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Conserved domains on  [gi|19111992|ref|NP_595200|]
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Ctf18 RFC-like complex subunit Ctf18 [Schizosaccharomyces pombe]

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
 353-618 9.06e-39

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: 151.23  E-value: 9.06e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  353 WVDTYRPQLFRDLLGDERVHRAAMHWIKAWDpcvfgksRLQPSKSMrfnprftnitsdsdrpdkrimMLTGLAGAGKTTL 432
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWL-------KGKPKKAL---------------------LLYGPPGVGKTSL 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  433 AHVIAHQAGYKVLEINASDDRTAHTVHEKVSSAISNHSALSSQPTCVIVDEIDG----GDPAFVRALLSLLEsdekatey 508
Cdd:PRK04195  56 AHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGihgnEDRGGARAILELIK-------- 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  509 sQAGNskkkkkfkklcrPIICICNDLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNS 588
Cdd:PRK04195 128 -KAKQ------------PIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGG 194

                        250       260       270
                 ....*....|....*....|....*....|
gi 19111992  589 DIRSCINSLQLLSLNNKRIDSETIKLLQPK 618
Cdd:PRK04195 195 DLRSAINDLQAIAEGYGKLTLEDVKTLGRR 224
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 353-618 9.06e-39

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 151.23  E-value: 9.06e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  353 WVDTYRPQLFRDLLGDERVHRAAMHWIKAWDpcvfgksRLQPSKSMrfnprftnitsdsdrpdkrimMLTGLAGAGKTTL 432
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWL-------KGKPKKAL---------------------LLYGPPGVGKTSL 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  433 AHVIAHQAGYKVLEINASDDRTAHTVHEKVSSAISNHSALSSQPTCVIVDEIDG----GDPAFVRALLSLLEsdekatey 508
Cdd:PRK04195  56 AHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGihgnEDRGGARAILELIK-------- 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  509 sQAGNskkkkkfkklcrPIICICNDLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNS 588
Cdd:PRK04195 128 -KAKQ------------PIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGG 194

                        250       260       270
                 ....*....|....*....|....*....|
gi 19111992  589 DIRSCINSLQLLSLNNKRIDSETIKLLQPK 618
Cdd:PRK04195 195 DLRSAINDLQAIAEGYGKLTLEDVKTLGRR 224
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 554-615 2.48e-14

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: 68.32  E-value: 2.48e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19111992 554 PPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQLLSLNNKRIDSETIKLL 615
Cdd:cd18140   1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGGVITEEDVYEV 62
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 416-554 1.59e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992    416 KRIMMLTGLAGAGKTTLAHVIAHQA---GYKVLEINASDDRTAHTVHEKVSSAISNHS--------------ALSSQPTC 478
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKAsgsgelrlrlalalARKLKPDV 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19111992    479 VIVDEIDGGDPAFVRALLSLLESDEKATEYSQAGNskkkkkfkklcRPIICICNDLYTPALRPLRPYAQ-IIYFRPP 554
Cdd:smart00382  82 LILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN-----------LTVILTTNDEKDLGPALLRRRFDrRIVLLLI 147
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
419-602 9.34e-09

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 57.68  E-value: 9.34e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 419 MMLTGLAGAGKTTLAHVIAH---------------------QAGYK--VLEINA---SDDRTAHTVhEKVSSAISNHSAL 472
Cdd:COG0470  21 LLLHGPPGIGKTTLALALARdllcenpeggkacgqchsrlmAAGNHpdLLELNPeekSDQIGIDQI-RELGEFLSLTPLE 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 473 SSQPTcVIVDEIDGGDPAFVRALLSLLEsdekatEYSqaGNSkkkkkfkklcrPIICICNDLYTPaLRPLRPYAQIIYFR 552
Cdd:COG0470 100 GGRKV-VIIDEADAMNEAAANALLKTLE------EPP--KNT-----------PFILIANDPSRL-LPTIRSRCQVIRFR 158

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 19111992 553 PPPQASLVGRLRTicrnENIAVDsrSLTLLTDIYNSDIRSCINSLQLLSL 602
Cdd:COG0470 159 PPSEEEALAWLRE----EGVDED--ALEAILRLAGGDPRAAINLLQALAG 202
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 419-540 1.50e-07

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: 51.05  E-value: 1.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992   419 MMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDDR------TAHTVHEKVSSAISNhsalssQPTCVIVDEID------- 485
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL------APCVIFIDEIDalagsrg 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111992   486 -GGDPAFVR---ALLSLLESDEKATEYsqagnskkkkkfkklcRPIICICN--DLYTPALR 540
Cdd:pfam00004  75 sGGDSESRRvvnQLLTELDGFTSSNSK----------------VIVIAATNrpDKLDPALL 119
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 353-618 9.06e-39

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 151.23  E-value: 9.06e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  353 WVDTYRPQLFRDLLGDERVHRAAMHWIKAWDpcvfgksRLQPSKSMrfnprftnitsdsdrpdkrimMLTGLAGAGKTTL 432
Cdd:PRK04195   4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWL-------KGKPKKAL---------------------LLYGPPGVGKTSL 55

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  433 AHVIAHQAGYKVLEINASDDRTAHTVHEKVSSAISNHSALSSQPTCVIVDEIDG----GDPAFVRALLSLLEsdekatey 508
Cdd:PRK04195  56 AHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGihgnEDRGGARAILELIK-------- 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  509 sQAGNskkkkkfkklcrPIICICNDLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNS 588
Cdd:PRK04195 128 -KAKQ------------PIILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGG 194

                        250       260       270
                 ....*....|....*....|....*....|
gi 19111992  589 DIRSCINSLQLLSLNNKRIDSETIKLLQPK 618
Cdd:PRK04195 195 DLRSAINDLQAIAEGYGKLTLEDVKTLGRR 224
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 554-615 2.48e-14

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: 68.32  E-value: 2.48e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19111992 554 PPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQLLSLNNKRIDSETIKLL 615
Cdd:cd18140   1 LSKEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGGVITEEDVYEV 62
rfc PRK00440
replication factor C small subunit; Reviewed
 349-612 6.17e-14

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 73.75  E-value: 6.17e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  349 SQKLWVDTYRPQLFRDLLGDERVhraamhwikawdpcvfgKSRLQP---SKSMrfnPRftnitsdsdrpdkriMMLTGLA 425
Cdd:PRK00440   3 MEEIWVEKYRPRTLDEIVGQEEI-----------------VERLKSyvkEKNM---PH---------------LLFAGPP 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  426 GAGKTTLAHVIAHQ---AGYK--VLEINASDDRTAHTVHEKVSSaISNHSALSSQP-TCVIVDEIDGGDPAFVRALLSLL 499
Cdd:PRK00440  48 GTGKTTAALALARElygEDWRenFLELNASDERGIDVIRNKIKE-FARTAPVGGAPfKIIFLDEADNLTSDAQQALRRTM 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  500 ESdekateYSQAgnskkkkkfkklCRPIIcICNdlYTPAL-RPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRS 578
Cdd:PRK00440 127 EM------YSQN------------TRFIL-SCN--YSSKIiDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDA 185

                        250       260       270
                 ....*....|....*....|....*....|....
gi 19111992  579 LTLLTDIYNSDIRSCINSLQLLSLNNKRIDSETI 612
Cdd:PRK00440 186 LEAIYYVSEGDMRKAINALQAAAATGKEVTEEAV 219
44 PHA02544
clamp loader, small subunit; Provisional
 352-651 8.09e-14

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 73.49  E-value: 8.09e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  352 LWVDTYRPQLFrdllgdervhraamhwikawDPCVFgksrlqPSksmRFNPRFTNITSDSDRPDkrIMMLTGLAGAGKTT 431
Cdd:PHA02544  10 MWEQKYRPSTI--------------------DECIL------PA---ADKETFKSIVKKGRIPN--MLLHSPSPGTGKTT 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  432 LAHVIAHQAGYKVLEINASDDR--TAHTVHEKVSSAISnhsaLSSQPTCVIVDEID-GGDPAFVRALLSLLEsdekatEY 508
Cdd:PHA02544  59 VAKALCNEVGAEVLFVNGSDCRidFVRNRLTRFASTVS----LTGGGKVIIIDEFDrLGLADAQRHLRSFME------AY 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  509 SqaGNskkkkkfkklCRPIIcICNDLyTPALRPLRPYAQIIYFRPPPQA-------SLVGRLRTICRNENIAVDSRSLTL 581
Cdd:PHA02544 129 S--KN----------CSFII-TANNK-NGIIEPLRSRCRVIDFGVPTKEeqiemmkQMIVRCKGILEAEGVEVDMKVLAA 194

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  582 LTDIYNSDIRSCINSLQLLSLNNKrIDSETIKLLqpksnsfsTSSLIQSLFLQLDNKQIRAIEASQPTYS 651
Cdd:PHA02544 195 LVKKNFPDFRRTINELQRYASTGK-IDAGILSEV--------TNSDIDDVVEALKAKDFKAVRALAPNYA 255
PLN03025 PLN03025
replication factor C subunit; Provisional
 353-598 5.02e-12

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 68.22  E-value: 5.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  353 WVDTYRPQLFRDLLGDERVhraamhwikawdpcvfgKSRLQpsksmrfnprftNITSDSDRPDkriMMLTGLAGAGKTTL 432
Cdd:PLN03025   3 WVEKYRPTKLDDIVGNEDA-----------------VSRLQ------------VIARDGNMPN---LILSGPPGTGKTTS 50

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  433 AHVIAHQ---AGYK--VLEINASDDRTAHTVHEKVSSAISNHSAL-SSQPTCVIVDEIDGGDPAFVRALLSLLESDEKAT 506
Cdd:PLN03025  51 ILALAHEllgPNYKeaVLELNASDDRGIDVVRNKIKMFAQKKVTLpPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTT 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  507 EYSQAgnskkkkkfkklcrpiiciCNdLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIY 586
Cdd:PLN03025 131 RFALA-------------------CN-TSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTA 190

                        250
                 ....*....|..
gi 19111992  587 NSDIRSCINSLQ 598
Cdd:PLN03025 191 DGDMRQALNNLQ 202
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 412-553 1.19e-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: 63.70  E-value: 1.19e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 412 DRPDKRIMMLTGLAGAGKTTLAHVIAHQA---GYKVLEINASDDRTAHTVHEKVSSAISNHS---ALSSQPTCVIVDEID 485
Cdd:cd00009  15 ELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHFLVRLLfelAEKAKPGVLFIDEID 94

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 486 GGDPAFVRALLSLLESDEKATEYSQAgnskkkkkfkklcRPIICICNDLYTPALRPLRPYA--QIIYFRP 553
Cdd:cd00009  95 SLSRGAQNALLRVLETLNDLRIDREN-------------VRVIGATNRPLLGDLDRALYDRldIRIVIPL 151
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 416-554 1.59e-09

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.38  E-value: 1.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992    416 KRIMMLTGLAGAGKTTLAHVIAHQA---GYKVLEINASDDRTAHTVHEKVSSAISNHS--------------ALSSQPTC 478
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKAsgsgelrlrlalalARKLKPDV 81

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19111992    479 VIVDEIDGGDPAFVRALLSLLESDEKATEYSQAGNskkkkkfkklcRPIICICNDLYTPALRPLRPYAQ-IIYFRPP 554
Cdd:smart00382  82 LILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN-----------LTVILTTNDEKDLGPALLRRRFDrRIVLLLI 147
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 419-622 6.41e-09

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 59.33  E-value: 6.41e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  419 MMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDDRTAHtVHEKVSSAISNHSalSSQPTCVIVDEI--------Dggdpa 490
Cdd:PRK13342  39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVKD-LREVIEEARQRRS--AGRRTILFIDEIhrfnkaqqD----- 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  491 fvrALLSLLESDE-----KATEysqagNskkkkkfkklcrPIICIcndlyTPALRPlRpyAQIIYFRPPPQASLVGRLRT 565
Cdd:PRK13342 111 ---ALLPHVEDGTitligATTE-----N------------PSFEV-----NPALLS-R--AQVFELKPLSEEDIEQLLKR 162

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111992  566 ICRNEN---IAVDSRSLTLLTDIYNSDIRSCINSLQLLSLNNKRIDSETIK-LLQPKSNSF 622
Cdd:PRK13342 163 ALEDKErglVELDDEALDALARLANGDARRALNLLELAALGVDSITLELLEeALQKRAARY 223
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
419-602 9.34e-09

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 57.68  E-value: 9.34e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 419 MMLTGLAGAGKTTLAHVIAH---------------------QAGYK--VLEINA---SDDRTAHTVhEKVSSAISNHSAL 472
Cdd:COG0470  21 LLLHGPPGIGKTTLALALARdllcenpeggkacgqchsrlmAAGNHpdLLELNPeekSDQIGIDQI-RELGEFLSLTPLE 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 473 SSQPTcVIVDEIDGGDPAFVRALLSLLEsdekatEYSqaGNSkkkkkfkklcrPIICICNDLYTPaLRPLRPYAQIIYFR 552
Cdd:COG0470 100 GGRKV-VIIDEADAMNEAAANALLKTLE------EPP--KNT-----------PFILIANDPSRL-LPTIRSRCQVIRFR 158

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 19111992 553 PPPQASLVGRLRTicrnENIAVDsrSLTLLTDIYNSDIRSCINSLQLLSL 602
Cdd:COG0470 159 PPSEEEALAWLRE----EGVDED--ALEAILRLAGGDPRAAINLLQALAG 202
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 350-642 5.70e-08

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 55.77  E-value: 5.70e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  350 QKLWVDTYRPQLFRDLLGDERVhraamhwikawdpcvfgKSRLQpsksmrfnprftnitSDSDRPDKRIMMLTGLAGAGK 429
Cdd:PRK12402   2 APLWTEKYRPALLEDILGQDEV-----------------VERLS---------------RAVDSPNLPHLLVQGPPGSGK 49

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  430 TTLAHVIAHQAgY------KVLEINAS------------DDRTAH---TVHEKVSSAISN----------HSALSSQPTC 478
Cdd:PRK12402  50 TAAVRALAREL-YgdpwenNFTEFNVAdffdqgkkylveDPRFAHflgTDKRIRSSKIDNfkhvlkeyasYRPLSADYKT 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  479 VIVDEIDGGDPAFVRALLSLLEsdekatEYSQAgnskkkkkfkklCRPIICICNdlytPA--LRPLRPYAQIIYFRPPPQ 556
Cdd:PRK12402 129 ILLDNAEALREDAQQALRRIME------QYSRT------------CRFIIATRQ----PSklIPPIRSRCLPLFFRAPTD 186

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  557 ASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQLLSLNNKRIDSETIkllQPKSNSFSTSSLIQSLFLQLD 636
Cdd:PRK12402 187 DELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAA---YEALGDVGTDEVIESLLDAAE 263


                 ....*.
gi 19111992  637 NKQIRA 642
Cdd:PRK12402 264 AGDFTD 269
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 419-540 1.50e-07

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: 51.05  E-value: 1.50e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992   419 MMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDDR------TAHTVHEKVSSAISNhsalssQPTCVIVDEID------- 485
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL------APCVIFIDEIDalagsrg 74

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111992   486 -GGDPAFVR---ALLSLLESDEKATEYsqagnskkkkkfkklcRPIICICN--DLYTPALR 540
Cdd:pfam00004  75 sGGDSESRRvvnQLLTELDGFTSSNSK----------------VIVIAATNrpDKLDPALL 119
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 350-612 1.36e-06

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 51.84  E-value: 1.36e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 350 QKLWVDTYRPQLFRDLLGDERVhRAAMHWIKAW---DPCVFGKSRLQPSKSMrfnprftnitsdsdrpdkrimMLTGLAG 426
Cdd:COG0464 144 LEEELLELREAILDDLGGLEEV-KEELRELVALplkRPELREEYGLPPPRGL---------------------LLYGPPG 201

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 427 AGKTTLAHVIAHQAGYKVLEINASDDR------TAHTVHEKVssaisnHSALSSQPTCVIVDEID--------GGDPAFV 492
Cdd:COG0464 202 TGKTLLARALAGELGLPLIEVDLSDLVskyvgeTEKNLREVF------DKARGLAPCVLFIDEADalagkrgeVGDGVGR 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 493 RA---LLSLLESDEKATeysqagnskkkkkfkklcrPIICICN--DLYTPALrpLRPYAQIIYFRPPPQASLVGRLRTIC 567
Cdd:COG0464 276 RVvntLLTEMEELRSDV-------------------VVIAATNrpDLLDPAL--LRRFDEIIFFPLPDAEERLEIFRIHL 334

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 19111992 568 RNENIA--VDSRSLTLLTDIYN-SDIRSCINS--LQLLSLNNKRIDSETI 612
Cdd:COG0464 335 RKRPLDedVDLEELAEATEGLSgADIRNVVRRaaLQALRLGREPVTTEDL 384
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 396-507 2.13e-06

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


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 48.43  E-value: 2.13e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 396 KSMRFNPRFTNITSDSDRPDKRIMMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDDRTAH--TVHEKVSSAISnhSALS 473
Cdd:cd19481   6 REAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYvgESEKNLRKIFE--RARR 83

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 19111992 474 SQPTCVIVDEID--------GGDPAFVRALLS--LLESDEKATE 507
Cdd:cd19481  84 LAPCILFIDEIDaigrkrdsSGESGELRRVLNqlLTELDGVNSR 127
HLD_clamp cd18133
helical lid domain of clamp loader-like AAA+ proteins; Clamp loader complexes are multisubunit ...
 554-612 3.84e-04

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: 39.38  E-value: 3.84e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19111992 554 PPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQ--LLSLNNKRIDSETI 612
Cdd:cd18133   1 LDQEQLKRRLAAIAEQEKLKLDDAALQALAYISEGDLRKALNALQraAALGDDGKISLDRV 61
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 419-484 7.61e-04

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 43.12  E-value: 7.61e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19111992 419 MMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDDRTAhTVHEKVSSAisNHSALSSQPTCVIVDEI 484
Cdd:COG2256  52 MILWGPPGTGKTTLARLIANATDAEFVALSAVTSGVK-DIREVIEEA--RERRAYGRRTILFVDEI 114
AAA_22 pfam13401
AAA domain;
413-506 1.16e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.02  E-value: 1.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992   413 RPDKRIMMLTGLAGAGKTTLAHVIA---HQAGYKVLEINASDDRTAHTVHEKVSSAI--SNHSALSSQP----------- 476
Cdd:pfam13401   2 RFGAGILVLTGESGTGKTTLLRRLLeqlPEVRDSVVFVDLPSGTSPKDLLRALLRALglPLSGRLSKEEllaalqqllla 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 19111992   477 ----TCVIVDEIDGGDPAFVRALLSLLESDEKAT 506
Cdd:pfam13401  82 lavaVVLIIDEAQHLSLEALEELRDLLNLSSKLL 115
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
410-484 1.16e-03

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 42.24  E-value: 1.16e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 19111992 410 DSDRPDKRIMMLTGLAGAGKTTLAHVIAHQAGyKVLEINASDDRTAHTVHEKVSSAISNHSALSSQPTCVIVDEI 484
Cdd:COG1373  14 LKLLDNRKAVVITGPRQVGKTTLLKQLAKELE-NILYINLDDPRLRALAEEDPDDLLEALKELYPGKTYLFLDEI 87
PRK04132 PRK04132
replication factor C small subunit; Provisional
 445-644 1.50e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 42.52  E-value: 1.50e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  445 LEINASDDRTAHTVHEKVSSAISnhsalsSQPTcvivdeidgGDPAFvrALLSLLESDeKATEYSQAGNSKKKKKFKKLC 524
Cdd:PRK04132 600 LELNASDERGINVIREKVKEFAR------TKPI---------GGASF--KIIFLDEAD-ALTQDAQQALRRTMEMFSSNV 661

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992  525 RPIICiCNdLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQLLSLNN 604
Cdd:PRK04132 662 RFILS-CN-YSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD 739

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 19111992  605 KRIDSETIKLLQPKSNSFSTSSLIQslfLQLDNKQIRAIE 644
Cdd:PRK04132 740 DKITDENVFLVASRARPEDIREMML---LALKGNFLKARE 776
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
547-616 2.44e-03

DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 41.33  E-value: 2.44e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19111992 547 QIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCInSL--QLLSLNNKRIDSETIKLLQ 616
Cdd:COG2812 166 QRFDFRRLPPEEIAEHLAKIAEREGIEIEPEALALIARAADGSMRDAL-SLldQAIAFGLLDRRELLLDLLE 236
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 417-485 3.75e-03

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like 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: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 39.31  E-value: 3.75e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19111992 417 RIMMLTGLAGAGKTTLAHVIAHQAGYKVLEINASDdrtahtvhekVSSAISNHS----------ALSSQPTCVIVDEID 485
Cdd:cd19518  35 RGVLLHGPPGCGKTMLANAIAGELKVPFLKISATE----------IVSGVSGESeekirelfdqAISNAPCIVFIDEID 103
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 525-600 4.04e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 40.96  E-value: 4.04e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19111992  525 RPIICICNDLYTPALRPLRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRsciNSLQLL 600
Cdd:PRK14953 149 RTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMR---DAASLL 221
HolA COG1466
DNA polymerase III, delta subunit [Replication, recombination and repair];
542-645 4.20e-03

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


Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 40.24  E-value: 4.20e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 542 LRPYAQIIYFRPPPQASLVGRLRTICRNENIAVDSRSLTLLTDIYNSDIRSCINSLQLLSL---NNKRIDSETIKLLQPK 618
Cdd:COG1466 114 LEKAGVVVECYPLKERELPAWIRQRLKAAGLRIDPDAAQLLAERVGGDLLALAQELEKLALyagDGGTITLEDVEALVGD 193

                        90       100
                ....*....|....*....|....*..
gi 19111992 619 SNSFSTSSLIQSLflqLDNKQIRAIEA 645
Cdd:COG1466 194 SAEFNVFDLADAL---LAGDAARALRI 217
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 415-484 4.38e-03

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 40.73  E-value: 4.38e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 415 DKRIMMLTGLAGAGKTTLAHVIA---HQAGYKVL----------EINASDDRTAHTVhekvssaisnHSALSSQP----- 476
Cdd:COG0507 139 TRRVSVLTGGAGTGKTTTLRALLaalEALGLRVAlaaptgkaakRLSESTGIEARTI----------HRLLGLRPdsgrf 208

                        90
                ....*....|....*....
gi 19111992 477 -----------TCVIVDEI 484
Cdd:COG0507 209 rhnrdnpltpaDLLVVDEA 227
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 407-483 6.63e-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: 38.70  E-value: 6.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992   407 ITSDSDRpdkrIMMLTGLAGAGKTT-LAHV--IAHQAGYKVLEInASDDRTAHTVHEKVSSAISN-HSALSSQ------- 475
Cdd:pfam13604  13 LLTSGDR----VAVLVGPAGTGKTTaLKALreAWEAAGYRVIGL-APTGRAAKVLGEELGIPADTiAKLLHRLggragld 87


                  ....*....
gi 19111992   476 -PTCVIVDE 483
Cdd:pfam13604  88 pGTLLIVDE 96
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 413-606 7.87e-03

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 39.60  E-value: 7.87e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 413 RPDKRIMmLTGLAGAGKTTLAHVIAHQAGYKVLEINASD------DRTAHTVHEkVSSAISNHSalssqPTCVIVDEID- 485
Cdd:COG1222 110 EPPKGVL-LYGPPGTGKTLLAKAVAGELGAPFIRVRGSElvskyiGEGARNVRE-VFELAREKA-----PSIIFIDEIDa 182

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19111992 486 -------GGDPAFVRALLS--LLESDekatEYSQAGNSKkkkkfkklcrpIICICN--DLYTPAL-RPLRpYAQIIYFRP 553
Cdd:COG1222 183 iaarrtdDGTSGEVQRTVNqlLAELD----GFESRGDVL-----------IIAATNrpDLLDPALlRPGR-FDRVIEVPL 246

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19111992 554 PPQASLVGRLRTICRNENIA--VDSRSLTLLTDIYN-SDIRSCINSLQLLSLNNKR 606
Cdd:COG1222 247 PDEEAREEILKIHLRDMPLAddVDLDKLAKLTEGFSgADLKAIVTEAGMFAIREGR 302
CysC COG0529
Adenylylsulfate kinase or related kinase [Inorganic ion transport and metabolism]; ...
 421-444 8.54e-03

Adenylylsulfate kinase or related kinase [Inorganic ion transport and metabolism]; Adenylylsulfate kinase or related kinase is part of the Pathway/BioSystem: Cysteine biosynthesis


Pssm-ID: 440295 [Multi-domain]  Cd Length: 189  Bit Score: 38.53  E-value: 8.54e-03
                        10        20
                ....*....|....*....|....*..
gi 19111992 421 LTGLAGAGKTTLAHVIA---HQAGYKV 444
Cdd:COG0529  21 FTGLSGSGKSTLANALErrlFERGRHV 47
 
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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