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Conserved domains on  [gi|148690490|gb|EDL22437|]
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CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae), isoform CRA_a [Mus musculus]

Protein Classification

ATP-binding protein( domain architecture ID 1005821)

ATP-binding protein with an AAA (ATPases Associated with various cellular Activities) domain, similar to human ATPase family AAA domain-containing protein 5 that is involved in DNA damage response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 342-588 4.04e-31

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: 128.50  E-value: 4.04e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 342 HEQALEEMLE-AELDPSQRPrQKVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSPEAFRTRIEAATQMESVLGV 420
Cdd:PRK04195  19 NEKAKEQLREwIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 421 GGRpncLVI-DEIDGaptaaINVllgilnrkgpqEADQGGTAVaaggrrrraegglLTR-------PIICICNDQFTPSL 492
Cdd:PRK04195  98 RRK---LILlDEVDG-----IHG-----------NEDRGGARA-------------ILElikkakqPIILTANDPYDPSL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 493 RQLKQQALLLHVPPtLPSR-LVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFLyGRGRRELSVKAVQTthV 571
Cdd:PRK04195 146 RELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--L 221

                        250
                 ....*....|....*..
gi 148690490 572 GLKDQRKGLFSVWQEVF 588
Cdd:PRK04195 222 GRRDREESIFDALDAVF 238
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 342-588 4.04e-31

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 128.50  E-value: 4.04e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 342 HEQALEEMLE-AELDPSQRPrQKVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSPEAFRTRIEAATQMESVLGV 420
Cdd:PRK04195  19 NEKAKEQLREwIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 421 GGRpncLVI-DEIDGaptaaINVllgilnrkgpqEADQGGTAVaaggrrrraegglLTR-------PIICICNDQFTPSL 492
Cdd:PRK04195  98 RRK---LILlDEVDG-----IHG-----------NEDRGGARA-------------ILElikkakqPIILTANDPYDPSL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 493 RQLKQQALLLHVPPtLPSR-LVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFLyGRGRRELSVKAVQTthV 571
Cdd:PRK04195 146 RELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--L 221

                        250
                 ....*....|....*..
gi 148690490 572 GLKDQRKGLFSVWQEVF 588
Cdd:PRK04195 222 GRRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 347-516 2.99e-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: 71.02  E-value: 2.99e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 347 EEMLEAELDPSQRPRQKVALLCGPPGLGKTTLAHVVARHAGYC---VVEMNASDDRSPEAFRTRIEA-ATQMESVLGVGG 422
Cdd:cd00009    4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 423 RPNCLVIDEIDGAPTAAINVLLGILNrkgpqeadqggtavaaggRRRRAEGGLLTRPIICICNDqftpslrqlkqqALLL 502
Cdd:cd00009   84 KPGVLFIDEIDSLSRGAQNALLRVLE------------------TLNDLRIDRENVRVIGATNR------------PLLG 133

                        170
                 ....*....|....
gi 148690490 503 HVPPTLPSRLVQRL 516
Cdd:cd00009  134 DLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 366-433 6.66e-12

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: 63.77  E-value: 6.66e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 148690490  366 LLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDR------SPEAFRTRIEAATQMesvlgvggRPNCLVIDEID 433
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL--------APCVIFIDEID 67
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 361-490 3.81e-07

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: 50.45  E-value: 3.81e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490   361 RQKVALLCGPPGLGKTTLAHVVARHA---GYCVVEMNASDDRSPEAFRTRIEAATQMESVLGVGGR------------PN 425
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRlrlalalarklkPD 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148690490   426 CLVIDEIDGAPTAAINVLLGILNRkgpqeadqggtavaagGRRRRAEGGLLTRPIICICNDQFTP 490
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEE----------------LRLLLLLKSEKNLTVILTTNDEKDL 129
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 366-396 4.86e-06

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 49.69  E-value: 4.86e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 148690490 366 LLCGPPGLGKTTLAHVVARhagycvvEMNAS 396
Cdd:COG2255   58 LLYGPPGLGKTTLAHIIAN-------EMGVN 81
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 340-552 3.10e-04

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: 44.56  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  340 KSHEQALEEMLEAELDPSQRPRqkVALLCGPPGLGKTTLAHVVARHAGYCVVE-MNASDDRSP----------------- 401
Cdd:TIGR00602  90 KKKIEEVETWLKAQVLENAPKR--ILLITGPSGCGKSTTIKILSKELGIQVQEwSNPTLPDFQkndhkvtlslescfsnf 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  402 ----EAFRTRIEAATQMESVLG--VGGRPNCLVIDEI----DGAPTAAINVLLGILNRKGP-------QEADQGGTAVAA 464
Cdd:TIGR00602 168 qsqiEVFSEFLLRATNKLQMLGddLMTDKKIILVEDLpnqfYRDTRALHEILRWKYVSIGRcplvfiiTESLEGDNNQRR 247

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  465 ggrrrraegglLTRPIICICND--QFTPSLRQLKqqalllhVPPTLPSRLVQRLQEISLQHGMRSDPGALVA-------L 535
Cdd:TIGR00602 248 -----------LLFPAETIMNKeiLEEPRVSNIS-------FNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPkktsvelL 309

                         250
                  ....*....|....*..
gi 148690490  536 CEKTDNDIRACINTLQF 552
Cdd:TIGR00602 310 CQGCSGDIRSAINSLQF 326
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 342-588 4.04e-31

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 128.50  E-value: 4.04e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 342 HEQALEEMLE-AELDPSQRPrQKVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSPEAFRTRIEAATQMESVLGV 420
Cdd:PRK04195  19 NEKAKEQLREwIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGA 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 421 GGRpncLVI-DEIDGaptaaINVllgilnrkgpqEADQGGTAVaaggrrrraegglLTR-------PIICICNDQFTPSL 492
Cdd:PRK04195  98 RRK---LILlDEVDG-----IHG-----------NEDRGGARA-------------ILElikkakqPIILTANDPYDPSL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 493 RQLKQQALLLHVPPtLPSR-LVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFLyGRGRRELSVKAVQTthV 571
Cdd:PRK04195 146 RELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--L 221

                        250
                 ....*....|....*..
gi 148690490 572 GLKDQRKGLFSVWQEVF 588
Cdd:PRK04195 222 GRRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 347-516 2.99e-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: 71.02  E-value: 2.99e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 347 EEMLEAELDPSQRPRQKVALLCGPPGLGKTTLAHVVARHAGYC---VVEMNASDDRSPEAFRTRIEA-ATQMESVLGVGG 422
Cdd:cd00009    4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPgapFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 423 RPNCLVIDEIDGAPTAAINVLLGILNrkgpqeadqggtavaaggRRRRAEGGLLTRPIICICNDqftpslrqlkqqALLL 502
Cdd:cd00009   84 KPGVLFIDEIDSLSRGAQNALLRVLE------------------TLNDLRIDRENVRVIGATNR------------PLLG 133

                        170
                 ....*....|....
gi 148690490 503 HVPPTLPSRLVQRL 516
Cdd:cd00009  134 DLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 366-433 6.66e-12

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: 63.77  E-value: 6.66e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 148690490  366 LLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDR------SPEAFRTRIEAATQMesvlgvggRPNCLVIDEID 433
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL--------APCVIFIDEID 67
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 509-569 8.84e-12

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: 61.01  E-value: 8.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 148690490 509 PSRLVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFLYgRGRRELSVKAVQTT 569
Cdd:cd18140    3 KEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAA-AGGGVITEEDVYEV 62
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 366-450 2.81e-08

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 53.45  E-value: 2.81e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  366 LLCGPPGLGKTTLAHVVARH-AGYCVVEMNASDDRSPEAFRTRIEAATQM----ESVLGVGGRPNC-LVIDEIDGAPTAA 439
Cdd:pfam07728   3 LLVGPPGTGKTELAERLAAAlSNRPVFYVQLTRDTTEEDLFGRRNIDPGGaswvDGPLVRAAREGEiAVLDEINRANPDV 82

                          90
                  ....*....|.
gi 148690490  440 INVLLGILNRK 450
Cdd:pfam07728  83 LNSLLSLLDER 93
PLN03025 PLN03025
replication factor C subunit; Provisional
 366-439 2.94e-08

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 56.66  E-value: 2.94e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148690490 366 LLCGPPGLGKTTLAHVVARH---AGY--CVVEMNASDDRSPEAFRTRIEAATQMESVLGVgGRPNCLVIDEIDGAPTAA 439
Cdd:PLN03025  38 ILSGPPGTGKTTSILALAHEllgPNYkeAVLELNASDDRGIDVVRNKIKMFAQKKVTLPP-GRHKIVILDEADSMTSGA 115
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 361-490 3.81e-07

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: 50.45  E-value: 3.81e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490   361 RQKVALLCGPPGLGKTTLAHVVARHA---GYCVVEMNASDDRSPEAFRTRIEAATQMESVLGVGGR------------PN 425
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRlrlalalarklkPD 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 148690490   426 CLVIDEIDGAPTAAINVLLGILNRkgpqeadqggtavaagGRRRRAEGGLLTRPIICICNDQFTP 490
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEE----------------LRLLLLLKSEKNLTVILTTNDEKDL 129
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 346-433 9.05e-07

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: 49.59  E-value: 9.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 346 LEEMLEAELDPSQRPRQ-----KVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASD------DRSPEAFRTRIEAATQM 414
Cdd:cd19481    5 LREAVEAPRRGSRLRRYglglpKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSllskyvGESEKNLRKIFERARRL 84

                         90
                 ....*....|....*....
gi 148690490 415 esvlgvggRPNCLVIDEID 433
Cdd:cd19481   85 --------APCILFIDEID 95
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 334-432 1.12e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 52.01  E-value: 1.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 334 TAPGKwksheqALEEMLEAELDPSqrprqkvALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSPEaFRTRIEAATQ 413
Cdd:PRK13342  21 LGPGK------PLRRMIEAGRLSS-------MILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVKD-LREVIEEARQ 86

                         90
                 ....*....|....*....
gi 148690490 414 MESvlgvGGRPNCLVIDEI 432
Cdd:PRK13342  87 RRS----AGRRTILFIDEI 101
AAA_22 pfam13401
AAA domain;
358-448 3.23e-06

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 47.34  E-value: 3.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  358 QRPRQKVALLCGPPGLGKTTLA-HVVARHAGYC--VVEMNASDDRSPEAFRTRIEAAT---------------QMESVLG 419
Cdd:pfam13401   1 IRFGAGILVLTGESGTGKTTLLrRLLEQLPEVRdsVVFVDLPSGTSPKDLLRALLRALglplsgrlskeellaALQQLLL 80

                          90       100
                  ....*....|....*....|....*....
gi 148690490  420 VGGRPNCLVIDEIDGAPTAAINVLLGILN 448
Cdd:pfam13401  81 ALAVAVVLIIDEAQHLSLEALEELRDLLN 109
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 366-396 4.86e-06

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 49.69  E-value: 4.86e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 148690490 366 LLCGPPGLGKTTLAHVVARhagycvvEMNAS 396
Cdd:COG2255   58 LLYGPPGLGKTTLAHIIAN-------EMGVN 81
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 366-396 9.44e-06

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: 46.72  E-value: 9.44e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 148690490  366 LLCGPPGLGKTTLAHVVARhagycvvEMNAS 396
Cdd:pfam05496  37 LLYGPPGLGKTTLANIIAN-------EMGVN 60
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
366-396 1.17e-05

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 48.59  E-value: 1.17e-05
                         10        20        30
                 ....*....|....*....|....*....|.
gi 148690490 366 LLCGPPGLGKTTLAHVVARhagycvvEMNAS 396
Cdd:PRK00080  55 LLYGPPGLGKTTLANIIAN-------EMGVN 78
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 342-433 1.22e-05

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: 48.75  E-value: 1.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 342 HEQALEEMLEAELDPSQRPRQ---------KVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSP------EAFRT 406
Cdd:COG0464  162 LEEVKEELRELVALPLKRPELreeyglpppRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteKNLRE 241

                         90       100
                 ....*....|....*....|....*..
gi 148690490 407 RIEAATQMESVLgvggrpncLVIDEID 433
Cdd:COG0464  242 VFDKARGLAPCV--------LFIDEAD 260
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 334-432 3.15e-05

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 47.36  E-value: 3.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 334 TAPGKWksheqaLEEMLEAELDPSqrprqkvALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDDRSPEaFRTRIEAAtq 413
Cdd:COG2256   34 LGPGKP------LRRAIEAGRLSS-------MILWGPPGTGKTTLARLIANATDAEFVALSAVTSGVKD-IREVIEEA-- 97

                         90
                 ....*....|....*....
gi 148690490 414 mESVLGVGGRPnCLVIDEI 432
Cdd:COG2256   98 -RERRAYGRRT-ILFVDEI 114
44 PHA02544
clamp loader, small subunit; Provisional
 366-557 4.83e-05

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 46.52  E-value: 4.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 366 LLCGP-PGLGKTTLAHVVARHAGYCVVEMNASDDRSpEAFRTRIeaaTQMESVLGVGGRPNCLVIDEIDGAPTAAINVLL 444
Cdd:PHA02544  46 LLHSPsPGTGKTTVAKALCNEVGAEVLFVNGSDCRI-DFVRNRL---TRFASTVSLTGGGKVIIIDEFDRLGLADAQRHL 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 445 gilnrKGPQEADQGGTAvaaggrrrraegglltrpIICICNDQ--FTPSLR------------QLKQQALLlhvpptlpS 510
Cdd:PHA02544 122 -----RSFMEAYSKNCS------------------FIITANNKngIIEPLRsrcrvidfgvptKEEQIEMM--------K 170

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 148690490 511 RLVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFLYGRG 557
Cdd:PHA02544 171 QMIVRCKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYASTG 217
rfc PRK00440
replication factor C small subunit; Reviewed
 366-551 1.05e-04

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 45.63  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 366 LLCGPPGLGKTTLAHVVARHAgYC------VVEMNASDDRSPEAFRTRIE--AATQMesvlgVGGRPNCLVI-DEIDGAP 436
Cdd:PRK00440  42 LFAGPPGTGKTTAALALAREL-YGedwrenFLELNASDERGIDVIRNKIKefARTAP-----VGGAPFKIIFlDEADNLT 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 437 TAAINVllgiLNRKGPQEADQggtavaaggrrrraeggllTRPIIcICN------D---------QFTPslrqLKQQAll 501
Cdd:PRK00440 116 SDAQQA----LRRTMEMYSQN-------------------TRFIL-SCNysskiiDpiqsrcavfRFSP----LKKEA-- 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 148690490 502 lhvpptlpsrLVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQ 551
Cdd:PRK00440 166 ----------VAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQ 205
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 343-434 1.76e-04

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 44.61  E-value: 1.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 343 EQALEEMLEAELDPSQR----------PRQKVaLLCGPPGLGKTTLAHVVARHAGYCVVEMNASDdrspeafrtrieaat 412
Cdd:COG1222   84 DEQIEEIREAVELPLKNpelfrkygiePPKGV-LLYGPPGTGKTLLAKAVAGELGAPFIRVRGSE--------------- 147

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 148690490 413 QMESVLGVGGR-------------PNCLVIDEIDG 434
Cdd:COG1222  148 LVSKYIGEGARnvrevfelarekaPSIIFIDEIDA 182
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 344-436 2.98e-04

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: 42.28  E-value: 2.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 344 QALEEMLEAeldPSQRPRQ---------KVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASD------DRSPEAFRTRI 408
Cdd:cd19503   10 ASLKELIEL---PLKYPELfralglkppRGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSivskylGESEKNLREIF 86

                         90       100
                 ....*....|....*....|....*....
gi 148690490 409 EAATQMEsvlgvggrPNCLVIDEIDG-AP 436
Cdd:cd19503   87 EEARSHA--------PSIIFIDEIDAlAP 107
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 340-552 3.10e-04

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: 44.56  E-value: 3.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  340 KSHEQALEEMLEAELDPSQRPRqkVALLCGPPGLGKTTLAHVVARHAGYCVVE-MNASDDRSP----------------- 401
Cdd:TIGR00602  90 KKKIEEVETWLKAQVLENAPKR--ILLITGPSGCGKSTTIKILSKELGIQVQEwSNPTLPDFQkndhkvtlslescfsnf 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  402 ----EAFRTRIEAATQMESVLG--VGGRPNCLVIDEI----DGAPTAAINVLLGILNRKGP-------QEADQGGTAVAA 464
Cdd:TIGR00602 168 qsqiEVFSEFLLRATNKLQMLGddLMTDKKIILVEDLpnqfYRDTRALHEILRWKYVSIGRcplvfiiTESLEGDNNQRR 247

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490  465 ggrrrraegglLTRPIICICND--QFTPSLRQLKqqalllhVPPTLPSRLVQRLQEISLQHGMRSDPGALVA-------L 535
Cdd:TIGR00602 248 -----------LLFPAETIMNKeiLEEPRVSNIS-------FNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPkktsvelL 309

                         250
                  ....*....|....*..
gi 148690490  536 CEKTDNDIRACINTLQF 552
Cdd:TIGR00602 310 CQGCSGDIRSAINSLQF 326
Rad17 pfam03215
Rad17 P-loop domain;
340-416 4.03e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 42.64  E-value: 4.03e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 148690490  340 KSHEQALEEMLEAELDPSQRPRqkVALLCGPPGLGKTTLAHVVARHAGYCVVE-MNASDDRSPEAFRTRIEAATQMES 416
Cdd:pfam03215  25 KRKIKDVQEWLDAMFLENAKHR--ILLISGPSGCGKSTVIKELSKELGPKYREwSNPTSFRSPPNQVTDFRGDCIVNS 100
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 317-447 7.48e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 42.94  E-value: 7.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 317 ARKPRPGVETTRVGKEATApgkwKSHEQALEEMLEAEldpsqrprqkVALLCGPPGLGKTTLAHVVAR------------ 384
Cdd:PRK14970   8 ARKYRPQTFDDVVGQSHIT----NTLLNAIENNHLAQ----------ALLFCGPRGVGKTTCARILARkinqpgyddpne 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148690490 385 HAGYCVVEMNASDDRSPEAFRTRIEAATQMESVlgvgGRPNCLVIDEIDGAPTAAINVLLGIL 447
Cdd:PRK14970  74 DFSFNIFELDAASNNSVDDIRNLIDQVRIPPQT----GKYKIYIIDEVHMLSSAAFNAFLKTL 132
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 366-396 1.44e-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: 41.90  E-value: 1.44e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 148690490  366 LLCGPPGLGKTTLAHVVARhagycvvEMNAS 396
Cdd:TIGR00635  34 LLYGPPGLGKTTLAHIIAN-------EMGVN 57
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
342-566 1.64e-03

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 41.50  E-value: 1.64e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 342 HEQALEEMLEAeldpSQRPRQKVALL-CGPPGLGKTTLAHVVARH-----------AGYC------------VVEMNA-- 395
Cdd:COG0470    1 QEEAWEQLLAA----AESGRLPHALLlHGPPGIGKTTLALALARDllcenpeggkaCGQChsrlmaagnhpdLLELNPee 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 396 -SDDRSPEAFRTRIEAATQMesvlGVGGRPNCLVIDEIDGAPTAAINVLLGILNRkgPQEadqggtavaaggrrrraegg 474
Cdd:COG0470   77 kSDQIGIDQIRELGEFLSLT----PLEGGRKVVIIDEADAMNEAAANALLKTLEE--PPK-------------------- 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 475 llTRPIICICND--QFTPSLRQLKQQallLHVPPTLPSRLVQRLQeislQHGMrsDPGALVALCEKTDNDIRACINTLQF 552
Cdd:COG0470  131 --NTPFILIANDpsRLLPTIRSRCQV---IRFRPPSEEEALAWLR----EEGV--DEDALEAILRLAGGDPRAAINLLQA 199

                        250
                 ....*....|....
gi 148690490 553 LYGRGRRELSVKAV 566
Cdd:COG0470  200 LAGRKELLEDLAAL 213
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 343-433 1.87e-03

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and 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: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 40.29  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 343 EQALEEMLEAeLDPSQRPRQ---------KVALLCGPPGLGKTTLAHVVARHAGYCVVEMNASDdrspeaFrtrieaatq 413
Cdd:cd19501   10 EEAKEELKEV-VEFLKNPEKftklgakipKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSD------F--------- 73

                         90       100       110
                 ....*....|....*....|....*....|...
gi 148690490 414 MESVLGVGG------------RPNCLV-IDEID 433
Cdd:cd19501   74 VEMFVGVGAsrvrdlfeqakkNAPCIVfIDEID 106
PRK13341 PRK13341
AAA family ATPase;
365-432 3.35e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 41.19  E-value: 3.35e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 148690490 365 ALLCGPPGLGKTTLAHVVARHAGYCVVEMNA-----SDdrspeaFRTRIEAATQMesvLGVGGRPNCLVIDEI 432
Cdd:PRK13341  55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAvlagvKD------LRAEVDRAKER---LERHGKRTILFIDEV 118
DNA_pol3_delta pfam06144
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 486-553 4.21e-03

DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA.


Pssm-ID: 428788 [Multi-domain]  Cd Length: 174  Bit Score: 39.19  E-value: 4.21e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 148690490  486 DQFTPSLRQLKQQALLLHV-PPTLpSRLVQRLQEISLQHGMRSDPGALVALCEKTDNDIRACINTLQFL 553
Cdd:pfam06144 105 DERKKLTKLLKKKATVVECfTLKE-EELIQWIQSRAQELGLQIEPEAIELLCELVENNLSALAQELEKL 172
COG2842 COG2842
Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]; ...
 365-443 4.72e-03

Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons];


Pssm-ID: 442090 [Multi-domain]  Cd Length: 254  Bit Score: 39.94  E-value: 4.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148690490 365 ALLCGPPGLGKT-TLAHVVARHAGYCVVEMNASDDRS------------PEAFRTRIEAATQMESVLGVGGRPncLVIDE 431
Cdd:COG2842   53 GVVYGESGVGKTtAAREYANRNPNVIYVTASPSWTSKelleelaeelgiPAPPGTIADLRDRILERLAGTGRL--LIIDE 130

                         90
                 ....*....|..
gi 148690490 432 IDGAPTAAINVL 443
Cdd:COG2842  131 ADHLKPKALEEL 142
AAA_18 pfam13238
AAA domain;
366-418 4.75e-03

AAA domain;


Pssm-ID: 433052 [Multi-domain]  Cd Length: 128  Bit Score: 38.18  E-value: 4.75e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 148690490  366 LLCGPPGLGKTTLAHVVARHAGY-----CVV-EMNASDDRSPEAFRTRIEAATQMESVL 418
Cdd:pfam13238   2 LITGTPGVGKTTLAKELSKRLGFgdnvrDLAlENGLVLGDDPETRESKRLDEDKLDRLL 60
 
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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