATPase component
12	cd03264	211	75	98.9	7.6E-09	[                                 -------------   ]	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.
13	cd03226	205	73	98.9	1.1E-08	[                                 ------------    ]	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.
14	cd03219	236	74	98.9	2.4E-08	[                                 -------------   ]	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).
15	cd03260	227	76	98.9	6.2E-08	[                                  ------------   ]	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).
16	cd03240	204	65	98.9	3.5E-08	[                                 ----------      ]	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.
17	COG1122	235	74	98.9	1.4E-08	[                                 -------------   ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
18	COG1195	363	88	98.8	6.6E-08	[                                --------------   ]	RecF	Recombinational DNA repair ATPase RecF
19	cd03230	173	71	98.8	3.1E-08	[                                  -----------    ]	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.
20	PRK00064	361	83	98.8	8.6E-08	[                                 ------------    ]	recF	recombination protein F; Reviewed
21	cd03235	213	68	98.7	6.8E-08	[                                 ------------    ]	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.
22	cd03262	213	70	98.7	1.4E-07	[                                  -----------    ]	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.
23	COG3910	233	53	98.6	2.7E-07	[                                      --------   ]	COG3910	Predicted ATPase
24	TIGR00611	365	45	98.6	5E-07	[------                                           ]	recf	recF protein. All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
25	cd03278	197	43	98.6	2.8E-07	[------                                           ]	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).
26	COG1121	254	81	98.6	1.3E-07	[                                 --------------  ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
27	COG4555	245	75	98.6	7.4E-07	[                                  ------------   ]	NatA	ABC-type Na+ transport system, ATPase component NatA
28	COG1126	240	72	98.6	7.5E-07	[                                  ------------   ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
29	COG0411	250	70	98.6	1.7E-07	[                                  -----------    ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
30	cd03224	222	73	98.5	9.3E-07	[                                  ------------   ]	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.
31	cd03269	210	75	98.5	2.9E-07	[                                 -------------   ]	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.
32	cd03256	241	75	98.5	2.5E-06	[                                 -------------   ]	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.
33	TIGR01166	190	58	98.5	2.2E-07	[                                 ----------      ]	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.
34	COG1117	253	57	98.5	1.2E-06	[                                  ---------      ]	PstB	ABC-type phosphate transport system, ATPase component
35	cd03263	220	76	98.5	9.6E-07	[                                 -------------   ]	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.
36	cd03245	220	71	98.5	1.9E-06	[                                  ------------   ]	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.
37	TIGR00972	247	73	98.5	2.5E-06	[                                  ------------   ]	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.
38	cd03272	243	62	98.4	9.3E-07	[                                 ----------      ]	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).
39	TIGR04521	277	81	98.4	3.2E-06	[                                  -------------- ]	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.
40	pfam13476	203	40	98.4	1.7E-07	[------                                           ]	AAA_23	AAA domain.
41	cd03266	218	75	98.4	3.8E-06	[                                 -------------   ]	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.
42	cd03261	235	74	98.4	3.6E-06	[                                 -------------   ]	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.
43	cd03242	270	77	98.4	4.2E-06	[                                  -----------    ]	ABC_RecF	ATP-binding cassette domain of RecF. RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
44	TIGR03522	301	75	98.3	1E-06	[                                 -------------   ]	GldA_ABC_ATP	gliding motility-associated ABC transporter ATP-binding subunit GldA. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
45	PRK11264	250	73	98.3	6.5E-06	[                                  ------------   ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
46	COG0410	237	75	98.3	3.8E-06	[                                  ------------   ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
47	COG3638	258	75	98.3	6.9E-06	[                                 -------------   ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
48	PRK10619	257	72	98.3	1.4E-05	[                                  ------------   ]	PRK10619	histidine/lysine/arginine/ornithine transporter subunit; Provisional
49	pfam13555	60	43	98.3	8.9E-07	[------                                           ]	AAA_29	P-loop containing region of AAA domain.
50	cd03268	208	74	98.3	5.7E-06	[                                 -------------   ]	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.
51	COG0419	908	44	98.3	5.5E-07	[------                                           ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
52	cd03229	178	69	98.3	6E-06	[                                  -----------    ]	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.
53	PRK11231	255	74	98.3	1.8E-05	[                                 -------------   ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
54	COG4604	252	75	98.3	3.6E-06	[                                 -------------   ]	CeuD	ABC-type enterochelin transport system, ATPase component
55	PRK14264	305	74	98.3	1.1E-05	[                                  ------------   ]	PRK14264	phosphate ABC transporter ATP-binding protein; Provisional
56	PRK13647	274	74	98.2	9.8E-07	[                                 -------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
57	COG1127	263	74	98.2	1.7E-05	[                                 -------------   ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
58	PRK09493	240	74	98.2	1.5E-05	[                                  ------------   ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
59	pfam11398	373	45	98.2	8.6E-06	[------                                           ]	DUF2813	Protein of unknown function (DUF2813). This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase.
60	PRK13539	207	58	98.2	6.2E-06	[                                 ----------      ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
61	TIGR03411	242	72	98.2	2.3E-05	[                                  -----------    ]	urea_trans_UrtD	urea ABC transporter, ATP-binding protein UrtD. 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.
62	cd03257	228	75	98.2	2.6E-05	[                                 -------------   ]	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.
63	COG4161	242	74	98.2	3.1E-05	[                                  ------------   ]	ArtP	ABC-type arginine transport system, ATPase component
64	COG0396	251	73	98.2	3.9E-05	[                                  ------------   ]	SufC	Fe-S cluster assembly ATPase SufC
65	cd03267	236	74	98.1	2E-05	[                                 ------------    ]	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.
66	pfam02463	1162	42	98.1	1.5E-06	[------                                           ]	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.
67	PRK14254	285	75	98.1	1.5E-05	[                                  ------------   ]	PRK14254	phosphate ABC transporter ATP-binding protein; Provisional
68	TIGR03873	256	74	98.1	1.1E-05	[                                 -------------   ]	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.
69	COG4586	325	76	98.1	2.3E-05	[                                 -------------   ]	COG4586	ABC-type uncharacterized transport system, ATPase component
70	PRK11124	242	74	98.1	3.2E-05	[                                  ------------   ]	artP	arginine transporter ATP-binding subunit; Provisional
71	TIGR02169	1164	44	98.1	1.4E-06	[------                                           ]	SMC_prok_A	chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
72	COG4598	256	72	98.1	0.00013	[                                  ------------   ]	HisP	ABC-type histidine transport system, ATPase component
73	PRK13651	305	72	98.1	1.1E-05	[                                  ------------   ]	PRK13651	cobalt transporter ATP-binding subunit; Provisional
74	cd03275	247	44	98.1	2E-06	[------                                           ]	ABC_SMC1_euk	ATP-binding cassette domain of eukaryotic SMC1 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
75	TIGR03375	694	72	98.1	2.7E-05	[                                  ------------   ]	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.
76	COG1118	345	77	98.1	4.2E-05	[                                 -------------   ]	CysA	ABC-type sulfate/molybdate transport systems, ATPase component
77	COG1196	1163	46	98.1	3.2E-06	[------                                           ]	Smc	Chromosome segregation ATPase
78	COG1136	226	73	98.1	6.8E-05	[                                 -------------   ]	LolD	ABC-type lipoprotein export system, ATPase component
79	TIGR04520	268	82	98.1	8.3E-05	[                                 --------------- ]	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.
80	TIGR02315	243	75	98.0	5.9E-05	[                                 -------------   ]	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.
81	PRK13639	275	83	98.0	2.5E-06	[                                 --------------- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
82	PRK03918	880	43	98.0	4.9E-06	[------                                           ]	PRK03918	chromosome segregation protein; Provisional
83	COG2884	223	72	98.0	5.6E-05	[                                  ------------   ]	FtsE	ABC-type ATPase involved in cell division
84	cd03259	213	76	98.0	5.6E-05	[                                 -------------   ]	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.
85	cd03239	178	43	98.0	1.8E-06	[------                                           ]	ABC_SMC_head	The SMC head domain belongs to the ATP-binding cassette superfamily. The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.
86	PRK13636	283	74	98.0	5.4E-06	[                                 -------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
87	COG1124	252	76	98.0	9.4E-05	[                                 -------------   ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
88	cd03255	218	73	98.0	0.00012	[                                 ------------    ]	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.
89	TIGR02168	1179	43	98.0	7E-06	[------                                           ]	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.
90	PRK14247	250	70	98.0	3.6E-05	[                               ------------      ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
91	PRK13548	258	81	98.0	9.6E-05	[                                 -------------   ]	hmuV	hemin importer ATP-binding subunit; Provisional
92	COG1135	339	75	97.9	8E-05	[                                 -------------   ]	AbcC	ABC-type methionine transport system, ATPase component
93	PRK14244	251	76	97.9	0.00017	[                                  ------------   ]	PRK14244	phosphate ABC transporter ATP-binding protein; Provisional
94	COG4988	559	72	97.9	9.7E-05	[                                  ------------   ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
95	cd03274	212	45	97.9	1.1E-05	[------                                           ]	ABC_SMC4_euk	ATP-binding cassette domain of eukaryotic SMC4 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
96	cd03271	261	66	97.9	0.00025	[                                 ----------      ]	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.
97	COG1101	263	75	97.9	0.00038	[                                 -------------   ]	PhnK	ABC-type uncharacterized transport system, ATPase component
98	TIGR04435	555	72	97.9	0.00014	[                                 ------------    ]	restrict_AAA_1	restriction system-associated AAA family ATPase. Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements.
99	PRK14240	250	73	97.9	0.00021	[                                  ------------   ]	PRK14240	phosphate transporter ATP-binding protein; Provisional
100	cd03277	213	42	97.8	1.6E-05	[------                                           ]	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).
101	PRK02224	880	45	97.8	1.3E-05	[------                                           ]	PRK02224	chromosome segregation protein; Provisional
102	TIGR03864	236	74	97.8	0.00014	[                                 -------------   ]	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.
103	COG1125	309	76	97.8	0.0002	[                                 -------------   ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
104	PRK14236	272	57	97.8	2.2E-05	[                                  ---------      ]	PRK14236	phosphate transporter ATP-binding protein; Provisional
105	COG0488	530	78	97.8	0.00026	[                                 -------------   ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
106	TIGR01188	302	75	97.8	9.7E-05	[                                 -------------   ]	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.
107	COG1119	257	74	97.8	0.00016	[                                 -------------   ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
108	PRK03695	248	54	97.8	8.7E-05	[                                      --------   ]	PRK03695	vitamin B12-transporter ATPase; Provisional
109	cd03228	171	68	97.8	0.00022	[                                  -----------    ]	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.
110	COG0444	316	76	97.8	0.00032	[                                 -------------   ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
111	cd03220	224	77	97.8	0.00054	[                                 -------------   ]	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.
112	cd03227	162	60	97.8	2.6E-05	[                                  ---------      ]	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.
113	PRK14253	249	56	97.8	0.0003	[                                  ---------      ]	PRK14253	phosphate ABC transporter ATP-binding protein; Provisional
114	PRK14242	253	56	97.7	0.00034	[                                  ---------      ]	PRK14242	phosphate transporter ATP-binding protein; Provisional
115	PRK14237	267	57	97.7	0.00019	[                                  ---------      ]	PRK14237	phosphate transporter ATP-binding protein; Provisional
116	PRK14262	250	58	97.7	0.00011	[                                  ---------      ]	PRK14262	phosphate ABC transporter ATP-binding protein; Provisional
117	COG4674	249	70	97.7	0.00016	[                                  -----------    ]	COG4674	ABC-type uncharacterized transport system, ATPase component
118	cd03279	213	45	97.7	4.1E-05	[------                                           ]	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.
119	COG1134	249	77	97.7	0.00095	[                                 -------------   ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
120	cd03295	242	76	97.7	0.00041	[                                 -------------   ]	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.
121	cd03241	276	65	97.7	0.00097	[----------                                       ]	ABC_RecN	ATP-binding cassette domain of RecN. RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
122	TIGR03005	252	82	97.7	0.00037	[                                  -------------- ]	ectoine_ehuA	ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.
123	COG2274	709	72	97.7	0.00023	[                                  ------------   ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
124	COG4152	300	60	97.7	0.00029	[                                 ----------      ]	YhaQ	ABC-type uncharacterized transport system, ATPase component
125	PRK14248	268	74	97.7	0.00033	[                                  ------------   ]	PRK14248	phosphate ABC transporter ATP-binding protein; Provisional
126	PRK14243	264	57	97.7	0.00028	[                                  ---------      ]	PRK14243	phosphate transporter ATP-binding protein; Provisional
127	COG1132	567	73	97.7	0.00053	[                                  ------------   ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
128	COG4133	209	60	97.7	0.00022	[                                 ----------      ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
129	PRK09536	402	74	97.7	0.00019	[                                 -------------   ]	btuD	corrinoid ABC transporter ATPase; Reviewed
130	COG3839	338	77	97.6	0.0004	[                                 -------------   ]	MalK	ABC-type sugar transport system, ATPase component
131	cd03265	220	75	97.6	0.00026	[                                 -------------   ]	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.
132	cd03273	251	46	97.6	2.8E-05	[------                                           ]	ABC_SMC2_euk	ATP-binding cassette domain of eukaryotic SMC2 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
133	PRK14079	349	270	97.6	0.00044	[------------------------------------------       ]	recF	recombination protein F; Provisional
134	COG0488	530	71	97.6	0.00084	[                                 ------------    ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
135	cd03217	200	55	97.6	0.00041	[                                      --------   ]	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.
136	PRK14263	261	56	97.6	0.00043	[                                  ---------      ]	PRK14263	phosphate ABC transporter ATP-binding protein; Provisional
137	TIGR03410	230	74	97.6	0.00095	[                                  ------------   ]	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.
138	COG1123	539	76	97.6	0.0011	[                                 -------------   ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
139	PRK14235	267	57	97.5	0.00025	[                                  ---------      ]	PRK14235	phosphate transporter ATP-binding protein; Provisional
140	cd03297	214	74	97.5	0.0018	[                                 -------------   ]	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.
141	PRK14267	253	57	97.5	0.00053	[                                  ---------      ]	PRK14267	phosphate ABC transporter ATP-binding protein; Provisional
142	cd03258	233	75	97.5	0.0012	[                                 -------------   ]	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.
143	TIGR01288	303	59	97.5	0.00027	[                                 ----------      ]	nodI	ATP-binding ABC transporter family nodulation protein NodI. This protein is required for normal nodulation by nitrogen-fixing root nodule bacteria such as Mesorhizobium loti. It is a member of the family of ABC transporter ATP binding proteins and works with NodJ to export a nodulation signal molecule. This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.
144	PRK14245	250	56	97.4	0.0021	[                                  ---------      ]	PRK14245	phosphate ABC transporter ATP-binding protein; Provisional
145	PRK14261	253	57	97.4	0.00033	[                                  ---------      ]	PRK14261	phosphate ABC transporter ATP-binding protein; Provisional
146	PRK14274	259	56	97.4	0.00057	[                                  ---------      ]	PRK14274	phosphate ABC transporter ATP-binding protein; Provisional
147	cd03292	214	70	97.4	0.0021	[                                  -----------    ]	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.
148	PRK13536	340	59	97.4	0.00033	[                                 ----------      ]	PRK13536	nodulation factor exporter subunit NodI; Provisional
149	PRK13649	280	88	97.4	0.00089	[                                  ---------------]	cbiO	cobalt transporter ATP-binding subunit; Provisional
150	COG4987	573	72	97.4	0.0021	[                                  ------------   ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
151	COG3842	352	78	97.4	0.00078	[                                 -------------   ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
152	PRK11153	343	74	97.4	0.0024	[                                  ------------   ]	metN	DL-methionine transporter ATP-binding subunit; Provisional
153	PRK14270	251	56	97.4	0.00016	[                                  ---------      ]	PRK14270	phosphate ABC transporter ATP-binding protein; Provisional
154	TIGR01978	243	73	97.4	0.0035	[                                  ------------   ]	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.
155	PRK13637	287	88	97.3	0.00035	[                                  ---------------]	cbiO	cobalt transporter ATP-binding subunit; Provisional
156	TIGR03740	223	58	97.3	0.00063	[                                 ----------      ]	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.
157	TIGR01277	213	75	97.3	0.0043	[                                  ------------   ]	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.
158	COG1123	539	76	97.3	0.0044	[                                 -------------   ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
159	cd03254	229	73	97.3	0.0084	[                                  ------------   ]	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.
160	COG4619	223	77	97.3	0.0035	[                                 -------------   ]	FetA	ABC-type iron transport system FetAB, ATPase component
161	pfam00005	150	26	97.3	0.00024	[  ----                                           ]	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.
162	TIGR03771	223	68	97.3	0.00069	[                                 ------------    ]	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.
163	COG1129	500	75	97.3	0.0043	[                                 -------------   ]	MglA	ABC-type sugar transport system, ATPase component
164	cd03294	269	77	97.2	0.0052	[                                 -------------   ]	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.
165	COG3840	231	76	97.2	0.0073	[                                 -------------   ]	ThiQ	ABC-type thiamine transport system, ATPase component
166	TIGR02673	214	70	97.2	0.0015	[                                  -----------    ]	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.
167	PRK14252	265	55	97.2	0.0017	[                                  ---------      ]	PRK14252	phosphate ABC transporter ATP-binding protein; Provisional
168	PRK13631	320	72	97.2	0.0004	[                                  ------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
169	PRK10744	260	57	97.2	0.00084	[                                  ---------      ]	pstB	phosphate transporter ATP-binding protein; Provisional
170	TIGR00618	1042	44	97.2	0.00038	[------                                           ]	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).
171	cd00267	157	69	97.2	0.00029	[                                  -----------    ]	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.
172	TIGR03719	552	69	97.1	0.0044	[                                -----------      ]	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.
173	PRK11701	258	75	97.1	0.0019	[                                  ------------   ]	phnK	phosphonate C-P lyase system protein PhnK; Provisional
174	TIGR00958	711	73	97.1	0.004	[                                  ------------   ]	3a01208	Conjugate Transporter-2 (CT2) Family protein.
175	PRK13537	306	72	97.1	0.0033	[                                 ------------    ]	PRK13537	nodulation ABC transporter NodI; Provisional
176	COG4618	580	71	97.1	0.0062	[                                  ------------   ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
177	PRK14275	286	73	97.0	0.0031	[                                  ------------   ]	PRK14275	phosphate ABC transporter ATP-binding protein; Provisional
178	cd03298	211	75	97.0	0.011	[                                 -------------   ]	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.
179	PRK14268	258	55	97.0	0.0013	[                                  ---------      ]	PRK14268	phosphate ABC transporter ATP-binding protein; Provisional
180	COG1137	243	72	97.0	0.011	[                                  ------------   ]	LptB	ABC-type lipopolysaccharide export system, ATPase component
181	PRK11819	556	69	97.0	0.0085	[                                -----------      ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
182	PRK11300	255	71	97.0	0.0011	[                                  -----------    ]	livG	leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
183	COG4175	386	76	97.0	0.011	[                                 -------------   ]	ProV	ABC-type proline/glycine betaine transport system, ATPase component
184	cd03218	232	72	96.9	0.011	[                                  ------------   ]	ABC_YhbG	ATP-binding cassette component of YhbG transport system. The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.
185	PRK14241	258	57	96.9	0.0078	[                                  ---------      ]	PRK14241	phosphate transporter ATP-binding protein; Provisional
186	COG4559	259	82	96.9	0.00061	[                                 -------------   ]	COG4559	ABC-type hemin transport system, ATPase component
187	PRK14246	257	73	96.9	0.01	[                                 -------------   ]	PRK14246	phosphate ABC transporter ATP-binding protein; Provisional
188	COG4172	534	76	96.9	0.013	[                                 -------------   ]	YejF	ABC-type microcin C transport system, duplicated ATPase component YejF
189	TIGR02857	529	57	96.9	0.008	[                                  ---------      ]	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
190	TIGR03415	382	83	96.9	0.0077	[                               ---------------   ]	ABC_choXWV_ATP	choline ABC transporter, ATP-binding protein. Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.
191	cd03299	235	76	96.9	0.02	[                                 -------------   ]	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.
192	PRK14258	261	46	96.9	0.013	[                                  -------        ]	PRK14258	phosphate ABC transporter ATP-binding protein; Provisional
193	cd03301	213	76	96.8	0.016	[                                 -------------   ]	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.
194	COG1116	248	69	96.8	0.016	[                                  -----------    ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
195	cd03221	144	66	96.8	0.00092	[                                  -----------    ]	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.
196	PRK14257	329	56	96.8	0.025	[                                  ---------      ]	PRK14257	phosphate ABC transporter ATP-binding protein; Provisional
197	PRK11147	635	76	96.8	0.0083	[                                 -------------   ]	PRK11147	ABC transporter ATPase component; Reviewed
198	TIGR00606	1311	40	96.7	0.00087	[------                                           ]	rad50	rad50. All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
199	TIGR01186	363	75	96.7	0.03	[                                  ------------   ]	proV	glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature.
200	PRK11288	501	95	96.7	0.074	[                                 ----------------]	araG	L-arabinose transporter ATP-binding protein; Provisional
201	PRK13409	590	77	96.7	0.023	[                                 -------------   ]	PRK13409	putative ATPase RIL; Provisional
202	PRK01156	895	44	96.7	0.0015	[------                                           ]	PRK01156	chromosome segregation protein; Provisional
203	COG3845	501	74	96.6	0.02	[                                 -------------   ]	YufO	ABC-type uncharacterized transport system, ATPase component
204	cd03253	236	71	96.6	0.015	[                                  ------------   ]	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.
205	PRK11160	574	82	96.6	0.024	[                                  -------------- ]	PRK11160	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
206	TIGR00630	925	66	96.6	0.0048	[                                 ----------      ]	uvra	excinuclease ABC, A subunit. This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
207	cd00267	157	26	96.6	0.012	[  ----                                           ]	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.
208	PRK14249	251	66	96.6	0.0066	[                                  -----------    ]	PRK14249	phosphate ABC transporter ATP-binding protein; Provisional
209	TIGR02142	354	74	96.5	0.014	[                                 -------------   ]	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.
210	TIGR02868	530	45	96.5	0.0095	[                                  -------        ]	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.
211	COG4172	534	75	96.5	0.0088	[                                 -------------   ]	YejF	ABC-type microcin C transport system, duplicated ATPase component YejF
212	cd03236	255	77	96.5	0.043	[                                 -------------   ]	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.
213	cd03293	220	75	96.5	0.033	[                                 -------------   ]	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.
214	PRK14238	271	71	96.4	0.0059	[                                  ------------   ]	PRK14238	phosphate transporter ATP-binding protein; Provisional
215	COG1245	591	75	96.4	0.041	[                                 ------------    ]	Rli1	Translation initiation factor RLI1, contains Fe-S and AAA+ ATPase domains
216	PRK14266	250	56	96.4	0.0045	[                                  ---------      ]	PRK14266	phosphate ABC transporter ATP-binding protein; Provisional
217	TIGR00956	1394	49	96.4	0.01	[                                      -------    ]	3a01205	Pleiotropic Drug Resistance (PDR) Family protein.
218	PRK14265	274	56	96.3	0.0085	[                                  ---------      ]	PRK14265	phosphate ABC transporter ATP-binding protein; Provisional
219	cd03244	221	74	96.3	0.094	[                                  ------------   ]	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.
220	cd03231	201	58	96.3	0.0028	[                                 ----------      ]	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.
221	PRK13643	288	53	96.3	0.011	[                                      --------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
222	PRK14251	251	60	96.3	0.0042	[                                 ----------      ]	PRK14251	phosphate ABC transporter ATP-binding protein; Provisional
223	TIGR02982	220	57	96.2	0.03	[                                  ---------      ]	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.
224	COG0178	935	66	96.2	0.0065	[                                 ----------      ]	UvrA	Excinuclease UvrABC ATPase subunit
225	COG0497	557	43	96.2	0.0055	[------                                           ]	RecN	DNA repair ATPase RecN
226	COG4148	352	85	96.2	0.021	[                                  -------------- ]	ModC	ABC-type molybdate transport system, ATPase component
227	PRK10419	268	77	96.2	0.13	[                                 -------------   ]	nikE	nickel transporter ATP-binding protein NikE; Provisional
228	cd03289	275	74	96.2	0.031	[                                  ------------   ]	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.
229	TIGR02324	224	51	96.1	0.0068	[                                 ---------       ]	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.
230	TIGR01271	1490	57	96.1	0.022	[                                  ---------      ]	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.
231	TIGR01842	544	56	96.1	0.031	[                                  ---------      ]	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.
232	PRK14272	252	61	96.0	0.017	[                                 ----------      ]	PRK14272	phosphate ABC transporter ATP-binding protein; Provisional
233	TIGR03797	686	73	96.0	0.066	[                                  ------------   ]	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.
234	PRK00349	943	62	96.0	0.028	[                                 ----------      ]	uvrA	excinuclease ABC subunit A; Reviewed
235	PRK13634	290	72	96.0	0.029	[                                  ------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
236	COG4138	248	35	96.0	0.0041	[                                      -----      ]	BtuD	ABC-type cobalamin transport system, ATPase component
237	PRK10771	232	74	96.0	0.14	[                                  ------------   ]	thiQ	thiamine transporter ATP-binding subunit; Provisional
238	cd00009	151	25	96.0	0.0066	[  ----                                           ]	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.
239	PRK14256	252	57	95.9	0.006	[                                  ---------      ]	PRK14256	phosphate ABC transporter ATP-binding protein; Provisional
240	PRK11174	588	72	95.9	0.16	[                                  ------------   ]	PRK11174	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
241	PRK14271	276	92	95.9	0.019	[                                  ---------------]	PRK14271	phosphate ABC transporter ATP-binding protein; Provisional
242	TIGR01189	198	58	95.9	0.0059	[                                 ----------      ]	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.
243	cd03276	198	42	95.8	0.011	[------                                           ]	ABC_SMC6_euk	ATP-binding cassette domain of eukaryotic SM6 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
244	PRK13409	590	59	95.8	0.046	[                                 ----------      ]	PRK13409	putative ATPase RIL; Provisional
245	cd03216	163	72	95.8	0.0074	[                                  ------------   ]	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.
246	PRK14260	259	56	95.8	0.012	[                                  ---------      ]	PRK14260	phosphate ABC transporter ATP-binding protein; Provisional
247	cd03234	226	50	95.7	0.14	[                                 ---------       ]	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.
248	PRK14250	241	77	95.7	0.069	[                                 -------------   ]	PRK14250	phosphate ABC transporter ATP-binding protein; Provisional
249	cd03243	202	26	95.7	0.0091	[  ----                                           ]	ABC_MutS_homologs	ATP-binding cassette domain of MutS homologs. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
250	PRK13632	271	73	95.7	0.059	[                                 -------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
251	cd03286	218	24	95.6	0.011	[  ----                                           ]	ABC_MSH6_euk	ATP-binding cassette domain of eukaryotic MutS6 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
252	pfam13207	114	23	95.6	0.012	[  ----                                           ]	AAA_17	AAA domain.
253	COG4717	984	78	95.6	0.019	[------------                                     ]	YhaN	Uncharacterized protein YhaN, contains AAA domain
254	PRK15056	272	79	95.6	0.016	[                                 -------------   ]	PRK15056	manganese/iron transporter ATP-binding protein; Provisional
255	PRK14255	252	73	95.6	0.012	[                                  ------------   ]	PRK14255	phosphate ABC transporter ATP-binding protein; Provisional
256	cd03248	226	50	95.5	0.011	[                                  --------       ]	ABCC_TAP	ATP-binding cassette domain of the Transporter Associated with Antigen Processing, subfamily C. TAP (Transporter Associated with Antigen Processing) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
257	COG4167	267	76	95.5	0.1	[                                 -------------   ]	SapF	ABC-type antimicrobial peptide transport system, ATPase component
258	PRK14239	252	73	95.5	0.01	[                                  ------------   ]	PRK14239	phosphate transporter ATP-binding protein; Provisional
259	PRK10636	638	59	95.5	0.024	[                                 ----------      ]	PRK10636	putative ABC transporter ATP-binding protein; Provisional
260	cd03237	246	59	95.5	0.011	[                                 ----------      ]	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.
261	pfam00488	235	24	95.4	0.02	[  ----                                           ]	MutS_V	MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.
262	cd03300	232	76	95.4	0.11	[                                 -------------   ]	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.
263	TIGR03265	353	74	95.4	0.41	[                                  ------------   ]	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.
264	PRK11144	352	85	95.4	0.099	[                                  -------------- ]	modC	molybdate transporter ATP-binding protein; Provisional
265	PRK10253	265	50	95.4	0.014	[                                 ---------       ]	PRK10253	iron-enterobactin transporter ATP-binding protein; Provisional
266	PRK13549	506	75	95.3	0.24	[                                 -------------   ]	PRK13549	xylose transporter ATP-binding subunit; Provisional
267	TIGR02769	265	77	95.3	0.25	[                                 -------------   ]	nickel_nikE	nickel import ATP-binding protein NikE. This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.
268	PRK11147	635	26	95.3	0.011	[  ----                                           ]	PRK11147	ABC transporter ATPase component; Reviewed
269	PRK14269	246	48	95.3	0.087	[                                  --------       ]	PRK14269	phosphate ABC transporter ATP-binding protein; Provisional
270	TIGR03185	650	45	95.3	0.011	[------                                           ]	DNA_S_dndD	DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
271	pfam00004	131	22	95.3	0.014	[   ---                                           ]	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.
272	cd03296	239	79	95.1	0.019	[                                 -------------   ]	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.
273	PRK13650	279	84	95.1	0.008	[                                 --------------- ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
274	COG4778	235	35	95.1	0.028	[-----                                            ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
275	cd03249	238	73	95.0	0.62	[                                  ------------   ]	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.
276	TIGR00968	237	76	95.0	0.018	[                                  ------------   ]	3a0106s01	sulfate ABC transporter, ATP-binding protein.
277	PRK10522	547	67	95.0	0.11	[                                -----------      ]	PRK10522	multidrug transporter membrane component/ATP-binding component; Provisional
278	TIGR00634	563	43	95.0	0.0095	[------                                           ]	recN	DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
279	PRK15064	530	58	95.0	0.12	[                                 ----------      ]	PRK15064	ABC transporter ATP-binding protein; Provisional
280	cd03284	216	24	95.0	0.022	[  ----                                           ]	ABC_MutS1	ATP-binding cassette domain of MutS1 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
281	TIGR02314	343	72	94.9	0.27	[                                  ------------   ]	ABC_MetN	D-methionine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.
282	PRK13652	277	53	94.9	0.043	[                                      --------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
283	PRK13640	282	91	94.9	0.037	[                                 ----------------]	cbiO	cobalt transporter ATP-binding subunit; Provisional
284	COG4615	546	68	94.8	0.23	[                                -----------      ]	PvdE	ABC-type siderophore export system, fused ATPase and permease components
285	pfam13166	713	71	94.8	0.021	[                                 ----------      ]	AAA_13	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.
286	PRK09984	262	67	94.6	0.05	[                                 -----------     ]	PRK09984	phosphonate/organophosphate ester transporter subunit; Provisional
287	COG1245	591	51	94.5	0.27	[                                 ---------       ]	Rli1	Translation initiation factor RLI1, contains Fe-S and AAA+ ATPase domains
288	cd03222	177	22	94.4	0.026	[  ---                                            ]	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.
289	PRK14259	269	57	94.4	0.042	[                                  ---------      ]	PRK14259	phosphate ABC transporter ATP-binding protein; Provisional
290	TIGR02204	576	90	94.3	0.6	[                                  ---------------]	MsbA_rel	ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.
291	PRK05399	854	24	94.3	0.049	[  ----                                           ]	PRK05399	DNA mismatch repair protein MutS; Provisional
292	cd03282	204	24	94.2	0.039	[  ----                                           ]	ABC_MSH4_euk	ATP-binding cassette domain of eukaryotic MutS4 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
293	PRK13538	204	61	94.2	0.049	[                                 ----------      ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
294	COG0249	843	24	94.2	0.042	[  ----                                           ]	MutS	DNA mismatch repair ATPase MutS
295	PRK11650	356	40	94.1	0.041	[                                 -------         ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
296	PRK11000	369	23	94.1	0.041	[  ----                                           ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
297	cd03223	166	49	94.1	0.039	[                                  --------       ]	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).
298	cd03213	194	71	94.1	0.048	[                                  -----------    ]	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.
299	cd03246	173	56	93.9	0.06	[                                  ---------      ]	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.
300	TIGR01187	325	76	93.9	0.2	[                                 -------------   ]	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).
301	TIGR00955	617	72	93.9	0.8	[                                  ------------   ]	3a01204	The Eye Pigment Precursor Transporter (EPP) Family protein.
302	PRK13646	286	72	93.9	0.05	[                                  ------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
303	cd03250	204	68	93.8	0.061	[                                  -----------    ]	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.
304	COG2805	353	26	93.8	0.069	[  ----                                           ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
305	pfam13191	156	26	93.6	0.081	[  ----                                           ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
306	cd03216	163	26	93.5	0.5	[  ----                                           ]	ABC_Carb_Monos_I	First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
307	TIGR02770	230	73	93.4	0.19	[                                  ------------   ]	nickel_nikD	nickel import ATP-binding protein NikD. This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.
308	PRK11819	556	58	93.3	0.058	[                                 ----------      ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
309	PRK10246	1047	44	93.3	0.062	[------                                           ]	PRK10246	exonuclease subunit SbcC; Provisional
310	PRK15064	530	51	93.3	0.081	[                                     --------    ]	PRK15064	ABC transporter ATP-binding protein; Provisional
311	cd01131	198	21	93.2	0.066	[  ---                                            ]	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.
312	PRK13547	272	32	93.1	0.068	[                                     -----       ]	hmuV	hemin importer ATP-binding subunit; Provisional
313	PRK13641	287	54	93.1	0.94	[                                     ---------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
314	PRK10247	225	28	93.1	0.041	[  ----                                           ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
315	pfam13521	162	22	93.0	0.079	[  ----                                           ]	AAA_28	AAA domain.
316	TIGR03719	552	58	92.9	0.072	[                                 ----------      ]	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.
317	cd03221	144	23	92.8	0.42	[  ----                                           ]	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.
318	cd00071	137	48	92.8	0.084	[  --------                                       ]	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.
319	PRK09270	229	27	92.7	0.11	[  ----                                           ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
320	PRK10575	265	29	92.6	0.09	[                                      ----       ]	PRK10575	iron-hydroxamate transporter ATP-binding subunit; Provisional
321	pfam13671	143	21	92.6	0.092	[  ---                                            ]	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.
322	PRK09544	251	27	92.6	0.024	[  ----                                           ]	znuC	high-affinity zinc transporter ATPase; Reviewed
323	cd03270	226	61	92.5	0.088	[                                 ----------      ]	ABC_UvrA_I	ATP-binding cassette domain I of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
324	PRK13635	279	74	92.4	0.093	[                                 -------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
325	cd03251	234	73	92.3	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.
326	PRK08118	167	25	92.2	0.13	[  ----                                           ]	PRK08118	topology modulation protein; Reviewed
327	PRK10938	490	16	92.2	0.034	[   --                                            ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
328	COG0563	178	22	92.1	0.13	[  ----                                           ]	Adk	Adenylate kinase or related kinase
329	PRK14974	336	26	92.1	0.13	[  ----                                           ]	PRK14974	cell division protein FtsY; Provisional
330	PRK13652	277	27	91.9	0.11	[  ----                                           ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
331	PRK04863	1486	41	91.9	0.13	[------                                           ]	mukB	cell division protein MukB; Provisional
332	PRK10982	491	75	91.9	0.68	[                                 -------------   ]	PRK10982	galactose/methyl galaxtoside transporter ATP-binding protein; Provisional
333	cd03281	213	27	91.9	0.13	[  ----                                           ]	ABC_MSH5_euk	ATP-binding cassette domain of eukaryotic MutS5 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
334	cd03283	199	24	91.7	0.15	[  ----                                           ]	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.
335	pfam05729	165	25	91.7	0.19	[  ----                                           ]	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.
336	TIGR04406	239	30	91.6	0.099	[----                                             ]	LPS_export_lptB	LPS export ABC transporter ATP-binding protein. Members of this fmaily are LptB, the ATP-binding cassette protein of an ABC transporter involved in lipopolysaccharide export.
337	COG3172	187	27	91.6	0.078	[  ----                                           ]	NadR3	Nicotinamide riboside kinase
338	COG0194	191	47	91.5	0.16	[  --------                                       ]	Gmk	Guanylate kinase
339	pfam00448	195	26	91.5	0.2	[  ----                                           ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
340	cd03285	222	23	91.5	0.14	[  ----                                           ]	ABC_MSH2_euk	ATP-binding cassette domain of eukaryotic MutS2 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.
341	PRK09700	510	75	91.4	0.85	[                                  ------------   ]	PRK09700	D-allose transporter ATP-binding protein; Provisional
342	TIGR01420	343	24	91.4	0.14	[  ----                                           ]	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.
343	cd03213	194	24	91.4	0.26	[  ----                                           ]	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.
344	pfam13401	124	24	91.3	0.2	[  ----                                           ]	AAA_22	AAA domain.
345	PRK09580	248	55	91.3	0.092	[                                     ---------   ]	sufC	cysteine desulfurase ATPase component; Reviewed
346	COG4181	228	71	91.3	0.16	[                                  ------------   ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
347	COG4608	268	76	91.2	0.75	[                                 -------------   ]	AppF	ABC-type oligopeptide transport system, ATPase component
348	cd04170	268	26	91.2	0.14	[   ---                                           ]	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.
349	cd03287	222	26	91.1	0.16	[  ----                                           ]	ABC_MSH3_euk	ATP-binding cassette domain of eukaryotic MutS3 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.
350	pfam03193	161	24	91.1	0.17	[  ----                                           ]	DUF258	Protein of unknown function, DUF258.
351	pfam13245	72	25	90.8	0.31	[  ----                                           ]	AAA_19	Part of AAA domain.
352	cd02021	150	26	90.7	0.21	[  ----                                           ]	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.
353	PRK13638	271	74	90.6	0.13	[                                 -------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
354	PRK13830	818	26	90.6	0.25	[  ----                                           ]	PRK13830	conjugal transfer protein TrbE; Provisional
355	PRK00635	1809	77	90.5	0.38	[                             -------------       ]	PRK00635	excinuclease ABC subunit A; Provisional
356	TIGR03263	179	47	90.5	0.24	[  --------                                       ]	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.
357	COG1222	406	23	90.4	0.19	[  ----                                           ]	RPT1	ATP-dependent 26S proteasome regulatory subunit
358	cd03232	192	29	90.3	0.23	[                                      ----       ]	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.
359	cd01882	231	27	90.3	0.23	[  ----                                           ]	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.
360	pfam00910	105	23	90.2	0.29	[   ---                                           ]	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.
361	PRK11432	351	48	90.2	0.8	[                                  --------       ]	fbpC	ferric transporter ATP-binding subunit; Provisional
362	cd03369	207	75	90.1	0.33	[                                  ------------   ]	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.
363	PRK15112	267	74	90.1	0.2	[                                 -------------   ]	PRK15112	antimicrobial peptide ABC system ATP-binding protein SapF; Provisional
364	cd03252	237	80	89.8	4.9	[                                  -------------- ]	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.
365	cd03238	176	55	89.8	0.41	[--------                                         ]	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.
366	cd02019	69	22	89.8	0.37	[   ---                                           ]	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.
367	TIGR02211	221	73	89.7	0.34	[                                 -------------   ]	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.
368	PRK04195	482	27	89.7	0.25	[  ----                                           ]	PRK04195	replication factor C large subunit; Provisional
369	PRK03992	389	23	89.7	0.22	[  ----                                           ]	PRK03992	proteasome-activating nucleotidase; Provisional
370	cd00464	154	25	89.7	0.31	[   ---                                           ]	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.
371	pfam13238	128	24	89.6	0.28	[   ---                                           ]	AAA_18	AAA domain.
372	PRK13648	269	58	89.6	0.24	[                                 ----------      ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
373	cd01854	211	22	89.5	0.26	[  ---                                            ]	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.
374	cd03247	178	73	89.4	0.34	[                                  ------------   ]	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.
375	pfam07728	135	23	89.4	0.35	[   ---                                           ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
376	pfam03205	138	26	89.2	0.43	[  ----                                           ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
377	pfam13173	127	22	89.2	0.39	[  ---                                            ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
378	pfam01637	223	25	89.1	0.37	[  ----                                           ]	Arch_ATPase	Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family.
379	COG4185	187	25	88.9	0.1	[  ----                                           ]	COG4185	Predicted ABC-type ATPase
380	PRK14273	254	56	88.9	0.43	[                                  ---------      ]	PRK14273	phosphate ABC transporter ATP-binding protein; Provisional
381	COG2804	500	26	88.8	0.38	[  ----                                           ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
382	COG5008	375	20	88.7	0.42	[  ---                                            ]	PilU	Tfp pilus assembly protein, ATPase PilU
383	COG4639	168	19	88.5	0.31	[  ---                                            ]	COG4639	Predicted kinase
384	COG4525	259	67	88.3	0.41	[                                  -----------    ]	TauB	ABC-type taurine transport system, ATPase component
385	COG0703	172	26	88.3	0.4	[  ----                                           ]	AroK	Shikimate kinase
386	COG4240	300	26	88.2	0.46	[  ----                                           ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
387	PRK00300	205	44	88.2	0.44	[  --------                                       ]	gmk	guanylate kinase; Provisional
388	PRK13633	280	73	88.1	0.26	[                                 -------------   ]	PRK13633	cobalt transporter ATP-binding subunit; Provisional
389	TIGR03608	206	29	88.1	0.47	[ -----                                           ]	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.
390	COG2401	593	59	88.0	1.1	[                                 ----------      ]	MK0520	ABC-type ATPase fused to a predicted acetyltransferase domain
391	PRK15079	331	75	87.9	3.9	[                                 -------------   ]	PRK15079	oligopeptide ABC transporter ATP-binding protein OppF; Provisional
392	PRK13342	413	26	87.9	0.42	[  ----                                           ]	PRK13342	recombination factor protein RarA; Reviewed
393	COG0552	340	26	87.8	0.46	[  ----                                           ]	FtsY	Signal recognition particle GTPase
394	cd04164	159	21	87.8	0.48	[  ---                                            ]	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.
395	TIGR00455	184	27	87.8	0.47	[  ----                                           ]	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.
396	PRK10851	353	77	87.7	0.36	[                                 -------------   ]	PRK10851	sulfate/thiosulfate transporter subunit; Provisional
397	PRK11308	327	58	87.7	6.8	[                                 ----------      ]	dppF	dipeptide transporter ATP-binding subunit; Provisional
398	TIGR02533	486	26	87.7	0.37	[  ----                                           ]	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.
399	PRK13543	214	47	87.6	0.58	[                                 --------        ]	PRK13543	cytochrome c biogenesis protein CcmA; Provisional
400	PRK05342	412	27	87.3	0.49	[  ----                                           ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
401	cd01129	264	26	87.2	0.4	[  ----                                           ]	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.
402	pfam01926	114	19	87.1	0.54	[   --                                            ]	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.
403	COG4107	258	75	87.0	0.62	[                                  ------------   ]	PhnK	ABC-type phosphonate transport system, ATPase component
404	COG2256	436	26	86.6	0.51	[  ----                                           ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
405	PRK00098	298	27	86.6	0.5	[  ----                                           ]	PRK00098	GTPase RsgA; Reviewed
406	PRK12289	352	24	86.6	0.51	[  ----                                           ]	PRK12289	GTPase RsgA; Reviewed
407	PRK06762	166	26	86.6	0.72	[  ----                                           ]	PRK06762	hypothetical protein; Provisional
408	COG4107	258	26	86.5	2.5	[  ----                                           ]	PhnK	ABC-type phosphonate transport system, ATPase component
409	PRK00131	175	27	86.5	0.57	[  ----                                           ]	aroK	shikimate kinase; Reviewed
410	TIGR00954	659	57	86.4	0.53	[                                  ---------      ]	3a01203	Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein.
411	COG4178	604	46	86.3	0.52	[                                  -------        ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
412	PRK13541	195	27	86.2	0.39	[  ----                                           ]	PRK13541	cytochrome c biogenesis protein CcmA; Provisional
413	pfam02456	370	21	86.2	0.58	[  ---                                            ]	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.
414	TIGR01846	694	87	86.1	5.7	[                                  ---------------]	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.
415	PRK13657	588	73	86.1	0.6	[                                  ------------   ]	PRK13657	cyclic beta-1,2-glucan ABC transporter; Provisional
416	TIGR02525	372	25	86.1	0.55	[  ----                                           ]	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).
417	TIGR01070	840	23	86.0	0.61	[  ----                                           ]	mutS1	DNA mismatch repair protein MutS.
418	PRK13540	200	27	86.0	0.6	[  ----                                           ]	PRK13540	cytochrome c biogenesis protein CcmA; Provisional
419	PRK11248	255	55	85.8	0.66	[                                  ---------      ]	tauB	taurine transporter ATP-binding subunit; Provisional
420	TIGR00630	925	44	85.8	0.45	[------                                           ]	uvra	excinuclease ABC, A subunit. This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
421	TIGR03689	512	27	85.6	0.7	[  ----                                           ]	pup_AAA	proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
422	COG0178	935	63	85.4	0.42	[                                 ----------      ]	UvrA	Excinuclease UvrABC ATPase subunit
423	TIGR01526	325	52	85.3	0.38	[  --------                                       ]	nadR_NMN_Atrans	nicotinamide-nucleotide adenylyltransferase, NadR type. The NadR protein of E. coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal to the region covered by this model, is a DNA-binding helix-turn-helix domain (pfam01381) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity.
424	cd01120	165	24	85.1	0.74	[  ----                                           ]	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.
425	PRK10789	569	57	85.0	0.55	[                                  ---------      ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
426	pfam00437	273	26	84.9	0.77	[  ----                                           ]	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.
427	COG3854	308	25	84.8	0.82	[   ---                                           ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
428	COG0529	197	26	84.7	1.1	[  ----                                           ]	CysC	Adenylylsulfate kinase or related kinase
429	PRK12727	559	36	84.7	0.63	[-----                                            ]	PRK12727	flagellar biosynthesis regulator FlhF; Provisional
430	COG3911	183	27	84.6	0.93	[  ----                                           ]	COG3911	Predicted ATPase
431	cd01124	187	21	84.5	0.82	[  ---                                            ]	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.
432	COG1219	408	27	84.4	0.82	[  ----                                           ]	ClpX	ATP-dependent protease Clp, ATPase subunit
433	cd02020	147	25	84.3	0.91	[   ---                                           ]	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.
434	TIGR01242	364	22	84.3	0.75	[  ---                                            ]	26Sp45	26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
435	TIGR03499	282	23	84.2	0.89	[  ----                                           ]	FlhF	flagellar biosynthetic protein FlhF.
436	PRK11831	269	53	84.2	0.94	[                                 ---------       ]	PRK11831	putative ABC transporter ATP-binding protein YrbF; Provisional
437	cd00880	161	19	84.2	0.64	[   --                                            ]	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.
438	TIGR02323	253	74	84.1	1.7	[                                  ------------   ]	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.
439	PRK00635	1809	45	84.1	0.64	[------                                           ]	PRK00635	excinuclease ABC subunit A; Provisional
440	TIGR01192	585	72	84.1	1.1	[                                  ------------   ]	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.
441	cd01130	186	26	84.1	0.92	[  ----                                           ]	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.
442	PRK06547	172	23	83.8	0.95	[  ----                                           ]	PRK06547	hypothetical protein; Provisional
443	PRK13341	725	22	83.6	0.97	[  ---                                            ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
444	pfam02492	178	22	83.6	1	[  ---                                            ]	cobW	CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.
445	pfam03266	168	24	83.5	1.2	[   ---                                           ]	NTPase_1	NTPase. This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue.
446	TIGR02323	253	26	83.4	1.1	[  ----                                           ]	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.
447	pfam05272	198	21	83.4	0.93	[  ---                                            ]	VirE	Virulence-associated protein E. This family contains several bacterial virulence-associated protein E like proteins. These proteins contain a P-loop motif.
448	cd01672	200	25	83.4	1.3	[  ----                                           ]	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).
449	COG5192	1077	25	83.2	1.1	[  ----                                           ]	BMS1	GTP-binding protein required for 40S ribosome biogenesis
450	TIGR00064	277	26	83.1	0.96	[  ----                                           ]	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.
451	pfam05673	248	26	82.9	1.2	[  ----                                           ]	DUF815	Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
452	COG1100	219	21	82.9	1	[  ---                                            ]	Gem1	GTPase SAR1 family domain
453	PRK13873	811	58	82.8	1	[                                    ---------    ]	PRK13873	conjugal transfer ATPase TrbE; Provisional
454	PRK11614	237	19	82.7	0.67	[  ---                                            ]	livF	leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
455	TIGR02203	571	90	82.7	0.92	[                                  ---------------]	MsbA_lipidA	lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.
456	PRK10418	254	74	82.6	3.1	[                                  ------------   ]	nikD	nickel transporter ATP-binding protein NikD; Provisional
457	PRK13768	253	25	82.6	1.3	[  ----                                           ]	PRK13768	GTPase; Provisional
458	cd03232	192	23	82.3	1.5	[  ----                                           ]	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.
459	PRK05057	172	24	82.3	0.96	[   ---                                           ]	aroK	shikimate kinase I; Reviewed
460	cd00882	161	20	82.2	0.89	[   ---                                           ]	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.
461	cd03247	178	28	81.8	6.4	[  ----                                           ]	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.
462	COG0470	325	25	81.7	1.2	[  ----                                           ]	HolB	DNA polymerase III, delta prime subunit
463	TIGR02173	171	25	81.7	1.1	[  ----                                           ]	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.
464	TIGR01241	495	21	81.6	1.1	[  ---                                            ]	FtsH_fam	ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
465	PRK10416	318	26	81.5	1.4	[  ----                                           ]	PRK10416	signal recognition particle-docking protein FtsY; Provisional
466	COG4608	268	27	81.3	1	[  ----                                           ]	AppF	ABC-type oligopeptide transport system, ATPase component
467	PRK13645	289	73	81.2	1.6	[                                  ------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
468	PRK12402	337	27	81.1	1.4	[  ----                                           ]	PRK12402	replication factor C small subunit 2; Reviewed
469	PRK00349	943	33	81.0	0.86	[-----                                            ]	uvrA	excinuclease ABC subunit A; Reviewed
470	pfam13481	192	25	80.9	1.7	[  ----                                           ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
471	pfam08477	118	25	80.9	1.4	[  ----                                           ]	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.
472	COG0467	260	24	80.8	1.5	[  ----                                           ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
473	PRK10895	241	30	80.7	0.88	[----                                             ]	PRK10895	lipopolysaccharide ABC transporter ATP-binding protein; Provisional
474	TIGR03922	557	27	80.5	1.2	[  ----                                           ]	T7SS_EccA	type VII secretion AAA-ATPase EccA. This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc.
475	COG2607	287	35	80.4	0.48	[ -----                                           ]	COG2607	Predicted ATPase, AAA+ superfamily
476	cd03233	202	73	80.3	1.5	[                                  -----------    ]	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.
477	cd02028	179	26	80.3	1.5	[  ----                                           ]	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).
478	cd03116	159	27	80.3	1.9	[  ----                                           ]	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.
479	TIGR00929	785	84	80.2	1.4	[                                 ------------    ]	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).
480	COG4088	261	27	80.1	1.7	[  ----                                           ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
481	COG4913	1104	42	80.1	1.8	[------                                           ]	COG4913	Uncharacterized protein, contains a C-terminal ATPase domain
482	cd01892	180	17	80.1	1.3	[   --                                            ]	Miro2	Mitochondrial Rho family 2 (Miro2), C-terminal. Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
483	TIGR00382	413	27	80.1	1.5	[  ----                                           ]	clpX	endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
484	COG1162	301	22	80.0	1.3	[  ---                                            ]	RsgA	Putative ribosome biogenesis GTPase RsgA
485	PRK10869	553	44	79.9	1.2	[------                                           ]	PRK10869	recombination and repair protein; Provisional
486	PRK15439	510	52	79.6	1.2	[                                      --------   ]	PRK15439	autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional
487	cd02027	149	24	79.6	1.8	[   ---                                           ]	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.
488	COG0802	149	26	79.3	1.9	[  ----                                           ]	TsaE	tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE
489	PRK13642	277	73	79.3	1.1	[                                  ------------   ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
490	PRK11247	257	73	79.1	1.7	[                                  ------------   ]	ssuB	aliphatic sulfonates transport ATP-binding subunit; Provisional
491	cd04105	202	21	79.0	1.6	[  ---                                            ]	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.
492	TIGR00176	155	26	78.9	1.9	[  ----                                           ]	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.
493	COG0283	222	26	78.4	2	[  ----                                           ]	Cmk	Cytidylate kinase
494	cd03115	173	25	78.2	2.3	[  ----                                           ]	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.
495	pfam00350	168	20	78.2	1.6	[   --                                            ]	Dynamin_N	Dynamin family.
496	COG2255	332	26	78.1	1.8	[  ----                                           ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
497	pfam01583	157	25	78.1	2.7	[   ---                                           ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
498	PRK09452	375	17	78.0	1.4	[   --                                            ]	potA	putrescine/spermidine ABC transporter ATPase protein; Reviewed
499	TIGR03796	710	72	77.9	1.7	[                                  ------------   ]	NHLM_micro_ABC1	NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes a multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHLM, Nitrile Hydratase Leader Microcin.
500	TIGR03269	520	74	77.8	12	[                                  ------------   ]	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.