match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam04465	1025	935	100.0	1E-82	[   ----------------------------------------------]	DUF499	Protein of unknown function (DUF499). Family of uncharacterized hypothetical prokaryotic proteins.
2	COG1483	774	712	100.0	1.6E-49	[---------------------------------                ]	COG1483	Predicted ATPase, AAA+ superfamily
3	pfam13401	124	111	97.5	0.00051	[  ------                                         ]	AAA_22	AAA domain.
4	cd00009	151	27	97.1	0.0008	[  -                                              ]	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.
5	pfam13191	156	26	96.8	0.0028	[  -                                              ]	AAA_16	AAA ATPase domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
6	COG1474	366	180	96.6	0.01	[ ---------                                       ]	CDC6	Cdc6-related protein, AAA superfamily ATPase
7	pfam09820	279	206	96.6	0.016	[  ---------                                      ]	AAA-ATPase_like	Predicted AAA-ATPase. This family contains many hypothetical bacterial proteins. This family was previously the N-terminal part of the Pfam DUF1703 (pfam08011) family before it was split into two. This region is predicted to be an AAA-ATPase domain.
8	pfam00006	213	133	95.8	0.072	[  -------                                        ]	ATP-synt_ab	ATP synthase alpha/beta family, nucleotide-binding domain. This family includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.
9	COG1484	254	26	94.5	0.024	[  -                                              ]	DnaC	DNA replication protein DnaC
10	pfam13207	114	23	94.5	0.029	[  -                                              ]	AAA_17	AAA domain.
11	COG0593	408	93	94.3	0.24	[      ----                                       ]	DnaA	Chromosomal replication initiation ATPase DnaA
12	pfam00931	287	99	94.3	0.098	[  -----                                          ]	NB-ARC	NB-ARC domain.
13	cd01120	165	125	93.5	0.78	[  ------                                         ]	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.
14	pfam03266	168	129	93.2	0.1	[  -------                                        ]	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.
15	COG0541	451	291	92.7	0.36	[-------------                                    ]	Ffh	Signal recognition particle GTPase
16	pfam13476	203	26	92.6	0.09	[  -                                              ]	AAA_23	AAA domain.
17	PRK13695	174	133	92.5	0.03	[  -------                                        ]	PRK13695	putative NTPase; Provisional
18	TIGR02928	365	15	92.4	0.66	[  -                                              ]	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.
19	TIGR03420	226	25	92.1	0.13	[  -                                              ]	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.
20	PRK00411	394	141	92.0	2.8	[ -------                                         ]	cdc6	cell division control protein 6; Reviewed
21	cd03115	173	114	91.3	0.5	[  -----                                          ]	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.
22	cd03225	211	146	91.2	0.15	[  --------                                       ]	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.
23	PRK08116	268	23	90.9	0.13	[  -                                              ]	PRK08116	hypothetical protein; Validated
24	PRK06835	329	38	90.8	0.23	[ --                                              ]	PRK06835	DNA replication protein DnaC; Validated
25	PRK13342	413	206	90.0	1.2	[-----------                                      ]	PRK13342	recombination factor protein RarA; Reviewed
26	PRK10867	433	285	89.6	1.2	[-------------                                    ]	PRK10867	signal recognition particle protein; Provisional
27	PRK14974	336	157	89.4	1.8	[ -------                                         ]	PRK14974	cell division protein FtsY; Provisional
28	TIGR00362	437	25	89.3	0.22	[  -                                              ]	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).
29	TIGR00959	428	272	89.3	2.5	[ ------------                                    ]	ffh	signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
30	pfam00448	195	129	89.1	0.78	[  ------                                         ]	SRP54	SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
31	pfam00004	131	22	88.8	0.25	[  -                                              ]	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.
32	pfam04851	103	26	88.1	0.86	[  -                                              ]	ResIII	Type III restriction enzyme, res subunit.
33	cd03255	218	21	87.9	0.28	[  -                                              ]	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.
34	pfam13304	144	22	87.7	0.35	[  -                                              ]	AAA_21	AAA domain.
35	pfam01580	201	135	87.7	3.5	[  ------                                         ]	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.
36	COG1136	226	25	87.7	0.3	[  -                                              ]	LolD	ABC-type lipoprotein export system, ATPase component
37	pfam00308	219	59	87.6	0.3	[        --                                       ]	Bac_DnaA	Bacterial dnaA protein.
38	pfam09848	348	119	87.4	1.1	[  ------                                         ]	DUF2075	Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function.
39	TIGR03185	650	120	87.3	8.9	[        ------                                   ]	DNA_S_dndD	DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
40	COG1120	258	57	87.0	0.28	[ ---                                             ]	FepC	ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component
41	cd00267	157	25	86.7	0.43	[  -                                              ]	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.
42	pfam00005	150	31	86.7	0.32	[  -                                              ]	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.
43	cd01364	353	34	86.6	0.29	[ --                                              ]	KISc_BimC_Eg5	Kinesin motor domain, BimC/Eg5 spindle pole proteins. Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division. 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.
44	pfam13086	183	22	86.5	0.67	[  -                                              ]	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.
45	pfam07693	301	30	86.5	1.9	[  -                                              ]	KAP_NTPase	KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.
46	cd01363	170	39	86.4	0.39	[ --                                              ]	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.
47	pfam12846	298	57	86.3	1.4	[  ---                                            ]	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.
48	cd00046	144	130	86.3	3	[  ------                                         ]	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.
49	PRK08084	235	58	86.3	0.59	[ ---                                             ]	PRK08084	DNA replication initiation factor; Provisional
50	PRK08939	306	23	86.2	0.51	[  -                                              ]	PRK08939	primosomal protein DnaI; Reviewed
51	COG1157	441	128	86.1	4	[  -------                                        ]	FliI	Flagellar biosynthesis/type III secretory pathway ATPase
52	pfam10236	293	133	85.6	3.4	[  ------                                         ]	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).
53	TIGR03864	236	76	85.6	0.8	[ -----                                           ]	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.
54	COG2256	436	237	85.5	0.84	[-------------                                    ]	RarA	Replication-associated recombination protein RarA (DNA-dependent ATPase)
55	TIGR00954	659	37	85.3	0.38	[ --                                              ]	3a01203	Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein.
56	cd03223	166	38	85.3	0.31	[ --                                              ]	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).
57	pfam13238	128	21	85.2	0.49	[  -                                              ]	AAA_18	AAA domain.
58	COG3598	402	142	85.1	2.7	[ -------                                         ]	RepA	RecA-family ATPase
59	pfam01935	219	28	85.0	0.45	[  -                                              ]	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.
60	PRK08181	269	18	84.9	0.64	[  -                                              ]	PRK08181	transposase; Validated
61	pfam01637	223	27	84.8	3.3	[  -                                              ]	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.
62	COG0552	340	146	84.7	1	[ -------                                         ]	FtsY	Signal recognition particle GTPase
63	COG1122	235	146	84.4	0.96	[  --------                                       ]	EcfA2	Energy-coupling factor transporter ATP-binding protein EcfA2
64	cd01130	186	47	84.2	1.1	[ --                                              ]	VirB11-like_ATPase	Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
65	PRK08727	233	39	84.0	0.93	[ --                                              ]	PRK08727	hypothetical protein; Validated
66	cd03228	171	33	83.9	0.5	[  -                                              ]	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.
67	pfam07728	135	26	83.8	0.76	[  -                                              ]	AAA_5	AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
68	COG0464	494	109	83.7	0.69	[  ------                                         ]	SpoVK	AAA+-type ATPase, SpoVK/Ycf46/Vps4 family
69	cd01136	326	155	83.6	5.6	[  ---------                                      ]	ATPase_flagellum-secretory_path_III	Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.
70	TIGR02315	243	88	83.5	0.22	[  ----                                           ]	ABC_phnC	phosphonate ABC transporter, ATP-binding protein. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.
71	pfam01695	178	97	83.3	0.84	[  -----                                          ]	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.
72	PRK00149	450	107	83.3	0.71	[      -----                                      ]	dnaA	chromosomal replication initiation protein; Reviewed
73	PRK13539	207	37	83.3	0.44	[ --                                              ]	PRK13539	cytochrome c biogenesis protein CcmA; Provisional
74	cd02019	69	22	83.1	0.92	[  -                                              ]	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.
75	cd03214	180	35	82.8	0.51	[  -                                              ]	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.
76	PRK06762	166	97	82.6	2.1	[  -----                                          ]	PRK06762	hypothetical protein; Provisional
77	cd01367	328	30	82.6	0.57	[  -                                              ]	KISc_KIF2_like	Kinesin motor domain, KIF2-like group. Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. 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 this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-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 (KIF2 may be slower). 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.
78	COG2884	223	24	82.6	0.85	[  -                                              ]	FtsE	ABC-type ATPase involved in cell division
79	TIGR04521	277	63	82.4	1.1	[  ---                                            ]	ECF_ATPase_2	energy-coupling factor transporter ATPase. Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the downstream member of the pair of ECF ATPases in Firmicutes and Mollicutes.
80	PRK03992	389	25	82.2	0.65	[  -                                              ]	PRK03992	proteasome-activating nucleotidase; Provisional
81	COG1222	406	51	82.1	0.78	[ --                                              ]	RPT1	ATP-dependent 26S proteasome regulatory subunit
82	pfam13555	60	24	82.0	1.2	[  -                                              ]	AAA_29	P-loop containing region of AAA domain.
83	pfam00225	324	30	81.9	0.75	[  -                                              ]	Kinesin	Kinesin motor domain.
84	PRK12422	445	34	81.6	1.2	[  -                                              ]	PRK12422	chromosomal replication initiation protein; Provisional
85	COG1121	254	22	81.4	0.9	[  -                                              ]	ZnuC	ABC-type Mn2+/Zn2+ transport system, ATPase component
86	TIGR02673	214	81	81.2	0.87	[  ---                                            ]	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.
87	PRK04182	180	25	81.1	1.4	[  -                                              ]	PRK04182	cytidylate kinase; Provisional
88	TIGR01613	304	60	80.5	2.6	[ --                                              ]	primase_Cterm	phage/plasmid primase, P4 family, C-terminal domain. This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.
89	COG3845	501	118	80.4	3.1	[  -----                                          ]	YufO	ABC-type uncharacterized transport system, ATPase component
90	PRK05541	176	25	80.2	2.9	[  -                                              ]	PRK05541	adenylylsulfate kinase; Provisional
91	COG1485	367	129	79.9	1.2	[  ------                                         ]	YhcM	Predicted ATPase
92	COG1223	368	28	79.8	0.91	[  -                                              ]	COG1223	Predicted ATPase, AAA+ superfamily
93	pfam13245	72	26	79.8	1.6	[  -                                              ]	AAA_19	Part of AAA domain.
94	TIGR02546	422	51	79.7	11	[      ---                                        ]	III_secr_ATP	type III secretion apparatus H+-transporting two-sector ATPase.
95	PRK09270	229	25	79.5	1.8	[  -                                              ]	PRK09270	nucleoside triphosphate hydrolase domain-containing protein; Reviewed
96	cd00106	326	30	79.3	1	[  -                                              ]	KISc	Kinesin motor domain. Kinesin motor domain. 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), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-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.
97	COG0563	178	26	79.3	1.8	[  -                                              ]	Adk	Adenylate kinase or related kinase
98	TIGR00064	277	123	79.1	2.5	[  ------                                         ]	ftsY	signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
99	cd03235	213	21	79.1	1.2	[  -                                              ]	ABC_Metallic_Cations	ATP-binding cassette domain of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.
100	cd03221	144	33	79.0	0.84	[  -                                              ]	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.
101	cd03230	173	142	78.8	1.3	[  --------                                       ]	ABC_DR_subfamily_A	ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A. This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
102	COG2255	332	49	78.6	2.9	[ --                                              ]	RuvB	Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit
103	cd01370	345	27	78.5	0.86	[  -                                              ]	KISc_KIP3_like	Kinesin motor domain, KIP3-like subgroup. Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. 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.
104	COG1116	248	21	78.5	1.3	[  -                                              ]	TauB	ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
105	COG2805	353	157	78.4	1.4	[ ----------                                      ]	PilT	Tfp pilus assembly protein PilT, pilus retraction ATPase
106	TIGR01186	363	39	78.3	2	[  -                                              ]	proV	glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature.
107	TIGR03496	411	124	78.2	18	[      -------                                    ]	FliI_clade1	flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
108	COG5008	375	34	77.9	1.3	[ --                                              ]	PilU	Tfp pilus assembly protein, ATPase PilU
109	PRK00771	437	285	77.8	6.8	[ --------------                                  ]	PRK00771	signal recognition particle protein Srp54; Provisional
110	cd03293	220	21	77.7	1.4	[  -                                              ]	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.
111	pfam13671	143	20	77.5	1.4	[  -                                              ]	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.
112	PRK08903	227	28	77.5	1.8	[  -                                              ]	PRK08903	DnaA regulatory inactivator Hda; Validated
113	COG1061	442	50	77.4	4.1	[ --                                              ]	SSL2	Superfamily II DNA or RNA helicase
114	cd03244	221	37	77.3	1.5	[ --                                              ]	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.
115	COG0419	908	29	77.0	1.6	[  -                                              ]	SbcC	DNA repair exonuclease SbcCD ATPase subunit
116	pfam00910	105	21	77.0	1.6	[  -                                              ]	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.
117	pfam13479	201	19	76.4	0.83	[  -                                              ]	AAA_24	AAA domain. This AAA domain is found in a wide variety of presumed phage proteins.
118	PRK00080	328	50	76.3	3.4	[ --                                              ]	ruvB	Holliday junction DNA helicase RuvB; Reviewed
119	COG1224	450	28	75.8	2.3	[  -                                              ]	TIP49	DNA helicase TIP49, TBP-interacting protein
120	COG3451	796	84	75.4	2.4	[  ---                                            ]	VirB4	Type IV secretory pathway, VirB4 component
121	cd03292	214	22	75.4	1.8	[  -                                              ]	ABC_FtsE_transporter	ATP-binding cassette domain of the cell division transporter. FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane. The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.
122	COG0470	325	28	75.4	2.2	[  -                                              ]	HolB	DNA polymerase III, delta prime subunit
123	COG5635	824	104	75.3	3.9	[  -----                                          ]	COG5635	Predicted NTPase, NACHT family domain
124	COG4559	259	23	75.1	1.6	[  -                                              ]	COG4559	ABC-type hemin transport system, ATPase component
125	cd03264	211	24	75.1	1.5	[  -                                              ]	ABC_drug_resistance_like	ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
126	COG3839	338	23	75.1	1.8	[  -                                              ]	MalK	ABC-type sugar transport system, ATPase component
127	cd03253	236	35	75.0	1.6	[ --                                              ]	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.
128	COG4167	267	55	74.7	2.2	[ --                                              ]	SapF	ABC-type antimicrobial peptide transport system, ATPase component
129	PRK05342	412	56	74.7	2	[ --                                              ]	clpX	ATP-dependent protease ATP-binding subunit ClpX; Provisional
130	cd01376	319	29	74.6	1.1	[ --                                              ]	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.
131	PRK10416	318	207	74.5	3.9	[---------                                        ]	PRK10416	signal recognition particle-docking protein FtsY; Provisional
132	COG1126	240	24	74.3	1.9	[  -                                              ]	GlnQ	ABC-type polar amino acid transport system, ATPase component
133	PRK13634	290	64	73.8	1.8	[       ---                                       ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
134	TIGR01242	364	25	73.6	1.8	[  -                                              ]	26Sp45	26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
135	TIGR02173	171	25	73.5	2.7	[  -                                              ]	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.
136	COG4988	559	141	73.3	1.9	[  ------                                         ]	CydD	ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components
137	COG1119	257	148	73.1	2.2	[  ------                                         ]	ModF	ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA
138	TIGR03922	557	51	73.0	5.6	[ --                                              ]	T7SS_EccA	type VII secretion AAA-ATPase EccA. This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc.
139	cd04170	268	111	72.7	5.7	[  -----                                          ]	EF-G_bact	Elongation factor G (EF-G) family. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members.
140	TIGR01420	343	155	72.6	2.3	[  ---------                                      ]	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.
141	cd03231	201	150	72.5	2.3	[ -------                                         ]	ABC_CcmA_heme_exporter	Cytochrome c biogenesis ATP-binding export protein. CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperon that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.
142	cd03220	224	34	72.5	1.7	[  -                                              ]	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.
143	pfam08477	118	27	72.3	2.3	[  -                                              ]	Miro	Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis.
144	COG1100	219	22	72.2	2.4	[  -                                              ]	Gem1	GTPase SAR1 family domain
145	cd03254	229	26	72.1	2.6	[  -                                              ]	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.
146	TIGR02868	530	140	72.0	2.2	[ -------                                         ]	CydC	thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.
147	cd04105	202	32	71.5	3.7	[  -                                              ]	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.
148	cd01673	193	20	71.2	3.3	[  -                                              ]	dNK	Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
149	cd01898	170	24	70.9	2	[  -                                              ]	Obg	Obg GTPase. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain.
150	pfam13521	162	21	70.8	2.8	[  -                                              ]	AAA_28	AAA domain.
151	pfam03969	361	29	70.7	2.9	[  -                                              ]	AFG1_ATPase	AFG1-like ATPase. This family of proteins contains a P-loop motif and are predicted to be ATPases.
152	cd03216	163	39	70.6	2.3	[  --                                             ]	ABC_Carb_Monos_I	First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
153	cd03251	234	35	70.5	2.6	[ --                                              ]	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.
154	pfam01926	114	19	70.5	2.9	[  -                                              ]	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.
155	cd01851	224	21	70.4	2.5	[  -                                              ]	GBP	Guanylate-binding protein (GBP) family (N-terminal domain). Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach.
156	cd03295	242	42	70.4	2.8	[  --                                             ]	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.
157	pfam13654	509	36	70.1	36	[ --                                              ]	AAA_32	AAA domain. This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop.
158	COG1131	293	23	70.1	2.8	[  -                                              ]	CcmA	ABC-type multidrug transport system, ATPase component
159	cd03259	213	24	70.0	2.9	[  -                                              ]	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.
160	PRK13641	287	75	69.9	5.2	[ -----                                           ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
161	cd03262	213	21	69.8	2.8	[  -                                              ]	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.
162	cd00464	154	25	69.6	3.4	[  -                                              ]	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.
163	cd01131	198	136	69.6	3.6	[  --------                                       ]	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.
164	TIGR00382	413	100	69.5	5	[ -----                                           ]	clpX	endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
165	COG1674	858	130	69.5	19	[  ------                                         ]	FtsK	DNA segregation ATPase FtsK/SpoIIIE and related proteins
166	COG1936	180	31	69.5	4	[  -                                              ]	Fap7	Broad-specificity NMP kinase
167	COG3842	352	27	69.4	2.8	[  -                                              ]	PotA	ABC-type Fe3+/spermidine/putrescine transport systems, ATPase components
168	PRK03695	248	38	69.4	2.8	[  --                                             ]	PRK03695	vitamin B12-transporter ATPase; Provisional
169	PRK13548	258	23	69.3	2.2	[  -                                              ]	hmuV	hemin importer ATP-binding subunit; Provisional
170	cd03301	213	24	69.3	3	[  -                                              ]	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.
171	PRK11231	255	35	69.3	3	[ --                                              ]	fecE	iron-dicitrate transporter ATP-binding subunit; Provisional
172	TIGR03499	282	20	69.2	6.1	[  -                                              ]	FlhF	flagellar biosynthetic protein FlhF.
173	cd03219	236	157	69.2	2.2	[  --------                                       ]	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).
174	cd01849	146	25	68.7	2.1	[  -                                              ]	YlqF_related_GTPase	Circularly permuted YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases.
175	cd01368	345	31	68.7	2.3	[ --                                              ]	KISc_KIF23_like	Kinesin motor domain, KIF23-like subgroup. Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role 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.
176	TIGR03015	269	222	68.7	3.9	[  ----------                                     ]	pepcterm_ATPase	putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
177	pfam00437	273	26	68.7	3.4	[  -                                              ]	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.
178	cd03224	222	139	68.3	3.4	[  -------                                        ]	ABC_TM1139_LivF_branched	ATP-binding cassette domain of branched-chain amino acid transporter. LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.
179	COG1132	567	130	68.3	2.7	[  ------                                         ]	MdlB	ABC-type multidrug transport system, ATPase and permease component
180	COG0410	237	136	68.1	3.3	[  -------                                        ]	LivF	ABC-type branched-chain amino acid transport system, ATPase component
181	cd00882	161	19	67.4	3	[  -                                              ]	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.
182	PRK11701	258	31	67.4	3.6	[  -                                              ]	phnK	phosphonate C-P lyase system protein PhnK; Provisional
183	cd03247	178	116	67.3	3.5	[ ------                                          ]	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.
184	PRK07261	171	25	67.1	6.1	[  -                                              ]	PRK07261	topology modulation protein; Provisional
185	PRK06921	266	32	66.9	8.5	[ --                                              ]	PRK06921	hypothetical protein; Provisional
186	PRK13549	506	99	66.8	3	[  ------                                         ]	PRK13549	xylose transporter ATP-binding subunit; Provisional
187	COG0714	329	26	66.7	4.3	[  -                                              ]	MoxR	MoxR-like ATPase
188	cd01918	149	23	66.6	3.6	[  -                                              ]	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.
189	COG1134	249	32	66.5	3.7	[  -                                              ]	TagH	ABC-type polysaccharide/polyol phosphate transport system, ATPase component
190	COG1125	309	39	66.3	3.6	[  --                                             ]	OpuBA	ABC-type proline/glycine betaine transport system, ATPase component
191	cd03294	269	23	66.2	3.6	[  -                                              ]	ABC_Pro_Gly_Betaine	ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system. This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
192	COG1102	179	25	66.2	5.4	[  -                                              ]	CmkB	Cytidylate kinase
193	COG4586	325	53	66.1	4.4	[ --                                              ]	COG4586	ABC-type uncharacterized transport system, ATPase component
194	cd01371	334	23	66.0	2.7	[  -                                              ]	KISc_KIF3	Kinesin motor domain, kinesins II or KIF3_like proteins. Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and 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 this group 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.
195	PRK11147	635	25	65.9	3.9	[  -                                              ]	PRK11147	ABC transporter ATPase component; Reviewed
196	cd03249	238	33	65.5	3.2	[ --                                              ]	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.
197	COG1219	408	101	65.5	7	[ -----                                           ]	ClpX	ATP-dependent protease Clp, ATPase subunit
198	TIGR01243	733	35	65.5	4.3	[  -                                              ]	CDC48	AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
199	COG0468	279	94	65.5	12	[  -----                                          ]	RecA	RecA/RadA recombinase
200	COG0488	530	38	65.4	2.5	[ --                                              ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
201	TIGR01618	220	16	65.1	3.2	[  -                                              ]	phage_P_loop	phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
202	PRK11174	588	35	64.6	4.1	[  -                                              ]	PRK11174	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
203	cd03229	178	23	64.5	4.6	[  -                                              ]	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.
204	PRK11784	345	36	64.3	7.4	[ --                                              ]	PRK11784	tRNA 2-selenouridine synthase; Provisional
205	TIGR04520	268	80	64.3	4.3	[       ---                                       ]	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.
206	cd01393	226	25	64.1	4.2	[  -                                              ]	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.
207	TIGR03928	1296	66	64.1	12	[      ---                                        ]	T7_EssCb_Firm	type VII secretion protein EssC, C-terminal domain. This model describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria.
208	PRK11650	356	41	63.9	4.3	[  --                                             ]	ugpC	glycerol-3-phosphate transporter ATP-binding subunit; Provisional
209	cd03261	235	25	63.9	4.4	[  -                                              ]	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.
210	COG0467	260	38	63.9	7.1	[ --                                              ]	RAD55	RecA-superfamily ATPase, KaiC/GvpD/RAD55 family
211	cd03256	241	26	63.9	4.4	[  -                                              ]	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.
212	cd03246	173	32	63.8	3.2	[  -                                              ]	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.
213	PRK13538	204	144	63.8	3.1	[ --------                                        ]	PRK13538	cytochrome c biogenesis protein CcmA; Provisional
214	cd01366	329	33	63.7	4.2	[ --                                              ]	KISc_C_terminal	Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. 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 this subgroup the motor domain is found at the C-terminus (C-type). C-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.
215	TIGR03608	206	22	63.7	4.8	[  -                                              ]	L_ocin_972_ABC	putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.
216	pfam06414	194	145	63.6	34	[  -------                                        ]	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.
217	pfam13481	192	22	63.3	5.6	[  -                                              ]	AAA_25	AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins.
218	cd03260	227	33	63.0	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).
219	cd03227	162	31	62.9	6.3	[  -                                              ]	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.
220	COG1127	263	35	62.7	2.7	[ --                                              ]	MlaF	ABC-type transporter Mla maintaining outer membrane lipid asymmetry, ATPase component MlaF
221	TIGR00635	305	49	62.5	11	[ --                                              ]	ruvB	Holliday junction DNA helicase, RuvB subunit. All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
222	COG3910	233	35	62.5	7.2	[  -                                              ]	COG3910	Predicted ATPase
223	PRK10733	644	61	62.4	8.4	[---                                              ]	hflB	ATP-dependent metalloprotease; Reviewed
224	TIGR03263	179	24	62.3	2.6	[  -                                              ]	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.
225	PRK12299	335	23	62.3	3.2	[  -                                              ]	obgE	GTPase CgtA; Reviewed
226	COG1124	252	34	62.2	5	[ --                                              ]	DppF	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
227	pfam06068	395	37	62.0	6.8	[ --                                              ]	TIP49	TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.
228	PRK10771	232	30	61.8	4.3	[  -                                              ]	thiQ	thiamine transporter ATP-binding subunit; Provisional
229	pfam05970	362	37	61.7	6.9	[ --                                              ]	PIF1	PIF1-like helicase. This family includes homologues of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.
230	COG0606	490	46	61.6	4	[  --                                             ]	YifB	Predicted ATPase with chaperone activity
231	cd03238	176	118	61.5	18	[  -----                                          ]	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.
232	TIGR02324	224	35	61.2	4.4	[ --                                              ]	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.
233	COG3950	440	49	61.1	6.5	[  --                                             ]	COG3950	Predicted ATP-binding protein involved in virulence
234	TIGR01026	440	239	60.9	48	[  --------------                                 ]	fliI_yscN	ATPase, FliI/YscN family. This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.
235	PRK06315	442	158	60.8	34	[  ---------                                      ]	PRK06315	type III secretion system ATPase; Provisional
236	PRK05922	434	132	60.8	9.6	[  -------                                        ]	PRK05922	type III secretion system ATPase; Validated
237	cd01850	275	21	60.6	5.6	[  -                                              ]	CDC_Septin	CDC/Septin GTPase family. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
238	cd03279	213	27	60.5	7.2	[  -                                              ]	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.
239	COG2804	500	135	60.5	6.4	[  --------                                       ]	PulE	Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB
240	COG0488	530	25	60.5	5.2	[  -                                              ]	Uup	ATPase components of ABC transporters with duplicated ATPase domains
241	PRK13341	725	281	60.3	5	[---------------                                  ]	PRK13341	recombination factor protein RarA/unknown domain fusion protein; Reviewed
242	PRK15112	267	58	60.2	6.7	[ --                                              ]	PRK15112	antimicrobial peptide ABC system ATP-binding protein SapF; Provisional
243	COG3638	258	23	60.2	5.6	[  -                                              ]	PhnC	ABC-type phosphate/phosphonate transport system, ATPase component
244	pfam13166	713	24	60.1	5.3	[  -                                              ]	AAA_13	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.
245	pfam13604	195	25	59.8	8.1	[  -                                              ]	AAA_30	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
246	cd03300	232	62	59.7	5.8	[       --                                        ]	ABC_PotA_N	ATP-binding cassette domain of the polyamine transporter. PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
247	pfam05707	183	32	59.6	8.2	[      -                                          ]	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
248	TIGR03719	552	60	59.6	2.6	[---                                              ]	ABC_ABC_ChvD	ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown.
249	cd01129	264	146	59.1	6.5	[  ---------                                      ]	PulE-GspE	PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
250	TIGR03819	340	25	59.0	5.6	[  -                                              ]	heli_sec_ATPase	helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.
251	TIGR01241	495	88	58.9	5	[      ----                                       ]	FtsH_fam	ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
252	pfam01293	451	43	58.8	6.4	[ --                                              ]	PEPCK_ATP	Phosphoenolpyruvate carboxykinase.
253	COG4604	252	25	58.8	5.6	[  -                                              ]	CeuD	ABC-type enterochelin transport system, ATPase component
254	COG4178	604	37	58.5	4.2	[ --                                              ]	YddA	ABC-type uncharacterized transport system, permease and ATPase components
255	PRK13647	274	111	58.4	4.4	[  ------                                         ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
256	PRK10247	225	36	58.4	6.2	[ --                                              ]	PRK10247	putative ABC transporter ATP-binding protein YbbL; Provisional
257	cd03257	228	31	58.1	6.4	[  -                                              ]	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.
258	cd03268	208	22	58.0	5.5	[  -                                              ]	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.
259	PRK09452	375	50	57.8	6.3	[  ---                                            ]	potA	putrescine/spermidine ABC transporter ATPase protein; Reviewed
260	cd00071	137	20	57.7	7.1	[  -                                              ]	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.
261	COG4133	209	37	57.7	4.6	[ --                                              ]	CcmA	ABC-type transport system involved in cytochrome c biogenesis, ATPase component
262	TIGR01166	190	35	57.3	6.5	[ --                                              ]	cbiO	cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.
263	COG1221	403	36	57.1	13	[ --                                              ]	PspF	Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain
264	COG4136	213	20	57.0	6.8	[  -                                              ]	YnjD	ABC-type uncharacterized transport system YnjBCD, ATPase component
265	cd03240	204	21	56.7	7.1	[  -                                              ]	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.
266	PRK00440	319	35	56.7	6.1	[  --                                             ]	rfc	replication factor C small subunit; Reviewed
267	COG1135	339	81	56.5	12	[  ---                                            ]	AbcC	ABC-type methionine transport system, ATPase component
268	pfam03193	161	30	56.3	8.5	[  -                                              ]	DUF258	Protein of unknown function, DUF258.
269	COG0194	191	23	56.3	7.8	[  -                                              ]	Gmk	Guanylate kinase
270	PRK09087	226	22	56.2	6.6	[  -                                              ]	PRK09087	hypothetical protein; Validated
271	PRK14087	450	19	56.0	7.3	[  -                                              ]	dnaA	chromosomal replication initiation protein; Provisional
272	cd03234	226	36	55.7	7.3	[  -                                              ]	ABCG_White	White pigment protein homolog of ABCG transporter subfamily. The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners.
273	PRK11819	556	60	55.5	2.6	[---                                              ]	PRK11819	putative ABC transporter ATP-binding protein; Reviewed
274	cd03275	247	24	55.5	6.1	[  -                                              ]	ABC_SMC1_euk	ATP-binding cassette domain of eukaryotic SMC1 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).
275	COG4619	223	24	55.4	7.4	[  -                                              ]	FetA	ABC-type iron transport system FetAB, ATPase component
276	COG4175	386	24	55.3	7.1	[  -                                              ]	ProV	ABC-type proline/glycine betaine transport system, ATPase component
277	COG4987	573	57	55.2	7	[ ---                                             ]	CydC	ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components
278	COG0396	251	152	54.8	6.4	[  --------                                       ]	SufC	Fe-S cluster assembly ATPase SufC
279	PRK06936	439	128	54.6	65	[  -------                                        ]	PRK06936	type III secretion system ATPase; Provisional
280	PRK14086	617	63	54.4	8	[ --                                              ]	dnaA	chromosomal replication initiation protein; Provisional
281	COG4107	258	31	54.2	7.9	[  -                                              ]	PhnK	ABC-type phosphonate transport system, ATPase component
282	COG4181	228	19	54.1	8.1	[  -                                              ]	YbbA	Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
283	cd03226	205	22	54.1	8.4	[  -                                              ]	ABC_cobalt_CbiO_domain2	Second domain of the ATP-binding cassette component of cobalt transport system. Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
284	pfam05496	234	48	54.0	17	[ --                                              ]	RuvB_N	Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
285	TIGR01447	582	22	53.9	1.3E+02	[  -                                              ]	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.
286	PRK06761	282	46	53.9	9.6	[  ---                                            ]	PRK06761	hypothetical protein; Provisional
287	cd03213	194	20	53.9	8.1	[  -                                              ]	ABCG_EPDR	Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette superfamily. ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
288	TIGR00602	637	22	53.7	8.9	[  -                                              ]	rad24	checkpoint protein rad24. All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
289	PRK13631	320	92	53.4	6.4	[ -----                                           ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
290	pfam10923	417	127	53.3	9.3	[      ------                                     ]	DUF2791	P-loop Domain of unknown function (DUF2791). This is a family of proteins found in archaea and bacteria. This domain contains a P-loop motif suggesting it binds to a nucleotide such as ATP.
291	COG2274	709	141	53.2	7.7	[  ------                                         ]	SunT	ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain
292	cd03298	211	113	52.9	7.3	[  -----                                          ]	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.
293	TIGR01277	213	28	52.7	8.9	[  -                                              ]	thiQ	thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.
294	PRK14250	241	23	52.5	8.9	[  -                                              ]	PRK14250	phosphate ABC transporter ATP-binding protein; Provisional
295	COG1618	179	144	52.3	25	[  -------                                        ]	THEP1	Nucleoside-triphosphatase THEP1
296	PRK13764	602	24	52.2	9.5	[  -                                              ]	PRK13764	ATPase; Provisional
297	cd03250	204	51	52.2	9.2	[      --                                         ]	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.
298	cd01372	341	40	52.2	9.5	[ --                                              ]	KISc_KIF4	Kinesin motor domain, KIF4-like subfamily. Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during 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.
299	PRK09361	225	96	52.1	17	[  -----                                          ]	radB	DNA repair and recombination protein RadB; Provisional
300	COG1419	407	24	51.9	17	[  -                                              ]	FlhF	Flagellar biosynthesis GTPase FlhF
301	COG4962	355	26	51.8	8.9	[  -                                              ]	CpaF	Pilus assembly protein, ATPase of CpaF family
302	pfam03215	517	26	51.7	10	[  -                                              ]	Rad17	Rad17 cell cycle checkpoint protein.
303	PRK00300	205	23	51.6	10	[  -                                              ]	gmk	guanylate kinase; Provisional
304	cd01854	211	30	51.6	11	[  -                                              ]	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.
305	PRK14088	440	28	51.4	10	[  -                                              ]	dnaA	chromosomal replication initiation protein; Provisional
306	cd01374	321	27	51.3	7.1	[  -                                              ]	KISc_CENP_E	Kinesin motor domain, CENP-E/KIP2-like subgroup. Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during 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.
307	TIGR02633	500	74	51.3	6.8	[  -----                                          ]	xylG	D-xylose ABC transporter, ATP-binding protein. Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).
308	pfam02456	370	37	51.3	8.1	[ --                                              ]	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.
309	TIGR02903	615	190	51.3	19	[ ----------                                      ]	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.
310	PRK04195	482	40	51.1	10	[  --                                             ]	PRK04195	replication factor C large subunit; Provisional
311	TIGR02729	328	24	50.7	6.6	[  -                                              ]	Obg_CgtA	Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal.
312	cd03217	200	127	50.7	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.
313	TIGR00416	454	42	50.7	9.9	[  --                                             ]	sms	DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
314	COG5019	373	128	50.3	12	[  ------                                         ]	CDC3	Septin family protein
315	pfam13173	127	22	50.2	13	[  -                                              ]	AAA_14	AAA domain. This family of domains contain a P-loop motif that is characteristic of the AAA superfamily.
316	cd02027	149	104	50.2	10	[  -----                                          ]	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.
317	TIGR02525	372	21	50.0	9.1	[  -                                              ]	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).
318	pfam06048	285	49	50.0	35	[ --                                              ]	DUF927	Domain of unknown function (DUF927). Family of bacterial proteins of unknown function. The C-terminal half of this family contains a P-loop motif.
319	COG1204	766	128	49.6	38	[ ------                                          ]	BRR2	Replicative superfamily II helicase
320	PRK10938	490	22	49.5	4.5	[  -                                              ]	PRK10938	putative molybdenum transport ATP-binding protein ModF; Provisional
321	cd03269	210	34	49.4	10	[  -                                              ]	ABC_putative_ATPase	ATP-binding cassette domain of an uncharacterized transporter. This subgroup is related to the subfamily A transporters involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two integral membranes. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
322	COG4778	235	20	49.4	11	[  -                                              ]	PhnL	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL
323	PRK11247	257	38	49.4	12	[ --                                              ]	ssuB	aliphatic sulfonates transport ATP-binding subunit; Provisional
324	TIGR00376	636	16	49.4	6.6	[  -                                              ]	TIGR00376	DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
325	TIGR02782	299	46	49.3	12	[ --                                              ]	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.
326	TIGR02236	310	120	49.0	37	[  ------                                         ]	recomb_radA	DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
327	PRK08118	167	27	48.9	13	[  -                                              ]	PRK08118	topology modulation protein; Reviewed
328	PRK09493	240	21	48.6	12	[  -                                              ]	glnQ	glutamine ABC transporter ATP-binding protein; Reviewed
329	COG0703	172	28	48.5	15	[  -                                              ]	AroK	Shikimate kinase
330	COG1195	363	54	48.5	14	[            --                                   ]	RecF	Recombinational DNA repair ATPase RecF
331	COG5059	568	24	48.4	7.1	[  -                                              ]	KIP1	Kinesin-like protein
332	COG4608	268	132	48.4	9.5	[ -------                                         ]	AppF	ABC-type oligopeptide transport system, ATPase component
333	COG0630	312	26	48.4	13	[  -                                              ]	VirB11	Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase
334	TIGR03498	418	123	48.3	1.1E+02	[  -------                                        ]	FliI_clade3	flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.
335	cd02021	150	40	48.2	14	[  --                                             ]	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.
336	COG0572	218	25	48.2	11	[  -                                              ]	Udk	Uridine kinase
337	PRK13635	279	59	48.1	11	[       --                                        ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
338	PRK05537	568	51	47.7	18	[ --                                              ]	PRK05537	bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated
339	PRK06893	229	21	47.6	12	[  -                                              ]	PRK06893	DNA replication initiation factor; Validated
340	PRK10253	265	45	47.6	19	[  --                                             ]	PRK10253	iron-enterobactin transporter ATP-binding protein; Provisional
341	TIGR03574	249	42	47.5	18	[  --                                             ]	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.
342	COG3840	231	107	47.3	12	[  -----                                          ]	ThiQ	ABC-type thiamine transport system, ATPase component
343	COG0536	369	24	47.3	8.6	[  -                                              ]	Obg	GTPase involved in cell partioning and DNA repair
344	TIGR02982	220	21	47.2	14	[  -                                              ]	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.
345	COG1493	308	23	47.0	11	[  -                                              ]	HprK	Serine kinase of the HPr protein, regulates carbohydrate metabolism
346	pfam00735	273	75	47.0	16	[  ---                                            ]	Septin	Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
347	cd01365	361	29	46.9	8.4	[  -                                              ]	KISc_KIF1A_KIF1B	Kinesin motor domain, KIF1_like proteins. Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. 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. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively.
348	TIGR02211	221	27	46.8	13	[  -                                              ]	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.
349	pfam05673	248	43	46.7	25	[ --                                              ]	DUF815	Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function.
350	cd02023	198	27	46.7	14	[  -                                              ]	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.
351	PRK09183	259	20	46.4	14	[  -                                              ]	PRK09183	transposase/IS protein; Provisional
352	PRK13894	319	113	46.3	21	[ ------                                          ]	PRK13894	conjugal transfer ATPase TrbB; Provisional
353	COG0444	316	35	46.3	13	[  -                                              ]	DppD	ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component
354	TIGR03797	686	42	46.0	9.4	[  --                                             ]	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.
355	TIGR02857	529	35	46.0	10	[ --                                              ]	CydD	thiol reductant ABC exporter, CydD subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD
356	COG1129	500	23	45.9	12	[  -                                              ]	MglA	ABC-type sugar transport system, ATPase component
357	cd02020	147	67	45.9	15	[  ---                                            ]	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.
358	cd03267	236	25	45.9	12	[  -                                              ]	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.
359	PRK11160	574	59	45.6	13	[ ---                                             ]	PRK11160	cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
360	cd01124	187	26	45.1	16	[  -                                              ]	KaiC	KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
361	TIGR01193	708	76	45.0	14	[---                                              ]	bacteriocin_ABC	ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
362	TIGR01978	243	39	44.7	14	[        -                                        ]	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.
363	TIGR00955	617	78	44.5	16	[  ----                                           ]	3a01204	The Eye Pigment Precursor Transporter (EPP) Family protein.
364	PRK09344	526	42	44.3	15	[ --                                              ]	PRK09344	phosphoenolpyruvate carboxykinase; Provisional
365	COG3267	269	178	44.1	1.5E+02	[  ---------                                      ]	ExeA	Type II secretory pathway, component ExeA (predicted ATPase)
366	TIGR01189	198	35	44.1	11	[ --                                              ]	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.
367	COG0056	504	94	44.1	45	[  -----                                          ]	AtpA	FoF1-type ATP synthase, alpha subunit
368	PRK10789	569	85	44.0	11	[  ----                                           ]	PRK10789	putative multidrug transporter membrane\ATP-binding components; Provisional
369	COG1866	529	19	43.9	11	[            -                                    ]	PckA	Phosphoenolpyruvate carboxykinase, ATP-dependent
370	TIGR00929	785	68	43.9	17	[  ---                                            ]	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).
371	pfam08433	267	68	43.7	1.3E+02	[      ---                                        ]	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.
372	cd03263	220	172	43.6	16	[ ---------                                       ]	ABC_subfamily_A	ATP-binding cassette domain of the lipid transporters, subfamily A. The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.
373	pfam01078	207	42	43.3	15	[  --                                             ]	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.
374	COG0466	782	30	43.3	31	[  -                                              ]	Lon	ATP-dependent Lon protease, bacterial type
375	PRK08472	434	187	43.2	93	[  ----------                                     ]	fliI	flagellum-specific ATP synthase; Validated
376	PRK06526	254	19	43.1	13	[  -                                              ]	PRK06526	transposase; Provisional
377	cd03369	207	26	43.1	17	[  -                                              ]	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.
378	pfam03029	235	21	43.0	11	[  -                                              ]	ATP_bind_1	Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.
379	PRK07952	244	41	42.9	24	[ --                                              ]	PRK07952	DNA replication protein DnaC; Validated
380	COG1241	682	48	42.9	13	[           --                                    ]	Mcm2	DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family
381	TIGR02237	209	96	42.9	71	[  -----                                          ]	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).
382	COG0529	197	126	42.8	17	[  ------                                         ]	CysC	Adenylylsulfate kinase or related kinase
383	COG4615	546	34	42.7	15	[  -                                              ]	PvdE	ABC-type siderophore export system, fused ATPase and permease components
384	COG4240	300	25	42.0	42	[  -                                              ]	Tda10	Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein)
385	TIGR03689	512	19	41.9	17	[  -                                              ]	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.
386	COG5265	497	48	41.9	16	[  --                                             ]	ATM1	ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components
387	TIGR01194	555	20	41.7	15	[  -                                              ]	cyc_pep_trnsptr	cyclic peptide transporter. This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.
388	cd01123	235	96	41.6	16	[  -----                                          ]	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 .
389	PRK05703	424	20	41.5	37	[  -                                              ]	flhF	flagellar biosynthesis regulator FlhF; Validated
390	cd03239	178	23	41.3	11	[  -                                              ]	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.
391	pfam00493	330	23	41.3	16	[  -                                              ]	MCM	MCM2/3/5 family.
392	PRK11144	352	49	41.2	15	[  --                                             ]	modC	molybdate transporter ATP-binding protein; Provisional
393	TIGR01846	694	148	41.2	20	[  ------                                         ]	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.
394	TIGR02881	261	22	41.2	18	[  -                                              ]	spore_V_K	stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.
395	TIGR02323	253	30	41.0	18	[  -                                              ]	CP_lyasePhnK	phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.
396	PRK13951	488	33	40.7	20	[  -                                              ]	PRK13951	bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
397	PRK11124	242	20	40.5	18	[  -                                              ]	artP	arginine transporter ATP-binding subunit; Provisional
398	PRK06851	367	33	40.5	12	[  -                                              ]	PRK06851	hypothetical protein; Provisional
399	PRK12297	424	24	40.4	12	[  -                                              ]	obgE	GTPase CgtA; Reviewed
400	COG4618	580	35	40.2	14	[  -                                              ]	ArpD	ABC-type protease/lipase transport system, ATPase and permease components
401	cd01428	194	25	40.1	45	[  -                                              ]	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.
402	COG0411	250	22	40.1	7.6	[  -                                              ]	LivG	ABC-type branched-chain amino acid transport system, ATPase component
403	COG3911	183	20	40.0	19	[  -                                              ]	COG3911	Predicted ATPase
404	pfam05729	165	23	40.0	22	[  -                                              ]	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.
405	cd03277	213	27	40.0	17	[  -                                              ]	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).
406	TIGR03522	301	34	39.8	10	[ --                                              ]	GldA_ABC_ATP	gliding motility-associated ABC transporter ATP-binding subunit GldA. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
407	COG3265	161	131	39.7	61	[                            -------              ]	GntK	Gluconate kinase
408	pfam01583	157	110	39.7	22	[  -----                                          ]	APS_kinase	Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
409	cd01369	325	25	39.7	12	[  -                                              ]	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.
410	TIGR00235	207	45	39.6	18	[  --                                             ]	udk	uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below
411	cd03222	177	19	39.5	18	[  -                                              ]	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.
412	pfam03205	138	19	39.3	19	[  -                                              ]	MobB	Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
413	COG1101	263	43	39.3	14	[ --                                              ]	PhnK	ABC-type uncharacterized transport system, ATPase component
414	PRK13768	253	24	39.3	20	[  -                                              ]	PRK13768	GTPase; Provisional
415	TIGR02788	308	27	39.3	21	[  -                                              ]	VirB11	P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.
416	cd03283	199	42	39.2	22	[  -                                              ]	ABC_MutS-like	ATP-binding cassette domain of MutS-like homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
417	cd00154	159	20	39.2	20	[  -                                              ]	Rab	Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases). Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible.
418	PRK09473	330	33	38.8	19	[ --                                              ]	oppD	oligopeptide transporter ATP-binding component; Provisional
419	PRK12608	380	29	38.6	21	[  -                                              ]	PRK12608	transcription termination factor Rho; Provisional
420	TIGR03345	852	28	38.5	20	[  -                                              ]	VI_ClpV1	type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
421	COG3596	296	79	38.4	30	[      ---                                        ]	YeeP	Predicted GTPase
422	COG1643	845	125	38.3	63	[ ------                                          ]	HrpA	HrpA-like RNA helicase
423	PRK05563	559	39	38.3	25	[ --                                              ]	PRK05563	DNA polymerase III subunits gamma and tau; Validated
424	PRK11147	635	23	38.1	20	[  -                                              ]	PRK11147	ABC transporter ATPase component; Reviewed
425	TIGR02397	355	39	38.1	29	[ --                                              ]	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.
426	COG2766	649	47	38.0	29	[ --                                              ]	PrkA	Predicted Ser/Thr protein kinase
427	TIGR02533	486	28	37.9	20	[  -                                              ]	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.
428	COG2874	235	139	37.9	1.9E+02	[  -------                                        ]	FlaH	Archaellum biogenesis protein FlaH, an ATPase
429	PRK14248	268	76	37.7	31	[  ---                                            ]	PRK14248	phosphate ABC transporter ATP-binding protein; Provisional
430	TIGR00455	184	124	37.6	28	[  ------                                         ]	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.
431	TIGR03005	252	35	37.6	19	[ --                                              ]	ectoine_ehuA	ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.
432	PRK06002	450	129	37.5	81	[  -------                                        ]	fliI	flagellum-specific ATP synthase; Validated
433	COG1392	217	70	37.4	4.7E+02	[         ---                                     ]	YkaA	Uncharacterized conserved protein YkaA, distantly related to PhoU, UPF0111/DUF47 family
434	PRK06547	172	21	37.3	22	[  -                                              ]	PRK06547	hypothetical protein; Provisional
435	pfam00625	183	67	37.1	23	[  ----                                           ]	Guanylate_kin	Guanylate kinase.
436	COG4674	249	22	36.7	9.4	[  -                                              ]	COG4674	ABC-type uncharacterized transport system, ATPase component
437	cd01128	249	133	36.6	80	[  -------                                        ]	rho_factor	Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
438	cd01983	99	22	36.6	27	[  -                                              ]	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.
439	pfam02463	1162	23	36.5	21	[  -                                              ]	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.
440	cd03237	246	23	36.4	22	[  -                                              ]	ABC_RNaseL_inhibitor_domain2	The ATP-binding cassette domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
441	cd03276	198	18	36.4	20	[  -                                              ]	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).
442	PRK00131	175	28	36.3	30	[  -                                              ]	aroK	shikimate kinase; Reviewed
443	PRK14246	257	26	36.3	27	[  -                                              ]	PRK14246	phosphate ABC transporter ATP-binding protein; Provisional
444	COG1123	539	20	36.1	21	[  -                                              ]	GsiA	ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain
445	PRK11000	369	32	36.0	23	[             -                                   ]	PRK11000	maltose/maltodextrin transporter ATP-binding protein; Provisional
446	TIGR04249	292	25	35.5	19	[  -                                              ]	SCM_chp_ScmC	SynChlorMet cassette protein ScmC. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are designated ScmC.
447	COG4555	245	23	35.3	22	[  -                                              ]	NatA	ABC-type Na+ transport system, ATPase component NatA
448	COG1117	253	29	35.3	25	[  -                                              ]	PstB	ABC-type phosphate transport system, ATPase component
449	PRK13541	195	51	35.3	8.6	[  ---                                            ]	PRK13541	cytochrome c biogenesis protein CcmA; Provisional
450	cd03296	239	24	35.3	24	[  -                                              ]	ABC_CysA_sulfate_importer	ATP-binding cassette domain of the sulfate transporter. Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
451	COG5192	1077	160	35.2	19	[  --------                                       ]	BMS1	GTP-binding protein required for 40S ribosome biogenesis
452	PRK11308	327	37	35.2	25	[ --                                              ]	dppF	dipeptide transporter ATP-binding subunit; Provisional
453	cd00880	161	84	35.1	21	[  -----                                          ]	Era_like	E. coli Ras-like protein (Era)-like GTPase. The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family.
454	pfam00158	168	23	35.1	49	[  -                                              ]	Sigma54_activat	Sigma-54 interaction domain.
455	pfam10412	386	21	35.1	25	[  -                                              ]	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.
456	PRK13833	323	53	35.0	40	[ --                                              ]	PRK13833	conjugal transfer protein TrbB; Provisional
457	TIGR01243	733	21	34.8	23	[  -                                              ]	CDC48	AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
458	cd04162	164	56	34.7	27	[  ---                                            ]	Arl9_Arfrp2_like	Arf-like 9 (Arl9)/Arfrp2-like GTPase. Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date.
459	COG0645	170	20	34.6	24	[  -                                              ]	COG0645	Predicted kinase
460	PRK06851	367	22	34.4	25	[  -                                              ]	PRK06851	hypothetical protein; Provisional
461	PRK07165	507	158	34.3	62	[  --------                                       ]	PRK07165	F0F1 ATP synthase subunit alpha; Validated
462	cd01672	200	24	34.3	61	[  -                                              ]	TMPK	Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
463	cd03258	233	78	34.2	26	[  ---                                            ]	ABC_MetN_methionine_transporter	ATP-binding cassette domain of methionine transporter. MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
464	cd01882	231	161	34.1	24	[  --------                                       ]	BMS1	Bms1, an essential GTPase, promotes assembly of preribosomal RNA processing complexes. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
465	PRK10436	462	44	34.1	23	[ --                                              ]	PRK10436	hypothetical protein; Provisional
466	cd01900	274	23	34.0	21	[  -                                              ]	YchF	YchF GTPase. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor.
467	PRK13830	818	32	33.9	30	[  -                                              ]	PRK13830	conjugal transfer protein TrbE; Provisional
468	cd03245	220	26	33.8	30	[  -                                              ]	ABCC_bacteriocin_exporters	ATP-binding cassette domain of bacteriocin exporters, subfamily C. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
469	cd03116	159	22	33.7	34	[  -                                              ]	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.
470	TIGR03873	256	22	33.7	22	[  -                                              ]	F420-0_ABC_ATP	proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.
471	PRK14490	369	32	33.5	19	[  -                                              ]	PRK14490	putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional
472	cd01893	168	19	33.3	26	[  -                                              ]	Miro1	Mitochondrial Rho family 1 (Miro1), N-terminal. Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature.
473	TIGR03410	230	157	33.3	30	[  --------                                       ]	urea_trans_UrtE	urea ABC transporter, ATP-binding protein UrtE. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
474	cd00878	158	92	33.2	28	[  ----                                           ]	Arf_Arl	ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions.
475	cd03243	202	31	33.1	35	[  -                                              ]	ABC_MutS_homologs	ATP-binding cassette domain of MutS homologs. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange.
476	PRK10535	648	22	33.0	27	[  -                                              ]	PRK10535	macrolide transporter ATP-binding /permease protein; Provisional
477	COG4152	300	38	33.0	18	[ --                                              ]	YhaQ	ABC-type uncharacterized transport system, ATPase component
478	PRK13632	271	137	32.9	33	[ ------                                          ]	cbiO	cobalt transporter ATP-binding subunit; Provisional
479	COG4598	256	110	32.8	30	[  ------                                         ]	HisP	ABC-type histidine transport system, ATPase component
480	cd01862	172	17	32.8	24	[  -                                              ]	Rab7	Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation.
481	PRK00409	782	85	32.8	41	[  -----                                          ]	PRK00409	recombination and DNA strand exchange inhibitor protein; Reviewed
482	TIGR01184	230	90	32.8	28	[     ----                                        ]	ntrCD	nitrate transport ATP-binding subunits C and D. This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.
483	COG0237	201	24	32.6	41	[  -                                              ]	CoaE	Dephospho-CoA kinase
484	COG1118	345	27	32.6	29	[  -                                              ]	CysA	ABC-type sulfate/molybdate transport systems, ATPase component
485	TIGR03415	382	23	32.4	29	[  -                                              ]	ABC_choXWV_ATP	choline ABC transporter, ATP-binding protein. Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.
486	TIGR03596	276	113	32.4	48	[  ------                                         ]	GTPase_YlqF	ribosome biogenesis GTP-binding protein YlqF. Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members.
487	COG4650	531	37	32.4	47	[ --                                              ]	RtcR	Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain
488	TIGR03265	353	147	32.3	29	[  -------                                        ]	PhnT2	putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
489	PRK12724	432	24	32.2	36	[  -                                              ]	PRK12724	flagellar biosynthesis regulator FlhF; Provisional
490	TIGR03411	242	19	32.1	12	[  -                                              ]	urea_trans_UrtD	urea ABC transporter, ATP-binding protein UrtD. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.
491	cd11383	140	18	32.1	20	[  -                                              ]	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.
492	cd01125	239	135	32.0	67	[  ------                                         ]	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.
493	TIGR02203	571	26	31.9	26	[  -                                              ]	MsbA_lipidA	lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.
494	TIGR00958	711	56	31.9	28	[ ---                                             ]	3a01208	Conjugate Transporter-2 (CT2) Family protein.
495	pfam10662	143	21	31.8	30	[  -                                              ]	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.
496	PRK08233	182	24	31.7	35	[  -                                              ]	PRK08233	hypothetical protein; Provisional
497	PRK11264	250	148	31.7	28	[  --------                                       ]	PRK11264	putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
498	cd01394	218	91	31.7	2.2E+02	[  -----                                          ]	radB	RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
499	pfam02562	205	19	31.7	33	[  -                                              ]	PhoH	PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
500	PRK05298	652	40	31.7	41	[ --                                              ]	PRK05298	excinuclease ABC subunit B; Provisional