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Conserved domains on  [gi|1390249137|ref|NP_001350425|]
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replication factor C subunit 1 isoform 4 [Homo sapiens]

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

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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 ...
 889-1042 4.28e-78

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: 252.88  E-value: 4.28e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  889 ICDGDLVDSQIRSKQNWSLLPAQAIYASVLPGELMRGYMTQFPTFPSWLGKHSSTGKHDRIVQDLALHMSLRTYSSKRTV 968
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1390249137  969 NMDYLSLLRDALVQPLTSQGVDGVQDVVALMDTYYLMKEDFENIMEISSWG----GKPSPFSKLDPKVKAAFTRAYNK 1042
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 558-977 9.76e-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: 189.75  E-value: 9.76e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  558 LLWVDKYKPTSLKTIIGQQgdqSCANKLLRWLRNWQKsssedkkhaakfgkfsgkddGSSFKAALLSGPPGVGKTTTASL 637
Cdd:PRK04195     2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLK--------------------GKPKKALLLYGPPGVGKTSLAHA 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  638 VCQELGYSYVELNASDTRSKSSLKAIVAESLNNTSIKGFysngaassvstKHALI-MDEVDGMAGNEDRGGIQELIGLIK 716
Cdd:PRK04195    59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA-----------RRKLIlLDEVDGIHGNEDRGGARAILELIK 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  717 HTKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKGAMMSIAFKEGLKIPPPAMNEIILGANQDIRQVLHNLSMWC 796
Cdd:PRK04195   128 KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIA 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  797 ARSKALTYDQAKAdshRAKKDIKMGPFDVARKVFA---AGEETAHMSLVDKS-DLFFHdysiaplFVQEN----YIHVKP 868
Cdd:PRK04195   208 EGYGKLTLEDVKT---LGRRDREESIFDALDAVFKarnADQALEASYDVDEDpDDLIE-------WIDENipkeYDDPED 277

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  869 VAAGGDMkkhlmlLSRAadsicdgDLVDSQIRSKQNWSLLPaqaiYASvlpgELM------------RGYmTQFpTFPSW 936
Cdd:PRK04195   278 IARAYDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSY 334

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|.
gi 1390249137  937 LGKHSSTGKHDRIVQDLALHMSLRTYSSKRTVNMDYLSLLR 977
Cdd:PRK04195   335 WRLLSKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 376-454 5.33e-46

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: 159.30  E-value: 5.33e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1390249137  376 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 454
Cdd:cd17752      1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
PTZ00121 super family cl31754
MAEBL; Provisional
 14-378 3.09e-06

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 3.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEETLKAKKGIKEIKVNSSRKEDDFKQKQPSKKKRIIYDSDSESEETLQVKNAKKPPEKLP--- 90
Cdd:PTZ00121  1328 KKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKkka 1407

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   91 --VSSKPGKISRQDPVTYISETDEEDDFMCKKA--ASKSKENGRSTNSHLGTSNMKKNEENTKTKNKplSPIKLTPTSVL 166
Cdd:PTZ00121  1408 deLKKAAAAKKKADEAKKKAEEKKKADEAKKKAeeAKKADEAKKKAEEAKKAEEAKKKAEEAKKADE--AKKKAEEAKKA 1485

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  167 DYFGTGSVQRSNKKMVASKRKELSQNTDESGLNDEAiAKQLQLDEDAEARKDTEAGETFSSVQAN-LSKAE---KHKYPH 242
Cdd:PTZ00121  1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEA-KKADEAKKAEEAKKADEAKKAEEKKKADeLKKAEelkKAEEKK 1564

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  243 KVKTAQVSDERKSYSPRKQS-----------------KYESSKESQQHSKSSADKIGEVSSPKASS---KLAIMKRKEES 302
Cdd:PTZ00121  1565 KAEEAKKAEEDKNMALRKAEeakkaeearieevmklyEEEKKMKAEEAKKAEEAKIKAEELKKAEEekkKVEQLKKKEAE 1644

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  303 SYKEIEPVASKRKENAIKLKGETKTPKKTKSspaKKESVSPEDSEKKRTNYQayrsyLNREGPKALGSKEIPKGAE 378
Cdd:PTZ00121  1645 EKKKAEELKKAEEENKIKAAEEAKKAEEDKK---KAEEAKKAEEDEKKAAEA-----LKKEAEEAKKAEELKKKEA 1712
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 889-1042 4.28e-78

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: 252.88  E-value: 4.28e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  889 ICDGDLVDSQIRSKQNWSLLPAQAIYASVLPGELMRGYMTQFPTFPSWLGKHSSTGKHDRIVQDLALHMSLRTYSSKRTV 968
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1390249137  969 NMDYLSLLRDALVQPLTSQGVDGVQDVVALMDTYYLMKEDFENIMEISSWG----GKPSPFSKLDPKVKAAFTRAYNK 1042
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 558-977 9.76e-52

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 189.75  E-value: 9.76e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  558 LLWVDKYKPTSLKTIIGQQgdqSCANKLLRWLRNWQKsssedkkhaakfgkfsgkddGSSFKAALLSGPPGVGKTTTASL 637
Cdd:PRK04195     2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLK--------------------GKPKKALLLYGPPGVGKTSLAHA 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  638 VCQELGYSYVELNASDTRSKSSLKAIVAESLNNTSIKGFysngaassvstKHALI-MDEVDGMAGNEDRGGIQELIGLIK 716
Cdd:PRK04195    59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA-----------RRKLIlLDEVDGIHGNEDRGGARAILELIK 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  717 HTKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKGAMMSIAFKEGLKIPPPAMNEIILGANQDIRQVLHNLSMWC 796
Cdd:PRK04195   128 KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIA 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  797 ARSKALTYDQAKAdshRAKKDIKMGPFDVARKVFA---AGEETAHMSLVDKS-DLFFHdysiaplFVQEN----YIHVKP 868
Cdd:PRK04195   208 EGYGKLTLEDVKT---LGRRDREESIFDALDAVFKarnADQALEASYDVDEDpDDLIE-------WIDENipkeYDDPED 277

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  869 VAAGGDMkkhlmlLSRAadsicdgDLVDSQIRSKQNWSLLPaqaiYASvlpgELM------------RGYmTQFpTFPSW 936
Cdd:PRK04195   278 IARAYDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSY 334

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|.
gi 1390249137  937 LGKHSSTGKHDRIVQDLALHMSLRTYSSKRTVNMDYLSLLR 977
Cdd:PRK04195   335 WRLLSKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 376-454 5.33e-46

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: 159.30  E-value: 5.33e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1390249137  376 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 454
Cdd:cd17752      1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
372-453 9.36e-28

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 120.51  E-value: 9.36e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  372 EIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKIIDEDGLLN 451
Cdd:COG0272    587 EAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLE 665


                   ..
gi 1390249137  452 LI 453
Cdd:COG0272    666 LL 667
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 366-453 1.48e-25

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 113.68  E-value: 1.48e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  366 KALGSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKIID 445
Cdd:PRK07956   576 LEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLD 654


                   ....*...
gi 1390249137  446 EDGLLNLI 453
Cdd:PRK07956   655 EEEFLRLL 662
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 622-750 5.41e-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: 5.41e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKsslkaIVAESLNNtsIKGFYSNgaASSVStKHALIMDEVDGMAG 701
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-----YVGESEKR--LRELFEA--AKKLA-PCVIFIDEIDALAG 71

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1390249137  702 NEDRGGIQELIGLI------------KHTKIPIICMCNdrNHPKIRSLVHYCFDLRFQRPR 750
Cdd:pfam00004   72 SRGSGGDSESRRVVnqllteldgftsSNSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 378-453 5.16e-15

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: 70.79  E-value: 5.16e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  378 ENCLEGLIFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMgrDSGQSKSDKAAALGTKIIDEDGLLNLI 453
Cdd:pfam00533    3 EKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 617-746 2.95e-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: 71.41  E-value: 2.95e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  617 SFKAALLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSksslKAIVAESLNNTSIKGFYSNGAASSVSTkhaLIM 693
Cdd:cd00009     18 PPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLE----GLVVAELFGHFLVRLLFELAEKAKPGV---LFI 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1390249137  694 DEVDGMAGNEDRGGIQEL----IGLIKHTKIPIICMCNDRNHPKIRSLVHYCFDLRF 746
Cdd:cd00009     91 DEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
BRCT smart00292
breast cancer carboxy-terminal domain;
378-453 2.62e-13

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 66.24  E-value: 2.62e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1390249137   378 ENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA--LGTKIIDEDGLLNLI 453
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKAiaLGIPIVKEEWLLDCL 78
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 622-752 6.92e-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: 55.84  E-value: 6.92e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   622 LLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKSSLKAIVAESLNNTSIKGFYSNGA-----ASSVSTKhALIM 693
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRlalalARKLKPD-VLIL 84

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1390249137   694 DEVDGMAGNEDRGGIQE------LIGLIKHTKIPIICMCNDRNHPKIRSLVHyCFDLRFQRPRVE 752
Cdd:smart00382   85 DEITSLLDAEQEALLLLleelrlLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 619-707 2.99e-06

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: 51.07  E-value: 2.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  619 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK------SSLKAIVAESLnntsikgfysnGAASSVstkhaLI 692
Cdd:COG0464    192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteKNLREVFDKAR-----------GLAPCV-----LF 255

                           90
                   ....*....|....*
gi 1390249137  693 MDEVDGMAGNEDRGG 707
Cdd:COG0464    256 IDEADALAGKRGEVG 270
PTZ00121 PTZ00121
MAEBL; Provisional
 14-378 3.09e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 3.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEETLKAKKGIKEIKVNSSRKEDDFKQKQPSKKKRIIYDSDSESEETLQVKNAKKPPEKLP--- 90
Cdd:PTZ00121  1328 KKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKkka 1407

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   91 --VSSKPGKISRQDPVTYISETDEEDDFMCKKA--ASKSKENGRSTNSHLGTSNMKKNEENTKTKNKplSPIKLTPTSVL 166
Cdd:PTZ00121  1408 deLKKAAAAKKKADEAKKKAEEKKKADEAKKKAeeAKKADEAKKKAEEAKKAEEAKKKAEEAKKADE--AKKKAEEAKKA 1485

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  167 DYFGTGSVQRSNKKMVASKRKELSQNTDESGLNDEAiAKQLQLDEDAEARKDTEAGETFSSVQAN-LSKAE---KHKYPH 242
Cdd:PTZ00121  1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEA-KKADEAKKAEEAKKADEAKKAEEKKKADeLKKAEelkKAEEKK 1564

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  243 KVKTAQVSDERKSYSPRKQS-----------------KYESSKESQQHSKSSADKIGEVSSPKASS---KLAIMKRKEES 302
Cdd:PTZ00121  1565 KAEEAKKAEEDKNMALRKAEeakkaeearieevmklyEEEKKMKAEEAKKAEEAKIKAEELKKAEEekkKVEQLKKKEAE 1644

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  303 SYKEIEPVASKRKENAIKLKGETKTPKKTKSspaKKESVSPEDSEKKRTNYQayrsyLNREGPKALGSKEIPKGAE 378
Cdd:PTZ00121  1645 EKKKAEELKKAEEENKIKAAEEAKKAEEDKK---KAEEAKKAEEDEKKAAEA-----LKKEAEEAKKAEELKKKEA 1712
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 511-648 2.29e-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: 48.41  E-value: 2.29e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  511 SLAKTIKKETDVFWKSLDFKEQVAEETSGDSKARNLADD-------SSENKVENLLWVDKYKPTSlktiigqQGDQSCAN 583
Cdd:TIGR00602   18 SLISTITKWSLSRPTSSHRRKNSPSTDIHARKRGFLSLEqdtglelSSENLDGNEPWVEKYKPET-------QHELAVHK 90

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  584 KLLRWLRNWQKSSS-EDKKHaakfgkfsgkddgssfKAALLSGPPGVGKTTTASLVCQELGYSYVE 648
Cdd:TIGR00602   91 KKIEEVETWLKAQVlENAPK----------------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 ...
 889-1042 4.28e-78

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: 252.88  E-value: 4.28e-78
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  889 ICDGDLVDSQIRSKQNWSLLPAQAIYASVLPGELMRGYMTQFPTFPSWLGKHSSTGKHDRIVQDLALHMSLRTYSSKRTV 968
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1390249137  969 NMDYLSLLRDALVQPLTSQGVDGVQDVVALMDTYYLMKEDFENIMEISSWG----GKPSPFSKLDPKVKAAFTRAYNK 1042
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 558-977 9.76e-52

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 189.75  E-value: 9.76e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  558 LLWVDKYKPTSLKTIIGQQgdqSCANKLLRWLRNWQKsssedkkhaakfgkfsgkddGSSFKAALLSGPPGVGKTTTASL 637
Cdd:PRK04195     2 MPWVEKYRPKTLSDVVGNE---KAKEQLREWIESWLK--------------------GKPKKALLLYGPPGVGKTSLAHA 58

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  638 VCQELGYSYVELNASDTRSKSSLKAIVAESLNNTSIKGFysngaassvstKHALI-MDEVDGMAGNEDRGGIQELIGLIK 716
Cdd:PRK04195    59 LANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA-----------RRKLIlLDEVDGIHGNEDRGGARAILELIK 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  717 HTKIPIICMCNDRNHPKIRSLVHYCFDLRFQRPRVEQIKGAMMSIAFKEGLKIPPPAMNEIILGANQDIRQVLHNLSMWC 796
Cdd:PRK04195   128 KAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIA 207

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  797 ARSKALTYDQAKAdshRAKKDIKMGPFDVARKVFA---AGEETAHMSLVDKS-DLFFHdysiaplFVQEN----YIHVKP 868
Cdd:PRK04195   208 EGYGKLTLEDVKT---LGRRDREESIFDALDAVFKarnADQALEASYDVDEDpDDLIE-------WIDENipkeYDDPED 277

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  869 VAAGGDMkkhlmlLSRAadsicdgDLVDSQIRSKQNWSLLPaqaiYASvlpgELM------------RGYmTQFpTFPSW 936
Cdd:PRK04195   278 IARAYDA------LSRA-------DIFLGRVKRTQNYDLWR----YAS----DLMtagvalakekkkRGF-TRY-QPPSY 334

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|.
gi 1390249137  937 LGKHSSTGKHDRIVQDLALHMSLRTYSSKRTVNMDYLSLLR 977
Cdd:PRK04195   335 WRLLSKTKEKRETRDSIAKKIAEKLHTSKRKVRREVLPFLS 375
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 376-454 5.33e-46

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: 159.30  E-value: 5.33e-46
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1390249137  376 GAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIR 454
Cdd:cd17752      1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
372-453 9.36e-28

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 120.51  E-value: 9.36e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  372 EIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKIIDEDGLLN 451
Cdd:COG0272    587 EAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILDEAEFLE 665


                   ..
gi 1390249137  452 LI 453
Cdd:COG0272    666 LL 667
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 366-453 1.48e-25

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 113.68  E-value: 1.48e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  366 KALGSKEIPKGAENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGqSKSDKAAALGTKIID 445
Cdd:PRK07956   576 LEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLD 654


                   ....*...
gi 1390249137  446 EDGLLNLI 453
Cdd:PRK07956   655 EEEFLRLL 662
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 381-452 5.58e-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: 96.40  E-value: 5.58e-24
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  381 LEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSD----KAAALGTKIIDEDGLLNL 452
Cdd:cd17748      1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKgeelKAKGLGIKIISEEEFLDL 76
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 622-750 5.41e-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: 5.41e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKsslkaIVAESLNNtsIKGFYSNgaASSVStKHALIMDEVDGMAG 701
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-----YVGESEKR--LRELFEA--AKKLA-PCVIFIDEIDALAG 71

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1390249137  702 NEDRGGIQELIGLI------------KHTKIPIICMCNdrNHPKIRSLVHYCFDLRFQRPR 750
Cdd:pfam00004   72 SRGSGGDSESRRVVnqllteldgftsSNSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 378-453 5.16e-15

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: 70.79  E-value: 5.16e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  378 ENCLEGLIFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMgrDSGQSKSDKAAALGTKIIDEDGLLNLI 453
Cdd:pfam00533    3 EKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 617-746 2.95e-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: 71.41  E-value: 2.95e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  617 SFKAALLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSksslKAIVAESLNNTSIKGFYSNGAASSVSTkhaLIM 693
Cdd:cd00009     18 PPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLE----GLVVAELFGHFLVRLLFELAEKAKPGV---LFI 90

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1390249137  694 DEVDGMAGNEDRGGIQEL----IGLIKHTKIPIICMCNDRNHPKIRSLVHYCFDLRF 746
Cdd:cd00009     91 DEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
BRCT smart00292
breast cancer carboxy-terminal domain;
378-453 2.62e-13

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 66.24  E-value: 2.62e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1390249137   378 ENCLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAA--LGTKIIDEDGLLNLI 453
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLKAiaLGIPIVKEEWLLDCL 78
PLN03025 PLN03025
replication factor C subunit; Provisional
 560-792 4.22e-11

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 65.52  E-value: 4.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  560 WVDKYKPTSLKTIIGQQGDQSCANKLLRwlrnwqksssedkkhaakfgkfsgkdDGSsFKAALLSGPPGVGKTTTA-SLV 638
Cdd:PLN03025     3 WVEKYRPTKLDDIVGNEDAVSRLQVIAR--------------------------DGN-MPNLILSGPPGTGKTTSIlALA 55

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  639 CQELGYSY----VELNASDTRSKSSLKaivaeslnnTSIKGFYSNGAASSVSTKHALIMDEVDGMAGnedrGGIQELIGL 714
Cdd:PLN03025    56 HELLGPNYkeavLELNASDDRGIDVVR---------NKIKMFAQKKVTLPPGRHKIVILDEADSMTS----GAQQALRRT 122

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  715 IK----HTKIPIICMCNDRNHPKIRSlvhYCFDLRFQRPRVEQIKGAMMSIAFKEGLKIPPPAMNEIILGANQDIRQVLH 790
Cdd:PLN03025   123 MEiysnTTRFALACNTSSKIIEPIQS---RCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADGDMRQALN 199


                   ..
gi 1390249137  791 NL 792
Cdd:PLN03025   200 NL 201
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 749-805 2.06e-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: 2.06e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1390249137  749 PRVEQIKGAMMSIAFKEGLKIPPPAMNEIILGANQDIRQVLHNLSMWCARSKALTYD 805
Cdd:cd18140      1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGGVITEE 57
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 622-752 6.92e-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: 55.84  E-value: 6.92e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   622 LLSGPPGVGKTTTASLVCQEL---GYSYVELNASDTRSKSSLKAIVAESLNNTSIKGFYSNGA-----ASSVSTKhALIM 693
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRlalalARKLKPD-VLIL 84

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1390249137   694 DEVDGMAGNEDRGGIQE------LIGLIKHTKIPIICMCNDRNHPKIRSLVHyCFDLRFQRPRVE 752
Cdd:smart00382   85 DEITSLLDAEQEALLLLleelrlLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 384-447 8.66e-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: 53.13  E-value: 8.66e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1390249137  384 LIFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDED 447
Cdd:cd00027      1 LVICFSG-LDDEEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEKYYLAALAWGIPIVSPE 63
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 300-454 2.18e-08

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 57.10  E-value: 2.18e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  300 EESSYKEIEPVASKRKENAIKLKGETKTPKKTKSSPAKKESvsPEDSEKKRtnyqayrsylnregpkalgsKEIPKGAEN 379
Cdd:PRK06195   162 KELNSKDINEISKLLGVTLGYVNENGYKPSSRKGRILKRSN--RQAPRKKK--------------------KIIESFGFT 219

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  380 CLEGLIFVITGVLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMG--------RDSGQSKSDKAAAL-----GTKIIDE 446
Cdd:PRK06195   220 AFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNtkdiedlnREEMSNKLKKAIDLkkkgqNIKFLNE 299


                   ....*...
gi 1390249137  447 DGLLNLIR 454
Cdd:PRK06195   300 EEFLQKCK 307
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 562-672 1.23e-07

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 55.48  E-value: 1.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  562 DKYKPTSLKTIIGQQ---GdqscANKLLRwlrnwqksssedkkHAAKFGKFSgkddgsSFkaaLLSGPPGVGKTTTASLV 638
Cdd:PRK13342     4 ERMRPKTLDEVVGQEhllG----PGKPLR--------------RMIEAGRLS------SM---ILWGPPGTGKTTLARII 56

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1390249137  639 CQELGYSYVELNASDTrSKSSLKAIVAESLNNTS 672
Cdd:PRK13342    57 AGATDAPFEALSAVTS-GVKDLREVIEEARQRRS 89
44 PHA02544
clamp loader, small subunit; Provisional
 558-792 6.72e-07

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 52.68  E-value: 6.72e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  558 LLWVDKYKPTSLKTIIGQQGDQscankllrwlrnwqksssedkkhaAKFGKFSgkDDGSSFKAALLSGPPGVGKTTTASL 637
Cdd:PHA02544     9 FMWEQKYRPSTIDECILPAADK------------------------ETFKSIV--KKGRIPNMLLHSPSPGTGKTTVAKA 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  638 VCQELGYSYVELNASDTRsksslkaivAESLNNtSIKGFysngaASSVSTK---HALIMDEVD--GMAGNED--RGGIQE 710
Cdd:PHA02544    63 LCNEVGAEVLFVNGSDCR---------IDFVRN-RLTRF-----ASTVSLTgggKVIIIDEFDrlGLADAQRhlRSFMEA 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  711 LiglikHTKIPIICMCNDRN--HPKIRSlvhYCFDLRFQRP-RVEQI--KGAM----MSIAFKEGLKIPPPAMNEIILGA 781
Cdd:PHA02544   128 Y-----SKNCSFIITANNKNgiIEPLRS---RCRVIDFGVPtKEEQIemMKQMivrcKGILEAEGVEVDMKVLAALVKKN 199

                          250
                   ....*....|.
gi 1390249137  782 NQDIRQVLHNL 792
Cdd:PHA02544   200 FPDFRRTINEL 210
rfc PRK00440
replication factor C small subunit; Reviewed
 554-655 1.22e-06

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 51.80  E-value: 1.22e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  554 KVENLLWVDKYKPTSLKTIIGQQgdqscanKLLRWLRNWQKSssEDKKHAakfgkfsgkddgssfkaaLLSGPPGVGKTT 633
Cdd:PRK00440     1 AMMEEIWVEKYRPRTLDEIVGQE-------EIVERLKSYVKE--KNMPHL------------------LFAGPPGTGKTT 53

                           90       100
                   ....*....|....*....|....*..
gi 1390249137  634 TASLVCQEL-GYSY----VELNASDTR 655
Cdd:PRK00440    54 AALALARELyGEDWrenfLELNASDER 80
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 619-707 2.99e-06

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: 51.07  E-value: 2.99e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  619 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK------SSLKAIVAESLnntsikgfysnGAASSVstkhaLI 692
Cdd:COG0464    192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteKNLREVFDKAR-----------GLAPCV-----LF 255

                           90
                   ....*....|....*
gi 1390249137  693 MDEVDGMAGNEDRGG 707
Cdd:COG0464    256 IDEADALAGKRGEVG 270
PTZ00121 PTZ00121
MAEBL; Provisional
 14-378 3.09e-06

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 51.68  E-value: 3.09e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEETLKAKKGIKEIKVNSSRKEDDFKQKQPSKKKRIIYDSDSESEETLQVKNAKKPPEKLP--- 90
Cdd:PTZ00121  1328 KKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKKAEEDKkka 1407

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   91 --VSSKPGKISRQDPVTYISETDEEDDFMCKKA--ASKSKENGRSTNSHLGTSNMKKNEENTKTKNKplSPIKLTPTSVL 166
Cdd:PTZ00121  1408 deLKKAAAAKKKADEAKKKAEEKKKADEAKKKAeeAKKADEAKKKAEEAKKAEEAKKKAEEAKKADE--AKKKAEEAKKA 1485

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  167 DYFGTGSVQRSNKKMVASKRKELSQNTDESGLNDEAiAKQLQLDEDAEARKDTEAGETFSSVQAN-LSKAE---KHKYPH 242
Cdd:PTZ00121  1486 DEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEA-KKADEAKKAEEAKKADEAKKAEEKKKADeLKKAEelkKAEEKK 1564

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  243 KVKTAQVSDERKSYSPRKQS-----------------KYESSKESQQHSKSSADKIGEVSSPKASS---KLAIMKRKEES 302
Cdd:PTZ00121  1565 KAEEAKKAEEDKNMALRKAEeakkaeearieevmklyEEEKKMKAEEAKKAEEAKIKAEELKKAEEekkKVEQLKKKEAE 1644

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  303 SYKEIEPVASKRKENAIKLKGETKTPKKTKSspaKKESVSPEDSEKKRTNYQayrsyLNREGPKALGSKEIPKGAE 378
Cdd:PTZ00121  1645 EKKKAEELKKAEEENKIKAAEEAKKAEEDKK---KAEEAKKAEEDEKKAAEA-----LKKEAEEAKKAEELKKKEA 1712
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
620-798 3.84e-06

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 49.97  E-value: 3.84e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  620 AALLSGPPGVGKTTTA-----SLVCQELGYS------------------YVELNA---SDTRSKSSLKAIVaESLNNTSI 673
Cdd:COG0470     20 ALLLHGPPGIGKTTLAlalarDLLCENPEGGkacgqchsrlmaagnhpdLLELNPeekSDQIGIDQIRELG-EFLSLTPL 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  674 KGFYSngaassvstkhALIMDEVDGMAGNEDRGGIQELIGLIKHTkiPIICMCNDRNH--PKIRSLvhyCFDLRFQRPRV 751
Cdd:COG0470     99 EGGRK-----------VVIIDEADAMNEAAANALLKTLEEPPKNT--PFILIANDPSRllPTIRSR---CQVIRFRPPSE 162

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*..
gi 1390249137  752 EQIKGAMmsiafkEGLKIPPPAMNEIILGANQDIRQVLHNLSMWCAR 798
Cdd:COG0470    163 EEALAWL------REEGVDEDALEAILRLAGGDPRAAINLLQALAGR 203
BRCT_PARP1 cd17747
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ...
 381-447 7.44e-06

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: 44.83  E-value: 7.44e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  381 LEGLIFVITGVLeSIERDEAKSLIERYGGKVTGNVSKKTNYLV---MGRDSGQSKSDKAAALGTKIIDED 447
Cdd:cd17747      1 LTGMKFALIGKL-SKSKDELKKLIEKLGGKVASKVTKKVTLCIstkAEVEKMSKKMKEAKEAGVPVVSED 69
PTZ00121 PTZ00121
MAEBL; Provisional
 14-350 1.25e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 49.75  E-value: 1.25e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEETLKAKKGIKeiKVNSSRKEDDFKQKQPSKKK-----RIIYDSDSESEETLQVKNAKKPPEK 88
Cdd:PTZ00121  1437 KKKAEEAKKADEAKKKAEEAKKAEEAKK--KAEEAKKADEAKKKAEEAKKadeakKKAEEAKKKADEAKKAAEAKKKADE 1514

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   89 LPVSSKPGKISRQDPVTYISETDEEDDFMCKKAAS--KSKENGRSTNSHLGTSNMKKNEENTKTKNKPLSPIKLTPTSVL 166
Cdd:PTZ00121  1515 AKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADelKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARI 1594

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  167 DYFGTGSVQRSNKKMVASKRKELSQNTDESGLNDEAIAKQLQLDEDAEARKDTEAGETFSSVQANLSKAEkhkyphKVKT 246
Cdd:PTZ00121  1595 EEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAA------EEAK 1668

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  247 AQVSDERKSYSPRKQSKYESSKESQQHSKSSADKigevsspkassKLAIMKRKEESSYKEIEPVASKRKENAIKLKgetK 326
Cdd:PTZ00121  1669 KAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAK-----------KAEELKKKEAEEKKKAEELKKAEEENKIKAE---E 1734

                          330       340
                   ....*....|....*....|....
gi 1390249137  327 TPKKTKSSPAKKESVSPEDSEKKR 350
Cdd:PTZ00121  1735 AKKEAEEDKKKAEEAKKDEEEKKK 1758
PTZ00121 PTZ00121
MAEBL; Provisional
 19-378 1.72e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 49.37  E-value: 1.72e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   19 ETVKKNEKTKSDEEtlKAKKGIKEIKVNSSRKEDDFKQKQPSKKKRIIYDSDSESEETLQVKNAKKPPEKLPVSSKPGKI 98
Cdd:PTZ00121  1227 EAVKKAEEAKKDAE--EAKKAEEERNNEEIRKFEEARMAHFARRQAAIKAEEARKADELKKAEEKKKADEAKKAEEKKKA 1304

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   99 SRQDPVTYISETDEEDDFMCKKAASKSKENGRSTNSHLGTSNMKKNEENTKTKnkplspikltptsvldyfgtgSVQRSN 178
Cdd:PTZ00121  1305 DEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAAD---------------------EAEAAE 1363

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  179 KKMVASKRK--ELSQNTDESGLNDEAIAKQLQLDEDAEarKDTEAGETFSSVQANLSKAEKHKypHKVKTAQVSDERKSY 256
Cdd:PTZ00121  1364 EKAEAAEKKkeEAKKKADAAKKKAEEKKKADEAKKKAE--EDKKKADELKKAAAAKKKADEAK--KKAEEKKKADEAKKK 1439

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  257 SPRKQSKYESSKESQQHSKS--SADKIGEVSSPKASSKLAIMKRKEESSYKEIEPvASKRKENAIKLKGETKTPKKTKSS 334
Cdd:PTZ00121  1440 AEEAKKADEAKKKAEEAKKAeeAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEE-AKKKADEAKKAAEAKKKADEAKKA 1518

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1390249137  335 PAKKESVSPEDSEKKRTNYQAYRSYLNREGPKALGSKEIPKGAE 378
Cdd:PTZ00121  1519 EEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEE 1562
BRCT_TopBP1_rpt2_like cd17731
second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; ...
 381-430 1.87e-05

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: 43.68  E-value: 1.87e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1390249137  381 LEGLIFVITGvLESIERDEAKSLIERYGGKVTGNVSKKTNYLVMGRDSGQ 430
Cdd:cd17731      3 FKGLVICVTG-FDSEERKEIQQLVEQNGGSYSPDLSKNCTHLIAGSPSGQ 51
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 619-727 1.87e-05

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: 46.12  E-value: 1.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  619 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSKSS------LKAI--VAESLnntsikgfysngaASSVstkha 690
Cdd:cd19481     27 KGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVgeseknLRKIfeRARRL-------------APCI----- 88

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1390249137  691 LIMDEVDGMAGNEDRGG------------IQELIGLIKHTKIPIICMCN 727
Cdd:cd19481     89 LFIDEIDAIGRKRDSSGesgelrrvlnqlLTELDGVNSRSKVLVIAATN 137
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 566-666 1.95e-05

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 48.51  E-value: 1.95e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  566 PTSLKTIIGQQgdqscanKLL---RWLRNWQKSssedkkhaakfGKFSgkddgsSFkaaLLSGPPGVGKTTTASLVCQEL 642
Cdd:COG2256     21 PRTLDEVVGQE-------HLLgpgKPLRRAIEA-----------GRLS------SM---ILWGPPGTGKTTLARLIANAT 73

                           90       100
                   ....*....|....*....|....
gi 1390249137  643 GYSYVELNASDTrSKSSLKAIVAE 666
Cdd:COG2256     74 DAEFVALSAVTS-GVKDIREVIEE 96
PTZ00121 PTZ00121
MAEBL; Provisional
 14-570 2.12e-05

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 48.98  E-value: 2.12e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEEtlkAKKGIKEIKvnssRKEDDFKQKQPSKKKRiiyDSDSESEETLQVKNAKKPPEKLPVSS 93
Cdd:PTZ00121  1301 KKKADEAKKKAEEAKKADE---AKKKAEEAK----KKADAAKKKAEEAKKA---AEAAKAEAEAAADEAEAAEEKAEAAE 1370

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   94 KPgkisrqdpvtyISETDEEDDFMCKKAASKSKengrstnshlgTSNMKKNEENTKTKNKPLspikltptsvldyfgtgs 173
Cdd:PTZ00121  1371 KK-----------KEEAKKKADAAKKKAEEKKK-----------ADEAKKKAEEDKKKADEL------------------ 1410

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  174 vqrsnKKMVASKRK--ELSQNTDESGLNDEAIAKQLQLDEDAEARKDTEAGEtfssvqanlsKAEKHKypHKVKTAQVSD 251
Cdd:PTZ00121  1411 -----KKAAAAKKKadEAKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAK----------KAEEAK--KKAEEAKKAD 1473

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  252 ERKSYSPRKQSKYESSKESQQHSKssadKIGEVSSPKASSKLAIMKRKEESSYKEIEpvaSKRKENAIKLKGETKTPKKT 331
Cdd:PTZ00121  1474 EAKKKAEEAKKADEAKKKAEEAKK----KADEAKKAAEAKKKADEAKKAEEAKKADE---AKKAEEAKKADEAKKAEEKK 1546

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  332 KSSPAKKESVSPEDSEKKRTNyQAYRSYLNREgpKALGSKEIPKGAEnclEGLIFVITGVLESIERDEAKSLIERYGGKV 411
Cdd:PTZ00121  1547 KADELKKAEELKKAEEKKKAE-EAKKAEEDKN--MALRKAEEAKKAE---EARIEEVMKLYEEEKKMKAEEAKKAEEAKI 1620

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  412 TGNVSKKTNYLVMGRDSGQSKSDKAAALGTKIIDEDGLLNLIRTMPGKKSKYEIAVETEMKKESKLERtpQKNVQGKRKI 491
Cdd:PTZ00121  1621 KAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK--KAAEALKKEA 1698

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  492 SPSKKESESKKSRPTSKRDslAKTIKKETDV-FWKSLDFKEQVAEETSGDSKARnlADDSSENKVENLLWVDKYKPTSLK 570
Cdd:PTZ00121  1699 EEAKKAEELKKKEAEEKKK--AEELKKAEEEnKIKAEEAKKEAEEDKKKAEEAK--KDEEEKKKIAHLKKEEEKKAEEIR 1774
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 511-648 2.29e-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: 48.41  E-value: 2.29e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  511 SLAKTIKKETDVFWKSLDFKEQVAEETSGDSKARNLADD-------SSENKVENLLWVDKYKPTSlktiigqQGDQSCAN 583
Cdd:TIGR00602   18 SLISTITKWSLSRPTSSHRRKNSPSTDIHARKRGFLSLEqdtglelSSENLDGNEPWVEKYKPET-------QHELAVHK 90

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1390249137  584 KLLRWLRNWQKSSS-EDKKHaakfgkfsgkddgssfKAALLSGPPGVGKTTTASLVCQELGYSYVE 648
Cdd:TIGR00602   91 KKIEEVETWLKAQVlENAPK----------------RILLITGPSGCGKSTTIKILSKELGIQVQE 140
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
621-766 1.47e-04

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 45.61  E-value: 1.47e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  621 ALLSGPPGVGKTTTASLVCQELGY---------SYVELNASDTRSKSS-LKAIVAESLNNTSIkgfysngAASSVSTKHA 690
Cdd:COG1474     54 VLIYGPTGTGKTAVAKYVLEELEEeaeergvdvRVVYVNCRQASTRYRvLSRILEELGSGEDI-------PSTGLSTDEL 126

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  691 ----------------LIMDEVDGMAGNEDRGGIQELIGL---IKHTKIPIICMCND---RNH--PKIRSlVHYCFDLRF 746
Cdd:COG1474    127 fdrlyealderdgvlvVVLDEIDYLVDDEGDDLLYQLLRAneeLEGARVGVIGISNDlefLENldPRVKS-SLGEEEIVF 205

                          170       180
                   ....*....|....*....|...
gi 1390249137  747 QRPRVEQIKGAMM---SIAFKEG 766
Cdd:COG1474    206 PPYDADELRDILEdraELAFYDG 228
PTZ00121 PTZ00121
MAEBL; Provisional
 14-349 2.27e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 45.52  E-value: 2.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKNEKTKSDEETLKA---KKGIKEIKVNSSRKEDDFKQKQPSKKKRIIYDSDS--ESEETLQVKNAKKPPEK 88
Cdd:PTZ00121  1496 KKKADEAKKAAEAKKKADEAKKAeeaKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEElkKAEEKKKAEEAKKAEED 1575

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   89 LPVSSKPGKISRQDPVTYISETDEEDDFMCKKAASKSKengRSTNSHLGTSNMKKNEENTKtknkplspikltptsvldy 168
Cdd:PTZ00121  1576 KNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAK---KAEEAKIKAEELKKAEEEKK------------------- 1633

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  169 fgtgSVQRSNKKMVASKRK--ELSQNTDESGLNDEAIAKQlqldEDAEARKDTEAgetfssvqanlSKAEKHKyphkvKT 246
Cdd:PTZ00121  1634 ----KVEQLKKKEAEEKKKaeELKKAEEENKIKAAEEAKK----AEEDKKKAEEA-----------KKAEEDE-----KK 1689

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  247 AQVSDERKSYSPRKQSKYESSKESQQHSKSSADKIGEVSSPKASSklaiMKRKEESSYKEIEPVASKRKENAIKLKGETK 326
Cdd:PTZ00121  1690 AAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEE----AKKEAEEDKKKAEEAKKDEEEKKKIAHLKKE 1765

                          330       340
                   ....*....|....*....|...
gi 1390249137  327 TPKKTKSSPAKKESVSPEDSEKK 349
Cdd:PTZ00121  1766 EEKKAEEIRKEKEAVIEEELDEE 1788
Rad17 pfam03215
Rad17 P-loop domain;
552-658 2.74e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 43.02  E-value: 2.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  552 ENKVENLLWVDKYKPTSlktiigqQGDQSCANKLLRWLRNWQKSSS-EDKKHaakfgkfsgkddgssfKAALLSGPPGVG 630
Cdd:pfam03215    1 INDDGGEQWYEKYKPNC-------LEQLAVHKRKIKDVQEWLDAMFlENAKH----------------RILLISGPSGCG 57

                           90       100
                   ....*....|....*....|....*....
gi 1390249137  631 KTTTASLVCQELGYSYVE-LNASDTRSKS 658
Cdd:pfam03215   58 KSTVIKELSKELGPKYREwSNPTSFRSPP 86
PTZ00121 PTZ00121
MAEBL; Provisional
 25-378 3.73e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.75  E-value: 3.73e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   25 EKTKSDEETLKAKKGIKEIKVNSSRKEDDFKQKQPSKKKRiiyDSDSESEETLQVKNAKKPPE-KLPVSSKPGKISRQDP 103
Cdd:PTZ00121  1085 EDNRADEATEEAFGKAEEAKKTETGKAEEARKAEEAKKKA---EDARKAEEARKAEDARKAEEaRKAEDAKRVEIARKAE 1161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  104 VTYISETDEEDDFMCKKAASKSKENGRSTNSHLGTSNMKKNEENTKTKNKPLSPIKLTPTSVLDYFGTGSVQRSNKKMVA 183
Cdd:PTZ00121  1162 DARKAEEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKAEDAKKAEAVKKAEEAKKDAEE 1241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  184 SKRKELSQNTDESGLNDEAIAKQLQLDEDA----EARKDTEAGETFSSVQAN-LSKAEKHK----YPHKVKTAQVSDERK 254
Cdd:PTZ00121  1242 AKKAEEERNNEEIRKFEEARMAHFARRQAAikaeEARKADELKKAEEKKKADeAKKAEEKKkadeAKKKAEEAKKADEAK 1321

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  255 SYSPRKQSKYESSKESQQHSKsSADKIGEVSSPKASSKLAIMKRKEESSYKEIEpvASKRKENAIKLKGETK-----TPK 329
Cdd:PTZ00121  1322 KKAEEAKKKADAAKKKAEEAK-KAAEAAKAEAEAAADEAEAAEEKAEAAEKKKE--EAKKKADAAKKKAEEKkkadeAKK 1398

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*....
gi 1390249137  330 KTKSSPAKKESVSPEDSEKKRTNYQAYRSYLNREGPKALGSKEIPKGAE 378
Cdd:PTZ00121  1399 KAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKAD 1447
Fap7 COG1936
Broad-specificity NMP kinase [Nucleotide transport and metabolism];
622-650 1.41e-03

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


Pssm-ID: 441539 [Multi-domain]  Cd Length: 173  Bit Score: 40.95  E-value: 1.41e-03
                           10        20
                   ....*....|....*....|....*....
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELGYSYVELN 650
Cdd:COG1936      4 AITGTPGTGKTTVAKLLAERLGLEVIHLN 32
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 622-643 2.07e-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: 2.07e-03
                           10        20
                   ....*....|....*....|..
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELG 643
Cdd:pfam05496   37 LLYGPPGLGKTTLANIIANEMG 58
CMPK cd02020
Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine ...
 623-647 2.09e-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: 39.78  E-value: 2.09e-03
                           10        20
                   ....*....|....*....|....*
gi 1390249137  623 LSGPPGVGKTTTASLVCQELGYSYV 647
Cdd:cd02020      4 IDGPAGSGKSTVAKLLAKKLGLPYL 28
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
622-652 2.20e-03

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 41.02  E-value: 2.20e-03
                           10        20        30
                   ....*....|....*....|....*....|.
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELGYSYVELNAS 652
Cdd:COG1223     39 LFYGPPGTGKTMLAEALAGELKLPLLTVRLD 69
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 622-643 2.92e-03

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: 41.13  E-value: 2.92e-03
                           10        20
                   ....*....|....*....|..
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELG 643
Cdd:TIGR00635   34 LLYGPPGLGKTTLAHIIANEMG 55
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 619-657 3.54e-03

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 40.76  E-value: 3.54e-03
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1390249137  619 KAALLSGPPGVGKTTTASLVCQELGYSYVELNASDTRSK 657
Cdd:COG1222    113 KGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSK 151
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 622-643 3.79e-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: 3.79e-03
                           10        20
                   ....*....|....*....|..
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELG 643
Cdd:COG2255     58 LLYGPPGLGKTTLAHIIANEMG 79
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
622-643 4.82e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 40.50  E-value: 4.82e-03
                           10        20
                   ....*....|....*....|..
gi 1390249137  622 LLSGPPGVGKTTTASLVCQELG 643
Cdd:PRK00080    55 LLYGPPGLGKTTLANIIANEMG 76
AAA_17 pfam13207
AAA domain;
624-653 5.35e-03

AAA domain;


Pssm-ID: 463810 [Multi-domain]  Cd Length: 136  Bit Score: 38.37  E-value: 5.35e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 1390249137  624 SGPPGVGKTTTASLVCQELGYSYVelNASD 653
Cdd:pfam13207    1 TGVPGSGKTTQLKKLAEKLGFPHI--SAGD 28
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 14-348 6.44e-03

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 40.80  E-value: 6.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   14 KKLVSETVKKN-----EKTKSDEETLKAKKGIKEIKVNSSRKEDDFKQKQPSKK-----KRIIYDSDSESEETL--QVKN 81
Cdd:PTZ00108  1034 KDLVKELKKLGyvrfkDIIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSydyllSMPIWSLTKEKVEKLnaELEK 1113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137   82 AKKPPEKLpVSSKPGKISRQDPVTYISETDEEDDFMCKKAASKSKENGRSTNSHLGTSNMKKNEENTKTKNKPLSPIKLT 161
Cdd:PTZ00108  1114 KEKELEKL-KNTTPKDMWLEDLDKFEEALEEQEEVEEKEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKA 1192

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  162 PTSVldyfGTGSVQRSNKKMVASKRKELSQNTDESGLNDEAIAKQLQLDEDAEARKDTEAGETFSSVQANLSKAEKHKYP 241
Cdd:PTZ00108  1193 SVVG----NSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKE 1268

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1390249137  242 HKVKTAQVSDERKSYSPRKQSKyESSKESQQHSKSSADKIGEVSSPKASSKLAIMKRKEEssyKEIEPVASKRKENAIKL 321
Cdd:PTZ00108  1269 GKPKNAPKRVSAVQYSPPPPSK-RPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKS---EKKTARKKKSKTRVKQA 1344

                          330       340
                   ....*....|....*....|....*..
gi 1390249137  322 KGETKTPkkTKSSPAKKESVSPEDSEK 348
Cdd:PTZ00108  1345 SASQSSR--LLRRPRKKKSDSSSEDDD 1369
 
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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