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 metabolism and recombination.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952     1 MEEPYLDGIQYNCVAPGKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESaREHM 80
Cdd:pfam02463 1053 PDDPFSGGIEISARPPGKGVKNLDLLSGGEKTLVALALIFAIQKYKPAPFYLLDEIDAALDDQNVSRVANLLKEL-SKNA 1131

                           90       100       110
                   ....*....|....*....|....*....|
gi 351061952    81 QIIVISLKEEFYNKADSLIGIFPYPAACTT 110
Cdd:pfam02463 1132 QFIVISLREEMLEKADKLVGVTMVENGVST 1161

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952     8 GIQYNCVAPGKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYIcESAREHMQIIVISl 87
Cdd:TIGR02168 1072 GIEIFAQPPGKKNQNLSLLSGGEKALTALALLFAIFKVKPAPFCILDEVDAPLDDANVERFANLL-KEFSKNTQFIVIT- 1149

                           90
                   ....*....|....*....
gi 351061952    88 keefYNK-----ADSLIGI 101
Cdd:TIGR02168 1150 ----HNKgtmevADQLYGV 1164

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 metabolism and recombination.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952     1 MEEPYLDGIQYNCVAPGKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESaREHM 80
Cdd:pfam02463 1053 PDDPFSGGIEISARPPGKGVKNLDLLSGGEKTLVALALIFAIQKYKPAPFYLLDEIDAALDDQNVSRVANLLKEL-SKNA 1131

                           90       100       110
                   ....*....|....*....|....*....|
gi 351061952    81 QIIVISLKEEFYNKADSLIGIFPYPAACTT 110
Cdd:pfam02463 1132 QFIVISLREEMLEKADKLVGVTMVENGVST 1161

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 351061952  16 PGKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESArEHMQIIVISLKEEFYNKA 95
Cdd:cd03274  118 PKKSWKNISNLSGGEKTLSSLALVFALHHYKPTPLYVMDEIDAALDFRNVSIVANYIKERT-KNAQFIVISLRNNMFELA 196

                 ....*..
gi 351061952  96 DSLIGIF 102
Cdd:cd03274  197 DRLVGIY 203

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 351061952  26 LSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVISLKEEFYNKADSLIGI 101
Cdd:cd03239   95 LSGGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITLKKEMFENADKLIGV 170

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 351061952     2 EEPYLDGIQYNCVAPGKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESAREhMQ 81
Cdd:TIGR02169 1051 DDPFAGGLELSAKPKGKPVQRLEAMSGGEKSLTALSFIFAIQRYKPSPFYAFDEVDMFLDGVNVERVAKLIREKAGE-AQ 1129

                           90       100
                   ....*....|....*....|
gi 351061952    82 IIVISLKEEFYNKADSLIGI 101
Cdd:TIGR02169 1130 FIVVSLRSPMIEYADRAIGV 1149

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 351061952  23 MDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESArEHMQIIVISLKEEFYNKADSLIGIF 102
Cdd:cd03272  156 MQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALDAQYRTAVANMIKELS-DGAQFITTTFRPELLEVADKFYGVK 234

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 351061952  20 FRPMDNLSGGEKTIAALALLFAVH--GRNPAPFFVLDEIDAALDNTNIGKVASYICESARE--HMQIIVISLKEEFYNKA 95
Cdd:cd03240  110 LDMRGRCSGGEKVLASLIIRLALAetFGSNCGILALDEPTTNLDEENIEESLAEIIEERKSqkNFQLIVITHDEELVDAA 189

                 ....
gi 351061952  96 DSLI 99
Cdd:cd03240  190 DHIY 193

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        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 351061952  17 GKRFRPMDNLSGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESARE--HMQIIVIS 86
Cdd:cd03276  101 KAAVRDVKTLSGGERSFSTVCLLLSLWEVMESPFRCLDEFDVFMDMVNRKISTDLLVKEAKKqpGRQFIFIT 172

Predicted ATPase [General function prediction only];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 351061952  22 PMDNLSGGekTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESAREHmQIIVIS 86
Cdd:COG4637  255 PARELSDG--TLRFLALLAALLSPRPPPLLCIEEPENGLHPDLLPALAELLREASERT-QVIVTT 316

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).

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 351061952  19 RFRPMDNL--------SGGEKTIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESA 76
Cdd:cd03277  112 KFREGEQLqeldphhqSGGERSVSTMLYLLSLQELTRCPFRVVDEINQGMDPTNERKVFDMLVETA 177

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952  17 GKRFRPMDNLSGGEKTIAALALLFAvhgRNPaPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVIS 86
Cdd:cd03225  126 GLRDRSPFTLSGGQKQRVAIAGVLA---MDP-DILLLDEPTAGLDPAGRRELLELLKKLKAEGKTIIIVT 191

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952  21 RPMDNLSGGEKTIAALALLFAVHGRNpaPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVISLKEEFYNKADSLIG 100
Cdd:cd03238   83 QKLSTLSGGELQRVKLASELFSEPPG--TLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNLDVLSSADWIID 160

                 ....*
gi 351061952 101 IFPYP 105
Cdd:cd03238  161 FGPGS 165

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 351061952  21 RPMDNLSGGEKTIAALALLFAV------HGRNPAPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVIS----LKEE 90
Cdd:cd03279  119 RPVSTLSGGETFLASLSLALALsevlqnRGGARLEALFIDEGFGTLDPEALEAVATALELIRTENRMVGVIShveeLKER 198

                 .
gi 351061952  91 F 91
Cdd:cd03279  199 I 199

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 351061952  20 FRPMDNLSGGEKTIAALALLFAVHGRnpapFFVLDEIDAALDNTNIGKVASYICESAREH-MQIIVISLKEEFYN 93
Cdd:COG2401  131 LRRFKELSTGQKFRFRLALLLAERPK----LLVIDEFCSHLDRQTAKRVARNLQKLARRAgITLVVATHHYDVID 201

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        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 351061952  21 RPMDNLSGGEKTIAALALLFAvhgRNPaPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVISL 87
Cdd:cd03214   93 RPFNELSGGERQRVLLARALA---QEP-PILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVL 155

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 351061952  21 RPMDNLSGGEK---TIAALALLFAVHGRNPAPFFVLDEIDAALDNTNIGKVASYICESAREHMQIIV 84
Cdd:COG3593  158 LPLDRLGSGFQrliLLALLSALAELKRAPANPILLIEEPEAHLHPQAQRRLLKLLKELSEKPNQVII 224

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 351061952  24 DNLSGGEKT---IAALALLfavhgrNPApFFVLDEIDAALDNTNIGKVASYICESAREHMQIIVISLKEEF--YNKAD 96
Cdd:cd03217  103 EGFSGGEKKrneILQLLLL------EPD-LAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQRLldYIKPD 173