P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717   31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAGKHM-VGGKnvVQVLDRSAFHDTELVCSGDLSYLGgswsktagsaGDIPL 109
Cdd:pfam00005   3 NVSLTLNPGEILALVGPNGAGKSTLLKLIAGLLSpTEGT--ILLDGQDLTDDERKSLRKEIGYVF----------QDPQL 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334717  110 QGDFSA-EHMIFGVEGIDPFRREK------------LIDLLDINLQWRMHKVSDGQRRRVQICMGLL 163
Cdd:pfam00005  71 FPRLTVrENLRLGLLLKGLSKREKdaraeealeklgLGDLADRPVGERPGTLSGGQRQRVAIARALL 137

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717   31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAGKHM-VGGKnvVQVLDRSAFHDTELVCSGDLSYLGgswsktagsaGDIPL 109
Cdd:pfam00005   3 NVSLTLNPGEILALVGPNGAGKSTLLKLIAGLLSpTEGT--ILLDGQDLTDDERKSLRKEIGYVF----------QDPQL 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334717  110 QGDFSA-EHMIFGVEGIDPFRREK------------LIDLLDINLQWRMHKVSDGQRRRVQICMGLL 163
Cdd:pfam00005  71 FPRLTVrENLRLGLLLKGLSKREKdaraeealeklgLGDLADRPVGERPGTLSGGQRQRVAIARALL 137

First domain of the ATP-binding cassette component of cobalt transport system; Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  20 FSYDVQD-PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG-KHMVGGKnvVQVLDRSAFHDTelvcsgdlsylGGSW 97
Cdd:cd03225    7 FSYPDGArPALDDISLTIKKGEFVLIVGPNGSGKSTLLRLLNGlLGPTSGE--VLVDGKDLTKLS-----------LKEL 73

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145334717  98 SKTAGSAgdipLQgdfSAEHMIFG--VE----------GIDPFRREKLID------LLDINLQWRMHKVSDGQRRRVQI 158
Cdd:cd03225   74 RRKVGLV----FQ---NPDDQFFGptVEeevafglenlGLPEEEIEERVEealelvGLEGLRDRSPFTLSGGQKQRVAI 145

ABC transporter ATP-binding protein; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  12 AIRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:PRK15064 319 ALEVENLTKGFD-NGPLFKNLNLLLEAGERLAIIGENGVGKTTLLRTLVG 367

ribosome-associated ATPase/putative transporter RbbA;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 145334717  31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAG-KHMVGGKnvVQVLD---RSAFH 80
Cdd:NF033858  19 DVSLDIPAGCMVGLIGPDGVGKSSLLSLIAGaRKIQQGR--VEVLGgdmADARH 70

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717   31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAGKHM-VGGKnvVQVLDRSAFHDTELVCSGDLSYLGgswsktagsaGDIPL 109
Cdd:pfam00005   3 NVSLTLNPGEILALVGPNGAGKSTLLKLIAGLLSpTEGT--ILLDGQDLTDDERKSLRKEIGYVF----------QDPQL 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334717  110 QGDFSA-EHMIFGVEGIDPFRREK------------LIDLLDINLQWRMHKVSDGQRRRVQICMGLL 163
Cdd:pfam00005  71 FPRLTVrENLRLGLLLKGLSKREKdaraeealeklgLGDLADRPVGERPGTLSGGQRQRVAIARALL 137

ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  13 IRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILA-------GKHMVGGKNVVQvlDRSAFHdtelv 85
Cdd:COG4133    3 LEAENLSCRRG-ERLLFSGLSFTLAAGEALALTGPNGSGKTTLLRILAgllppsaGEVLWNGEPIRD--AREDYR----- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  86 csGDLSYLGgswsktagsaGDIPLQGDFSA-EHMIF-----GVegidPFRREKLIDLLD-INLQWRMHK----VSDGQRR 154
Cdd:COG4133   75 --RRLAYLG----------HADGLKPELTVrENLRFwaalyGL----RADREAIDEALEaVGLAGLADLpvrqLSAGQKR 138

                        170
                 ....*....|.
gi 145334717 155 RVQICMGLLHP 165
Cdd:COG4133  139 RVALARLLLSP 149

ABC-type Na+ transport system, ATPase component NatA [Energy production and conversion, Inorganic ion transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  13 IRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGKhMVGGKNVVQVLDRSAFHDTELVcSGDLSY 92
Cdd:COG4555    2 IEVENLSKKYG-KVPALKDVSFTAKDGEITGLLGPNGAGKTTLLRMLAGL-LKPDSGSILIDGEDVRKEPREA-RRQIGV 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  93 LGgswsktagsaGDIPLQGDFSAEHMI------FGVEGID-PFRREKLIDLLDIN--LQWRMHKVSDGQRRRVQICMGLL 163
Cdd:COG4555   79 LP----------DERGLYDRLTVRENIryfaelYGLFDEElKKRIEELIELLGLEefLDRRVGELSTGMKKKVALARALV 148

                 .
gi 145334717 164 H 164
Cdd:COG4555  149 H 149

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  13 IRVSGMQFSYDVQdPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGK 62
Cdd:cd03221    1 IELENLSKTYGGK-LLLKDISLTINPGDRIGLVGRNGAGKSTLLKLIAGE 49

ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  13 IRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGK 62
Cdd:COG0488  316 LELEGLSKSYG-DKTLLDDLSLRIDRGDRIGLIGPNGAGKSTLLKLLAGE 364

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717    7 SAVDGAIRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGkHMVGGKNVVQVLDRSAFHDTELVC 86
Cdd:TIGR02857 316 AAPASSLEFSGVSVAYPGRRPALRPVSFTVPPGERVALVGPSGAGKSTLLNLLLG-FVDPTEGSIAVNGVPLADADADSW 394

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717   87 SGDLSYLGGSWSKTAGS-AGDIPL-QGDFSAEHMIFGVE--GIDPFRREkLIDLLDINLQWRMHKVSDGQRRRVQICMGL 162
Cdd:TIGR02857 395 RDQIAWVPQHPFLFAGTiAENIRLaRPDASDAEIREALEraGLDEFVAA-LPQGLDTPIGEGGAGLSGGQAQRLALARAF 473

                  ...
gi 145334717  163 LHP 165
Cdd:TIGR02857 474 LRD 476

ABC-type multidrug transport system, ATPase component [Defense mechanisms];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAG-KHMVGGKnvVQVLDRSAFHDTELVCSgDLSYLggswsktagsAGDIPL 109
Cdd:COG1131   18 GVSLTVEPGEIFGLLGPNGAGKTTTIRMLLGlLRPTSGE--VRVLGEDVARDPAEVRR-RIGYV----------PQEPAL 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 145334717 110 QGDFSA-EHMIF--GVEGIDPFRREKLID-LLDI-NLQWRMHKV----SDGQRRRVQICMGLLH 164
Cdd:COG1131   85 YPDLTVrENLRFfaRLYGLPRKEARERIDeLLELfGLTDAADRKvgtlSGGMKQRLGLALALLH 148

ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component [Inorganic ion transport and metabolism, Coenzyme transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  12 AIRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGKH-------MVGGKNVVQvLDRSAF----- 79
Cdd:COG1120    1 MLEAENLSVGYG-GRPVLDDVSLSLPPGEVTALLGPNGSGKSTLLRALAGLLkpssgevLLDGRDLAS-LSRRELarria 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  80 -----HDT-------ELVCSGDLSYLG--GSWSKTagsagDiplqgdfsaEHMIfgvegidpfrrEKLIDLLDI-NLQWR 144
Cdd:COG1120   79 yvpqePPApfgltvrELVALGRYPHLGlfGRPSAE-----D---------REAV-----------EEALERTGLeHLADR 133

                        170
                 ....*....|....*....
gi 145334717 145 -MHKVSDGQRRRVQICMGL 162
Cdd:COG1120  134 pVDELSGGERQRVLIARAL 152

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 145334717    6 ASAVDGA-IRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:TIGR02868 327 AVGLGKPtLELRDLSAGYPGAPPVLDGVSLDLPPGERVAILGPSGSGKSTLLATLAG 383

ABC-type molybdenum transport system, ATPase component ModF/photorepair protein PhrA [Inorganic ion transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  27 PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGKHMVGGKNVVQVLDR-----SAFhdtEL-----VCSGDLsylggs 96
Cdd:COG1119   17 TILDDISWTVKPGEHWAILGPNGAGKSTLLSLITGDLPPTYGNDVRLFGErrggeDVW---ELrkrigLVSPAL------ 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 145334717  97 wsktagsAGDIPlqGDFSAEHMI----FGVegIDPFRR---------EKLIDLLDIN--LQWRMHKVSDGQRRRVQI 158
Cdd:COG1119   88 -------QLRFP--RDETVLDVVlsgfFDS--IGLYREptdeqreraRELLELLGLAhlADRPFGTLSQGEQRRVLI 153

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 145334717  14 RVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03214    1 EVENLSVGYG-GRTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTLAG 47

ABC-type lipoprotein export system, ATPase component [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145334717  12 AIRVSGMQFSYDVQD---PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILA-------GKHMVGGKNV 70
Cdd:COG1136    4 LLELRNLTKSYGTGEgevTALRGVSLSIEAGEFVAIVGPSGSGKSTLLNILGgldrptsGEVLIDGQDI 72

ATPase subunit MlaF of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  12 AIRVSGMQFSYDVQdPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:COG1127    5 MIEVRNLTKSFGDR-VVLDGVSLDVPRGEILAIIGGSGSGKSVLLKLIIG 53

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 145334717  14 RVSGMQFSYDVQdPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03235    1 EVEDLTVSYGGH-PVLEDVSFEVKPGEFLAIVGPNGAGKSTLLKAILG 47

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.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 145334717  31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03220   40 DVSFEVPRGERIGLIGRNGAGKSTLLRLLAG 70

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 145334717  11 GAIRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03254    1 GEIEFENVNFSYDEKKPVLKDINFSIKPGETVAIVGPTGAGKTTLINLLMR 51

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  13 IRVSGMQFSYDVQD-PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03247    1 LSINNVSFSYPEQEqQVLKNLSLELKQGEKIALLGRSGSGKSTLLQLLTG 50

ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only];

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 145334717  27 PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:COG4178  377 PLLEDLSLSLKPGERLLITGPSGSGKSTLLRAIAG 411

ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  12 AIRVSGMQFSYDVQD-PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGKHMVGGKNVVQVLdrsaFHDTELvcsgdl 90
Cdd:COG1123    4 LLEVRDLSVRYPGGDvPAVDGVSLTIAPGETVALVGESGSGKSTLALALMGLLPHGGRISGEVL----LDGRDL------ 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717  91 syLGGSWSKTAGSAGDIPLQGDFS------AEHMIFGVE--GIDPF-RREKLIDLLD-INLQWRM----HKVSDGQRRRV 156
Cdd:COG1123   74 --LELSEALRGRRIGMVFQDPMTQlnpvtvGDQIAEALEnlGLSRAeARARVLELLEaVGLERRLdrypHQLSGGQRQRV 151

                 ....*.
gi 145334717 157 QICMGL 162
Cdd:COG1123  152 AIAMAL 157

ABC-type sugar transport system, ATPase component MalK [Carbohydrate transport and metabolism];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 145334717  11 GAIRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:COG3839    2 ASLELENVSKSYG-GVEALKDIDLDIEDGEFLVLLGPSGCGKSTLLRMIAG 51

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 145334717  13 IRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKIL 59
Cdd:cd03253    1 IEFENVTFAYDPGRPVLKDVSFTIPAGKKVAIVGPSGSGKSTILRLL 47

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. [Protein fate, Protein and peptide secretion and trafficking, Protein fate, Protein modification and repair, Transport and binding proteins, Other]

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 145334717   11 GAIRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:TIGR01193 472 GDIVINDVSYSYGYGSNILSDISLTIKMNSKTTIVGMSGSGKSTLAKLLVG 522

ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only];

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 145334717  23 DVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAGKH 63
Cdd:COG2401   40 VVERYVLRDLNLEIEPGEIVLIVGASGSGKSTLLRLLAGAL 80

ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  10 DGAIRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKIL 59
Cdd:COG5265  355 GGEVRFENVSFGYDPERPILKGVSFEVPAGKTVAIVGPSGAGKSTLARLL 404

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.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 145334717  27 PIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03224   14 QILFGVSLTVPEGEIVALLGRNGAGKTTLLKTIMG 48

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 145334717  14 RVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03226    1 RIENISFSYKKGTEILDDLSLDLYAGEIIALTGKNGAGKTTLAKILAG 48

ATP-binding cassette transport system involved in resistance 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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 145334717  13 IRVSGMQFSYDVQdPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03261    1 IELRGLTKSFGGR-TVLKGVDLDVRRGEILAIIGPSGSGKSTLLRLIVG 48

SmdB family multidrug efflux ABC transporter permease/ATP-binding protein;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 145334717  11 GAIRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:PRK10790 339 GRIDIDNVSFAYRDDNLVLQNINLSVPSRGFVALVGHTGSGKSTLASLLMG 389

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. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145334717   26 DPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG-KHMVGGknvVQVLDRSAFHDTELVCSGDLSYLGGSwsktAGsa 104
Cdd:TIGR01189  13 RMLFEGLSFTLNAGEALQVTGPNGIGKTTLLRILAGlLRPDSG---EVRWNGTPLAEQRDEPHENILYLGHL----PG-- 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 145334717  105 gdipLQGDFSAE------HMIFGVEGIDPFRREKLIDLLDINlQWRMHKVSDGQRRRV 156
Cdd:TIGR01189  84 ----LKPELSALenlhfwAAIHGGAQRTIEDALAAVGLTGFE-DLPAAQLSAGQQRRL 136

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.

                         10        20
                 ....*....|....*....|....*....
gi 145334717  33 NLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03216   20 SLSVRRGEVHALLGENGAGKSTLMKILSG 48

hemin importer ATP-binding subunit; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 145334717  12 AIRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:PRK13548   2 MLEARNLSVRLG-GRTLLDDVSLTLRPGEVVAILGPNGAGKSTLLRALSG 50

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 145334717  13 IRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILA-------GKHMVGGKNVVQV 73
Cdd:cd03300    1 IELENVSKFYG-GFVALDGVSLDIKEGEFFTLLGPSGCGKTTLLRLIAgfetptsGEILLDGKDITNL 67

sulfate/thiosulfate ABC transporter ATP-binding protein CysA;

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 145334717  31 DFNLDLPAGSRCLLVGANGSGKTTLLKILAG-KHMVGGK 68
Cdd:PRK10851  20 DISLDIPSGQMVALLGPSGSGKTTLLRIIAGlEHQTSGH 58

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).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 145334717  13 IRVSGMQFSYDVQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03223    1 IELENLSLATPDGRVLLKDLSFEIKPGDRLLITGPSGTGKSSLFRALAG 49

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 145334717  13 IRVSGMQFSYDvQDPIFFDFNLDLPAGSRCLLVGANGSGKTTLLKILAG 61
Cdd:cd03229    1 LELKNVSKRYG-QKTVLNDVSLNIEAGEIVALLGPSGSGKSTLLRCIAG 48