match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG0514	590	343	100.0	6.5E-65	[            ------------------                   ]	RecQ	Superfamily II DNA helicase RecQ
2	TIGR01389	591	343	100.0	3.9E-55	[            ------------------                   ]	recQ	ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
3	TIGR00614	470	341	100.0	8.1E-55	[            ------------------                   ]	recQ_fam	ATP-dependent DNA helicase, RecQ family. All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
4	PRK11057	607	354	100.0	3.4E-45	[            -------------------                  ]	PRK11057	ATP-dependent DNA helicase RecQ; Provisional
5	COG0513	513	347	99.9	7.6E-24	[           -------------------                   ]	SrmB	Superfamily II DNA and RNA helicase
6	COG1205	851	312	99.8	2.6E-20	[              ----------------                   ]	YprA	ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain
7	pfam00270	167	153	99.8	2.4E-20	[             --------                            ]	DEAD	DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
8	COG1061	442	311	99.8	3.6E-19	[             -----------------                   ]	SSL2	Superfamily II DNA or RNA helicase
9	cd00079	131	104	99.8	5.4E-19	[                        ------                   ]	HELICc	Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
10	COG1201	814	308	99.7	4.6E-16	[             ----------------                    ]	Lhr	Lhr-like helicase
11	cd00046	144	142	99.7	1.5E-16	[              -------                            ]	DEXDc	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
12	PRK11192	434	303	99.5	1.1E-13	[              ----------------                   ]	PRK11192	ATP-dependent RNA helicase SrmB; Provisional
13	pfam00271	78	71	99.5	5.6E-15	[                          ---                    ]	Helicase_C	Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
14	COG1204	766	457	99.5	7.8E-13	[              --------------------------         ]	BRR2	Replicative superfamily II helicase
15	COG1111	542	351	99.5	8.5E-13	[             ------------------                  ]	MPH1	ERCC4-related helicase
16	TIGR04121	804	308	99.5	1.1E-12	[             ----------------                    ]	DEXH_lig_assoc	DEXH box helicase, DNA ligase-associated. Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE
17	COG1203	733	316	99.4	1.5E-12	[             ----------------                    ]	Cas3	CRISPR/Cas system-associated endonuclease/helicase Cas3
18	PRK11776	460	288	99.4	4.4E-13	[              ----------------                   ]	PRK11776	ATP-dependent RNA helicase DbpA; Provisional
19	PRK13767	876	352	99.3	1.6E-10	[              ------------------                 ]	PRK13767	ATP-dependent helicase; Provisional
20	TIGR01587	359	282	99.2	6.3E-11	[              ---------------                    ]	cas3_core	CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
21	TIGR03817	742	302	99.2	2.5E-10	[              ---------------                    ]	DECH_helic	helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
22	PRK13766	773	336	99.2	9.6E-10	[              -----------------                  ]	PRK13766	Hef nuclease; Provisional
23	cd09639	353	295	99.1	3.3E-10	[              ----------------                   ]	Cas3_I	CRISPR/Cas system-associated protein Cas3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
24	PRK05580	679	310	99.1	6.8E-10	[             ----------------                    ]	PRK05580	primosome assembly protein PriA; Validated
25	COG1202	830	283	99.0	3.1E-09	[             ----------------                    ]	COG1202	Superfamily II helicase, archaea-specific
26	PRK10917	681	296	98.8	6.6E-08	[             ----------------                    ]	PRK10917	ATP-dependent DNA helicase RecG; Provisional
27	TIGR04095	451	317	98.7	1E-07	[             ----------------                    ]	dnd_restrict_1	DNA phosphorothioation system restriction enzyme. The DNA phosphorothioate modification system dnd (DNA instability during electrophoresis) recently has been shown to provide a modification essential to a restriction system. This protein family was detected by Partial Phylogenetic Profiling as linked to dnd, and its members usually are clustered with the dndABCDE genes.
28	pfam04851	103	58	98.7	3E-08	[             ---                                 ]	ResIII	Type III restriction enzyme, res subunit.
29	TIGR00595	505	127	98.6	2.8E-07	[              -------                            ]	priA	primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
30	PRK04837	423	291	98.6	4.9E-08	[              ----------------                   ]	PRK04837	ATP-dependent RNA helicase RhlB; Provisional
31	COG1200	677	297	98.5	2.2E-06	[             -----------------                   ]	RecG	RecG-like helicase
32	TIGR00643	630	294	98.5	3.4E-06	[             ----------------                    ]	recG	ATP-dependent DNA helicase RecG.
33	COG1198	730	148	98.5	3.3E-07	[             --------                            ]	PriA	Primosomal protein N' (replication factor Y) - superfamily II helicase
34	PRK04537	572	287	98.5	2.6E-06	[              ----------------                   ]	PRK04537	ATP-dependent RNA helicase RhlB; Provisional
35	PRK10590	456	303	98.5	8.8E-07	[             -----------------                   ]	PRK10590	ATP-dependent RNA helicase RhlE; Provisional
36	cd00268	203	168	98.2	6E-06	[             ---------                           ]	DEADc	DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
37	cd09710	353	293	98.2	1.3E-05	[              ---------------                    ]	Cas3_I-D	CRISPR/Cas system-associated protein Cas3; Distinct diverged subfamily of Cas3 helicase domain. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Diverged DNA helicase Cas3'; signature gene for Type I and subtype I-D
38	PRK09751	1490	312	98.1	7.2E-05	[              ----------------                   ]	PRK09751	putative ATP-dependent helicase Lhr; Provisional
39	cd00009	151	43	98.1	1.1E-05	[             --                                  ]	AAA	The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
40	COG1197	1139	332	98.0	3.3E-05	[             -------------------                 ]	Mfd	Transcription-repair coupling factor (superfamily II helicase)
41	TIGR00580	926	331	98.0	3.6E-05	[             -------------------                 ]	mfd	transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.
42	PRK01297	475	300	98.0	9.3E-06	[              ----------------                   ]	PRK01297	ATP-dependent RNA helicase RhlB; Provisional
43	PRK00254	720	403	97.8	0.00077	[              ----------------------             ]	PRK00254	ski2-like helicase; Provisional
44	PRK02362	737	324	97.8	0.00036	[           ------------------                    ]	PRK02362	ski2-like helicase; Provisional
45	PRK09401	1176	281	97.8	0.00038	[             ---------------                     ]	PRK09401	reverse gyrase; Reviewed
46	COG1110	1187	280	97.8	0.00052	[            ----------------                     ]	TopG2	Reverse gyrase
47	pfam13401	124	34	97.7	7.5E-05	[                  ---                            ]	AAA_22	AAA domain.
48	COG1643	845	290	97.5	0.00069	[              ----------------                   ]	HrpA	HrpA-like RNA helicase
49	pfam00176	286	223	97.2	0.0026	[              ------------                       ]	SNF2_N	SNF2 family N-terminal domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1).
50	COG0553	866	164	97.2	0.0032	[                        --------                 ]	HepA	Superfamily II DNA or RNA helicase, SNF2 family
51	COG4096	875	327	97.1	0.0042	[             -----------------                   ]	HsdR	Type I site-specific restriction endonuclease, part of a restriction-modification system
52	pfam13191	156	42	97.1	0.0084	[             --                                  ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
53	PRK01172	674	290	96.8	0.015	[             ----------------                    ]	PRK01172	ski2-like helicase; Provisional
54	COG1199	654	67	96.7	0.0015	[             ---                                 ]	DinG	Rad3-related DNA helicase
55	PRK11634	629	308	96.7	0.00098	[             ------------------                  ]	PRK11634	ATP-dependent RNA helicase DeaD; Provisional
56	TIGR02928	365	77	96.1	0.017	[              ---                                ]	TIGR02928	orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
57	PRK14701	1638	145	95.8	0.028	[            --------                             ]	PRK14701	reverse gyrase; Provisional
58	TIGR03158	357	290	95.8	0.0067	[              ---------------                    ]	cas3_cyano	CRISPR-associated helicase Cas3, subtype CYANO. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
59	pfam13173	127	74	95.6	0.013	[              ------                             ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
60	TIGR01054	1171	252	95.5	0.036	[              --------------                     ]	rgy	reverse gyrase. This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
61	PRK11747	697	66	95.1	0.025	[             ---                                 ]	dinG	ATP-dependent DNA helicase DinG; Provisional
62	COG1132	567	93	95.1	0.0073	[              -----                              ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
63	pfam09848	348	136	95.1	0.036	[              --------                           ]	DUF2075	Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
64	PRK11448	1123	313	95.0	0.15	[              ----------------                   ]	hsdR	type I restriction enzyme EcoKI subunit R; Provisional
65	TIGR00348	667	350	94.6	1.1	[            ------------------                   ]	hsdR	type I site-specific deoxyribonuclease, HsdR family. This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity.
66	TIGR01407	850	42	94.1	0.02	[              --                                 ]	dinG_rel	DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
67	pfam13207	114	21	94.0	0.02	[              -                                  ]	AAA_17	AAA domain.
68	COG1484	254	85	93.8	0.14	[              ----                               ]	DnaC	DNA replication protein DnaC
69	COG4581	1041	78	93.6	0.081	[                          ----                   ]	Dob10	Superfamily II RNA helicase
70	COG1219	408	27	93.6	0.025	[              -                                  ]	ClpX	ATP-dependent protease Clp, ATPase subunit
71	COG0610	962	189	93.5	0.16	[            ----------                           ]	COG0610	Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ...
72	TIGR02621	862	188	93.5	0.27	[                   ----------                    ]	cas3_GSU0051	CRISPR-associated helicase Cas3, subtype Dpsyc. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
73	pfam13671	143	86	93.4	0.059	[              ----                               ]	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.
74	pfam05707	183	15	93.4	0.043	[              -                                  ]	Zot	Zonular occludens toxin (Zot). This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers
75	PRK13342	413	60	93.2	0.059	[             ---                                 ]	PRK13342	recombination factor protein RarA; Reviewed
76	pfam07724	168	105	92.9	0.091	[              ------                             ]	AAA_2	AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
77	PRK05342	412	27	92.6	0.04	[              -                                  ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
78	TIGR00382	413	26	92.5	0.047	[              -                                  ]	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.
79	PRK09361	225	114	92.4	0.34	[              -------                            ]	radB	DNA repair and recombination protein RadB; Provisional
80	PRK10689	1147	289	91.9	2.6	[             ----------------                    ]	PRK10689	transcription-repair coupling factor; Provisional
81	COG1110	1187	123	91.4	0.38	[                        -------                  ]	TopG2	Reverse gyrase
82	pfam13555	60	30	91.3	0.023	[              --                                 ]	AAA_29	P-loop containing region of AAA domain.
83	COG1435	201	107	90.9	0.45	[              -------                            ]	Tdk	Thymidine kinase
84	COG0470	325	46	90.9	0.29	[             --                                  ]	HolB	DNA polymerase III, delta prime subunit
85	PRK12724	432	69	90.5	0.14	[            ----                                 ]	PRK12724	flagellar biosynthesis regulator FlhF; Provisional
86	cd09708	632	47	90.2	0.16	[              --                                 ]	Csf4_U	CRISPR/Cas system-associated DinG family helicase Csf4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase
87	TIGR03117	636	47	90.2	0.16	[              --                                 ]	cas_csf4	CRISPR type AFERR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
88	PRK04296	190	106	90.2	0.28	[              -------                            ]	PRK04296	thymidine kinase; Provisional
89	pfam07728	135	92	89.9	0.15	[              -----                              ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
90	cd01120	165	29	89.9	0.42	[              -                                  ]	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.
91	COG1444	758	262	89.9	0.89	[             ----------------                    ]	TmcA	tRNA(Met) C34 N-acetyltransferase TmcA
92	pfam13238	128	21	89.7	0.1	[              -                                  ]	AAA_18	AAA domain.
93	COG0529	197	66	89.5	0.24	[             ----                                ]	CysC	Adenylylsulfate kinase or related kinase
94	cd02027	149	82	89.1	0.25	[              -----                              ]	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.
95	pfam13245	72	42	88.2	0.35	[              --                                 ]	AAA_19	Part of AAA domain.
96	cd01393	226	90	88.1	0.97	[                -----                            ]	recA_like	RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
97	PRK05298	652	189	88.1	1.2	[                   -----------                   ]	PRK05298	excinuclease ABC subunit B; Provisional
98	COG2804	500	34	87.9	0.19	[       --                                        ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
99	cd09696	843	184	87.7	1.8	[                   ----------                    ]	Cas3_I	CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to C-termus of Helicase domain. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DNA helicase Cas3; This protein includes both DEAH and HD motifs; signature gene for Type I
100	cd02023	198	73	87.4	0.37	[              ----                               ]	UMPK	Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
101	COG0593	408	80	87.2	0.9	[             ----                                ]	DnaA	Chromosomal replication initiation ATPase DnaA
102	COG0556	663	193	87.1	1.6	[                   -----------                   ]	UvrB	Excinuclease UvrABC helicase subunit UvrB
103	pfam00005	150	125	86.7	0.67	[              --------                           ]	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.
104	TIGR01054	1171	172	86.6	1.2	[                       ---------                 ]	rgy	reverse gyrase. This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
105	COG4098	441	276	86.3	2.2	[              ----------------                   ]	comFA	Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein)
106	pfam13481	192	133	86.2	1.9	[              -------                            ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
107	cd01129	264	28	86.1	0.34	[             --                                  ]	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.
108	pfam03266	168	125	85.8	0.41	[              -------                            ]	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.
109	cd03225	211	40	85.7	0.18	[              --                                 ]	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.
110	COG2812	515	120	85.6	1.4	[            --------                             ]	DnaX	DNA polymerase III, gamma/tau subunits
111	cd01131	198	21	85.6	0.35	[                  -                              ]	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.
112	COG0468	279	110	85.2	2.5	[              -------                            ]	RecA	RecA/RadA recombinase
113	TIGR01420	343	25	84.8	0.69	[                               -                 ]	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.
114	COG2256	436	61	84.7	0.57	[             ---                                 ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
115	PRK12422	445	94	84.6	1.2	[             -------                             ]	PRK12422	chromosomal replication initiation protein; Provisional
116	COG2805	353	68	84.0	0.4	[             ------                              ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
117	COG0553	866	224	83.9	5.1	[              ------------                       ]	HepA	Superfamily II DNA or RNA helicase, SNF2 family
118	COG1618	179	109	83.9	0.53	[              ------                             ]	THEP1	Nucleoside-triphosphatase THEP1
119	cd03228	171	38	83.7	0.28	[              --                                 ]	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.
120	pfam13304	144	21	83.6	0.3	[              -                                  ]	AAA_21	AAA domain.
121	pfam06414	194	90	83.4	2.5	[              ----                               ]	Zeta_toxin	Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.
122	pfam00004	131	46	83.1	0.92	[              --                                 ]	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.
123	pfam13476	203	22	82.6	0.38	[              -                                  ]	AAA_23	AAA domain.
124	COG0467	260	106	82.5	2.9	[              -----                              ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
125	pfam13604	195	151	81.7	1.6	[             ----------                          ]	AAA_30	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
126	pfam02463	1162	46	81.6	0.42	[              --                                 ]	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.
127	PRK06835	329	84	81.6	2	[           -----                                 ]	PRK06835	DNA replication protein DnaC; Validated
128	PRK11664	812	258	81.5	41	[              --------------                     ]	PRK11664	ATP-dependent RNA helicase HrpB; Provisional
129	COG1122	235	27	81.3	0.68	[              -                                  ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
130	cd02019	69	22	81.3	2	[              -                                  ]	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.
131	cd00984	242	145	81.2	5	[              -------                            ]	DnaB_C	DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
132	pfam05127	160	36	81.0	1.2	[                 --                              ]	Helicase_RecD	Helicase. This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases.
133	TIGR02237	209	86	80.6	3.8	[              -----                              ]	recomb_radB	DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
134	pfam01637	223	63	80.3	11	[             ---                                 ]	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.
135	TIGR02169	1164	75	80.3	0.94	[              ----                               ]	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.
136	COG1136	226	44	80.0	0.61	[                    --                           ]	LolD	ABC-type lipoprotein export system, ATPase component
137	PRK09200	790	100	79.9	1.4	[                        -----                    ]	PRK09200	preprotein translocase subunit SecA; Reviewed
138	cd00267	157	23	79.5	0.66	[              -                                  ]	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.
139	PRK08074	928	57	79.5	1.2	[             ---                                 ]	PRK08074	bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
140	cd03279	213	14	79.4	0.58	[              -                                  ]	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.
141	COG1474	366	33	79.2	2.1	[              -                                  ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
142	cd03227	162	17	78.9	0.73	[              -                                  ]	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.
143	PRK00440	319	41	78.9	1.2	[             --                                  ]	rfc	replication factor C small subunit; Reviewed
144	TIGR00631	655	183	78.8	4.3	[                   ----------                    ]	uvrb	excinuclease ABC, B subunit. All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
145	PRK05480	209	35	78.3	1.2	[              --                                 ]	PRK05480	uridine/cytidine kinase; Provisional
146	PRK13695	174	106	78.2	1.1	[              ------                             ]	PRK13695	putative NTPase; Provisional
147	PRK05298	652	76	78.2	4.5	[             ----                                ]	PRK05298	excinuclease ABC subunit B; Provisional
148	COG1373	398	38	78.1	3.5	[                   --                            ]	COG1373	Predicted ATPase, AAA+ superfamily
149	COG0419	908	14	77.7	0.7	[              -                                  ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
150	cd01123	235	86	77.5	2.1	[                -----                            ]	Rad51_DMC1_radA	Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
151	TIGR02533	486	54	77.5	1.1	[      ---                                        ]	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.
152	TIGR03499	282	37	77.3	1.9	[              --                                 ]	FlhF	flagellar biosynthetic protein FlhF.
153	pfam00437	273	16	77.1	0.89	[                                                 ]	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.
154	cd01130	186	42	76.4	0.35	[              --                                 ]	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.
155	COG0563	178	22	75.8	1.4	[              -                                  ]	Adk	Adenylate kinase or related kinase
156	COG0556	663	76	75.7	5.8	[             ----                                ]	UvrB	Excinuclease UvrABC helicase subunit UvrB
157	PRK10436	462	74	75.1	1.5	[     ----                                        ]	PRK10436	hypothetical protein; Provisional
158	COG4987	573	78	74.4	1.3	[              ---                                ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
159	PRK09270	229	84	74.3	1.3	[              ----                               ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
160	COG1199	654	200	73.9	24	[                   ----------                    ]	DinG	Rad3-related DNA helicase
161	PRK13768	253	25	73.4	2	[              -                                  ]	PRK13768	GTPase; Provisional
162	cd01983	99	75	73.0	8.8	[              -----                              ]	Fer4_NifH	The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
163	TIGR04221	762	90	72.4	5.1	[                        -----                    ]	SecA2_Mycobac	accessory Sec system translocase SecA2, Actinobacterial type. Members of this family are the SecA2 subunit of the Mycobacterial type of accessory secretory system. This family is quite different SecA2 of the Staph/Strep type (TIGR03714).
164	cd03299	235	130	72.2	1.5	[              -------                            ]	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.
165	TIGR02538	564	41	72.1	1.9	[       --                                        ]	type_IV_pilB	type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
166	pfam01583	157	84	72.1	2.1	[              -----                              ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
167	TIGR00631	655	76	72.1	5.4	[             ----                                ]	uvrb	excinuclease ABC, B subunit. All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
168	cd03255	218	61	71.0	1.3	[              ----                               ]	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.
169	TIGR00174	287	74	70.8	2.8	[                           ----                  ]	miaA	tRNA dimethylallyltransferase. Alternate names include delta(2)-isopentenylpyrophosphate transferase, IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA modification enzyme. Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine. Understanding of substrate specificity has changed.
170	TIGR04521	277	32	70.7	1.2	[              -                                  ]	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.
171	cd01428	194	44	70.7	2.5	[              --                                 ]	ADK	Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
172	pfam02456	370	79	70.7	2.1	[            ----                                 ]	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.
173	pfam12846	298	35	70.4	2.4	[                            --                   ]	AAA_10	AAA-like domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
174	PRK08939	306	82	69.8	8.2	[              ----                               ]	PRK08939	primosomal protein DnaI; Reviewed
175	PRK00131	175	49	69.7	2	[              --                                 ]	aroK	shikimate kinase; Reviewed
176	PRK06762	166	30	69.5	7.9	[              -                                  ]	PRK06762	hypothetical protein; Provisional
177	pfam03205	138	28	69.0	2.8	[              -                                  ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
178	pfam10236	293	42	69.0	2.9	[             --                                  ]	DAP3	Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
179	pfam00270	167	69	68.7	11	[                        ---                      ]	DEAD	DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolizm, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
180	pfam13086	183	62	68.5	27	[             ---                                 ]	AAA_11	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
181	COG4185	187	80	68.4	19	[              ----                               ]	COG4185	Predicted ABC-type ATPase
182	COG5008	375	18	68.4	2.4	[                        -                        ]	PilU	Tfp pilus assembly protein, ATPase PilU
183	TIGR02173	171	23	68.3	1.8	[              -                                  ]	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.
184	cd03254	229	21	68.1	1.8	[              -                                  ]	ABCC_Glucan_exporter_like	ATP-binding cassette domain of glucan transporter and related proteins, subfamily C. Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virulence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
185	cd03276	198	24	67.9	2.2	[              -                                  ]	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).
186	cd03239	178	14	67.3	2.3	[                                                 ]	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.
187	COG3267	269	34	67.1	5.3	[              --                                 ]	ExeA	Type II secretory pathway, component ExeA (predicted ATPase)
188	pfam02078	105	19	67.0	1.9	[                   -                             ]	Synapsin	Synapsin, N-terminal domain.
189	PRK04837	423	89	66.6	8.6	[                       -----                     ]	PRK04837	ATP-dependent RNA helicase RhlB; Provisional
190	cd03247	178	49	66.5	3.3	[              --                                 ]	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.
191	COG0324	308	14	66.1	2.6	[                                                 ]	MiaA	tRNA A37 N6-isopentenylltransferase MiaA
192	TIGR04397	774	155	65.8	4.3	[                        --------                 ]	SecA2_Bac_anthr	accessory Sec system translocase SecA2, Bacillus type. Members of this family always occur in genomes with the preprotein translocase SecA (TIGR00963) and closely resemble it, hence the designation SecA2. However, this appears to mark a different type of accessory Sec system SecA2 (TIGR03714) from the serine-rich glycoprotein type found in Staphylococcus and Streptococcus, and the actinobacterial SecA2 (TIGR04221). This type occurs in species including Bacillus anthracis, Geobacillus thermoglucosidasius, Solibacillus silvestris, etc.
193	cd00502	225	37	65.3	38	[                    -                            ]	DHQase_I	Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase). Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase). Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism.
194	cd03278	197	43	65.3	2.1	[              --                                 ]	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).
195	TIGR02525	372	56	64.7	2.2	[       ---                                       ]	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).
196	COG1134	249	78	64.3	2	[           -----                                 ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
197	COG3839	338	26	63.9	2.5	[                            -                    ]	MalK	ABC-type sugar transport system, ATPase component
198	COG1196	1163	56	63.8	3	[              ---                                ]	Smc	Chromosome segregation ATPase
199	cd03293	220	33	63.6	1.7	[              -                                  ]	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.
200	PRK00091	307	43	63.4	2.4	[                   --                            ]	miaA	tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
201	cd00071	137	64	63.3	2.6	[              ----                               ]	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.
202	cd03262	213	58	63.0	3.6	[                     ----                        ]	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.
203	pfam06862	436	219	62.7	44	[                   ------------                  ]	DUF1253	Protein of unknown function (DUF1253). This family represents the C-terminal portion (approximately 500 residues) of several hypothetical eukaryotic proteins of unknown function.
204	COG4889	1518	44	62.5	10	[                           --                    ]	COG4889	Predicted helicase
205	pfam01935	219	14	62.4	3.5	[                                                 ]	DUF87	Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
206	TIGR03714	762	100	62.4	6	[                        -----                    ]	secA2	accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.
207	pfam01695	178	33	61.6	5.1	[             --                                  ]	IstB_IS21	IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.
208	TIGR02168	1179	14	61.5	2.8	[                                                 ]	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.
209	cd03238	176	113	61.5	2.3	[              ------                             ]	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.
210	PRK08116	268	101	61.4	5.5	[              -------                            ]	PRK08116	hypothetical protein; Validated
211	PRK12326	764	59	60.9	18	[                          ---                    ]	PRK12326	preprotein translocase subunit SecA; Reviewed
212	cd00464	154	29	60.5	3.1	[              -                                  ]	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.
213	cd03240	204	14	60.5	2.8	[              -                                  ]	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.
214	pfam07527	42	41	60.4	9	[                                          --     ]	Hairy_orange	Hairy Orange. The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute.
215	pfam01487	222	38	60.1	6.4	[                    -                            ]	DHquinase_I	Type I 3-dehydroquinase. Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) Catalyses the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyses the trans-dehydration of 3-dehydroshikimate see pfam01220.
216	COG4181	228	48	59.9	3.2	[              --                                 ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
217	pfam00158	168	99	59.5	4.4	[             -----                               ]	Sigma54_activat	Sigma-54 interaction domain.
218	PRK14526	211	27	59.3	6.4	[              -                                  ]	PRK14526	adenylate kinase; Provisional
219	COG0630	312	34	59.3	4	[              -                                  ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
220	pfam15162	162	63	59.2	1.2	[                  ----                           ]	DUF4580	Domain of unknown function (DUF4580). This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 185 amino acids in length.
221	TIGR00763	775	48	59.1	8.3	[             --                                  ]	lon	endopeptidase La. This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
222	COG1126	240	164	59.1	3.5	[              -----------                        ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
223	cd03253	236	59	58.9	3.1	[                     ----                        ]	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.
224	cd02021	150	22	58.8	3.1	[              -                                  ]	GntK	Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
225	cd03257	228	58	58.6	4.1	[              ----                               ]	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.
226	PRK13539	207	22	58.6	3.7	[              -                                  ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
227	TIGR03574	249	86	58.5	43	[              ----                               ]	selen_PSTK	L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
228	pfam00910	105	24	58.4	4.1	[              -                                  ]	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.
229	cd05572	262	73	58.2	8.7	[                 ------                          ]	STKc_cGK	Catalytic domain of the Serine/Threonine Kinase, cGMP-dependent protein kinase (cGK or PKG). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mammals have two cGK isoforms from different genes, cGKI and cGKII. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. cGK consists of an N-terminal regulatory domain containing a dimerization and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. cGKII is a membrane-bound protein that is most abundantly expressed in the intestine. It is also present in the brain nuclei, adrenal cortex, kidney, lung, and prostate. cGKI is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. cGKII plays a role in the regulation of secretion, such as renin secretion by the kidney and aldosterone secretion by the adrenal. It also regulates bone growth and the circadian rhythm. The cGK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
230	PRK10247	225	24	58.2	3.1	[              -                                  ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
231	COG2884	223	16	58.2	3.6	[                                                 ]	FtsE	ABC-type ATPase involved in cell division
232	COG0237	201	62	58.0	11	[              ---                                ]	CoaE	Dephospho-CoA kinase
233	cd03223	166	21	58.0	3.4	[              -                                  ]	ABCD_peroxisomal_ALDP	ATP-binding cassette domain of peroxisomal transporter, subfamily D. Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).
234	PRK08118	167	23	57.7	5.6	[              -                                  ]	PRK08118	topology modulation protein; Reviewed
235	TIGR00455	184	133	57.6	5.5	[              ---------                          ]	apsK	adenylyl-sulfate kinase. This protein, adenylylsulfate kinase, is often found as a fusion protein with sulfate adenylyltransferase. Important residue (active site in E.coli) is residue 100 of the seed alignment.
236	pfam02562	205	108	57.5	9.4	[             ------                              ]	PhoH	PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
237	pfam01078	207	49	57.3	3.6	[              --                                 ]	Mg_chelatase	Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
238	COG0703	172	39	57.2	3.7	[              --                                 ]	AroK	Shikimate kinase
239	PRK11634	629	69	56.8	11	[              ----                               ]	PRK11634	ATP-dependent RNA helicase DeaD; Provisional
240	COG4088	261	89	56.7	5.5	[              ----                               ]	Kti12	tRNA Uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein)
241	pfam03796	261	147	56.6	45	[              -------                            ]	DnaB_C	DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
242	cd01363	170	76	56.3	8.1	[             ----                                ]	Motor_domain	Myosin and Kinesin motor domain. Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes. Some of the names do not match with what is given in the sequence list. This is because they are based on the current nomenclature by Kollmar/Sebe-Pedros.
243	TIGR03420	226	34	56.3	6.3	[             --                                  ]	DnaA_homol_Hda	DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
244	PRK09694	878	304	55.9	63	[             ----------------                    ]	PRK09694	helicase Cas3; Provisional
245	pfam04665	241	40	55.8	7.4	[              --                                 ]	Pox_A32	Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging.
246	cd02020	147	22	55.1	4.5	[              -                                  ]	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.
247	cd03260	227	104	54.8	3.9	[                  ------                         ]	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).
248	PRK11160	574	103	54.8	4.1	[              -----                              ]	PRK11160	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
249	cd03250	204	14	54.6	4.5	[                                                 ]	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.
250	PRK10789	569	14	54.3	3.6	[                                                 ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
251	TIGR00602	637	41	54.3	5.7	[             --                                  ]	rad24	checkpoint protein rad24. All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
252	cd03249	238	73	54.2	4	[                    -----                        ]	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.
253	COG0542	786	114	53.9	8.1	[           -------                               ]	ClpA	ATP-dependent Clp protease ATP-binding subunit ClpA
254	COG1116	248	31	53.5	3.9	[              -                                  ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
255	COG4604	252	40	53.3	5.1	[              --                                 ]	CeuD	ABC-type enterochelin transport system, ATPase component
256	cd04105	202	16	53.3	4.6	[              -                                  ]	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.
257	pfam00448	195	59	53.2	14	[              ---                                ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
258	COG0466	782	49	52.9	11	[             --                                  ]	Lon	ATP-dependent Lon protease, bacterial type
259	TIGR02528	142	84	52.8	4.2	[              -----                              ]	EutP	ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.
260	TIGR02673	214	17	52.6	5.1	[              -                                  ]	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.
261	COG1120	258	23	52.5	4.5	[              -                                  ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
262	pfam00308	219	95	52.3	20	[             ----                                ]	Bac_DnaA	Bacterial dnaA protein.
263	cd03219	236	23	52.2	5	[              -                                  ]	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).
264	PRK13634	290	141	51.8	7.1	[              -------                            ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
265	pfam12846	298	43	51.5	18	[                   --                            ]	AAA_10	AAA-like domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
266	pfam08433	267	32	51.3	9.4	[              -                                  ]	KTI12	Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity.
267	PRK14950	585	114	51.3	8	[             -------                             ]	PRK14950	DNA polymerase III subunits gamma and tau; Provisional
268	PRK12901	1112	135	51.2	9	[                        --------                 ]	secA	preprotein translocase subunit SecA; Reviewed
269	TIGR00963	742	48	51.0	9.4	[                           --                    ]	secA	preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus. This model excludes SecA2 of the accessory secretory system.
270	COG1121	254	27	50.5	4.2	[              -                                  ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
271	cd03214	180	36	50.5	5.6	[              --                                 ]	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.
272	PRK13764	602	64	50.5	3.1	[             ---                                 ]	PRK13764	ATPase; Provisional
273	PRK09493	240	14	50.5	6.3	[                                                 ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
274	COG0444	316	33	50.2	11	[                 -                               ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
275	PRK04182	180	23	50.1	6.4	[              -                                  ]	PRK04182	cytidylate kinase; Provisional
276	COG1124	252	28	49.8	4.7	[              -                                  ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
277	PRK00149	450	84	49.6	19	[            ----                                 ]	dnaA	chromosomal replication initiation protein; Reviewed
278	PRK05703	424	159	49.6	9.3	[              -----------                        ]	flhF	flagellar biosynthesis regulator FlhF; Validated
279	TIGR02397	355	46	49.5	10	[             --                                  ]	dnaX_nterm	DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
280	PRK04301	317	111	49.5	25	[              -------                            ]	radA	DNA repair and recombination protein RadA; Validated
281	COG4240	300	29	49.3	7.9	[              -                                  ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
282	cd03277	213	21	49.2	7	[                                                 ]	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).
283	COG1224	450	58	49.2	13	[             --                                  ]	TIP49	DNA helicase TIP49, TBP-interacting protein
284	COG3596	296	23	49.1	9.5	[             -                                   ]	YeeP	Predicted GTPase
285	COG0606	490	63	48.7	7.2	[                            ---                  ]	YifB	Predicted ATPase with chaperone activity
286	PRK14952	584	49	48.7	7.6	[             --                                  ]	PRK14952	DNA polymerase III subunits gamma and tau; Provisional
287	PRK13341	725	56	48.5	4.6	[             ---                                 ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
288	PRK14974	336	39	48.3	16	[              --                                 ]	PRK14974	cell division protein FtsY; Provisional
289	COG1419	407	173	48.3	9.7	[              -----------                        ]	FlhF	Flagellar biosynthesis GTPase FlhF
290	TIGR00954	659	24	48.0	6.3	[              -                                  ]	3a01203	Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein.
291	PRK08760	476	146	47.9	92	[              -------                            ]	PRK08760	replicative DNA helicase; Provisional
292	cd01855	191	31	47.8	11	[             --                                  ]	YqeH	Circularly permuted YqeH GTPase. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.
293	PRK09087	226	39	47.8	12	[             --                                  ]	PRK09087	hypothetical protein; Validated
294	pfam00485	196	78	47.7	15	[              ----                               ]	PRK	Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
295	cd03298	211	31	47.6	5.8	[              -                                  ]	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.
296	cd03274	212	18	47.5	7.2	[                                                 ]	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).
297	PRK10917	681	127	47.4	33	[                    --------                     ]	PRK10917	ATP-dependent DNA helicase RecG; Provisional
298	cd03267	236	82	47.4	9.9	[           ------                                ]	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.
299	cd02035	217	34	47.1	11	[              -                                  ]	ArsA	ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.
300	TIGR00603	732	285	46.9	28	[             ----------------                    ]	rad25	DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
301	PRK05057	172	22	46.9	8.4	[              -                                  ]	aroK	shikimate kinase I; Reviewed
302	cd03244	221	18	46.8	6.1	[              -                                  ]	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.
303	PRK12906	796	117	46.8	7.6	[                        ------                   ]	secA	preprotein translocase subunit SecA; Reviewed
304	PRK05541	176	32	46.7	14	[              -                                  ]	PRK05541	adenylylsulfate kinase; Provisional
305	cd03301	213	21	46.5	8.8	[              -                                  ]	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.
306	PRK12898	656	80	46.4	15	[              ----                               ]	secA	preprotein translocase subunit SecA; Reviewed
307	PRK03695	248	15	46.4	7.3	[              -                                  ]	PRK03695	vitamin B12-transporter ATPase; Provisional
308	cd03229	178	15	46.2	7.5	[              -                                  ]	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.
309	cd03220	224	41	46.1	5.4	[              --                                 ]	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.
310	TIGR00618	1042	41	46.0	7.6	[              --                                 ]	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).
311	PRK13649	280	22	45.8	7	[              -                                  ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
312	PRK11650	356	17	45.8	7.4	[              -                                  ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
313	TIGR00929	785	33	45.3	9.9	[              -                                  ]	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).
314	PRK13646	286	129	45.3	7.6	[              --------                           ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
315	pfam06794	70	52	45.0	27	[               ---                               ]	UPF0270	Uncharacterized protein family (UPF0270).
316	TIGR02524	358	26	45.0	10	[             -                                   ]	dot_icm_DotB	Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.
317	PRK09401	1176	133	44.6	45	[                        ------                   ]	PRK09401	reverse gyrase; Reviewed
318	TIGR02903	615	39	44.5	16	[             --                                  ]	spore_lon_C	ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
319	PRK13657	588	57	44.5	7.9	[                     ----                        ]	PRK13657	cyclic beta-1,2-glucan ABC transporter; Provisional
320	TIGR02204	576	94	44.1	7.5	[              -----                              ]	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.
321	PRK13830	818	59	44.0	9.3	[            ---                                  ]	PRK13830	conjugal transfer protein TrbE; Provisional
322	cd03259	213	56	43.8	8.5	[                  ---                            ]	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.
323	COG0305	435	147	43.6	63	[              -------                            ]	DnaB	Replicative DNA helicase
324	cd03246	173	39	43.4	7.6	[              --                                 ]	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.
325	PRK00411	394	122	43.3	29	[            -------                              ]	cdc6	cell division control protein 6; Reviewed
326	COG3910	233	14	43.3	8.4	[                                                 ]	COG3910	Predicted ATPase
327	pfam03215	517	39	43.1	11	[             --                                  ]	Rad17	Rad17 cell cycle checkpoint protein.
328	COG1102	179	21	43.0	10	[              -                                  ]	CmkB	Cytidylate kinase
329	cd01394	218	120	43.0	91	[              -------                            ]	radB	RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
330	cd02034	116	34	42.9	14	[              -                                  ]	CooC	The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
331	COG2204	464	154	42.9	38	[          --------                               ]	AtoC	DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains
332	TIGR03744	893	70	42.9	11	[              ---                                ]	traC_PFL_4706	conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves.
333	cd03221	144	23	42.8	7.9	[              -                                  ]	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.
334	COG0194	191	15	42.7	9	[              -                                  ]	Gmk	Guanylate kinase
335	cd03275	247	40	42.7	9.5	[              --                                 ]	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).
336	PRK00300	205	14	42.5	9.2	[                                                 ]	gmk	guanylate kinase; Provisional
337	cd02028	179	15	42.5	11	[              -                                  ]	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).
338	TIGR03797	686	102	42.4	8.3	[                  ------                         ]	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.
339	PRK12900	1025	84	42.3	11	[                          -----                  ]	secA	preprotein translocase subunit SecA; Reviewed
340	cd03230	173	31	42.2	6.4	[              -                                  ]	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.
341	COG0411	250	29	42.2	13	[              -                                  ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
342	PRK13548	258	31	42.0	8.1	[              -                                  ]	hmuV	hemin importer ATP-binding subunit; Provisional
343	cd03235	213	17	42.0	9.5	[              -                                  ]	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.
344	COG3973	747	67	41.9	32	[             ---                                 ]	HelD	DNA helicase IV
345	pfam14532	138	93	41.9	42	[             -----                               ]	Sigma54_activ_2	Sigma-54 interaction domain.
346	COG4619	223	38	41.8	9.1	[                    --                           ]	FetA	ABC-type iron transport system FetAB, ATPase component
347	TIGR02211	221	27	41.7	10	[                     -                           ]	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.
348	PRK07246	820	49	41.5	28	[              --                                 ]	PRK07246	bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
349	TIGR02982	220	27	41.3	11	[             --                                  ]	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.
350	TIGR00362	437	86	41.2	43	[            ----                                 ]	DnaA	chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
351	TIGR03263	179	14	40.8	10	[                                                 ]	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.
352	COG3598	402	152	40.7	59	[             --------                            ]	RepA	RecA-family ATPase
353	COG0396	251	24	40.5	7.7	[                     -                           ]	SufC	Fe-S cluster assembly ATPase SufC
354	COG1119	257	23	40.3	8.3	[              -                                  ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
355	COG0714	329	60	40.3	14	[             ---                                 ]	MoxR	MoxR-like ATPase
356	PRK07764	824	49	40.3	11	[             --                                  ]	PRK07764	DNA polymerase III subunits gamma and tau; Validated
357	COG4133	209	31	40.2	11	[              -                                  ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
358	PRK13641	287	34	40.1	14	[              -                                  ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
359	COG0572	218	23	39.9	12	[              -                                  ]	Udk	Uridine kinase
360	PRK12402	337	56	39.7	26	[             --                                  ]	PRK12402	replication factor C small subunit 2; Reviewed
361	TIGR03600	420	235	39.6	26	[        -------------                            ]	phage_DnaB	phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
362	pfam01580	201	24	39.6	13	[              -                                  ]	FtsK_SpoIIIE	FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from Escherichia coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer.
363	cd11621	72	32	39.3	27	[                                               --]	HR1_PKC-like_1_fungi	First Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of fungal Protein Kinase C-like proteins. This subfamily is composed of fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity. They contain two HR1 domains, C2 and C1 domains, and a kinase domain. This model characterizes the first HR1 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. The HR1 domains of Pck1p and Pck2p interact with GTP-bound Rho1p and Rho2p.
364	COG1072	283	82	39.2	22	[             -----                               ]	CoaA	Panthothenate kinase
365	COG3950	440	18	38.9	14	[                                                 ]	COG3950	Predicted ATP-binding protein involved in virulence
366	cd03241	276	59	38.3	12	[                ---                              ]	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.
367	PRK03731	171	27	38.2	14	[              -                                  ]	aroL	shikimate kinase II; Reviewed
368	cd03116	159	14	38.1	16	[                                                 ]	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.
369	pfam13521	162	38	38.1	12	[              --                                 ]	AAA_28	AAA domain.
370	TIGR03158	357	11	38.0	17	[                                                 ]	cas3_cyano	CRISPR-associated helicase Cas3, subtype CYANO. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
371	PRK11000	369	17	37.7	12	[              -                                  ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
372	cd00046	144	60	37.7	61	[                        ---                      ]	DEXDc	DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
373	COG0378	202	28	37.5	17	[              -                                  ]	HypB	Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase
374	cd03115	173	63	37.3	80	[              ---                                ]	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.
375	cd02022	179	62	37.1	42	[              ---                                ]	DPCK	Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
376	TIGR03864	236	30	37.0	13	[              -                                  ]	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.
377	pfam10662	143	17	36.7	12	[              -                                  ]	PduV-EutP	Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood.
378	COG1100	219	30	36.6	12	[              -                                  ]	Gem1	GTPase SAR1 family domain
379	COG3451	796	33	36.6	18	[              -                                  ]	VirB4	Type IV secretory pathway, VirB4 component
380	COG3840	231	30	36.5	12	[              -                                  ]	ThiQ	ABC-type thiamine transport system, ATPase component
381	COG1131	293	20	36.4	9	[              -                                  ]	CcmA	ABC-type multidrug transport system, ATPase component
382	cd03217	200	25	36.3	10	[                 --                              ]	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.
383	cd03369	207	136	36.2	13	[              -------                            ]	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.
384	COG0464	494	27	35.9	19	[              -                                  ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
385	TIGR04291	566	110	35.7	28	[              -----                              ]	arsen_driv_ArsA	arsenical pump-driving ATPase. The broader family (TIGR00345) to which the current family belongs consists of transport-energizing ATPases, including to TRC40/GET3 family involved in post-translational insertion of protein C-terminal transmembrane anchors into membranes from the cyotosolic face. This family, however, is restricted to ATPases that energize pumps that export arsenite (or antimonite).
386	cd03231	201	78	35.4	14	[              ----                               ]	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.
387	COG4525	259	31	35.4	13	[              -                                  ]	TauB	ABC-type taurine transport system, ATPase component
388	PRK13651	305	14	35.3	21	[                                                 ]	PRK13651	cobalt transporter ATP-binding subunit; Provisional
389	PRK11784	345	29	35.1	21	[             --                                  ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
390	PRK07133	725	109	35.1	20	[             ------                              ]	PRK07133	DNA polymerase III subunits gamma and tau; Validated
391	PRK04132	846	40	35.1	31	[             -                                   ]	PRK04132	replication factor C small subunit; Provisional
392	COG1703	323	70	35.0	19	[                       ----                      ]	ArgK	Putative periplasmic protein kinase ArgK or related GTPase of G3E family
393	cd01369	325	21	34.9	35	[             --                                  ]	KISc_KHC_KIF5	Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
394	cd11383	140	20	34.8	9.3	[                  -                              ]	YfjP	YfjP GTPase. The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain.
395	cd03272	243	29	34.8	17	[              -                                  ]	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).
396	pfam02374	304	34	34.7	28	[              -                                  ]	ArsA_ATPase	Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
397	COG0513	513	54	34.7	66	[               ---                               ]	SrmB	Superfamily II DNA and RNA helicase
398	pfam14270	106	56	34.6	1.1E+02	[                         --                      ]	DUF4358	Domain of unknown function (DUF4358). This domain family is found in bacteria, and is approximately 110 amino acids in length.
399	TIGR01447	582	88	34.3	27	[              -----                              ]	recD	exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.
400	COG4615	546	74	34.3	15	[                ------                           ]	PvdE	ABC-type siderophore export system, fused ATPase and permease components
401	TIGR03880	224	86	34.2	99	[              -----                              ]	KaiC_arch_3	KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
402	cd01918	149	14	34.2	18	[                                                 ]	HprK_C	HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases.
403	TIGR00368	499	47	34.2	19	[              --                                 ]	TIGR00368	Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
404	TIGR01846	694	22	34.1	14	[              -                                  ]	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.
405	cd01854	211	16	34.0	14	[                                                 ]	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.
406	cd03268	208	33	34.0	12	[              -                                  ]	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.
407	COG1125	309	14	33.9	16	[                                                 ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
408	cd00882	161	12	33.8	13	[                                                 ]	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.
409	cd00079	131	55	33.7	1.3E+02	[               ---                               ]	HELICc	Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
410	PRK07940	394	74	33.6	27	[             ---                                 ]	PRK07940	DNA polymerase III subunit delta'; Validated
411	PRK14969	527	58	33.6	21	[            ---                                  ]	PRK14969	DNA polymerase III subunits gamma and tau; Provisional
412	PRK05563	559	46	33.5	23	[             --                                  ]	PRK05563	DNA polymerase III subunits gamma and tau; Validated
413	COG1195	363	26	33.5	22	[              -                                  ]	RecF	Recombinational DNA repair ATPase RecF
414	PRK11629	233	15	33.5	14	[              -                                  ]	lolD	lipoprotein transporter ATP-binding subunit; Provisional
415	COG1674	858	129	33.2	51	[              -------                            ]	FtsK	DNA segregation ATPase FtsK/SpoIIIE and related proteins
416	pfam08494	186	132	33.2	3.6E+02	[                        --------                 ]	DEAD_assoc	DEAD/H associated. This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain (pfam00270) and the pfam00271 domain.
417	cd03251	234	15	33.1	17	[              -                                  ]	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.
418	PRK09580	248	13	33.0	20	[                                                 ]	sufC	cysteine desulfurase ATPase component; Reviewed
419	TIGR02759	566	86	32.9	44	[                        -----                    ]	TraD_Ftype	type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM).
420	PRK09694	878	31	32.6	23	[               --                                ]	PRK09694	helicase Cas3; Provisional
421	pfam14091	152	109	32.6	33	[                           ------                ]	DUF4269	Domain of unknown function (DUF4269). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved KTE sequence motif.
422	TIGR01189	198	26	32.4	17	[              -                                  ]	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.
423	COG3640	255	98	32.2	26	[              -----                              ]	CooC	CO dehydrogenase nickel-insertion accessory protein CooC1
424	TIGR01978	243	26	32.2	15	[                     -                           ]	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.
425	pfam02534	468	39	32.0	37	[              --                                 ]	T4SS-DNA_transf	Type IV secretory system Conjugative DNA transfer. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. The family contains a number of different DNA transfer proteins.
426	COG0003	322	32	31.9	23	[              -                                  ]	ArsA	Anion-transporting ATPase, ArsA/GET3 family
427	PRK13873	811	34	31.5	17	[              -                                  ]	PRK13873	conjugal transfer ATPase TrbE; Provisional
428	cd03114	148	34	31.4	24	[              --                                 ]	ArgK-like	The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
429	pfam00225	324	20	31.4	38	[              -                                  ]	Kinesin	Kinesin motor domain.
430	PRK13851	344	55	31.2	25	[              ---                                ]	PRK13851	type IV secretion system protein VirB11; Provisional
431	COG4178	604	17	31.2	16	[              -                                  ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
432	TIGR02639	730	92	30.7	33	[             -----                               ]	ClpA	ATP-dependent Clp protease ATP-binding subunit clpA.
433	pfam05729	165	54	30.3	16	[              --                                 ]	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.
434	TIGR01967	1283	264	30.2	29	[             ---------------                     ]	DEAH_box_HrpA	RNA helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB.
435	cd01122	271	14	30.2	25	[                                                 ]	GP4d_helicase	GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
436	TIGR04520	268	139	30.2	20	[              -------                            ]	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.
437	COG0552	340	110	30.0	1.3E+02	[              ------                             ]	FtsY	Signal recognition particle GTPase
438	TIGR00958	711	14	29.9	18	[              -                                  ]	3a01208	Conjugate Transporter-2 (CT2) Family protein.
439	cd01376	319	41	29.8	47	[            ---                                  ]	KISc_KID_like	Kinesin motor domain, KIF22/Kid-like subgroup. Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward.
440	PRK13833	323	68	29.8	37	[             ----                                ]	PRK13833	conjugal transfer protein TrbB; Provisional
441	PRK04914	956	151	29.7	35	[              --------                           ]	PRK04914	ATP-dependent helicase HepA; Validated
442	cd03261	235	48	29.6	19	[              --                                 ]	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.
443	COG1074	1139	39	29.4	32	[              --                                 ]	RecB	ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains)
444	PRK00698	205	46	29.4	24	[              --                                 ]	tmk	thymidylate kinase; Validated
445	COG1855	604	51	29.4	19	[              --                                 ]	COG1855	Predicted ATPase, PilT family
446	COG3842	352	29	29.1	19	[                           --                    ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
447	COG4988	559	96	29.0	20	[              -----                              ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
448	cd10337	136	66	28.9	49	[                      ---                        ]	SH2_BCAR3	Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3. BCAR3 is part of a growing family of guanine nucleotide exchange factors is responsible for activation of Ras-family GTPases, including Sos1 and 2, GRF1 and 2, CalDAG-GEF/GRP1-4, C3G, cAMP-GEF/Epac 1 and 2, PDZ-GEFs, MR-GEF, RalGDS family members, RalGPS, RasGEF, Smg GDS, and phospholipase C(epsilon). 12102558 21262352 BCAR3 binds to the carboxy-terminus of BCAR1/p130Cas, a focal adhesion adapter protein. Over expression of BCAR1 (p130Cas) and BCAR3 induces estrogen independent growth in normally estrogen-dependent cell lines. They have been linked to resistance to anti-estrogens in breast cancer, Rac activation, and cell motility, though the BCAR3/p130Cas complex is not required for this activity in BCAR3. Many BCAR3-mediated signaling events in epithelial and mesenchymal cells are independent of p130Cas association. Structurally these proteins contain a single SH2 domain upstream of their RasGEF domain, which is responsible for the ability of BCAR3 to enhance p130Cas over-expression-induced migration. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
449	TIGR00073	208	27	28.9	26	[              -                                  ]	hypB	hydrogenase accessory protein HypB. A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs.
450	PRK03992	389	24	28.7	27	[             -                                   ]	PRK03992	proteasome-activating nucleotidase; Provisional
451	COG4559	259	15	28.3	19	[              -                                  ]	COG4559	ABC-type hemin transport system, ATPase component
452	cd03295	242	15	28.2	24	[                                                 ]	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.
453	PRK06547	172	22	28.1	36	[             -                                   ]	PRK06547	hypothetical protein; Provisional
454	cd01126	384	38	27.9	32	[              --                                 ]	TraG_VirD4	The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.
455	cd03248	226	63	27.9	18	[              ---                                ]	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.
456	PRK14701	1638	131	27.7	1.8E+02	[                        --------                 ]	PRK14701	reverse gyrase; Provisional
457	PRK14277	386	48	27.6	42	[                                  --             ]	PRK14277	chaperone protein DnaJ; Provisional
458	COG2519	256	34	27.6	66	[                        -                        ]	Gcd14	tRNA A58 N-methylase Trm61
459	pfam02492	178	14	27.5	22	[                                                 ]	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.
460	COG1117	253	121	27.5	20	[                  -------                        ]	PstB	ABC-type phosphate transport system, ATPase component
461	TIGR01016	386	78	27.2	1.5E+02	[                           -----                 ]	sucCoAbeta	succinyl-CoA synthetase, beta subunit. This model is designated subfamily because it does not discriminate the ADP-forming enzyme ((EC 6.2.1.5) from the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half is described by the CoA-ligases model (pfam00549). The C-terminal half is described by the ATP-grasp model (pfam02222). This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling
462	TIGR00611	365	21	27.1	28	[              -                                  ]	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).
463	TIGR01351	210	25	27.1	42	[              -                                  ]	adk	adenylate kinase. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is SP|Q9UIJ7, a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
464	pfam08442	202	78	26.9	1.3E+02	[                           -----                 ]	ATP-grasp_2	ATP-grasp domain.
465	pfam01926	114	15	26.9	22	[              -                                  ]	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.
466	PRK00080	328	260	26.9	22	[             ---------------                     ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
467	cd05779	204	108	26.5	32	[                                        ------   ]	DNA_polB_epsilon_exo	DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. The exonuclease domain of family-B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation
468	cd03222	177	59	26.5	29	[              ---                                ]	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.
469	cd01779	105	48	26.5	58	[                                            ---  ]	Myosin_IXb_RA	ubitquitin-like domain of Myosin_IXb_RA. Myosin_IXb_RA RasGTP binding domain from guanine nucleotide exchange factors. In some proteins the domain acts as a RasGTP effector (AF6, canoe and RalGDS, for example), but in other cases it may not bind to RasGTP at all.
470	PRK10867	433	87	26.3	1.4E+02	[              ----                               ]	PRK10867	signal recognition particle protein; Provisional
471	PRK07261	171	41	26.3	31	[              --                                 ]	PRK07261	topology modulation protein; Provisional
472	COG2274	709	71	26.2	21	[              ---                                ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
473	pfam10412	386	59	26.2	36	[              ---                                ]	TrwB_AAD_bind	Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export.
474	pfam00503	317	17	26.2	40	[              -                                  ]	G-alpha	G-protein alpha subunit. G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA.
475	PRK12904	830	82	26.2	41	[                        ----                     ]	PRK12904	preprotein translocase subunit SecA; Reviewed
476	pfam03193	161	16	26.0	25	[                                                 ]	DUF258	Protein of unknown function, DUF258.
477	TIGR00972	247	164	25.9	22	[              -----------                        ]	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.
478	PRK13637	287	133	25.9	20	[              -------                            ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
479	PRK13645	289	19	25.9	35	[              -                                  ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
480	PRK14247	250	83	25.9	25	[                    -----                        ]	PRK14247	phosphate ABC transporter ATP-binding protein; Provisional
481	cd01561	291	119	25.8	1.1E+02	[         ------                                  ]	CBS_like	CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine.
482	TIGR01822	393	30	25.8	60	[                                             -   ]	2am3keto_CoA	glycine C-acetyltransferase. This model represents a narrowly defined clade of animal and bacterial (almost exclusively Proteobacterial) 2-amino-3-ketobutyrate--CoA ligase, now called glycine C-acetyltransferase. This enzyme can act in threonine catabolism. The closest homolog from Bacillus subtilis, and sequences like it, may be functionally equivalent but were not included in the model because of difficulty in finding reports of function.
483	COG0667	316	122	25.8	1.8E+02	[                        --------                 ]	Tas	Predicted oxidoreductase (related to aryl-alcohol dehydrogenase)
484	PRK13538	204	79	25.7	26	[              ---                                ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
485	TIGR03689	512	50	25.7	50	[            ---                                  ]	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.
486	PRK00064	361	28	25.7	28	[              -                                  ]	recF	recombination protein F; Reviewed
487	cd03765	236	11	25.5	30	[                                                 ]	proteasome_beta_bacterial	Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
488	TIGR02782	299	70	25.5	39	[             ----                                ]	TrbB_P	P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
489	PRK12309	391	122	25.4	78	[                     -------                     ]	PRK12309	transaldolase/EF-hand domain-containing protein; Provisional
490	pfam09439	181	16	25.3	26	[              -                                  ]	SRPRB	Signal recognition particle receptor beta subunit. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane.
491	cd05579	272	29	25.1	33	[                  --                             ]	STKc_MAST_like	Catalytic domain of Microtubule-associated serine/threonine (MAST) kinase-like proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes MAST kinases, MAST-like (MASTL) kinases (also called greatwall kinase or Gwl), and fungal kinases with similarity to Saccharomyces cerevisiae Rim15 and Schizosaccharomyces pombe cek1. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. MASTL kinases carry only a catalytic domain which contains a long insert relative to other kinases. The fungal kinases in this subfamily harbor other domains in addition to a central catalytic domain, which like in MASTL, also contains an insert relative to MAST kinases. Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. MAST kinases are cytoskeletal associated kinases of unknown function that are also expressed at neuromuscular junctions and postsynaptic densities. MASTL/Gwl is involved in the regulation of mitotic entry, mRNA stabilization, and DNA checkpoint recovery. The fungal proteins Rim15 and cek1 are involved in the regulation of meiosis and mitosis, respectively. The MAST-like kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
492	PRK14528	186	25	24.9	49	[              -                                  ]	PRK14528	adenylate kinase; Provisional
493	PRK12903	925	114	24.9	60	[                        -----                    ]	secA	preprotein translocase subunit SecA; Reviewed
494	cd03256	241	163	24.9	28	[              -----------                        ]	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.
495	COG3854	308	37	24.8	48	[             --                                  ]	SpoIIIAA	Stage III sporulation protein SpoIIIAA
496	cd03218	232	121	24.7	35	[              --------                           ]	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.
497	cd01125	239	18	24.6	42	[              -                                  ]	repA	Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
498	TIGR02324	224	14	24.6	27	[                                                 ]	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.
499	PRK13652	277	38	24.5	29	[              --                                 ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
500	pfam00581	106	83	24.5	1.3E+02	[                      ----                       ]	Rhodanese	Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.