NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|188219597|ref|NP_035388|]
View 

replication factor C subunit 1 isoform 2 [Mus musculus]

Protein Classification

AAA and RFC1 domain-containing protein; BRCT_RFC1 and RFC1 domain-containing protein( domain architecture ID 13027101)

protein containing domains BRCT_RFC1, AAA, and RFC1; protein containing domains COG5275, BRCT_RFC1, AAA, and RFC1

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 899-1052 1.52e-75

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


:

Pssm-ID: 462507  Cd Length: 158  Bit Score: 245.95  E-value: 1.52e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   899 ICDGDLVDNQIRSKQNWSLLPTQAIYASVLPGELMRGYMTQFPSFPSWLGKHSSTGKHDRIVQDLSLHMSLRTYSSKRTV 978
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597   979 NMDYLSHIRDALVRPLTSQGVEGAQHVIKLMDTYYLMKEDFENIMEVSSWG----GKPSAFSKLDPKVKAAFTRAYNK 1052
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 568-987 1.61e-52

replication factor C large subunit; Provisional


The actual alignment was detected with superfamily member PRK04195:

Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 192.06  E-value: 1.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  568 LLWVDKYKPASLKNIIGQQgdqSCANKLLRWLRNWHKSSPEekkhaakfgklaskddgssfKAALLSGPPGVGKTTTASL 647
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLKGKPK--------------------KALLLYGPPGVGKTSLAHA 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  648 VCQELGYSYVELNASDTRSKNSLKAVVAESLNNTSIKGfytsgaapsvSARHALIMDEVDGMAGNEDRGGIQELIGLIKH 727
Cdd:PRK04195   59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG----------ARRKLILLDEVDGIHGNEDRGGARAILELIKK 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  728 TKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGANQDVRQVLHNLSMWCA 807
Cdd:PRK04195  129 AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  808 QSKALTYDQAKADSQRakkDIRLGPFDVTRKVFAA-GEETAHMSLMDkSDLFFHDYSiapLFVQEN----YLHVKPVAAG 882
Cdd:PRK04195  209 GYGKLTLEDVKTLGRR---DREESIFDALDAVFKArNADQALEASYD-VDEDPDDLI---EWIDENipkeYDDPEDIARA 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  883 GDMkkhlmlLSRAadsicdgDLVDNQIRSKQNWSLLPtqaiYASvlpgELM------------RGYmTQFpSFPSWLGKH 950
Cdd:PRK04195  282 YDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSYWRLL 338

                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 188219597  951 SSTGKHDRIVQDLSLHMSLRTYSSKRTVNMDYLSHIR 987
Cdd:PRK04195  339 SKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 399-477 3.25e-47

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


:

Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 162.77  E-value: 3.25e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 188219597  399 GAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKILDEDGLLDLIR 477
Cdd:cd17752     1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
PTZ00121 super family cl31754
MAEBL; Provisional
 14-372 1.84e-06

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 52.45  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   14 KKPVNETVKNE--KTKASEGTVKG---KKGVKEAKvnnsGKEDASKPKQHSKKKRIINDSDSESEETVQVKNAKKKSEkl 88
Cdd:PTZ00121 1308 KKKAEEAKKADeaKKKAEEAKKKAdaaKKKAEEAK----KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD-- 1381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   89 SLSYKPGKVSQKDPVTYVSETDEDD-DFVCKKAASKSKENGVSTNSylgtSNVKKNEENVKTKNKPLSPIKLTPTSVLDY 167
Cdd:PTZ00121 1382 AAKKKAEEKKKADEAKKKAEEDKKKaDELKKAAAAKKKADEAKKKA----EEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  168 FGTESVQRSGKKmvtSKRKESSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEFARTLALL------DEEPKIKKAR 241
Cdd:PTZ00121 1458 KAEEAKKKAEEA---KKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAeeakkaDEAKKAEEAK 1534

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  242 KDSEEGEESFSSVQDDLSKAEKQKSPNKAELFSTARKTySPAKHGKGRASEDAKQpcksAHRKEACSSPKASAKLALMKA 321
Cdd:PTZ00121 1535 KADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKA-EEDKNMALRKAEEAKK----AEEARIEEVMKLYEEEKKMKA 1609

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 188219597  322 KEESSYNETELLAARRKESATEPKGEKTTPKKTKVSPTKRESVSPEDSEKK 372
Cdd:PTZ00121 1610 EEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENK 1660
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 899-1052 1.52e-75

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


Pssm-ID: 462507  Cd Length: 158  Bit Score: 245.95  E-value: 1.52e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   899 ICDGDLVDNQIRSKQNWSLLPTQAIYASVLPGELMRGYMTQFPSFPSWLGKHSSTGKHDRIVQDLSLHMSLRTYSSKRTV 978
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597   979 NMDYLSHIRDALVRPLTSQGVEGAQHVIKLMDTYYLMKEDFENIMEVSSWG----GKPSAFSKLDPKVKAAFTRAYNK 1052
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 568-987 1.61e-52

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 192.06  E-value: 1.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  568 LLWVDKYKPASLKNIIGQQgdqSCANKLLRWLRNWHKSSPEekkhaakfgklaskddgssfKAALLSGPPGVGKTTTASL 647
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLKGKPK--------------------KALLLYGPPGVGKTSLAHA 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  648 VCQELGYSYVELNASDTRSKNSLKAVVAESLNNTSIKGfytsgaapsvSARHALIMDEVDGMAGNEDRGGIQELIGLIKH 727
Cdd:PRK04195   59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG----------ARRKLILLDEVDGIHGNEDRGGARAILELIKK 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  728 TKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGANQDVRQVLHNLSMWCA 807
Cdd:PRK04195  129 AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  808 QSKALTYDQAKADSQRakkDIRLGPFDVTRKVFAA-GEETAHMSLMDkSDLFFHDYSiapLFVQEN----YLHVKPVAAG 882
Cdd:PRK04195  209 GYGKLTLEDVKTLGRR---DREESIFDALDAVFKArNADQALEASYD-VDEDPDDLI---EWIDENipkeYDDPEDIARA 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  883 GDMkkhlmlLSRAadsicdgDLVDNQIRSKQNWSLLPtqaiYASvlpgELM------------RGYmTQFpSFPSWLGKH 950
Cdd:PRK04195  282 YDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSYWRLL 338

                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 188219597  951 SSTGKHDRIVQDLSLHMSLRTYSSKRTVNMDYLSHIR 987
Cdd:PRK04195  339 SKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 399-477 3.25e-47

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 162.77  E-value: 3.25e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 188219597  399 GAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKILDEDGLLDLIR 477
Cdd:cd17752     1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
395-476 9.22e-29

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 123.60  E-value: 9.22e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  395 EIPKGAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKILDEDGLLD 474
Cdd:COG0272   587 EAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLE 665


                  ..
gi 188219597  475 LI 476
Cdd:COG0272   666 LL 667
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 389-476 3.73e-26

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 115.61  E-value: 3.73e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  389 KALGSKEIPKGAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKILD 468
Cdd:PRK07956  576 LEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLD 654


                  ....*...
gi 188219597  469 EDGLLDLI 476
Cdd:PRK07956  655 EEEFLRLL 662
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 632-760 5.46e-17

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 78.40  E-value: 5.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   632 LLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKnslkaVVAESLNNtsIKGFYT--SGAAPSVsarhaLIMDEVDGM 709
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-----YVGESEKR--LRELFEaaKKLAPCV-----IFIDEIDAL 69

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 188219597   710 AGNEDRGGIQELIGLI------------KHTKIPIICMCNdrNHPKIRSLVHYCFDLRFQRPR 760
Cdd:pfam00004   70 AGSRGSGGDSESRRVVnqllteldgftsSNSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 401-476 3.71e-16

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 74.25  E-value: 3.71e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597   401 ENCLEGLTFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMgrDSGQSKSDKAAALGTKILDEDGLLDLI 476
Cdd:pfam00533    3 EKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
BRCT smart00292
breast cancer carboxy-terminal domain;
401-476 9.51e-15

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 70.10  E-value: 9.51e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597    401 ENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA--LGTKILDEDGLLDLI 476
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKAiaLGIPIVKEEWLLDCL 78
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 618-756 1.07e-14

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 72.56  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  618 KLASKDDGSSFKAALLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKNSLKAVVAESLNNtsIKGFYTSGAAPS 694
Cdd:cd00009     9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHFLVR--LLFELAEKAKPG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  695 VsarhaLIMDEVDGMAGNEDRGGIQEL----IGLIKHTKIPIICMCNDRNHPKIRSLVHYCFDLRF 756
Cdd:cd00009    87 V-----LFIDEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 632-762 1.98e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.98e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597    632 LLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKNSLKAVVaesLNNTSIKGFYTSGAAPSVSARHA-------L 701
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLL---IIVGGKKASGSGELRLRLALALArklkpdvL 82

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 188219597    702 IMDEVDGMAGNEDRGGIQE------LIGLIKHTKIPIICMCNDRNHPKIRSLVHyCFDLRFQRPRVE 762
Cdd:smart00382   83 ILDEITSLLDAEQEALLLLleelrlLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 629-717 3.90e-07

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 53.76  E-value: 3.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  629 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK------NSLKAVVAESLnntsikgfytsGAAPSVsarhaLI 702
Cdd:COG0464   192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteKNLREVFDKAR-----------GLAPCV-----LF 255

                          90
                  ....*....|....*
gi 188219597  703 MDEVDGMAGNEDRGG 717
Cdd:COG0464   256 IDEADALAGKRGEVG 270
PTZ00121 PTZ00121
MAEBL; Provisional
 14-372 1.84e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 52.45  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   14 KKPVNETVKNE--KTKASEGTVKG---KKGVKEAKvnnsGKEDASKPKQHSKKKRIINDSDSESEETVQVKNAKKKSEkl 88
Cdd:PTZ00121 1308 KKKAEEAKKADeaKKKAEEAKKKAdaaKKKAEEAK----KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD-- 1381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   89 SLSYKPGKVSQKDPVTYVSETDEDD-DFVCKKAASKSKENGVSTNSylgtSNVKKNEENVKTKNKPLSPIKLTPTSVLDY 167
Cdd:PTZ00121 1382 AAKKKAEEKKKADEAKKKAEEDKKKaDELKKAAAAKKKADEAKKKA----EEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  168 FGTESVQRSGKKmvtSKRKESSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEFARTLALL------DEEPKIKKAR 241
Cdd:PTZ00121 1458 KAEEAKKKAEEA---KKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAeeakkaDEAKKAEEAK 1534

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  242 KDSEEGEESFSSVQDDLSKAEKQKSPNKAELFSTARKTySPAKHGKGRASEDAKQpcksAHRKEACSSPKASAKLALMKA 321
Cdd:PTZ00121 1535 KADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKA-EEDKNMALRKAEEAKK----AEEARIEEVMKLYEEEKKMKA 1609

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 188219597  322 KEESSYNETELLAARRKESATEPKGEKTTPKKTKVSPTKRESVSPEDSEKK 372
Cdd:PTZ00121 1610 EEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENK 1660
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 551-658 4.61e-05

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 47.64  E-value: 4.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   551 LDVKETHG--NRSSNKEECLLWVDKYKPaslkniigqqgdqSCANKLLRwlrnwHKSSPEEKKHAAKFGKLASKDDgssf 628
Cdd:TIGR00602   53 LSLEQDTGleLSSENLDGNEPWVEKYKP-------------ETQHELAV-----HKKKIEEVETWLKAQVLENAPK---- 110

                           90       100       110
                   ....*....|....*....|....*....|
gi 188219597   629 KAALLSGPPGVGKTTTASLVCQELGYSYVE 658
Cdd:TIGR00602  111 RILLITGPSGCGKSTTIKILSKELGIQVQE 140
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 899-1052 1.52e-75

Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo.


Pssm-ID: 462507  Cd Length: 158  Bit Score: 245.95  E-value: 1.52e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   899 ICDGDLVDNQIRSKQNWSLLPTQAIYASVLPGELMRGYMTQFPSFPSWLGKHSSTGKHDRIVQDLSLHMSLRTYSSKRTV 978
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597   979 NMDYLSHIRDALVRPLTSQGVEGAQHVIKLMDTYYLMKEDFENIMEVSSWG----GKPSAFSKLDPKVKAAFTRAYNK 1052
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 568-987 1.61e-52

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 192.06  E-value: 1.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  568 LLWVDKYKPASLKNIIGQQgdqSCANKLLRWLRNWHKSSPEekkhaakfgklaskddgssfKAALLSGPPGVGKTTTASL 647
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLKGKPK--------------------KALLLYGPPGVGKTSLAHA 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  648 VCQELGYSYVELNASDTRSKNSLKAVVAESLNNTSIKGfytsgaapsvSARHALIMDEVDGMAGNEDRGGIQELIGLIKH 727
Cdd:PRK04195   59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG----------ARRKLILLDEVDGIHGNEDRGGARAILELIKK 128

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  728 TKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGANQDVRQVLHNLSMWCA 807
Cdd:PRK04195  129 AKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE 208

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  808 QSKALTYDQAKADSQRakkDIRLGPFDVTRKVFAA-GEETAHMSLMDkSDLFFHDYSiapLFVQEN----YLHVKPVAAG 882
Cdd:PRK04195  209 GYGKLTLEDVKTLGRR---DREESIFDALDAVFKArNADQALEASYD-VDEDPDDLI---EWIDENipkeYDDPEDIARA 281

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  883 GDMkkhlmlLSRAadsicdgDLVDNQIRSKQNWSLLPtqaiYASvlpgELM------------RGYmTQFpSFPSWLGKH 950
Cdd:PRK04195  282 YDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSYWRLL 338

                         410       420       430
                  ....*....|....*....|....*....|....*..
gi 188219597  951 SSTGKHDRIVQDLSLHMSLRTYSSKRTVNMDYLSHIR 987
Cdd:PRK04195  339 SKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 399-477 3.25e-47

BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349383 [Multi-domain]  Cd Length: 79  Bit Score: 162.77  E-value: 3.25e-47
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 188219597  399 GAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKILDEDGLLDLIR 477
Cdd:cd17752     1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
395-476 9.22e-29

NAD-dependent DNA ligase [Replication, recombination and repair];


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 123.60  E-value: 9.22e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  395 EIPKGAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKILDEDGLLD 474
Cdd:COG0272   587 EAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLE 665


                  ..
gi 188219597  475 LI 476
Cdd:COG0272   666 LL 667
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 389-476 3.73e-26

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 115.61  E-value: 3.73e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  389 KALGSKEIPKGAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKILD 468
Cdd:PRK07956  576 LEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLD 654


                  ....*...
gi 188219597  469 EDGLLDLI 476
Cdd:PRK07956  655 EEEFLRLL 662
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 404-475 1.06e-24

BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family.


Pssm-ID: 349379 [Multi-domain]  Cd Length: 76  Bit Score: 98.32  E-value: 1.06e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  404 LEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD----KAAALGTKILDEDGLLDL 475
Cdd:cd17748     1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKgeelKAKGLGIKIISEEEFLDL 76
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 632-760 5.46e-17

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 78.40  E-value: 5.46e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   632 LLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKnslkaVVAESLNNtsIKGFYT--SGAAPSVsarhaLIMDEVDGM 709
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-----YVGESEKR--LRELFEaaKKLAPCV-----IFIDEIDAL 69

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 188219597   710 AGNEDRGGIQELIGLI------------KHTKIPIICMCNdrNHPKIRSLVHYCFDLRFQRPR 760
Cdd:pfam00004   70 AGSRGSGGDSESRRVVnqllteldgftsSNSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 402-474 1.44e-16

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 84.81  E-value: 1.44e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  402 NCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKILDED---GLLD 474
Cdd:PRK14351  608 DALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEefeELLA 683
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 401-476 3.71e-16

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 74.25  E-value: 3.71e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597   401 ENCLEGLTFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMgrDSGQSKSDKAAALGTKILDEDGLLDLI 476
Cdd:pfam00533    3 EKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
BRCT smart00292
breast cancer carboxy-terminal domain;
401-476 9.51e-15

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 70.10  E-value: 9.51e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597    401 ENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA--LGTKILDEDGLLDLI 476
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKAiaLGIPIVKEEWLLDCL 78
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 618-756 1.07e-14

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 72.56  E-value: 1.07e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  618 KLASKDDGSSFKAALLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKNSLKAVVAESLNNtsIKGFYTSGAAPS 694
Cdd:cd00009     9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHFLVR--LLFELAEKAKPG 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  695 VsarhaLIMDEVDGMAGNEDRGGIQEL----IGLIKHTKIPIICMCNDRNHPKIRSLVHYCFDLRF 756
Cdd:cd00009    87 V-----LFIDEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
PLN03025 PLN03025
replication factor C subunit; Provisional
 570-802 1.36e-10

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 63.98  E-value: 1.36e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  570 WVDKYKPASLKNIIGQQGdqscankllrwlrnwhksspeekkhaaKFGKLASKDDGSSFKAALLSGPPGVGKTTTA-SLV 648
Cdd:PLN03025    3 WVEKYRPTKLDDIVGNED---------------------------AVSRLQVIARDGNMPNLILSGPPGTGKTTSIlALA 55

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  649 CQELGYSY----VELNASDTRSKNslkaVVaeslnNTSIKGFytsgAAPSVS---ARHAL-IMDEVDGMAGnedrGGIQE 720
Cdd:PLN03025   56 HELLGPNYkeavLELNASDDRGID----VV-----RNKIKMF----AQKKVTlppGRHKIvILDEADSMTS----GAQQA 118

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  721 LIGLIK----HTKIPIICMCNDRNHPKIRSlvhYCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGANQDVR 796
Cdd:PLN03025  119 LRRTMEiysnTTRFALACNTSSKIIEPIQS---RCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMR 195


                  ....*.
gi 188219597  797 QVLHNL 802
Cdd:PLN03025  196 QALNNL 201
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 759-815 1.71e-10

helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA+ superfamily.


Pssm-ID: 350842 [Multi-domain]  Cd Length: 63  Bit Score: 57.54  E-value: 1.71e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 188219597  759 PRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGANQDVRQVLHNLSMWCAQSKALTYD 815
Cdd:cd18140     1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGGVITEE 57
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 407-474 1.81e-09

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


Pssm-ID: 349339 [Multi-domain]  Cd Length: 68  Bit Score: 55.06  E-value: 1.81e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188219597  407 LTFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKILDEDGLLD 474
Cdd:cd00027     1 LVICFSG-LDDEEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEKYYLAALAWGIPIVSPEWLLD 67
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 632-762 1.98e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.98e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597    632 LLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKNSLKAVVaesLNNTSIKGFYTSGAAPSVSARHA-------L 701
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLL---IIVGGKKASGSGELRLRLALALArklkpdvL 82

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 188219597    702 IMDEVDGMAGNEDRGGIQE------LIGLIKHTKIPIICMCNDRNHPKIRSLVHyCFDLRFQRPRVE 762
Cdd:smart00382   83 ILDEITSLLDAEQEALLLLleelrlLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 572-682 2.31e-08

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 57.79  E-value: 2.31e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  572 DKYKPASLKNIIGQQ---GdqscANKLLRwlrnwhksspeekkHAAKFGKLASkddgssfkaALLSGPPGVGKTTTASLV 648
Cdd:PRK13342    4 ERMRPKTLDEVVGQEhllG----PGKPLR--------------RMIEAGRLSS---------MILWGPPGTGKTTLARII 56

                          90       100       110
                  ....*....|....*....|....*....|....
gi 188219597  649 CQELGYSYVELNASDTrSKNSLKAVVAESLNNTS 682
Cdd:PRK13342   57 AGATDAPFEALSAVTS-GVKDLREVIEEARQRRS 89
rfc PRK00440
replication factor C small subunit; Reviewed
 568-796 3.24e-08

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 56.80  E-value: 3.24e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  568 LLWVDKYKPASLKNIIGQQgdqSCANKLLRWLRNwhKSSPeekkHAakfgklaskddgssfkaaLLSGPPGVGKTTTASL 647
Cdd:PRK00440    5 EIWVEKYRPRTLDEIVGQE---EIVERLKSYVKE--KNMP----HL------------------LFAGPPGTGKTTAALA 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  648 VCQEL-GYSY----VELNASDTRSKNslkaVVaeslnNTSIKGFytSGAAPSVSARHALI-MDEVDGM---AGNEDRgGI 718
Cdd:PRK00440   58 LARELyGEDWrenfLELNASDERGID----VI-----RNKIKEF--ARTAPVGGAPFKIIfLDEADNLtsdAQQALR-RT 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  719 QELIGliKHTKIPIICmcndrNHP-KI------RslvhyCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIILGA 791
Cdd:PRK00440  126 MEMYS--QNTRFILSC-----NYSsKIidpiqsR-----CAVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVS 193


                  ....*
gi 188219597  792 NQDVR 796
Cdd:PRK00440  194 EGDMR 198
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 379-477 4.84e-08

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 55.94  E-value: 4.84e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  379 YRSYLNREGPKAlgsKEIPKGAENCLEGLTFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMG--------RD 450
Cdd:PRK06195  199 KRSNRQAPRKKK---KIIESFGFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNtkdiedlnRE 275

                          90       100       110
                  ....*....|....*....|....*....|..
gi 188219597  451 SGQSKSDKAAAL-----GTKILDEDGLLDLIR 477
Cdd:PRK06195  276 EMSNKLKKAIDLkkkgqNIKFLNEEEFLQKCK 307
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 629-717 3.90e-07

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 53.76  E-value: 3.90e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  629 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK------NSLKAVVAESLnntsikgfytsGAAPSVsarhaLI 702
Cdd:COG0464   192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteKNLREVFDKAR-----------GLAPCV-----LF 255

                          90
                  ....*....|....*
gi 188219597  703 MDEVDGMAGNEDRGG 717
Cdd:COG0464   256 IDEADALAGKRGEVG 270
BRCT_PARP1 cd17747
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ...
 404-476 4.74e-07

BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2.30), also termed ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1), or NAD(+) ADP-ribosyltransferase 1 (ADPRT 1), or poly[ADP-ribose] synthase 1, is involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism.


Pssm-ID: 349378 [Multi-domain]  Cd Length: 76  Bit Score: 48.30  E-value: 4.74e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  404 LEGLTFVITGVLeSIERDEAKSLIERYGGKVTGNVSKKTNYLV---MGRDSGQSKSDKAAALGTKILDEDGLLDLI 476
Cdd:cd17747     1 LTGMKFALIGKL-SKSKDELKKLIEKLGGKVASKVTKKVTLCIstkAEVEKMSKKMKEAKEAGVPVVSEDFLEDCI 75
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
630-812 5.15e-07

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 52.67  E-value: 5.15e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  630 AALLSGPPGVGKTTTA-----SLVCQELGYS------------------YVELNA---SDTRSKNSLKAVVaESLNNTSI 683
Cdd:COG0470    20 ALLLHGPPGIGKTTLAlalarDLLCENPEGGkacgqchsrlmaagnhpdLLELNPeekSDQIGIDQIRELG-EFLSLTPL 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  684 KGfytsgaapsvsARHALIMDEVDGMAGNEDRGGIQELIGLIKHTkiPIICMCNDRNH--PKIRSLvhyCFDLRFQRPRV 761
Cdd:COG0470    99 EG-----------GRKVVIIDEADAMNEAAANALLKTLEEPPKNT--PFILIANDPSRllPTIRSR---CQVIRFRPPSE 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 188219597  762 EQIKSAMlsiafkEGLKIPPPAMNEIILGANQDVRQVLHNLSMWcAQSKAL 812
Cdd:COG0470   163 EEALAWL------REEGVDEDALEAILRLAGGDPRAAINLLQAL-AGRKEL 206
44 PHA02544
clamp loader, small subunit; Provisional
 568-746 5.53e-07

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 52.68  E-value: 5.53e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  568 LLWVDKYKPASLKNIIGQQGDQscankllrwlrnwhksspeekkhaAKFGKLASKddGSSFKAALLSGPPGVGKTTTASL 647
Cdd:PHA02544    9 FMWEQKYRPSTIDECILPAADK------------------------ETFKSIVKK--GRIPNMLLHSPSPGTGKTTVAKA 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  648 VCQELGYSYVELNASDTR---SKNSLKAvvaeslnntsikgfYTSGAapSVSARH-ALIMDEVD--GMAGNED--RGGIQ 719
Cdd:PHA02544   63 LCNEVGAEVLFVNGSDCRidfVRNRLTR--------------FASTV--SLTGGGkVIIIDEFDrlGLADAQRhlRSFME 126

                         170       180
                  ....*....|....*....|....*....
gi 188219597  720 ELiglikHTKIPIICMCNDRN--HPKIRS 746
Cdd:PHA02544  127 AY-----SKNCSFIITANNKNgiIEPLRS 150
PTZ00121 PTZ00121
MAEBL; Provisional
 14-372 1.84e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 52.45  E-value: 1.84e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   14 KKPVNETVKNE--KTKASEGTVKG---KKGVKEAKvnnsGKEDASKPKQHSKKKRIINDSDSESEETVQVKNAKKKSEkl 88
Cdd:PTZ00121 1308 KKKAEEAKKADeaKKKAEEAKKKAdaaKKKAEEAK----KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD-- 1381

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   89 SLSYKPGKVSQKDPVTYVSETDEDD-DFVCKKAASKSKENGVSTNSylgtSNVKKNEENVKTKNKPLSPIKLTPTSVLDY 167
Cdd:PTZ00121 1382 AAKKKAEEKKKADEAKKKAEEDKKKaDELKKAAAAKKKADEAKKKA----EEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  168 FGTESVQRSGKKmvtSKRKESSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEFARTLALL------DEEPKIKKAR 241
Cdd:PTZ00121 1458 KAEEAKKKAEEA---KKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAeeakkaDEAKKAEEAK 1534

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  242 KDSEEGEESFSSVQDDLSKAEKQKSPNKAELFSTARKTySPAKHGKGRASEDAKQpcksAHRKEACSSPKASAKLALMKA 321
Cdd:PTZ00121 1535 KADEAKKAEEKKKADELKKAEELKKAEEKKKAEEAKKA-EEDKNMALRKAEEAKK----AEEARIEEVMKLYEEEKKMKA 1609

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 188219597  322 KEESSYNETELLAARRKESATEPKGEKTTPKKTKVSPTKRESVSPEDSEKK 372
Cdd:PTZ00121 1610 EEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENK 1660
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 629-737 2.78e-06

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 48.43  E-value: 2.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  629 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKnsLKAVVAESLNNTsikgF-YTSGAAPSVsarhaLIMDEVD 707
Cdd:cd19481    27 KGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSK--YVGESEKNLRKI----FeRARRLAPCI-----LFIDEID 95

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 188219597  708 GMAGNEDRGG------------IQELIGLIKHTKIPIICMCN 737
Cdd:cd19481    96 AIGRKRDSSGesgelrrvlnqlLTELDGVNSRSKVLVIAATN 137
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 576-676 3.74e-06

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 50.82  E-value: 3.74e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  576 PASLKNIIGQQgdqscanKLL---RWLRNWHKSspeekkhaakfGKLASkddgssfkaALLSGPPGVGKTTTASLVCQEL 652
Cdd:COG2256    21 PRTLDEVVGQE-------HLLgpgKPLRRAIEA-----------GRLSS---------MILWGPPGTGKTTLARLIANAT 73

                          90       100
                  ....*....|....*....|....
gi 188219597  653 GYSYVELNASDTrSKNSLKAVVAE 676
Cdd:COG2256    74 DAEFVALSAVTS-GVKDIREVIEE 96
PTZ00121 PTZ00121
MAEBL; Provisional
 18-401 7.45e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 50.52  E-value: 7.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   18 NETVKNEKTKASEGTVKGKKGVKEAKVNNSGK-EDASKPKQHSKKKRIINDSDS--ESEETVQVKNAKKKSEKlslsyKP 94
Cdd:PTZ00121 1079 FDFDAKEDNRADEATEEAFGKAEEAKKTETGKaEEARKAEEAKKKAEDARKAEEarKAEDARKAEEARKAEDA-----KR 1153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   95 GKVSQKDPVTYVSETDEDDDFVCKKAASKSKENGVSTNSYLGTSNVKKNEENVKTKNKPLSPIKLTPTSVLDYFGTESVQ 174
Cdd:PTZ00121 1154 VEIARKAEDARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAE 1233

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  175 RSGKKMVTSKRKESSQNTEDSRLNDEAIAKQLQLDEDAELERQLHEDEEF--ARTLALLDEEPKIKKARKDSEEGEESFS 252
Cdd:PTZ00121 1234 EAKKDAEEAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELkkAEEKKKADEAKKAEEKKKADEAKKKAEE 1313

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  253 SVQDDLSKAEKQKSPNKAE-LFSTARKTYSPAKHGKGRASEDAKQPCKSAHRKEAC----SSPKASAKLALMKAKEESSY 327
Cdd:PTZ00121 1314 AKKADEAKKKAEEAKKKADaAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAekkkEEAKKKADAAKKKAEEKKKA 1393

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 188219597  328 NETELLAARRKESATEPKGEKTTPKKTKVSPTKRESVSPEDSEKKRTNYQAYRSYLNREGPKALGSKEIPKGAE 401
Cdd:PTZ00121 1394 DEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAE 1467
BRCT_TopBP1_rpt2_like cd17731
second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; ...
 404-477 9.86e-06

second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the second BRCT domain.


Pssm-ID: 349363 [Multi-domain]  Cd Length: 77  Bit Score: 44.45  E-value: 9.86e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 188219597  404 LEGLTFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQsKSDKAAALGT-KILDEDGLLDLIR 477
Cdd:cd17731     3 FKGLVICVTG-FDSEERKEIQQLVEQNGGSYSPDLSKNCTHLIAGSPSGQ-KYEFARKWNSiHIVTPEWLYDSIE 75
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 573-817 3.97e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 47.18  E-value: 3.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  573 KYKPASLKNIIGQQgdqSCANKLLrwlrnwhksspeekkHAAKFGKLASkddgssfkAALLSGPPGVGKTTTASLVCQEL 652
Cdd:PRK14970   10 KYRPQTFDDVVGQS---HITNTLL---------------NAIENNHLAQ--------ALLFCGPRGVGKTTCARILARKI 63

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  653 ---GYSYVELNAS------DTRSKNSLkavvaESLNNTSIKGFYtsgaAPSVSARHALIMDEVDGMAGNEDRGGIQELIG 723
Cdd:PRK14970   64 nqpGYDDPNEDFSfnifelDAASNNSV-----DDIRNLIDQVRI----PPQTGKYKIYIIDEVHMLSSAAFNAFLKTLEE 134

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  724 LIKHTkipIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKSAMLSIAFKEGLKIPPPAMNEIIL---GANQDVRQVLH 800
Cdd:PRK14970  135 PPAHA---IFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQkadGALRDALSIFD 211

                         250
                  ....*....|....*..
gi 188219597  801 NLSMWCaqSKALTYDQA 817
Cdd:PRK14970  212 RVVTFC--GKNITRQAV 226
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 551-658 4.61e-05

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 47.64  E-value: 4.61e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   551 LDVKETHG--NRSSNKEECLLWVDKYKPaslkniigqqgdqSCANKLLRwlrnwHKSSPEEKKHAAKFGKLASKDDgssf 628
Cdd:TIGR00602   53 LSLEQDTGleLSSENLDGNEPWVEKYKP-------------ETQHELAV-----HKKKIEEVETWLKAQVLENAPK---- 110

                           90       100       110
                   ....*....|....*....|....*....|
gi 188219597   629 KAALLSGPPGVGKTTTASLVCQELGYSYVE 658
Cdd:TIGR00602  111 RILLITGPSGCGKSTTIKILSKELGIQVQE 140
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
579-662 4.12e-04

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 43.33  E-value: 4.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  579 LKNIIGQQgdqSCANKLLRWLRNWHKSspeekKHAAKFGKLASKDdgssfkaALLSGPPGVGKTTTASLVCQELGYSYVE 658
Cdd:COG1223     1 LDDVVGQE---EAKKKLKLIIKELRRR-----ENLRKFGLWPPRK-------ILFYGPPGTGKTMLAEALAGELKLPLLT 65


                  ....
gi 188219597  659 LNAS 662
Cdd:COG1223    66 VRLD 69
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 620-653 4.48e-04

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 43.83  E-value: 4.48e-04
                           10        20        30
                   ....*....|....*....|....*....|....
gi 188219597   620 ASKDDGSSFKAALLSGPPGVGKTTTASLVCQELG 653
Cdd:TIGR00635   22 AAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMG 55
Rad17 pfam03215
Rad17 P-loop domain;
563-666 5.11e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 42.25  E-value: 5.11e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   563 NKEECLLWVDKYKPASLKNIIgqqgdqscankllrwlrnWHKSSPEEKKHAAKFGKLASKDDgssfKAALLSGPPGVGKT 642
Cdd:pfam03215    2 NDDGGEQWYEKYKPNCLEQLA------------------VHKRKIKDVQEWLDAMFLENAKH----RILLISGPSGCGKS 59

                           90       100
                   ....*....|....*....|....*
gi 188219597   643 TTASLVCQELGYSYVE-LNASDTRS 666
Cdd:pfam03215   60 TVIKELSKELGPKYREwSNPTSFRS 84
PTZ00121 PTZ00121
MAEBL; Provisional
 14-539 7.85e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.98  E-value: 7.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   14 KKPVNETVKNEKTKASEGTVKGKKGVKEAKVNNSGKEDASKPKQHSKKKRiindSDSESEETVQVKNAKKKSEKLSLSYK 93
Cdd:PTZ00121 1289 KKKADEAKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKA----EEAKKAAEAAKAEAEAAADEAEAAEE 1364

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597   94 PGKVSQKDpvtyVSETDEDDDFVCKKAASKSKENGVSTNSylgtSNVKKNEENVKTKNKPLSPIKLTPTSVLDYFGTESV 173
Cdd:PTZ00121 1365 KAEAAEKK----KEEAKKKADAAKKKAEEKKKADEAKKKA----EEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEA 1436

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  174 QRSGKKmvTSKRKESSQNTEDSRLNDEAIAKQlqldEDAELERQLHEDEEFARTLALLDEEPKIKKARKDSEEGEESFSS 253
Cdd:PTZ00121 1437 KKKAEE--AKKADEAKKKAEEAKKAEEAKKKA----EEAKKADEAKKKAEEAKKADEAKKKAEEAKKKADEAKKAAEAKK 1510

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  254 VQDDLSKAEKQKSPNKAELFSTARKTYSPAKHGKGRASED---AKQPCKSAHRKEACSSPKASA-KLALMKAKEESSYNE 329
Cdd:PTZ00121 1511 KADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADElkkAEELKKAEEKKKAEEAKKAEEdKNMALRKAEEAKKAE 1590

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  330 TELLAARRKESATEPKGEKTTPKKTKVSPTKRESVSPEDSEKKRTnyqayrsylnrEGPKALGSKEIPKGAENCLEGLTF 409
Cdd:PTZ00121 1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV-----------EQLKKKEAEEKKKAEELKKAEEEN 1659

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  410 VITGVLESIERDEAKSLIERyggkvtgnvskktnylvmGRDSGQSKSDKAAALGTKILDEDGLLDLIRTMPGKRSKYEMA 489
Cdd:PTZ00121 1660 KIKAAEEAKKAEEDKKKAEE------------------AKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEEL 1721

                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|
gi 188219597  490 AEAEmKKEKSKLERTPQKNDQGKRKISPAKKESESKKCKLTLLKNSPMKA 539
Cdd:PTZ00121 1722 KKAE-EENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKEEEKKA 1770
Fap7 COG1936
Broad-specificity NMP kinase [Nucleotide transport and metabolism];
632-660 1.26e-03

Broad-specificity NMP kinase [Nucleotide transport and metabolism];


Pssm-ID: 441539 [Multi-domain]  Cd Length: 173  Bit Score: 40.95  E-value: 1.26e-03
                          10        20
                  ....*....|....*....|....*....
gi 188219597  632 LLSGPPGVGKTTTASLVCQELGYSYVELN 660
Cdd:COG1936     4 AITGTPGTGKTTVAKLLAERLGLEVIHLN 32
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 611-720 1.28e-03

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 40.73  E-value: 1.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  611 KHAAKFGKLASkddgSSFKAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKnslkaVVAESLNNTSiKGFYTS- 689
Cdd:cd19511    14 KHPDAFKRLGI----RPPKGVLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSK-----YVGESERAVR-EIFQKAr 83

                          90       100       110
                  ....*....|....*....|....*....|....
gi 188219597  690 GAAPSVsarhaLIMDEVDGMA---GNEDRGGIQE 720
Cdd:cd19511    84 QAAPCI-----IFFDEIDSLAprrGQSDSSGVTD 112
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 629-710 1.56e-03

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 40.35  E-value: 1.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  629 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK------NSLKAVVAESlnntsikgfytSGAAPSVsarhaLI 702
Cdd:cd19503    35 RGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKylgeseKNLREIFEEA-----------RSHAPSI-----IF 98


                  ....*...
gi 188219597  703 MDEVDGMA 710
Cdd:cd19503    99 IDEIDALA 106
CMPK cd02020
Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine ...
 633-657 1.63e-03

Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.


Pssm-ID: 238978 [Multi-domain]  Cd Length: 147  Bit Score: 40.16  E-value: 1.63e-03
                          10        20
                  ....*....|....*....|....*
gi 188219597  633 LSGPPGVGKTTTASLVCQELGYSYV 657
Cdd:cd02020     4 IDGPAGSGKSTVAKLLAKKLGLPYL 28
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 632-653 2.09e-03

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 40.18  E-value: 2.09e-03
                           10        20
                   ....*....|....*....|..
gi 188219597   632 LLSGPPGVGKTTTASLVCQELG 653
Cdd:pfam05496   37 LLYGPPGLGKTTLANIIANEMG 58
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 629-667 3.36e-03

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 41.15  E-value: 3.36e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 188219597  629 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK 667
Cdd:COG1222   113 KGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSK 151
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 632-653 3.83e-03

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 40.83  E-value: 3.83e-03
                          10        20
                  ....*....|....*....|..
gi 188219597  632 LLSGPPGVGKTTTASLVCQELG 653
Cdd:COG2255    58 LLYGPPGLGKTTLAHIIANEMG 79
AAA_17 pfam13207
AAA domain;
634-663 4.59e-03

AAA domain;


Pssm-ID: 463810 [Multi-domain]  Cd Length: 136  Bit Score: 38.76  E-value: 4.59e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 188219597   634 SGPPGVGKTTTASLVCQELGYSYVelNASD 663
Cdd:pfam13207    1 TGVPGSGKTTQLKKLAEKLGFPHI--SAGD 28
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
632-653 4.86e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.50  E-value: 4.86e-03
                          10        20
                  ....*....|....*....|..
gi 188219597  632 LLSGPPGVGKTTTASLVCQELG 653
Cdd:PRK00080   55 LLYGPPGLGKTTLANIIANEMG 76
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
631-776 5.51e-03

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 40.60  E-value: 5.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  631 ALLSGPPGVGKTTTASLVCQELGY---------SYVELNASDTRSKNSLKAVVAESLNNTsiKGFYTSGAAPSV------ 695
Cdd:COG1474    54 VLIYGPTGTGKTAVAKYVLEELEEeaeergvdvRVVYVNCRQASTRYRVLSRILEELGSG--EDIPSTGLSTDElfdrly 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188219597  696 ------SARHALIMDEVDGMAGNEDRGGIQELIGL---IKHTKIPIICMCND---RNH--PKIRSlVHYCFDLRFQRPRV 761
Cdd:COG1474   132 ealderDGVLVVVLDEIDYLVDDEGDDLLYQLLRAneeLEGARVGVIGISNDlefLENldPRVKS-SLGEEEIVFPPYDA 210

                         170
                  ....*....|....*...
gi 188219597  762 EQIKSAML---SIAFKEG 776
Cdd:COG1474   211 DELRDILEdraELAFYDG 228
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 573-648 7.94e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 40.15  E-value: 7.94e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 188219597  573 KYKPASLKNIIGQqgdqscaNKLLRWLRNwhksspeekkhAAKFGKLASkddgssfkAALLSGPPGVGKTTTASLV 648
Cdd:PRK14964    6 KYRPSSFKDLVGQ-------DVLVRILRN-----------AFTLNKIPQ--------SILLVGASGVGKTTCARII 55
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH