NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|62472391|ref|NP_001014605|]
View 

germ line transcription factor 1, isoform B [Drosophila melanogaster]

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 ...
 764-917 4.28e-71

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: 232.85  E-value: 4.28e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    764 LSLGDLVEKRIRANSAWSLLPTQAFFSSVLPGEHMCGHFTGQINFPGWLGKNSKSGKRARLAQELHDHTRVCTSGSRLSV 843
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391    844 RLDYAPFLLDNIVRPLAKDGQEGVPAALDVMKDYHLLREDLDSLVELTSWP----GKKSPLDAVDGRVKAALTRSYNK 917
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 421-969 7.70e-48

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: 178.19  E-value: 7.70e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   421 MAWVDKHKPTSIKEIVGQAgaasnvtnhnlklKAKQErvkvlhyfnfprLMNWLSKWyvnhdgnkkpqrpnpwaknDDGS 500
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE-------------KAKEQ------------LREWIESW-------------------LKGK 37

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   501 FYKAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEVSTLLSNKSLSGYftgqgqavsRKHVLIMDEVD 580
Cdd:PRK04195   38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA---------RRKLILLDEVD 108

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   581 GMAGNEDRGGMQELIALIKDSSIPIICMCNDRNHPKIRSLVNYCYDLRFQRPRLEQIKGKIMSICFKEKVKISPAKVEEI 660
Cdd:PRK04195  109 GIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEI 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   661 IAATNNDIRQSINHI-ALLSAKEDASQKSGQQVATKDLKLGPWEVVRKVFTADEHKH-----MSFADKSDLFFHdyslap 734
Cdd:PRK04195  189 AERSGGDLRSAINDLqAIAEGYGKLTLEDVKTLGRRDREESIFDALDAVFKARNADQaleasYDVDEDPDDLIE------ 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   735 lFVQQNylqvLPqgNKKDVLAKVAATADALSLGDLVEKRIRANSAWSLLPTqaFFSSVLPG-----EHMCGHFTgQINFP 809
Cdd:PRK04195  263 -WIDEN----IP--KEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRY--ASDLMTAGvalakEKKKRGFT-RYQPP 332

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   810 GWLGKNSKS----GKRARLAQEL--HDHTrvctsgSRLSVRLDYAPFLldnivRPLAKDGQEgVPAALDvmKDYHLlreD 883
Cdd:PRK04195  333 SYWRLLSKTkekrETRDSIAKKIaeKLHT------SKRKVRREVLPFL-----SIIFKHNPE-LAARLA--AFLEL---T 395

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   884 LDSLVELTswpGKKSPLDAVDGRVKAAlTRSYNKEVMAYSYSAQAGIKKKKSEAAGADDDylDEGPGEEDGAGGHLSSEE 963
Cdd:PRK04195  396 EEEIEFLT---GSKKATKKIKKIVEKA-EKKREEEKKEKKKKAFAGKKKEEEEEEEKEKK--EEEKEEEEEEAEEEKEEE 469


                  ....*.
gi 62472391   964 DEDKDN 969
Cdd:PRK04195  470 EEKKKK 475
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 232-310 2.68e-40

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: 142.74  E-value: 2.68e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62472391  232 GSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAVAEELNIPILSEDGLFDLIR 310
Cdd:cd17752    1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
PTZ00121 super family cl31754
MAEBL; Provisional
 12-434 7.27e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.59  E-value: 7.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    12 LPAKAKSAEAENGETPSKAPKRRKAVIISSDEDEVVSPPETKKRKASKTASSEddvvAATPEPIAKKARNGQKPAlsKLK 91
Cdd:PTZ00121 1396 AKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE----AKKKAEEAKKAEEAKKKA--EEA 1469

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    92 RHVDPTELFGGETKRVIVPKPKTKAVLEfENEDIDRSLMEVDLDESIKEAAPEKKVHSITRSSPSPKRAKNSSPEPPKPK 171
Cdd:PTZ00121 1470 KKADEAKKKAEEAKKADEAKKKAEEAKK-KADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKA 1548

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   172 STKSKATTPRVKKEKPAAdlESSVLTDEERHERKRASAVLYQKYKNRSSCLNPGSKEIPKGSPDCLSGltfvvtgvlESM 251
Cdd:PTZ00121 1549 DELKKAEELKKAEEKKKA--EEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK---------AEE 1617

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   252 EREEAESVIKEyggkvmTVVGKKLKYLVVGEEAGPKKlavAEELNipilsEDGLFDLIREKSGIAKQVKEEKKSPKKEHS 331
Cdd:PTZ00121 1618 AKIKAEELKKA------EEEKKKVEQLKKKEAEEKKK---AEELK-----KAEEENKIKAAEEAKKAEEDKKKAEEAKKA 1683

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   332 SEEKGKKEVKTSRRSSDKKEKEATKLKYGEKHDIAK--------HKVKEEHTSPKETKDKlndvpavtlkvKKEPSSQKE 403
Cdd:PTZ00121 1684 EEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEelkkaeeeNKIKAEEAKKEAEEDK-----------KKAEEAKKD 1752

                         410       420       430
                  ....*....|....*....|....*....|.
gi 62472391   404 HPPSPRTADLKTLDVVGMAWVDKHKPTSIKE 434
Cdd:PTZ00121 1753 EEEKKKIAHLKKEEEKKAEEIRKEKEAVIEE 1783
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 764-917 4.28e-71

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: 232.85  E-value: 4.28e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    764 LSLGDLVEKRIRANSAWSLLPTQAFFSSVLPGEHMCGHFTGQINFPGWLGKNSKSGKRARLAQELHDHTRVCTSGSRLSV 843
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391    844 RLDYAPFLLDNIVRPLAKDGQEGVPAALDVMKDYHLLREDLDSLVELTSWP----GKKSPLDAVDGRVKAALTRSYNK 917
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 421-969 7.70e-48

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 178.19  E-value: 7.70e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   421 MAWVDKHKPTSIKEIVGQAgaasnvtnhnlklKAKQErvkvlhyfnfprLMNWLSKWyvnhdgnkkpqrpnpwaknDDGS 500
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE-------------KAKEQ------------LREWIESW-------------------LKGK 37

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   501 FYKAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEVSTLLSNKSLSGYftgqgqavsRKHVLIMDEVD 580
Cdd:PRK04195   38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA---------RRKLILLDEVD 108

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   581 GMAGNEDRGGMQELIALIKDSSIPIICMCNDRNHPKIRSLVNYCYDLRFQRPRLEQIKGKIMSICFKEKVKISPAKVEEI 660
Cdd:PRK04195  109 GIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEI 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   661 IAATNNDIRQSINHI-ALLSAKEDASQKSGQQVATKDLKLGPWEVVRKVFTADEHKH-----MSFADKSDLFFHdyslap 734
Cdd:PRK04195  189 AERSGGDLRSAINDLqAIAEGYGKLTLEDVKTLGRRDREESIFDALDAVFKARNADQaleasYDVDEDPDDLIE------ 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   735 lFVQQNylqvLPqgNKKDVLAKVAATADALSLGDLVEKRIRANSAWSLLPTqaFFSSVLPG-----EHMCGHFTgQINFP 809
Cdd:PRK04195  263 -WIDEN----IP--KEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRY--ASDLMTAGvalakEKKKRGFT-RYQPP 332

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   810 GWLGKNSKS----GKRARLAQEL--HDHTrvctsgSRLSVRLDYAPFLldnivRPLAKDGQEgVPAALDvmKDYHLlreD 883
Cdd:PRK04195  333 SYWRLLSKTkekrETRDSIAKKIaeKLHT------SKRKVRREVLPFL-----SIIFKHNPE-LAARLA--AFLEL---T 395

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   884 LDSLVELTswpGKKSPLDAVDGRVKAAlTRSYNKEVMAYSYSAQAGIKKKKSEAAGADDDylDEGPGEEDGAGGHLSSEE 963
Cdd:PRK04195  396 EEEIEFLT---GSKKATKKIKKIVEKA-EKKREEEKKEKKKKAFAGKKKEEEEEEEKEKK--EEEKEEEEEEAEEEKEEE 469


                  ....*.
gi 62472391   964 DEDKDN 969
Cdd:PRK04195  470 EEKKKK 475
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 232-310 2.68e-40

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: 142.74  E-value: 2.68e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62472391  232 GSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAVAEELNIPILSEDGLFDLIR 310
Cdd:cd17752    1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
222-309 3.95e-23

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 105.49  E-value: 3.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  222 LNPGSKEIPKGSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGpKKLAVAEELNIPILS 301
Cdd:COG0272  581 VNMEEEEAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILD 659


                 ....*...
gi 62472391  302 EDGLFDLI 309
Cdd:COG0272  660 EAEFLELL 667
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 231-311 1.08e-18

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 91.34  E-value: 1.08e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   231 KGSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGpKKLAVAEELNIPILSEDGLFDLIR 310
Cdd:PRK07956  585 KGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLDEEEFLRLLG 663


                  .
gi 62472391   311 E 311
Cdd:PRK07956  664 E 664
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 232-309 3.49e-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: 73.87  E-value: 3.49e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391    232 GSPDCLSGLTFVVTGvLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVgeEAGPKKLAVAEELNIPILSEDGLFDLI 309
Cdd:pfam00533    1 PKEKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 506-633 8.83e-16

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: 74.94  E-value: 8.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    506 LLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEvstllsnKSLSGYFTGQGQavSRKHVLIMDEVDGMAGN 585
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESE-------KRLRELFEAAKK--LAPCVIFIDEIDALAGS 72

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    586 EDRGG-------MQELIALIKD-----SSIPIICMCNdrNHPKIRSLVNYCYDLRFQRPR 633
Cdd:pfam00004   73 RGSGGdsesrrvVNQLLTELDGftssnSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
BRCT smart00292
breast cancer carboxy-terminal domain;
234-309 5.34e-14

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 67.79  E-value: 5.34e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391     234 PDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLK-YLVVGEEAGPK-KLAVAEELNIPILSEDGLFDLI 309
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTtHVIVGSPEGGKlELLKAIALGIPIVKEEWLLDCL 78
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 502-629 5.43e-11

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: 61.78  E-value: 5.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  502 YKAALLSGPPGIGKTTTATLVVKEL---GFDAVEFNASDTRSKrllkdevsTLLSNKSLSGYFTGQGQAVSRKH--VLIM 576
Cdd:cd00009   19 PKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEG--------LVVAELFGHFLVRLLFELAEKAKpgVLFI 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 62472391  577 DEVDGMAGNEDRGGMQEL----IALIKDSSIPIICMCNDRNHPKIRSLVNYCYDLRF 629
Cdd:cd00009   91 DEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 506-635 2.33e-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: 57.00  E-value: 2.33e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391     506 LLSGPPGIGKTTTATLVVKEL---GFDAVEFNASDTRSKRLLKDEVSTLLSNKSLSGYFTGQGQAVS--RKH---VLIMD 577
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALAlaRKLkpdVLILD 85

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62472391     578 EVDGMAGNEDRGGMQELIAL------IKDSSIPIICMCNDRNHPkIRSLVNYCYDLRFQRPRLE 635
Cdd:smart00382   86 EITSLLDAEQEALLLLLEELrlllllKSEKNLTVILTTNDEKDL-GPALLRRRFDRRIVLLLIL 148
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
493-712 1.40e-08

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 57.29  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  493 WAKNDDGSfyKAALLSGPPGIGKTTTATLVVKELG-----------------------FDAVEFNAsDTRSKRLLKDEVS 549
Cdd:COG0470   11 AAESGRLP--HALLLHGPPGIGKTTLALALARDLLcenpeggkacgqchsrlmaagnhPDLLELNP-EEKSDQIGIDQIR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  550 TL---LSNKSLSGyftgqgqavSRKhVLIMDEVDGMAGNEDRGGMQELIALIKDSsiPIICMCNDRNH--PKIRSLvnyC 624
Cdd:COG0470   88 ELgefLSLTPLEG---------GRK-VVIIDEADAMNEAAANALLKTLEEPPKNT--PFILIANDPSRllPTIRSR---C 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  625 YDLRFQRPRLEQIKGKImsicfkEKVKISPAKVEEIIAATNNDIRQSINHIALLSAKEDASQKSGQQVATKDlklgPWEV 704
Cdd:COG0470  153 QVIRFRPPSEEEALAWL------REEGVDEDALEAILRLAGGDPRAAINLLQALAGRKELLEDLAALLSRDR----ALEL 222


                 ....*...
gi 62472391  705 VRKVFTAD 712
Cdd:COG0470  223 LDALLKAE 230
PTZ00121 PTZ00121
MAEBL; Provisional
 12-434 7.27e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.59  E-value: 7.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    12 LPAKAKSAEAENGETPSKAPKRRKAVIISSDEDEVVSPPETKKRKASKTASSEddvvAATPEPIAKKARNGQKPAlsKLK 91
Cdd:PTZ00121 1396 AKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE----AKKKAEEAKKAEEAKKKA--EEA 1469

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    92 RHVDPTELFGGETKRVIVPKPKTKAVLEfENEDIDRSLMEVDLDESIKEAAPEKKVHSITRSSPSPKRAKNSSPEPPKPK 171
Cdd:PTZ00121 1470 KKADEAKKKAEEAKKADEAKKKAEEAKK-KADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKA 1548

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   172 STKSKATTPRVKKEKPAAdlESSVLTDEERHERKRASAVLYQKYKNRSSCLNPGSKEIPKGSPDCLSGltfvvtgvlESM 251
Cdd:PTZ00121 1549 DELKKAEELKKAEEKKKA--EEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK---------AEE 1617

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   252 EREEAESVIKEyggkvmTVVGKKLKYLVVGEEAGPKKlavAEELNipilsEDGLFDLIREKSGIAKQVKEEKKSPKKEHS 331
Cdd:PTZ00121 1618 AKIKAEELKKA------EEEKKKVEQLKKKEAEEKKK---AEELK-----KAEEENKIKAAEEAKKAEEDKKKAEEAKKA 1683

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   332 SEEKGKKEVKTSRRSSDKKEKEATKLKYGEKHDIAK--------HKVKEEHTSPKETKDKlndvpavtlkvKKEPSSQKE 403
Cdd:PTZ00121 1684 EEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEelkkaeeeNKIKAEEAKKEAEEDK-----------KKAEEAKKD 1752

                         410       420       430
                  ....*....|....*....|....*....|.
gi 62472391   404 HPPSPRTADLKTLDVVGMAWVDKHKPTSIKE 434
Cdd:PTZ00121 1753 EEEKKKIAHLKKEEEKKAEEIRKEKEAVIEE 1783
Agg_substance NF033875
LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, ...
 25-223 1.01e-03

LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain.


Pssm-ID: 411439 [Multi-domain]  Cd Length: 1306  Bit Score: 43.16  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    25 ETPSKAPKRRKAViissdEDEVVSPPETKKRKASKTASSEDDvvAATP-------EPIAKKARNGQ-KPALSKLKRHV-- 94
Cdd:NF033875   67 ETPKTAVSEEATV-----QKDTTSQPTKVEEVASEKNGAEQS--SATPndttnaqQPTVGAEKSAQeQPVVSPETTNEpl 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    95 -DPTELFGGET---KRVIVPKpktkavlEFENEDIDRSLMEVDLDESIKEA-APEKKVHSITRSSPSPKRAKNSSPEPPK 169
Cdd:NF033875  140 gQPTEVAPAENeanKSTSIPK-------EFETPDVDKAVDEAKKDPNITVVeKPAEDLGNVSSKDLAAKEKEVDQLQKEQ 212

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 62472391   170 PKSTKSKATTPRVKKEKPA---ADLESSVLTDEERHERKRASavlYQKYKNRSSCLN 223
Cdd:NF033875  213 AKKIAQQAAELKAKNEKIAkenAEIAAKNKAEKERYEKEVAE---YNKHKNENGYVN 266
 
Name Accession Description Interval E-value
RFC1 pfam08519
Replication factor RFC1 C terminal domain; This is the C terminal domain of replication factor ...
 764-917 4.28e-71

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: 232.85  E-value: 4.28e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    764 LSLGDLVEKRIRANSAWSLLPTQAFFSSVLPGEHMCGHFTGQINFPGWLGKNSKSGKRARLAQELHDHTRVCTSGSRLSV 843
Cdd:pfam08519    1 ISDGDLVDRMIRGEQQWSLLPTHAVFSSVRPASFMRGSMTGRINFPSWLGKNSKTGKNKRLLQELQYHMRLKTSGDKSEL 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391    844 RLDYAPFLLDNIVRPLAKDGQEGVPAALDVMKDYHLLREDLDSLVELTSWP----GKKSPLDAVDGRVKAALTRSYNK 917
Cdd:pfam08519   81 RLDYLPLLRKRLTQPLLEEGKDGVDEVIDLMDEYYLTKEDWDNIVELSTWGvgpyGEEDPLKKIDTKVKAAFTRKYNK 158
PRK04195 PRK04195
replication factor C large subunit; Provisional
 421-969 7.70e-48

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 178.19  E-value: 7.70e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   421 MAWVDKHKPTSIKEIVGQAgaasnvtnhnlklKAKQErvkvlhyfnfprLMNWLSKWyvnhdgnkkpqrpnpwaknDDGS 500
Cdd:PRK04195    2 MPWVEKYRPKTLSDVVGNE-------------KAKEQ------------LREWIESW-------------------LKGK 37

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   501 FYKAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEVSTLLSNKSLSGYftgqgqavsRKHVLIMDEVD 580
Cdd:PRK04195   38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA---------RRKLILLDEVD 108

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   581 GMAGNEDRGGMQELIALIKDSSIPIICMCNDRNHPKIRSLVNYCYDLRFQRPRLEQIKGKIMSICFKEKVKISPAKVEEI 660
Cdd:PRK04195  109 GIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEI 188

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   661 IAATNNDIRQSINHI-ALLSAKEDASQKSGQQVATKDLKLGPWEVVRKVFTADEHKH-----MSFADKSDLFFHdyslap 734
Cdd:PRK04195  189 AERSGGDLRSAINDLqAIAEGYGKLTLEDVKTLGRRDREESIFDALDAVFKARNADQaleasYDVDEDPDDLIE------ 262

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   735 lFVQQNylqvLPqgNKKDVLAKVAATADALSLGDLVEKRIRANSAWSLLPTqaFFSSVLPG-----EHMCGHFTgQINFP 809
Cdd:PRK04195  263 -WIDEN----IP--KEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRY--ASDLMTAGvalakEKKKRGFT-RYQPP 332

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   810 GWLGKNSKS----GKRARLAQEL--HDHTrvctsgSRLSVRLDYAPFLldnivRPLAKDGQEgVPAALDvmKDYHLlreD 883
Cdd:PRK04195  333 SYWRLLSKTkekrETRDSIAKKIaeKLHT------SKRKVRREVLPFL-----SIIFKHNPE-LAARLA--AFLEL---T 395

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   884 LDSLVELTswpGKKSPLDAVDGRVKAAlTRSYNKEVMAYSYSAQAGIKKKKSEAAGADDDylDEGPGEEDGAGGHLSSEE 963
Cdd:PRK04195  396 EEEIEFLT---GSKKATKKIKKIVEKA-EKKREEEKKEKKKKAFAGKKKEEEEEEEKEKK--EEEKEEEEEEAEEEKEEE 469


                  ....*.
gi 62472391   964 DEDKDN 969
Cdd:PRK04195  470 EEKKKK 475
BRCT_RFC1 cd17752
BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins; RFC1, also termed ...
 232-310 2.68e-40

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: 142.74  E-value: 2.68e-40
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 62472391  232 GSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAVAEELNIPILSEDGLFDLIR 310
Cdd:cd17752    1 GAPNCLEGLTFVITGVLESLEREEAEDLIKRYGGKVTGSVSKKTSYLVVGRDAGPSKLEKAKELGTKIIDEDGLFDLIR 79
Lig COG0272
NAD-dependent DNA ligase [Replication, recombination and repair];
222-309 3.95e-23

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


Pssm-ID: 440042 [Multi-domain]  Cd Length: 668  Bit Score: 105.49  E-value: 3.95e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  222 LNPGSKEIPKGSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGpKKLAVAEELNIPILS 301
Cdd:COG0272  581 VNMEEEEAEAAADSPLAGKTFVLTGTLETMTRDEAKELIEALGGKVSGSVSKKTDYVVAGENAG-SKLDKAEELGVPILD 659


                 ....*...
gi 62472391  302 EDGLFDLI 309
Cdd:COG0272  660 EAEFLELL 667
BRCT_DNA_ligase_like cd17748
BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins; LigA, also ...
 237-308 6.42e-22

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: 90.23  E-value: 6.42e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62472391  237 LSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAV----AEELNIPILSEDGLFDL 308
Cdd:cd17748    1 LAGKTFVFTGTLSSMSRDEAEELIEALGGKVQSSVSKKTDYLVVGDNAGSKLKKGeelkAKGLGIKIISEEEFLDL 76
ligA PRK07956
NAD-dependent DNA ligase LigA; Validated
 231-311 1.08e-18

NAD-dependent DNA ligase LigA; Validated


Pssm-ID: 236137 [Multi-domain]  Cd Length: 665  Bit Score: 91.34  E-value: 1.08e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   231 KGSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGpKKLAVAEELNIPILSEDGLFDLIR 310
Cdd:PRK07956  585 KGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAG-SKLAKAQELGIEVLDEEEFLRLLG 663


                  .
gi 62472391   311 E 311
Cdd:PRK07956  664 E 664
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 232-309 3.49e-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: 73.87  E-value: 3.49e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391    232 GSPDCLSGLTFVVTGvLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVgeEAGPKKLAVAEELNIPILSEDGLFDLI 309
Cdd:pfam00533    1 PKEKLFSGKTFVITG-LDGLERDELKELIEKLGGKVTDSLSKKTTHVIV--EARTKKYLKAKELGIPIVTEEWLLDCI 75
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 506-633 8.83e-16

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: 74.94  E-value: 8.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    506 LLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEvstllsnKSLSGYFTGQGQavSRKHVLIMDEVDGMAGN 585
Cdd:pfam00004    2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESE-------KRLRELFEAAKK--LAPCVIFIDEIDALAGS 72

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    586 EDRGG-------MQELIALIKD-----SSIPIICMCNdrNHPKIRSLVNYCYDLRFQRPR 633
Cdd:pfam00004   73 RGSGGdsesrrvVNQLLTELDGftssnSKVIVIAATN--RPDKLDPALLGRFDRIIEFPL 130
BRCT smart00292
breast cancer carboxy-terminal domain;
234-309 5.34e-14

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 67.79  E-value: 5.34e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391     234 PDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLK-YLVVGEEAGPK-KLAVAEELNIPILSEDGLFDLI 309
Cdd:smart00292    1 PKLFKGKTFYITGSFDKEERDELKELIEALGGKVTSSLSSKTTtHVIVGSPEGGKlELLKAIALGIPIVKEEWLLDCL 78
PLN03025 PLN03025
replication factor C subunit; Provisional
 421-675 2.30e-13

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 72.45  E-value: 2.30e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   421 MAWVDKHKPTSIKEIVGQAGAASnvtnhnlklkakqeRVKVlhyfnfprlmnwlskwyVNHDGNKkpqrPNpwaknddgs 500
Cdd:PLN03025    1 LPWVEKYRPTKLDDIVGNEDAVS--------------RLQV-----------------IARDGNM----PN--------- 36

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   501 fykaALLSGPPGIGKTTTATLVVKEL----GFDAV-EFNASDTRSKRLLKDEVSTLLSNK-SLsgyftgqgqAVSRKHVL 574
Cdd:PLN03025   37 ----LILSGPPGTGKTTSILALAHELlgpnYKEAVlELNASDDRGIDVVRNKIKMFAQKKvTL---------PPGRHKIV 103

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   575 IMDEVDGM---AGNEDRGGMQelialIKDSSIPIICMCNdRNHPKIRSLVNYCYDLRFQRPRLEQIKGKIMSICFKEKVK 651
Cdd:PLN03025  104 ILDEADSMtsgAQQALRRTME-----IYSNTTRFALACN-TSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP 177

                         250       260
                  ....*....|....*....|....
gi 62472391   652 ISPAKVEEIIAATNNDIRQSINHI 675
Cdd:PLN03025  178 YVPEGLEAIIFTADGDMRQALNNL 201
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 502-629 5.43e-11

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: 61.78  E-value: 5.43e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  502 YKAALLSGPPGIGKTTTATLVVKEL---GFDAVEFNASDTRSKrllkdevsTLLSNKSLSGYFTGQGQAVSRKH--VLIM 576
Cdd:cd00009   19 PKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEG--------LVVAELFGHFLVRLLFELAEKAKpgVLFI 90

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 62472391  577 DEVDGMAGNEDRGGMQEL----IALIKDSSIPIICMCNDRNHPKIRSLVNYCYDLRF 629
Cdd:cd00009   91 DEIDSLSRGAQNALLRVLetlnDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
ligA PRK14351
NAD-dependent DNA ligase LigA; Provisional
 218-316 6.34e-11

NAD-dependent DNA ligase LigA; Provisional


Pssm-ID: 184640 [Multi-domain]  Cd Length: 689  Bit Score: 66.32  E-value: 6.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   218 RSSCLNPGSKEIPKGspDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAVAEELNI 297
Cdd:PRK14351  593 LDHGVDPQPAESEGG--DALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDV 670

                          90
                  ....*....|....*....
gi 62472391   298 PILSEDGLFDLIREkSGIA 316
Cdd:PRK14351  671 PTLDEEEFEELLAE-RGVA 688
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 632-683 1.69e-09

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: 54.84  E-value: 1.69e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 62472391  632 PRLEQIKGKIMSICFKEKVKISPAKVEEIIAATNNDIRQSINHIALLSAKED 683
Cdd:cd18140    1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGG 52
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 506-635 2.33e-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: 57.00  E-value: 2.33e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391     506 LLSGPPGIGKTTTATLVVKEL---GFDAVEFNASDTRSKRLLKDEVSTLLSNKSLSGYFTGQGQAVS--RKH---VLIMD 577
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALAlaRKLkpdVLILD 85

                            90       100       110       120       130       140
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62472391     578 EVDGMAGNEDRGGMQELIAL------IKDSSIPIICMCNDRNHPkIRSLVNYCYDLRFQRPRLE 635
Cdd:smart00382   86 EITSLLDAEQEALLLLLEELrlllllKSEKNLTVILTTNDEKDL-GPALLRRRFDRRIVLLLIL 148
44 PHA02544
clamp loader, small subunit; Provisional
 506-673 1.25e-08

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 57.69  E-value: 1.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   506 LLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKrLLKDEVSTLLSNKSLSGyftgqgqavsrKH-VLIMDEVD--GM 582
Cdd:PHA02544   47 LHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRID-FVRNRLTRFASTVSLTG-----------GGkVIIIDEFDrlGL 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   583 AGNED--RGGMQELialikDSSIPIICMCNDRN--HPKIRSlvnYCYDLRFQRP----RLE---QIKGKIMSICFKEKVK 651
Cdd:PHA02544  115 ADAQRhlRSFMEAY-----SKNCSFIITANNKNgiIEPLRS---RCRVIDFGVPtkeeQIEmmkQMIVRCKGILEAEGVE 186

                         170       180
                  ....*....|....*....|..
gi 62472391   652 ISPAKVEEIIAATNNDIRQSIN 673
Cdd:PHA02544  187 VDMKVLAALVKKNFPDFRRTIN 208
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
493-712 1.40e-08

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 57.29  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  493 WAKNDDGSfyKAALLSGPPGIGKTTTATLVVKELG-----------------------FDAVEFNAsDTRSKRLLKDEVS 549
Cdd:COG0470   11 AAESGRLP--HALLLHGPPGIGKTTLALALARDLLcenpeggkacgqchsrlmaagnhPDLLELNP-EEKSDQIGIDQIR 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  550 TL---LSNKSLSGyftgqgqavSRKhVLIMDEVDGMAGNEDRGGMQELIALIKDSsiPIICMCNDRNH--PKIRSLvnyC 624
Cdd:COG0470   88 ELgefLSLTPLEG---------GRK-VVIIDEADAMNEAAANALLKTLEEPPKNT--PFILIANDPSRllPTIRSR---C 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  625 YDLRFQRPRLEQIKGKImsicfkEKVKISPAKVEEIIAATNNDIRQSINHIALLSAKEDASQKSGQQVATKDlklgPWEV 704
Cdd:COG0470  153 QVIRFRPPSEEEALAWL------REEGVDEDALEAILRLAGGDPRAAINLLQALAGRKELLEDLAALLSRDR----ALEL 222


                 ....*...
gi 62472391  705 VRKVFTAD 712
Cdd:COG0470  223 LDALLKAE 230
rfc PRK00440
replication factor C small subunit; Reviewed
 423-673 2.25e-08

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 56.80  E-value: 2.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   423 WVDKHKPTSIKEIVGQagaasnvtnhnlklkakqERVKvlhyfnfPRLMNwlskwYVnhdgnKKPQRPNpwaknddgsfy 502
Cdd:PRK00440    7 WVEKYRPRTLDEIVGQ------------------EEIV-------ERLKS-----YV-----KEKNMPH----------- 40

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   503 kaALLSGPPGIGKTTTATLVVKELGFDA-----VEFNASDTRSKRLLKDEVSTLLSNKSLSGY-FtgqgqavsrkHVLIM 576
Cdd:PRK00440   41 --LLFAGPPGTGKTTAALALARELYGEDwrenfLELNASDERGIDVIRNKIKEFARTAPVGGApF----------KIIFL 108

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   577 DEVDGM---AGNEDRGGMqELIA------LIKDSSIPIIcmcndrnhPKIRSlvnYCYDLRFQRPRLEQIKGKIMSICFK 647
Cdd:PRK00440  109 DEADNLtsdAQQALRRTM-EMYSqntrfiLSCNYSSKII--------DPIQS---RCAVFRFSPLKKEAVAERLRYIAEN 176

                         250       260
                  ....*....|....*....|....*.
gi 62472391   648 EKVKISPAKVEEIIAATNNDIRQSIN 673
Cdd:PRK00440  177 EGIEITDDALEAIYYVSEGDMRKAIN 202
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 240-307 1.95e-07

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: 48.90  E-value: 1.95e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391  240 LTFVVTGvLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGPKKLAVAEELNIPILSEDGLFD 307
Cdd:cd00027    1 LVICFSG-LDDEEREELKKLIEALGGKVSESLSSKVTHLIAKSPSGEKYYLAALAWGIPIVSPEWLLD 67
BRCT_PARP1 cd17747
BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins; PARP-1 (EC 2.4.2. ...
 237-309 3.78e-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: 3.78e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62472391  237 LSGLTFVVTGVLeSMEREEAESVIKEYGGKVMTVVGKKLKYLVVGE---EAGPKKLAVAEELNIPILSEDGLFDLI 309
Cdd:cd17747    1 LTGMKFALIGKL-SKSKDELKKLIEKLGGKVASKVTKKVTLCISTKaevEKMSKKMKEAKEAGVPVVSEDFLEDCI 75
PRK06195 PRK06195
DNA polymerase III subunit epsilon; Validated
 227-312 5.26e-07

DNA polymerase III subunit epsilon; Validated


Pssm-ID: 235735 [Multi-domain]  Cd Length: 309  Bit Score: 52.48  E-value: 5.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   227 KEIPKGSPDCLSGLTFVVTGVLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVG--------EEAGPKKLAVAEEL--- 295
Cdd:PRK06195  211 KIIESFGFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNtkdiedlnREEMSNKLKKAIDLkkk 290

                          90
                  ....*....|....*....
gi 62472391   296 --NIPILSEDGLFDLIREK 312
Cdd:PRK06195  291 gqNIKFLNEEEFLQKCKEK 309
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 503-697 8.89e-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: 49.14  E-value: 8.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  503 KAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKrllkdevstllsnkslsgyFTGQ-GQAVSR---------KH 572
Cdd:COG0464  192 RGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSK-------------------YVGEtEKNLREvfdkarglaPC 252

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  573 VLIMDEVDGMAGNEDRGG---MQELIALI------KDSSIPIICMCNDRNH--PKIRSlvnycydlRFQR------PRLE 635
Cdd:COG0464  253 VLFIDEADALAGKRGEVGdgvGRRVVNTLltemeeLRSDVVVIAATNRPDLldPALLR--------RFDEiiffplPDAE 324

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 62472391  636 QIKgKIMSICFKEKVKISPAKVEEIIAATNN----DIRQsinhiALLSAKEDASQKSGQQVATKDL 697
Cdd:COG0464  325 ERL-EIFRIHLRKRPLDEDVDLEELAEATEGlsgaDIRN-----VVRRAALQALRLGREPVTTEDL 384
AAA_22 pfam13401
AAA domain;
506-606 3.48e-05

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 44.25  E-value: 3.48e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    506 LLSGPPGIGKTTTATLVVKEL---GFDAVEFNASDTRS--------KRLLKDEVSTLLSNKSLSGYFTGQGQAVSRKHVL 574
Cdd:pfam13401    9 VLTGESGTGKTTLLRRLLEQLpevRDSVVFVDLPSGTSpkdllralLRALGLPLSGRLSKEELLAALQQLLLALAVAVVL 88

                           90       100       110
                   ....*....|....*....|....*....|....
gi 62472391    575 IMDEVDGMagneDRGGMQELIAL--IKDSSIPII 606
Cdd:pfam13401   89 IIDEAQHL----SLEALEELRDLlnLSSKLLQLI 118
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 503-610 1.19e-04

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: 43.43  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  503 KAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLlkDEVSTLLSNkslsgYFtgqgqAVSRKH---VLIMDEV 579
Cdd:cd19481   27 KGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYV--GESEKNLRK-----IF-----ERARRLapcILFIDEI 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 62472391  580 DGMAGNEDRGGM------------QELIALIKDSSIPIICMCN 610
Cdd:cd19481   95 DAIGRKRDSSGEsgelrrvlnqllTELDGVNSRSKVLVIAATN 137
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
480-698 4.11e-04

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 43.33  E-value: 4.11e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  480 NHDGNKKPQRPNPWAKNDdgsfykaALLSGPPGIGKTTTATLVVKELGFDAVEFNASdtrskrllkdevstllsnkSLSG 559
Cdd:COG1223   20 ELRRRENLRKFGLWPPRK-------ILFYGPPGTGKTMLAEALAGELKLPLLTVRLD-------------------SLIG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  560 YFTGQG---------QAVSRKHVLIMDEVDGMAG----NEDRGGMQELI-AL------IKDSSIpIICMCndrNHPKI-- 617
Cdd:COG1223   74 SYLGETarnlrklfdFARRAPCVIFFDEFDAIAKdrgdQNDVGEVKRVVnALlqeldgLPSGSV-VIAAT---NHPELld 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  618 RSLVNYC-YDLRFQRPRLEQIKgKIMSIC---FKEKVKISPAK-VEEIIAATNNDIRQsinhiALLSAKEDASQKSGQQV 692
Cdd:COG1223  150 SALWRRFdEVIEFPLPDKEERK-EILELNlkkFPLPFELDLKKlAKKLEGLSGADIEK-----VLKTALKKAILEDREKV 223


                 ....*.
gi 62472391  693 ATKDLK 698
Cdd:COG1223  224 TKEDLE 229
PTZ00121 PTZ00121
MAEBL; Provisional
 12-434 7.27e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.59  E-value: 7.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    12 LPAKAKSAEAENGETPSKAPKRRKAVIISSDEDEVVSPPETKKRKASKTASSEddvvAATPEPIAKKARNGQKPAlsKLK 91
Cdd:PTZ00121 1396 AKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADE----AKKKAEEAKKAEEAKKKA--EEA 1469

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    92 RHVDPTELFGGETKRVIVPKPKTKAVLEfENEDIDRSLMEVDLDESIKEAAPEKKVHSITRSSPSPKRAKNSSPEPPKPK 171
Cdd:PTZ00121 1470 KKADEAKKKAEEAKKADEAKKKAEEAKK-KADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKA 1548

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   172 STKSKATTPRVKKEKPAAdlESSVLTDEERHERKRASAVLYQKYKNRSSCLNPGSKEIPKGSPDCLSGltfvvtgvlESM 251
Cdd:PTZ00121 1549 DELKKAEELKKAEEKKKA--EEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKK---------AEE 1617

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   252 EREEAESVIKEyggkvmTVVGKKLKYLVVGEEAGPKKlavAEELNipilsEDGLFDLIREKSGIAKQVKEEKKSPKKEHS 331
Cdd:PTZ00121 1618 AKIKAEELKKA------EEEKKKVEQLKKKEAEEKKK---AEELK-----KAEEENKIKAAEEAKKAEEDKKKAEEAKKA 1683

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391   332 SEEKGKKEVKTSRRSSDKKEKEATKLKYGEKHDIAK--------HKVKEEHTSPKETKDKlndvpavtlkvKKEPSSQKE 403
Cdd:PTZ00121 1684 EEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEelkkaeeeNKIKAEEAKKEAEEDK-----------KKAEEAKKD 1752

                         410       420       430
                  ....*....|....*....|....*....|.
gi 62472391   404 HPPSPRTADLKTLDVVGMAWVDKHKPTSIKE 434
Cdd:PTZ00121 1753 EEEKKKIAHLKKEEEKKAEEIRKEKEAVIEE 1783
BRCT_p53bp1_rpt1 cd17745
first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 236-313 7.47e-04

first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain.


Pssm-ID: 349376 [Multi-domain]  Cd Length: 99  Bit Score: 39.99  E-value: 7.47e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  236 CLSGLTFVVTGVLES---MEREEAESVIKEYGGKVM------------------------------TVVGKKLKYLvvge 282
Cdd:cd17745    1 IFSGCAFLLTGAEETdkpFDKERLESQIEANGGTVLedfdeelfndgrsstrksrskdlrfvfliaDSPSRTPKYL---- 76

                         90       100       110
                 ....*....|....*....|....*....|.
gi 62472391  283 eagpkkLAVAeeLNIPILSEDGLFDLIREKS 313
Cdd:cd17745   77 ------QALA--LGIPCVSHKWILDCIEAGK 99
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
498-611 8.84e-04

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 42.91  E-value: 8.84e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  498 DGSFYKAALLSGPPGIGKTTTATLVVKELGFDA---------VEFNASDTRSK-RLLKDEVSTLLSNKSLSgyFTGQG-- 565
Cdd:COG1474   47 RGERPSNVLIYGPTGTGKTAVAKYVLEELEEEAeergvdvrvVYVNCRQASTRyRVLSRILEELGSGEDIP--STGLStd 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 62472391  566 -------QAVSRK---HVLIMDEVDGMAGNEDRGGMQELI---ALIKDSSIPIICMCND 611
Cdd:COG1474  125 elfdrlyEALDERdgvLVVVLDEIDYLVDDEGDDLLYQLLranEELEGARVGVIGISND 183
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 506-527 9.35e-04

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: 40.95  E-value: 9.35e-04
                           10        20
                   ....*....|....*....|..
gi 62472391    506 LLSGPPGIGKTTTATLVVKELG 527
Cdd:pfam05496   37 LLYGPPGLGKTTLANIIANEMG 58
Agg_substance NF033875
LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, ...
 25-223 1.01e-03

LPXTG-anchored aggregation substance; Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain.


Pssm-ID: 411439 [Multi-domain]  Cd Length: 1306  Bit Score: 43.16  E-value: 1.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    25 ETPSKAPKRRKAViissdEDEVVSPPETKKRKASKTASSEDDvvAATP-------EPIAKKARNGQ-KPALSKLKRHV-- 94
Cdd:NF033875   67 ETPKTAVSEEATV-----QKDTTSQPTKVEEVASEKNGAEQS--SATPndttnaqQPTVGAEKSAQeQPVVSPETTNEpl 139

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    95 -DPTELFGGET---KRVIVPKpktkavlEFENEDIDRSLMEVDLDESIKEA-APEKKVHSITRSSPSPKRAKNSSPEPPK 169
Cdd:NF033875  140 gQPTEVAPAENeanKSTSIPK-------EFETPDVDKAVDEAKKDPNITVVeKPAEDLGNVSSKDLAAKEKEVDQLQKEQ 212

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 62472391   170 PKSTKSKATTPRVKKEKPA---ADLESSVLTDEERHERKRASavlYQKYKNRSSCLN 223
Cdd:NF033875  213 AKKIAQQAAELKAKNEKIAkenAEIAAKNKAEKERYEKEVAE---YNKHKNENGYVN 266
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 506-579 1.02e-03

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 42.76  E-value: 1.02e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62472391   506 LLSGPPGIGKTTTATLVVKELGFDAVEFNASDTrSKRLLKDEVSTLLSNKSLsgyftgqgqavSRKHVLIMDEV 579
Cdd:PRK13342   40 ILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-GVKDLREVIEEARQRRSA-----------GRRTILFIDEI 101
BRCT_TopBP1_rpt2_like cd17731
second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins; ...
 237-310 1.25e-03

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: 38.68  E-value: 1.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62472391  237 LSGLTFVVTGvLESMEREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAGpKKLAVAEELN-IPILSEDGLFDLIR 310
Cdd:cd17731    3 FKGLVICVTG-FDSEERKEIQQLVEQNGGSYSPDLSKNCTHLIAGSPSG-QKYEFARKWNsIHIVTPEWLYDSIE 75
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 506-527 1.46e-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: 41.99  E-value: 1.46e-03
                         10        20
                 ....*....|....*....|..
gi 62472391  506 LLSGPPGIGKTTTATLVVKELG 527
Cdd:COG2255   58 LLYGPPGLGKTTLAHIIANEMG 79
BRCT_PARP4_like cd17726
BRCT domain of poly [ADP-ribose] polymerase 4 (PARP-4) and similar proteins; PARP-4, also ...
 252-312 2.44e-03

BRCT domain of poly [ADP-ribose] polymerase 4 (PARP-4) and similar proteins; PARP-4, also termed 193 kDa vault protein, or ADP-ribosyltransferase diphtheria toxin-like 4 (ARTD4), or PARP-related/IalphaI-related H5/proline-rich (PH5P), or vault poly(ADP-ribose) polymerase (VPARP), shows poly(ADP-ribosyl)ation activity that catalyzes the formation of ADP-ribose polymers in response to DNA damage. PARP-4 is a component of the vault ribonucleoprotein particle, at least composed of MVP, PARP4 and one or more vault RNAs (vRNAs). The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this group.


Pssm-ID: 349358 [Multi-domain]  Cd Length: 85  Bit Score: 38.04  E-value: 2.44e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62472391  252 EREEAESVIKEYGGKVMTVVGKKLKYLVVGEEAG--PKKLAVAEELNIPILSEDGLFDLIREK 312
Cdd:cd17726   19 EKKKLKKKITENGGIISYIINKKCTHVVVNNAKAlsSYKCRMAQKYGIPVVSLDYIWKCVEAG 81
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
506-527 2.52e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 41.27  E-value: 2.52e-03
                          10        20
                  ....*....|....*....|..
gi 62472391   506 LLSGPPGIGKTTTATLVVKELG 527
Cdd:PRK00080   55 LLYGPPGLGKTTLANIIANEMG 76
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
503-548 7.49e-03

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 39.95  E-value: 7.49e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 62472391  503 KAALLSGPPGIGKTTTATLVVKELGFDA--VEFNASDTRSKRLLKDEV 548
Cdd:COG1224   65 KGILIVGPPGTGKTALAVAIARELGEDTpfVAISGSEIYSAELKKTEF 112
HLD_clamp cd18133
helical lid domain of clamp loader-like AAA+ proteins; Clamp loader complexes are multisubunit ...
 635-692 7.80e-03

helical lid domain of clamp loader-like AAA+ proteins; Clamp loader complexes are multisubunit complexes that play an important role in DNA replication. They open sliding clamps for assembly and close them around DNA, specifically targeting them to sites where DNA synthesis is initiated and orienting them correctly for replication. The subunits belong to the clamp loader clade of AAA+ superfamily.


Pssm-ID: 350838 [Multi-domain]  Cd Length: 65  Bit Score: 35.91  E-value: 7.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 62472391  635 EQIKGKIMSICFKEKVKISPAKVEEIIAATNNDIRQSINHIALLSAKEDASQKSGQQV 692
Cdd:cd18133    4 EQLKRRLAAIAEQEKLKLDDAALQALAYISEGDLRKALNALQRAAALGDDGKISLDRV 61
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 503-583 8.21e-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: 38.43  E-value: 8.21e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391  503 KAALLSGPPGIGKTTTATLVVKELGFDAVEFNASDTRSKRLLKDEvstllsnKSLSGYFtgqgqAVSRKH---VLIMDEV 579
Cdd:cd19503   35 RGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKYLGESE-------KNLREIF-----EEARSHapsIIFIDEI 102


                 ....
gi 62472391  580 DGMA 583
Cdd:cd19503  103 DALA 106
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 506-616 8.38e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 36.81  E-value: 8.38e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    506 LLSGPPGIGKTTTATLVVKELGfdavefnasdtRSKRLLKDEVSTL-LSNKSLSGYfTGQGqavsrkhVLIMDEVDGMAG 584
Cdd:pfam00910    2 WLYGPPGCGKSTLAKYLARALL-----------KKLGLPKDSVYSRnPDDDFWDGY-TGQP-------VVIIDDFGQNPD 62

                           90       100       110
                   ....*....|....*....|....*....|...
gi 62472391    585 NEDrggMQELIALIkdSSIPII-CMCNDRNHPK 616
Cdd:pfam00910   63 GPD---EAELIRLV--SSTPYPpPMAALEEKGT 90
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 505-617 8.98e-03

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.


Pssm-ID: 433343 [Multi-domain]  Cd Length: 191  Bit Score: 38.31  E-value: 8.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62472391    505 ALLSGPPGIGKTTTATLVVK---ELGFDAVEFNASDTRSKRLLKD---EVSTLlsnKSLsGYFTGQGQAVSRKHVLIMDE 578
Cdd:pfam13604   21 AVLVGPAGTGKTTALKALREaweAAGYRVIGLAPTGRAAKVLGEElgiPADTI---AKL-LHRLGGRAGLDPGTLLIVDE 96

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 62472391    579 VdGMAGNEDrggMQELIALIKDSSIPIICMCNDRNHPKI 617
Cdd:pfam13604   97 A-GMVGTRQ---MARLLKLAEDAGARVILVGDPRQLPSV 131
BRCT_Rad4_rpt4 cd17723
fourth BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and ...
 239-312 9.76e-03

fourth BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins; Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system, which couples S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the fourth one.


Pssm-ID: 349355 [Multi-domain]  Cd Length: 74  Bit Score: 36.08  E-value: 9.76e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 62472391  239 GLTFVVTGvLESMEREEAESVIKEYGGKVMTVVGKKLKYLVV-GEEAGPKKLAVAEELNIPILSEDGLFDLIREK 312
Cdd:cd17723    1 GLSISLTG-FSGVDLLHISKLIKLLGAKYHESLTKDRSLLIVnSTEKKSDKINFAKKWGIPVVSVEWLWDCLKEG 74
 
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