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Conserved domains on  [gi|25147160|ref|NP_509956|]
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Structural maintenance of chromosomes-like protein 1 [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 8-123 4.03e-15

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.


The actual alignment was detected with superfamily member cd03275:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 247  Bit Score: 75.30  E-value: 4.03e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160   8 LLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDYNI------RCVVSLK 81
Cdd:cd03275   1 LKRLELENFKSYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLKDLIYRARVgkpdsnSAYVTAV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 25147160  82 FEMPDGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLELGKMN 123
Cdd:cd03275  81 YEDDDGEEKTFRRIITGGSSSYRINGKVVSLKEYNEELEKIN 122
SMC_N super family cl47134
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 112-520 1.03e-11

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.


The actual alignment was detected with superfamily member pfam02463:

Pssm-ID: 481474 [Multi-domain]  Cd Length: 1161  Bit Score: 67.69  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    112 EEEYLLELGKMNFRFAGQNISVYNKTTLKVTRKSAEELGAFFDIVSNSIEFKPEYDELKAKLNFAESTVLRWAKMIDSIE 191
Cdd:pfam02463  735 NEELKLLKQKIDEEEEEEEKSRLKKEEKEEEKSELSLKEKELAEEREKTEKLKVEEEKEEKLKAQEEELRALEEELKEEA 814

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    192 LEKEKFITLTLYKLYLCDKEIQEtKEKFVAEQLKVNAKNAKmplRISRYSEAIpkqtpspnfKNNAIVVRPKTHNHYDNL 271
Cdd:pfam02463  815 ELLEEEQLLIEQEEKIKEEELEE-LALELKEEQKLEKLAEE---ELERLEEEI---------TKEELLQELLLKEEELEE 881

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    272 ITVDKLNSYLNEKVTERRELLQFAVNHPNMNIRFSEEGPNIYAREIDYTELPEYYKKESDDIIATSYKRSMLEKEIKKIR 351
Cdd:pfam02463  882 QKLKDELESKEEKEKEEKKELEEESQKLNLLEEKENEIEERIKEEAEILLKYEEEPEELLLEEADEKEKEENNKEEEEER 961

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    352 QCwLDENNIKDDANIDNINMRIKEATTKHTLALNIEsEARLNWEKLRV------MRSARFNNFM-APLQTSLSRIYAEIA 424
Cdd:pfam02463  962 NK-RLLLAKEELGKVNLMAIEEFEEKEERYNKDELE-KERLEEEKKKLiraiieETCQRLKEFLeLFVSINKGWNKVFFY 1039

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    425 QDEDSLAFLRPLDEEEPYLA-IDAFVKERHSEHISTRTFHGGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKK 503
Cdd:pfam02463 1040 LELGGSAELRLEDPDDPFSGgIEISARPPGKGVKNLDLLSGGEKTLVALALIFAIQKYKPAPFYLLDEIDAALDDQNVSR 1119

                          410
                   ....*....|....*...
gi 25147160    504 IEPYL-SRQKQTQFIVTT 520
Cdd:pfam02463 1120 VANLLkELSKNAQFIVIS 1137
 
Name Accession Description Interval E-value
ABC_SMC1_euk cd03275
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ...
 8-123 4.03e-15

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).


Pssm-ID: 213242 [Multi-domain]  Cd Length: 247  Bit Score: 75.30  E-value: 4.03e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160   8 LLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDYNI------RCVVSLK 81
Cdd:cd03275   1 LKRLELENFKSYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLKDLIYRARVgkpdsnSAYVTAV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 25147160  82 FEMPDGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLELGKMN 123
Cdd:cd03275  81 YEDDDGEEKTFRRIITGGSSSYRINGKVVSLKEYNEELEKIN 122
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 112-520 1.03e-11

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.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 67.69  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    112 EEEYLLELGKMNFRFAGQNISVYNKTTLKVTRKSAEELGAFFDIVSNSIEFKPEYDELKAKLNFAESTVLRWAKMIDSIE 191
Cdd:pfam02463  735 NEELKLLKQKIDEEEEEEEKSRLKKEEKEEEKSELSLKEKELAEEREKTEKLKVEEEKEEKLKAQEEELRALEEELKEEA 814

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    192 LEKEKFITLTLYKLYLCDKEIQEtKEKFVAEQLKVNAKNAKmplRISRYSEAIpkqtpspnfKNNAIVVRPKTHNHYDNL 271
Cdd:pfam02463  815 ELLEEEQLLIEQEEKIKEEELEE-LALELKEEQKLEKLAEE---ELERLEEEI---------TKEELLQELLLKEEELEE 881

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    272 ITVDKLNSYLNEKVTERRELLQFAVNHPNMNIRFSEEGPNIYAREIDYTELPEYYKKESDDIIATSYKRSMLEKEIKKIR 351
Cdd:pfam02463  882 QKLKDELESKEEKEKEEKKELEEESQKLNLLEEKENEIEERIKEEAEILLKYEEEPEELLLEEADEKEKEENNKEEEEER 961

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    352 QCwLDENNIKDDANIDNINMRIKEATTKHTLALNIEsEARLNWEKLRV------MRSARFNNFM-APLQTSLSRIYAEIA 424
Cdd:pfam02463  962 NK-RLLLAKEELGKVNLMAIEEFEEKEERYNKDELE-KERLEEEKKKLiraiieETCQRLKEFLeLFVSINKGWNKVFFY 1039

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    425 QDEDSLAFLRPLDEEEPYLA-IDAFVKERHSEHISTRTFHGGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKK 503
Cdd:pfam02463 1040 LELGGSAELRLEDPDDPFSGgIEISARPPGKGVKNLDLLSGGEKTLVALALIFAIQKYKPAPFYLLDEIDAALDDQNVSR 1119

                          410
                   ....*....|....*...
gi 25147160    504 IEPYL-SRQKQTQFIVTT 520
Cdd:pfam02463 1120 VANLLkELSKNAQFIVIS 1137
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 464-520 4.35e-08

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.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 53.08  E-value: 4.35e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSRQ--KQTQFIVTT 520
Cdd:cd03239  97 GGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMakHTSQFIVIT 155
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
7-94 5.01e-06

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 47.31  E-value: 5.01e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160   7 RLLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDyNIRCVVSLKFEMpD 86
Cdd:COG0419   1 KLLRLRLENFRSYRDTETIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRSDLINVG-SEEASVELEFEH-G 78


                ....*...
gi 25147160  87 GSTKRFTR 94
Cdd:COG0419  79 GKRYRIER 86
AAA_23 pfam13476
AAA domain;
13-119 3.33e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 44.79  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    13 ILNFKCYQHhKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDY-------NIRCVVSLKFEmp 85
Cdd:pfam13476   3 IENFRSFRD-QTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGDiriglegKGKAYVEITFE-- 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 25147160    86 DGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLEL 119
Cdd:pfam13476  80 NNDGRYTYAIERSRELSKKKGKTKKKEILEILEI 113
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 158-533 3.77e-05

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]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 46.60  E-value: 3.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    158 NSIEFKP---EYDELKAKLNFAESTVLRWAKMIDSIELEKEKfitLTLYKLYLCDK---------EIQETKEKFVAEQLK 225
Cdd:TIGR02169  782 NDLEARLshsRIPEIQAELSKLEEEVSRIEARLREIEQKLNR---LTLEKEYLEKEiqelqeqriDLKEQIKSIEKEIEN 858

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    226 VNAKNAKMPLRISRYSEAIpKQTPSP--NFKNNaivvRPKTHNHYDNL-ITVDKLNSYLNEKvteRRELLQFAVNHPNMN 302
Cdd:TIGR02169  859 LNGKKEELEEELEELEAAL-RDLESRlgDLKKE----RDELEAQLRELeRKIEELEAQIEKK---RKRLSELKAKLEALE 930

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    303 IRFSEEGPNIYAREIDYTELPEYykkesDDIIAtsyKRSMLEKEIKKirqcwLDENNIKDDANIDNINMRIKEATTKHTl 382
Cdd:TIGR02169  931 EELSEIEDPKGEDEEIPEEELSL-----EDVQA---ELQRVEEEIRA-----LEPVNMLAIQEYEEVLKRLDELKEKRA- 996

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    383 ALNIESEARL----NWEKLRvmRSARFNNFMApLQTSLSRIYAEIAQDEDSLAFLRPLDEEEPYLAIDAFVKERHSEHIS 458
Cdd:TIGR02169  997 KLEEERKAILerieEYEKKK--REVFMEAFEA-INENFNEIFAELSGGTGELILENPDDPFAGGLELSAKPKGKPVQRLE 1073

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 25147160    459 TRTfhGGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNL-YHEASKKIEPYLSRQKQTQFIVTTKEDSYFTEVTKTI 533
Cdd:TIGR02169 1074 AMS--GGEKSLTALSFIFAIQRYKPSPFYAFDEVDMFLdGVNVERVAKLIREKAGEAQFIVVSLRSPMIEYADRAI 1147
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 23-55 2.44e-03

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]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 2.44e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 25147160     23 KSFG-----PFDH-VTTFIGMNGCGKSIMIEAIAFVFGE 55
Cdd:TIGR02168   11 KSFAdpttiNFDKgITGIVGPNGCGKSNIVDAIRWVLGE 49
 
Name Accession Description Interval E-value
ABC_SMC1_euk cd03275
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ...
 8-123 4.03e-15

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).


Pssm-ID: 213242 [Multi-domain]  Cd Length: 247  Bit Score: 75.30  E-value: 4.03e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160   8 LLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDYNI------RCVVSLK 81
Cdd:cd03275   1 LKRLELENFKSYKGRHVIGPFDRFTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLKDLIYRARVgkpdsnSAYVTAV 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 25147160  82 FEMPDGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLELGKMN 123
Cdd:cd03275  81 YEDDDGEEKTFRRIITGGSSSYRINGKVVSLKEYNEELEKIN 122
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 112-520 1.03e-11

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.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 67.69  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    112 EEEYLLELGKMNFRFAGQNISVYNKTTLKVTRKSAEELGAFFDIVSNSIEFKPEYDELKAKLNFAESTVLRWAKMIDSIE 191
Cdd:pfam02463  735 NEELKLLKQKIDEEEEEEEKSRLKKEEKEEEKSELSLKEKELAEEREKTEKLKVEEEKEEKLKAQEEELRALEEELKEEA 814

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    192 LEKEKFITLTLYKLYLCDKEIQEtKEKFVAEQLKVNAKNAKmplRISRYSEAIpkqtpspnfKNNAIVVRPKTHNHYDNL 271
Cdd:pfam02463  815 ELLEEEQLLIEQEEKIKEEELEE-LALELKEEQKLEKLAEE---ELERLEEEI---------TKEELLQELLLKEEELEE 881

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    272 ITVDKLNSYLNEKVTERRELLQFAVNHPNMNIRFSEEGPNIYAREIDYTELPEYYKKESDDIIATSYKRSMLEKEIKKIR 351
Cdd:pfam02463  882 QKLKDELESKEEKEKEEKKELEEESQKLNLLEEKENEIEERIKEEAEILLKYEEEPEELLLEEADEKEKEENNKEEEEER 961

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    352 QCwLDENNIKDDANIDNINMRIKEATTKHTLALNIEsEARLNWEKLRV------MRSARFNNFM-APLQTSLSRIYAEIA 424
Cdd:pfam02463  962 NK-RLLLAKEELGKVNLMAIEEFEEKEERYNKDELE-KERLEEEKKKLiraiieETCQRLKEFLeLFVSINKGWNKVFFY 1039

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    425 QDEDSLAFLRPLDEEEPYLA-IDAFVKERHSEHISTRTFHGGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKK 503
Cdd:pfam02463 1040 LELGGSAELRLEDPDDPFSGgIEISARPPGKGVKNLDLLSGGEKTLVALALIFAIQKYKPAPFYLLDEIDAALDDQNVSR 1119

                          410
                   ....*....|....*...
gi 25147160    504 IEPYL-SRQKQTQFIVTT 520
Cdd:pfam02463 1120 VANLLkELSKNAQFIVIS 1137
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 464-520 4.35e-08

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.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 53.08  E-value: 4.35e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSRQ--KQTQFIVTT 520
Cdd:cd03239  97 GGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMakHTSQFIVIT 155
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 10-398 7.36e-08

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.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 55.36  E-value: 7.36e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160     10 TVDILNFKCYQHHKSfGPFDHVTTFI-GMNGCGKSIMIEAIAFVFGEDlpdpknpHNEHL---------FYDYN---IRC 76
Cdd:pfam02463    4 RIEIEGFKSYAKTVI-LPFSPGFTAIvGPNGSGKSNILDAILFVLGER-------SAKSLrserlsdliHSKSGafvNSA 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160     77 VVSLKFEMPDGSTKR-------FTRIGLKTTYTYMIFNKYVTEEEYLLELGKMNFRFAGQNISVYNKTTLKVTRKSAEEL 149
Cdd:pfam02463   76 EVEITFDNEDHELPIdkeevsiRRRVYRGGDSEYYINGKNVTKKEVAELLESQGISPEAYNFLVQGGKIEIIAMMKPERR 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    150 GAFFDIVSNSIEFKPEYDELKAKLNFAES-----------------TVLRWAKMIDSIELEKEKFITL--TLYKLYLcdK 210
Cdd:pfam02463  156 LEIEEEAAGSRLKRKKKEALKKLIEETENlaeliidleelklqelkLKEQAKKALEYYQLKEKLELEEeyLLYLDYL--K 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    211 EIQETKEKFVAEQLKVNAKNAKMpLRISRYSEAIPKQTPSPNFKNNAIVvrPKTHNHYDNLITVDKLNSYLNEKVTERRE 290
Cdd:pfam02463  234 LNEERIDLLQELLRDEQEEIESS-KQEIEKEEEKLAQVLKENKEEEKEK--KLQEEELKLLAKEEEELKSELLKLERRKV 310

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    291 LLQFAVNHPNMNIRF--SEEGPNIYAREIDYTELPEYYKKESDDIIATSYKRSMLEKEIKKirqcwLDENNIKDDANIDN 368
Cdd:pfam02463  311 DDEEKLKESEKEKKKaeKELKKEKEEIEELEKELKELEIKREAEEEEEEELEKLQEKLEQL-----EEELLAKKKLESER 385

                          410       420       430
                   ....*....|....*....|....*....|
gi 25147160    369 INMRIKEATTKHTLALNIESEARLNWEKLR 398
Cdd:pfam02463  386 LSSAAKLKEEELELKSEEEKEAQLLLELAR 415
ABC_SMC3_euk cd03272
ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of ...
 464-520 7.00e-07

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).


Pssm-ID: 213239 [Multi-domain]  Cd Length: 243  Bit Score: 50.72  E-value: 7.00e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNL---YHEASKKIEPYLSrqKQTQFIVTT 520
Cdd:cd03272 161 GGQKSLVALALIFAIQKCDPAPFYLFDEIDAALdaqYRTAVANMIKELS--DGAQFITTT 218
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 15-55 1.24e-06

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.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 48.84  E-value: 1.24e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 25147160  15 NFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGE 55
Cdd:cd03239   8 NFKSYRDETVVGGSNSFNAIVGPNGSGKSNIVDAICFVLGG 48
ABC_SMC1_euk cd03275
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ...
 464-527 1.98e-06

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).


Pssm-ID: 213242 [Multi-domain]  Cd Length: 247  Bit Score: 49.11  E-value: 1.98e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSRQ--KQTQFIVTTKEDSYFT 527
Cdd:cd03275 158 GGEKTMAALALLFAIHSYQPAPFFVLDEVDAALDNTNVGKVASYIREQagPNFQFIVISLKEEFFS 223
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 15-54 3.47e-06

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).


Pssm-ID: 213241 [Multi-domain]  Cd Length: 212  Bit Score: 48.06  E-value: 3.47e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 25147160  15 NFKCYQHHKSFGPFDH-VTTFIGMNGCGKSIMIEAIAFVFG 54
Cdd:cd03274  10 NFKSYAGEQVIGPFHKsFSAIVGPNGSGKSNVIDSMLFVFG 50
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 464-518 3.50e-06

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).


Pssm-ID: 213241 [Multi-domain]  Cd Length: 212  Bit Score: 48.06  E-value: 3.50e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYL-SRQKQTQFIV 518
Cdd:cd03274 130 GGEKTLSSLALVFALHHYKPTPLYVMDEIDAALDFRNVSIVANYIkERTKNAQFIV 185
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
7-94 5.01e-06

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 47.31  E-value: 5.01e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160   7 RLLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDyNIRCVVSLKFEMpD 86
Cdd:COG0419   1 KLLRLRLENFRSYRDTETIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRSDLINVG-SEEASVELEFEH-G 78


                ....*...
gi 25147160  87 GSTKRFTR 94
Cdd:COG0419  79 GKRYRIER 86
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 464-520 1.19e-05

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).


Pssm-ID: 213245 [Multi-domain]  Cd Length: 197  Bit Score: 46.30  E-value: 1.19e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSRQ-KQTQFIVTT 520
Cdd:cd03278 116 GGEKALTALALLFAIFRVRPSPFCVLDEVDAALDDANVERFARLLKEFsKETQFIVIT 173
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 464-520 1.27e-05

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.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 45.43  E-value: 1.27e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSR--QKQTQFIVTT 520
Cdd:cd03227  80 GGEKELSALALILALASLKPRPLYILDEIDRGLDPRDGQALAEAILEhlVKGAQVIVIT 138
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 23-55 1.31e-05

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).


Pssm-ID: 213245 [Multi-domain]  Cd Length: 197  Bit Score: 45.92  E-value: 1.31e-05
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 25147160  23 KSFG-----PFDH-VTTFIGMNGCGKSIMIEAIAFVFGE 55
Cdd:cd03278  10 KSFAdkttiPFPPgLTAIVGPNGSGKSNIIDAIRWVLGE 48
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
7-54 2.19e-05

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 46.14  E-value: 2.19e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 25147160   7 RLLTVDILNFKCYQHHK-SFGPFDHVTTFIGMNGCGKSIMIEAIAFVFG 54
Cdd:COG3950   2 RIKSLTIENFRGFEDLEiDFDNPPRLTVLVGENGSGKTTLLEAIALALS 50
AAA_23 pfam13476
AAA domain;
13-119 3.33e-05

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 44.79  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    13 ILNFKCYQHhKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDY-------NIRCVVSLKFEmp 85
Cdd:pfam13476   3 IENFRSFRD-QTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGGGFVKGDiriglegKGKAYVEITFE-- 79

                          90       100       110
                  ....*....|....*....|....*....|....
gi 25147160    86 DGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLEL 119
Cdd:pfam13476  80 NNDGRYTYAIERSRELSKKKGKTKKKEILEILEI 113
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 7-83 3.59e-05

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


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 46.15  E-value: 3.59e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 25147160   7 RLLTVDILNFKCYQHHkSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDYN-IRCVVSLKFE 83
Cdd:COG3593   2 KLEKIKIKNFRSIKDL-SIELSDDLTVLVGENNSGKSSILEALRLLLGPSSSRKFDEEDFYLGDDPDlPEIEIELTFG 78
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 158-533 3.77e-05

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]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 46.60  E-value: 3.77e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    158 NSIEFKP---EYDELKAKLNFAESTVLRWAKMIDSIELEKEKfitLTLYKLYLCDK---------EIQETKEKFVAEQLK 225
Cdd:TIGR02169  782 NDLEARLshsRIPEIQAELSKLEEEVSRIEARLREIEQKLNR---LTLEKEYLEKEiqelqeqriDLKEQIKSIEKEIEN 858

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    226 VNAKNAKMPLRISRYSEAIpKQTPSP--NFKNNaivvRPKTHNHYDNL-ITVDKLNSYLNEKvteRRELLQFAVNHPNMN 302
Cdd:TIGR02169  859 LNGKKEELEEELEELEAAL-RDLESRlgDLKKE----RDELEAQLRELeRKIEELEAQIEKK---RKRLSELKAKLEALE 930

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    303 IRFSEEGPNIYAREIDYTELPEYykkesDDIIAtsyKRSMLEKEIKKirqcwLDENNIKDDANIDNINMRIKEATTKHTl 382
Cdd:TIGR02169  931 EELSEIEDPKGEDEEIPEEELSL-----EDVQA---ELQRVEEEIRA-----LEPVNMLAIQEYEEVLKRLDELKEKRA- 996

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25147160    383 ALNIESEARL----NWEKLRvmRSARFNNFMApLQTSLSRIYAEIAQDEDSLAFLRPLDEEEPYLAIDAFVKERHSEHIS 458
Cdd:TIGR02169  997 KLEEERKAILerieEYEKKK--REVFMEAFEA-INENFNEIFAELSGGTGELILENPDDPFAGGLELSAKPKGKPVQRLE 1073

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 25147160    459 TRTfhGGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNL-YHEASKKIEPYLSRQKQTQFIVTTKEDSYFTEVTKTI 533
Cdd:TIGR02169 1074 AMS--GGEKSLTALSFIFAIQRYKPSPFYAFDEVDMFLdGVNVERVAKLIREKAGEAQFIVVSLRSPMIEYADRAI 1147
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 16-54 7.60e-05

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).


Pssm-ID: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 44.60  E-value: 7.60e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 25147160  16 FKCYQHHKSFGPFD-HVTTFIGMNGCGKSIMIEAIAFVFG 54
Cdd:cd03273  11 FKSYATRTVISGFDpQFNAITGLNGSGKSNILDAICFVLG 50
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 464-527 2.23e-04

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).


Pssm-ID: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 43.06  E-value: 2.23e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 25147160 464 GGSRMIVDLALIFAIHEWKPSPLVVIDDIDRNLYHEASKKIEPYLSRQ-KQTQFIVTTKEDSYFT 527
Cdd:cd03273 169 GGQRSLVALSLILALLLFKPAPMYILDEVDAALDLSHTQNIGRMIKTHfKGSQFIVVSLKEGMFN 233
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 13-87 1.65e-03

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.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 39.90  E-value: 1.65e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 25147160  13 ILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFV-FGEDLPDPK-NPHNEHLFYDYNIRCVVSLKFEMPDG 87
Cdd:cd03240   6 IRNIRSFHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYAlTGELPPNSKgGAHDPKLIREGEVRAQVKLAFENANG 82
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 23-55 2.44e-03

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]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.81  E-value: 2.44e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 25147160     23 KSFG-----PFDH-VTTFIGMNGCGKSIMIEAIAFVFGE 55
Cdd:TIGR02168   11 KSFAdpttiNFDKgITGIVGPNGCGKSNIVDAIRWVLGE 49
COG4637 COG4637
Predicted ATPase [General function prediction only];
7-52 2.74e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 40.30  E-value: 2.74e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 25147160   7 RLLTVDILNFKCYQH-HKSFGPFdhvTTFIGMNGCGKSIMIEAIAFV 52
Cdd:COG4637   1 MITRIRIKNFKSLRDlELPLGPL---TVLIGANGSGKSNLLDALRFL 44
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 464-520 3.10e-03

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]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.43  E-value: 3.10e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 25147160    464 GGSRMIVDLALIFAIHEWKPSPLVVIDDID---------R--NLYHEASkkiepylsrqKQTQFIVTT 520
Cdd:TIGR02168 1092 GGEKALTALALLFAIFKVKPAPFCILDEVDaplddanveRfaNLLKEFS----------KNTQFIVIT 1149
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 7-55 4.42e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 39.92  E-value: 4.42e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 25147160   7 RLLTVDILNFKcyqhhkSFG-----PFDH-VTTFIGMNGCGKS-ImIEAIAFVFGE 55
Cdd:COG1196   2 RLKRLELAGFK------SFAdpttiPFEPgITAIVGPNGSGKSnI-VDAIRWVLGE 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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