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 392896703 217 GDSETREMTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAE 296
Cdd:cd03272  149 KQDEQQEMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMIKELSDGAQFITTTFRPELLEVAD 228

                         90
                 ....*....|....*
gi 392896703 297 KFYGVRFRNKVSHID 311
Cdd:cd03272  229 KFYGVKFRNKVSTID 243

ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 217 GDSETREMTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAE 296
Cdd:cd03272  149 KQDEQQEMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMIKELSDGAQFITTTFRPELLEVAD 228

                         90
                 ....*....|....*
gi 392896703 297 KFYGVRFRNKVSHID 311
Cdd:cd03272  229 KFYGVKFRNKVSTID 243

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703     2 ESTRKQLATAISELQDYETKEKALQINIDNVLEQQRDLEKQQADFQLQYDKITAKEDEVKQKREDSLKKMRLLGALPTDT 81
Cdd:TIGR02169  864 EELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPKGED 943

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703    82 FSKWQNVKPRE-LEKKLLECVNELKKYENVNKKALDQYMTASSQKEELTKRMAEQKKSEDSIEELLKVLENRKYEAIDLT 160
Cdd:TIGR02169  944 EEIPEEELSLEdVQAELQRVEEEIRALEPVNMLAIQEYEEVLKRLDELKEKRAKLEEERKAILERIEEYEKKKREVFMEA 1023

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703   161 FKQVKKNFEQVFKQLvPHGRGKMQMrarEQRDDEeginsvelyegISVLVSFVSDDGDSETREMTQLSGGQKSLVALAII 240
Cdd:TIGR02169 1024 FEAINENFNEIFAEL-SGGTGELIL---ENPDDP-----------FAGGLELSAKPKGKPVQRLEAMSGGEKSLTALSFI 1088

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896703   241 FSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEKFYGV 301
Cdd:TIGR02169 1089 FAIQRYKPSPFYAFDEVDMFLDGVNVERVAKLIREKAGEAQFIVVSLRSPMIEYADRAIGV 1149

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896703  227 LSGGQKSLVALAIIFsiqkCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEK 297
Cdd:TIGR02857 459 LSGGQAQRLALARAF----LRDAPLLLLDEPTAHLDAETEAEVLEALRALAQGRTVLLVTHRLALAALADR 525

recombination protein F; Reviewed

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392896703 225 TQLSGGQKSLVALAIIFS-----IQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAqFVTTT 286
Cdd:PRK00064 272 DFGSTGQQKLLLLALKLAeaellKEETGEAPILLLDDVASELDDGRRAALLERLKGLGAQV-FITTT 337

ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 217 GDSETREMTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAE 296
Cdd:cd03272  149 KQDEQQEMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMIKELSDGAQFITTTFRPELLEVAD 228

                         90
                 ....*....|....*
gi 392896703 297 KFYGVRFRNKVSHID 311
Cdd:cd03272  229 KFYGVKFRNKVSTID 243

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 190 QRDDEEGINSVELYEGISVLvsfvsddGDSETREMtqLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSV 269
Cdd:cd03239   67 KAGINSASVEITFDKSYFLV-------LQGKVEQI--LSGGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRV 137

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 392896703 270 ADMIQSLSD-QAQFVTTTFRPELLATAEKFYGVRFRNKVSH 309
Cdd:cd03239  138 SDMIKEMAKhTSQFIVITLKKEMFENADKLIGVLFVHGVST 178

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703   2 ESTRKQLATAISELQDYETKEKALQINIDNVLEQQRDLEKQQADFQLQYDKITAKEDEVKQKREDSLKKMRLLGALPTDT 81
Cdd:COG1196  678 EAELEELAERLAEEELELEEALLAEEEEERELAEAEEERLEEELEEEALEEQLEAEREELLEELLEEEELLEEEALEELP 757

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703  82 fskwQNVKPRELEKKLLECVNELKKYENVNKKALDQYMTASSQKEELTKRMAEQKKSEDSIEELLKVLENRKYEAIDLTF 161
Cdd:COG1196  758 ----EPPDLEELERELERLEREIEALGPVNLLAIEEYEELEERYDFLSEQREDLEEARETLEEAIEEIDRETRERFLETF 833

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 162 KQVKKNFEQVFKQLVPHGRGKMQMRareqrDDEEGINSvelyeGISVLVSFvsddGDSETREMTQLSGGQKSLVALAIIF 241
Cdd:COG1196  834 DAVNENFQELFPRLFGGGEAELLLT-----DPDDPLET-----GIEIMAQP----PGKKLQRLSLLSGGEKALTALALLF 899

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 392896703 242 SIQKCDPAPFYLFDEIDAALDAQ--HRksVADMIQSLSDQAQFVTTTFRPELLATAEKFYGV 301
Cdd:COG1196  900 AIFRLNPSPFCVLDEVDAPLDDAnvER--FAELLKEMSEDTQFIVITHNKRTMEAADRLYGV 959

ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 224 MTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEKFYGVRF 303
Cdd:cd03278  111 LSLLSGGEKALTALALLFAIFRVRPSPFCVLDEVDAALDDANVERFARLLKEFSKETQFIVITHRKGTMEAADRLYGVTM 190

                 ....*.
gi 392896703 304 RNK-VS 308
Cdd:cd03278  191 QESgVS 196

ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 224 MTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEKFYGVRF 303
Cdd:cd03273  164 LTELSGGQRSLVALSLILALLLFKPAPMYILDEVDAALDLSHTQNIGRMIKTHFKGSQFIVVSLKEGMFNNANVLFRTRF 243

                 ....*...
gi 392896703 304 RNKVSHID 311
Cdd:cd03273  244 VDGTSTVT 251

ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 222 REMTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEKFYGV 301
Cdd:cd03274  123 KNISNLSGGEKTLSSLALVFALHHYKPTPLYVMDEIDAALDFRNVSIVANYIKERTKNAQFIVISLRNNMFELADRLVGI 202

Predicted ATP-binding protein involved in virulence [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 101 VNELKKYENVNKKALDQYMTASSQKEELtkrmaeqKKSEDSIEELLKVLENRKYEAIDLTFKQVKknfeQVFKQLVPHGR 180
Cdd:COG3950   92 LKKLERLKEEYFSRLDGYDSLLDEDSNL-------REFLEWLREYLEDLENKLSDELDEKLEAVR----EALNKLLPDFK 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 181 gkmQMRAREQRddeeginsvelyegisvlVSFVSDDGDSETREMTQLSGGQKSLVALA--IIFSIQKCDPAPFY------ 252
Cdd:COG3950  161 ---DIRIDRDP------------------GRLVILDKNGEELPLNQLSDGERSLLALVgdLARRLAELNPALENplegeg 219

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 392896703 253 --LFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEK 297
Cdd:COG3950  220 ivLIDEIDLHLHPKWQRRILPDLRKIFPNIQFIVTTHSPLILSSLED 266

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).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896703 211 SFVSDDgDSETREMTQLSGGQKSLVALAIIFSIQKCDPAPFYLFDEIDAALDAQHRKSVADMI 273
Cdd:cd03276   95 SFLTSN-KAAVRDVKTLSGGERSFSTVCLLLSLWEVMESPFRCLDEFDVFMDMVNRKISTDLL 156

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392896703  227 LSGGQKSLVALAIIFsiqkCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEK 297
Cdd:TIGR02857 459 LSGGQAQRLALARAF----LRDAPLLLLDEPTAHLDAETEAEVLEALRALAQGRTVLLVTHRLALAALADR 525

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703   87 NVKPRELEKKLLECVNELKKYENVNKKALDQYMTASSQKEELTKRMAEQKKSEDSIEELLKVLENRKYEAIDLTFKQVKK 166
Cdd:pfam13304  77 DLEREDVEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEELRLGLDVEERIELSLSELSDLISGLLLLSIISPLSFLLL 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703  167 NFEQVFKQLV------------PHGRGKMQMRAREQRDDEEGINSVELYEGISVLVSFVSDD--------GDSETREMTQ 226
Cdd:pfam13304 157 LDEGLLLEDWavldlaadlalfPDLKELLQRLVRGLKLADLNLSDLGEGIEKSLLVDDRLRErglillenGGGGELPAFE 236

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392896703  227 LSGGQKSLVALAIIFSIQkCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSD-QAQFVTTTFRPELLA 293
Cdd:pfam13304 237 LSDGTKRLLALLAALLSA-LPKGGLLLIDEPESGLHPKLLRRLLELLKELSRnGAQLILTTHSPLLLD 303

recombination protein F; Reviewed

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392896703 225 TQLSGGQKSLVALAIIFS-----IQKCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAqFVTTT 286
Cdd:PRK00064 272 DFGSTGQQKLLLLALKLAeaellKEETGEAPILLLDDVASELDDGRRAALLERLKGLGAQV-FITTT 337

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896703 227 LSGGQKSLVALAIIFsIQKcdpAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQFVTTTFRPELLATAEKFY 299
Cdd:cd03228   97 LSGGQRQRIAIARAL-LRD---PPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRLSTIRDADRII 165

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 392896703 224 MTQLSGGQKSLVALAIIFSiqkcDPAPFYLFDEIDAALDAQHRKSVADMIQS 275
Cdd:cd03221   68 FEQLSGGEKMRLALAKLLL----ENPNLLLLDEPTNHLDLESIEALEEALKE 115

ribosome biogenesis/translation initiation ATPase RLI;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 392896703 222 REMTQLSGG--QKSLVALAIIfsiqkcDPAPFYLFDEIDAALDAQHRKSVADMIQSLSD 278
Cdd:PRK13409 208 RDISELSGGelQRVAIAAALL------RDADFYFFDEPTSYLDIRQRLNVARLIRELAE 260

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 222 REMTQLSGGQKSLVALAIIFSIQK--CDPAPFYLFDEIDAALDAQHR-KSVADMIQSLSDQA--QFVTTTFRPELLATAE 296
Cdd:cd03240  111 DMRGRCSGGEKVLASLIIRLALAEtfGSNCGILALDEPTTNLDEENIeESLAEIIEERKSQKnfQLIVITHDEELVDAAD 190

                 ....*.
gi 392896703 297 KFYGVR 302
Cdd:cd03240  191 HIYRVE 196

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392896703 226 QLSGGQKSLVALAIIFSiqkCDPApFYLFDEIDAALDAQHRKSVADMIQSLSDQ 279
Cdd:COG1123  142 QLSGGQRQRVAIAMALA---LDPD-LLIADEPTTALDVTTQAEILDLLRELQRE 191

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392896703 215 DDGDSETREMTQLSGGQKSLVALAIIFSIQkcdpAPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQ----FVTT 285
Cdd:cd03259  119 GLEGLLNRYPHELSGGQQQRVALARALARE----PSLLLLDEPLSALDAKLREELREELKELQRELGittiYVTH 189

ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and Cell division ATP-binding protein FtsE; 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. The FtsEX complex resembles an ABC transporter, where FtsE is the ATPase and the membrane subunit FtsX resembles a permease subunit. But rather than transporting any substrate, the complex acts in cell division by undergoing conformational changes that alter the activity of cell wall hydrolases located outside the plasma membrane. The complex is widely conserved in bacteria, but also extremely divergent in sequence between different lineages. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392896703 217 GDSETREMTQLSGGQKSLVALA--IIfsiqkCDPaPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQ--FVTTTFRPELL 292
Cdd:cd03255  131 GDRLNHYPSELSGGQQQRVAIAraLA-----NDP-KIILADEPTGNLDSETGKEVMELLRELNKEAGttIVVVTHDPELA 204

                 ....*
gi 392896703 293 ATAEK 297
Cdd:cd03255  205 EYADR 209

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392896703 227 LSGGQKSLVALAIIFSIQkcdpaPFYLF-DEIDAALDAQHRKSVADMIQSLsdQAQFVTT---TFRPELLATAEK 297
Cdd:cd03246   97 LSGGQRQRLGLARALYGN-----PRILVlDEPNSHLDVEGERALNQAIAAL--KAAGATRiviAHRPETLASADR 164

energy-coupling factor ABC transporter ATP-binding protein;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 392896703 221 TREMTQLSGGQKSLVALAIIFSIQkcdPAPFYLfDEIDAALDAQHRKSVADMIQSLSDQ 279
Cdd:PRK13635 135 NREPHRLSGGQKQRVAIAGVLALQ---PDIIIL-DEATSMLDPRGRREVLETVRQLKEQ 189

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392896703 226 QLSGGQKSLVALAIIFSiqkCDPaPFYLFDEIDAALDAQHRKSVADMIQSLSDQ 279
Cdd:COG1123  404 ELSGGQRQRVAIARALA---LEP-KLLILDEPTSALDVSVQAQILNLLRDLQRE 453

glutamine ABC transporter ATP-binding protein GlnQ;

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 392896703 225 TQLSGGQKSLVALAIIFSIQkcdpAPFYLFDEIDAALDAQHRKSVADMIQSLSDQ 279
Cdd:PRK09493 135 SELSGGQQQRVAIARALAVK----PKLMLFDEPTSALDPELRHEVLKVMQDLAEE 185

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

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 392896703 226 QLSGGQKSLVALAIIFsiqkCDPAPFYLFDEIDAALDAQHRKSVADMIQSLSDQ 279
Cdd:COG4133  131 QLSAGQKRRVALARLL----LSPAPLWLLDEPFTALDAAGVALLAELIAAHLAR 180

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 392896703 226 QLSGGQKSLVALAIIFSIqkcDPaPFYLFDEIDAALDAQHRKSVADMIQSLSDQAQ----FVT 284
Cdd:cd03293  131 QLSGGMRQRVALARALAV---DP-DVLLLDEPFSALDALTREQLQEELLDIWRETGktvlLVT 189