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Conserved domains on  [gi|167860135|ref|NP_001103572|]
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chromosome transmission fidelity protein 18 homolog [Danio rerio]

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
 344-589 1.98e-30

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: 126.19  E-value: 1.98e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 344 KTKSQMTEEIlEAELDqyKRPKfKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDRSAELFQKRIDTATQMKSVLG 423
Cdd:PRK04195  21 KAKEQLREWI-ESWLK--GKPK-KALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 424 ANEKpncLII-DEID--------GAPAAAINILlatlnrKDSKDgeetgvnalkkkkkkqsvllrPIICICNDLYVPALR 494
Cdd:PRK04195  97 ARRK---LILlDEVDgihgnedrGGARAILELI------KKAKQ---------------------PIILTANDPYDPSLR 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 495 PLRQQAFLLVFPQtLPSR-LAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFLhSRGQKHLDQRSVSSmcVG 573
Cdd:PRK04195 147 ELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LG 222

                        250
                 ....*....|....*.
gi 167860135 574 LKDQNKGLFSVWQEIF 589
Cdd:PRK04195 223 RRDREESIFDALDAVF 238
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 344-589 1.98e-30

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 126.19  E-value: 1.98e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 344 KTKSQMTEEIlEAELDqyKRPKfKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDRSAELFQKRIDTATQMKSVLG 423
Cdd:PRK04195  21 KAKEQLREWI-ESWLK--GKPK-KALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 424 ANEKpncLII-DEID--------GAPAAAINILlatlnrKDSKDgeetgvnalkkkkkkqsvllrPIICICNDLYVPALR 494
Cdd:PRK04195  97 ARRK---LILlDEVDgihgnedrGGARAILELI------KKAKQ---------------------PIILTANDPYDPSLR 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 495 PLRQQAFLLVFPQtLPSR-LAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFLhSRGQKHLDQRSVSSmcVG 573
Cdd:PRK04195 147 ELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LG 222

                        250
                 ....*....|....*.
gi 167860135 574 LKDQNKGLFSVWQEIF 589
Cdd:PRK04195 223 RRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 362-505 2.25e-16

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: 77.19  E-value: 2.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 362 KRPKFKVALLSGPPGLGKTTLAHIIAKHA---GYNVVEINASDDRSAELFQKRIDT-ATQMKSVLGANEKPNCLIIDEID 437
Cdd:cd00009   15 ELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKAKPGVLFIDEID 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135 438 GAPAAAINILLATLNrkdskdgeetgvnalKKKKKKQSVLLRPIICICNDLYVPALRPLRQQAFLLVF 505
Cdd:cd00009   95 SLSRGAQNALLRVLE---------------TLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 370-494 9.89e-15

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: 71.86  E-value: 9.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDR------SAELFQKRIDTATQMksvlganeKPNCLIIDEID------ 437
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL--------APCVIFIDEIDalagsr 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167860135  438 -----GAPAAAINILLATLNRKDSKDGEetgvnalkkkkkkqsvllRPIICICN--DLYVPALR 494
Cdd:pfam00004  74 gsggdSESRRVVNQLLTELDGFTSSNSK------------------VIVIAATNrpDKLDPALL 119
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 365-497 5.36e-11

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: 61.62  E-value: 5.36e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135   365 KFKVALLSGPPGLGKTTLAHIIAKHAGYN---VVEINASDDRSAELFQKRIDTA-------TQMKSVLGANE-----KPN 429
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVggkkasgSGELRLRLALAlarklKPD 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135   430 CLIIDEIDGAPAAAINILLATLNRKDSKDGEETGVNalkkkkkkqsvllRPIICICNDLYVPALRPLR 497
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN-------------LTVILTTNDEKDLGPALLR 135
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 358-437 1.03e-08

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: 58.38  E-value: 1.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 358 LDQYKRPKFKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDdrsaeLFQKRI-DTATQMKSVL-GANEKPNC-LIID 434
Cdd:COG0464  183 REEYGLPPPRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSD-----LVSKYVgETEKNLREVFdKARGLAPCvLFID 257


                 ...
gi 167860135 435 EID 437
Cdd:COG0464  258 EAD 260
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 370-436 3.27e-07

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: 53.07  E-value: 3.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGYNVVEInasddrSAELFQKRIDTAtqmkSVLGANEKPNCLIIDEI 436
Cdd:TIGR00635  34 LLYGPPGLGKTTLAHIIANEMGVNLKIT------SGPALEKPGDLA----AILTNLEEGDVLFIDEI 90
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 344-589 1.98e-30

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 126.19  E-value: 1.98e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 344 KTKSQMTEEIlEAELDqyKRPKfKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDRSAELFQKRIDTATQMKSVLG 423
Cdd:PRK04195  21 KAKEQLREWI-ESWLK--GKPK-KALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFG 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 424 ANEKpncLII-DEID--------GAPAAAINILlatlnrKDSKDgeetgvnalkkkkkkqsvllrPIICICNDLYVPALR 494
Cdd:PRK04195  97 ARRK---LILlDEVDgihgnedrGGARAILELI------KKAKQ---------------------PIILTANDPYDPSLR 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 495 PLRQQAFLLVFPQtLPSR-LAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFLhSRGQKHLDQRSVSSmcVG 573
Cdd:PRK04195 147 ELRNACLMIEFKR-LSTRsIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LG 222

                        250
                 ....*....|....*.
gi 167860135 574 LKDQNKGLFSVWQEIF 589
Cdd:PRK04195 223 RRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 362-505 2.25e-16

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: 77.19  E-value: 2.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 362 KRPKFKVALLSGPPGLGKTTLAHIIAKHA---GYNVVEINASDDRSAELFQKRIDT-ATQMKSVLGANEKPNCLIIDEID 437
Cdd:cd00009   15 ELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKAKPGVLFIDEID 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135 438 GAPAAAINILLATLNrkdskdgeetgvnalKKKKKKQSVLLRPIICICNDLYVPALRPLRQQAFLLVF 505
Cdd:cd00009   95 SLSRGAQNALLRVLE---------------TLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 370-494 9.89e-15

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: 71.86  E-value: 9.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDR------SAELFQKRIDTATQMksvlganeKPNCLIIDEID------ 437
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVskyvgeSEKRLRELFEAAKKL--------APCVIFIDEIDalagsr 73

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167860135  438 -----GAPAAAINILLATLNRKDSKDGEetgvnalkkkkkkqsvllRPIICICN--DLYVPALR 494
Cdd:pfam00004  74 gsggdSESRRVVNQLLTELDGFTSSNSK------------------VIVIAATNrpDKLDPALL 119
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 510-571 3.31e-13

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: 65.24  E-value: 3.31e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 167860135 510 PSRLAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFLhSRGQKHLDQRSVSSMC 571
Cdd:cd18140    3 KEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAA-AAGGGVITEEDVYEVA 63
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 365-497 5.36e-11

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: 61.62  E-value: 5.36e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135   365 KFKVALLSGPPGLGKTTLAHIIAKHAGYN---VVEINASDDRSAELFQKRIDTA-------TQMKSVLGANE-----KPN 429
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVggkkasgSGELRLRLALAlarklKPD 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135   430 CLIIDEIDGAPAAAINILLATLNRKDSKDGEETGVNalkkkkkkqsvllRPIICICNDLYVPALRPLR 497
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN-------------LTVILTTNDEKDLGPALLR 135
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 370-436 5.88e-10

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 62.41  E-value: 5.88e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDRSAELfQKRIDTATQMKSvlgANEKPnCLIIDEI 436
Cdd:PRK13342  40 ILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVKDL-REVIEEARQRRS---AGRRT-ILFIDEI 101
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 357-437 2.17e-09

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: 57.29  E-value: 2.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 357 ELDQYKRPKFKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASddrsaELFQKRI-DTATQMKSVL-GANEKPNC-LII 433
Cdd:cd19481   17 RLRRYGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLS-----SLLSKYVgESEKNLRKIFeRARRLAPCiLFI 91


                 ....
gi 167860135 434 DEID 437
Cdd:cd19481   92 DEID 95
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 358-437 1.03e-08

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: 58.38  E-value: 1.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 358 LDQYKRPKFKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDdrsaeLFQKRI-DTATQMKSVL-GANEKPNC-LIID 434
Cdd:COG0464  183 REEYGLPPPRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSD-----LVSKYVgETEKNLREVFdKARGLAPCvLFID 257


                 ...
gi 167860135 435 EID 437
Cdd:COG0464  258 EAD 260
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 373-436 2.67e-08

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 57.37  E-value: 2.67e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167860135 373 GPPGLGKTTLAHIIAKHAGYNVVEINASDDRSAELfQKRIDTAtqmKSVLGANEKPnCLIIDEI 436
Cdd:COG2256   56 GPPGTGKTTLARLIANATDAEFVALSAVTSGVKDI-REVIEEA---RERRAYGRRT-ILFVDEI 114
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 351-438 5.19e-08

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 55.78  E-value: 5.19e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 351 EEILEAELDQYKRP-KF--------KVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASddrsaELFQKRI-DTATQMKS 420
Cdd:COG1222   88 EEIREAVELPLKNPeLFrkygieppKGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGS-----ELVSKYIgEGARNVRE 162

                         90       100
                 ....*....|....*....|
gi 167860135 421 VLG-ANEKPNCLI-IDEIDG 438
Cdd:COG1222  163 VFElAREKAPSIIfIDEIDA 182
44 PHA02544
clamp loader, small subunit; Provisional
 370-558 6.34e-08

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 55.38  E-value: 6.34e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDDrsaelfqkRIDT----ATQMKSVLGANEKPNCLIIDEIDGAPAAAIN 445
Cdd:PHA02544  47 LHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDC--------RIDFvrnrLTRFASTVSLTGGGKVIIIDEFDRLGLADAQ 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 446 ILLATLNRKDSKDGEetgvnalkkkkkkqsvllrpIICICNDL--YVPALRPLRQQAFLLVFPQT----LPSRLAQRLAE 519
Cdd:PHA02544 119 RHLRSFMEAYSKNCS--------------------FIITANNKngIIEPLRSRCRVIDFGVPTKEeqieMMKQMIVRCKG 178

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 167860135 520 ISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFLHSRG 558
Cdd:PHA02544 179 ILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYASTG 217
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 370-436 2.05e-07

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: 51.35  E-value: 2.05e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGynvVEINASddrSAELFQKRIDTAtqmkSVLGANEKPNCLIIDEI 436
Cdd:pfam05496  37 LLYGPPGLGKTTLANIIANEMG---VNIRIT---SGPAIERPGDLA----AILTNLEPGDVLFIDEI 93
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 370-454 2.36e-07

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: 50.75  E-value: 2.36e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  370 LLSGPPGLGKTTLAHIIAKH-AGYNVVEINASDD-RSAELFQkRIDTATQMKS-----VLGANEKPNCLIIDEIDGAPAA 442
Cdd:pfam07728   3 LLVGPPGTGKTELAERLAAAlSNRPVFYVQLTRDtTEEDLFG-RRNIDPGGASwvdgpLVRAAREGEIAVLDEINRANPD 81

                          90
                  ....*....|..
gi 167860135  443 AINILLATLNRK 454
Cdd:pfam07728  82 VLNSLLSLLDER 93
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 370-388 2.88e-07

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 53.55  E-value: 2.88e-07
                         10
                 ....*....|....*....
gi 167860135 370 LLSGPPGLGKTTLAHIIAK 388
Cdd:COG2255   58 LLYGPPGLGKTTLAHIIAN 76
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
352-467 3.19e-07

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 52.58  E-value: 3.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 352 EILEAELDQYKRP-KFKVA-----LLSGPPGLGKTTLAHIIAKHAGYNVVEINASddrsaELFQKRI-DTATQMKSVL-G 423
Cdd:COG1223   15 KLIIKELRRRENLrKFGLWpprkiLFYGPPGTGKTMLAEALAGELKLPLLTVRLD-----SLIGSYLgETARNLRKLFdF 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 167860135 424 ANEKPNCLIIDEIDgapaaAInillaTLNRKDSKDGEETG--VNAL 467
Cdd:COG1223   90 ARRAPCVIFFDEFD-----AI-----AKDRGDQNDVGEVKrvVNAL 125
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 370-436 3.27e-07

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: 53.07  E-value: 3.27e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGYNVVEInasddrSAELFQKRIDTAtqmkSVLGANEKPNCLIIDEI 436
Cdd:TIGR00635  34 LLYGPPGLGKTTLAHIIANEMGVNLKIT------SGPALEKPGDLA----AILTNLEEGDVLFIDEI 90
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
370-436 3.56e-07

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 53.21  E-value: 3.56e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEInasddrSAELFQKRIDTAtqmkSVLgANEKPN-CLIIDEI 436
Cdd:PRK00080  55 LLYGPPGLGKTTLANIIANEMGVNIRIT------SGPALEKPGDLA----AIL-TNLEEGdVLFIDEI 111
PLN03025 PLN03025
replication factor C subunit; Provisional
 370-571 4.69e-07

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 52.81  E-value: 4.69e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKH---AGYN--VVEINASDDRSAELFQKRIDTATQMKSVLgANEKPNCLIIDEIDGAPAAAI 444
Cdd:PLN03025  38 ILSGPPGTGKTTSILALAHEllgPNYKeaVLELNASDDRGIDVVRNKIKMFAQKKVTL-PPGRHKIVILDEADSMTSGAQ 116

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 445 NILLATLNRKDSkdgeeTGVNALKkkkkkqsvllrpiiciCNdLYVPALRPLRQQAFLLVFPQTLPSRLAQRLAEISRRQ 524
Cdd:PLN03025 117 QALRRTMEIYSN-----TTRFALA----------------CN-TSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAE 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 167860135 525 GMKADTGTLMALCEKTDNDIRSCINTLQFLHSrGQKHLDQRSVSSMC 571
Cdd:PLN03025 175 KVPYVPEGLEAIIFTADGDMRQALNNLQATHS-GFGFVNQENVFKVC 220
rfc PRK00440
replication factor C small subunit; Reviewed
 370-552 3.92e-06

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 49.87  E-value: 3.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAkHAGY------NVVEINASDDRSAELFQKRIDTATQMKSVLGANEKpnCLIIDEIDGAPAAA 443
Cdd:PRK00440  42 LFAGPPGTGKTTAALALA-RELYgedwreNFLELNASDERGIDVIRNKIKEFARTAPVGGAPFK--IIFLDEADNLTSDA 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 444 inillatlnrkdskdgeetgvnalkkkkkkQSVLLRPI---------ICICNdlYVPAL-------------RPLRQQAf 501
Cdd:PRK00440 119 ------------------------------QQALRRTMemysqntrfILSCN--YSSKIidpiqsrcavfrfSPLKKEA- 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 167860135 502 llvfpqtlpsrLAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQ 552
Cdd:PRK00440 166 -----------VAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQ 205
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 370-441 4.27e-06

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: 47.67  E-value: 4.27e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINA----------SDDRSAELFQKridtatqmksvlGANEKPNCLIIDEIDG- 438
Cdd:cd19503   38 LLHGPPGTGKTLLARAVANEAGANFLSISGpsivskylgeSEKNLREIFEE------------ARSHAPSIIFIDEIDAl 105


                 ...
gi 167860135 439 APA 441
Cdd:cd19503  106 APK 108
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
351-559 5.21e-06

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 49.20  E-value: 5.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 351 EEILEAELDQYKRPKFKVALL-SGPPGLGKTTLAHIIAKH---------------------AGY--NVVEINA---SDDR 403
Cdd:COG0470    2 EEAWEQLLAAAESGRLPHALLlHGPPGIGKTTLALALARDllcenpeggkacgqchsrlmaAGNhpDLLELNPeekSDQI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 404 SAELFqKRIDTATQMKSVLGANekpNCLIIDEIDGAPAAAINILLATLnrkdskdgEETGVNAlkkkkkkqsvllrPIIC 483
Cdd:COG0470   82 GIDQI-RELGEFLSLTPLEGGR---KVVIIDEADAMNEAAANALLKTL--------EEPPKNT-------------PFIL 136

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 167860135 484 ICNDLYVPaLRPLRQQAFLLVFPQTLPSRLAQRLaeisRRQGMKADtgTLMALCEKTDNDIRSCINTLQFLHSRGQ 559
Cdd:COG0470  137 IANDPSRL-LPTIRSRCQVIRFRPPSEEEALAWL----REEGVDED--ALEAILRLAGGDPRAAINLLQALAGRKE 205
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 370-437 9.09e-06

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: 47.01  E-value: 9.09e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINA----------SDDRSAELFQKRIDTAtqmksvlganekPNCLIIDEID 437
Cdd:cd19518   38 LLHGPPGCGKTMLANAIAGELKVPFLKISAteivsgvsgeSEEKIRELFDQAISNA------------PCIVFIDEID 103
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 351-437 1.39e-05

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: 46.46  E-value: 1.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 351 EEILEAeLDQYKRP-KF--------KVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASD----------DRSAELFQKr 411
Cdd:cd19501   14 EELKEV-VEFLKNPeKFtklgakipKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDfvemfvgvgaSRVRDLFEQ- 91

                         90       100
                 ....*....|....*....|....*..
gi 167860135 412 idtatqmksvlgANEKPNCLI-IDEID 437
Cdd:cd19501   92 ------------AKKNAPCIVfIDEID 106
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
353-436 1.48e-05

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 48.40  E-value: 1.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 353 ILEAELDQYKrPKFKVALLSGPPGLGKTTLAHIIAKHAGyNVVEINASDDRSAELFQKriDTATQMKSVLGANEKPNCLI 432
Cdd:COG1373    8 KILDKLLKLL-DNRKAVVITGPRQVGKTTLLKQLAKELE-NILYINLDDPRLRALAEE--DPDDLLEALKELYPGKTYLF 83


                 ....
gi 167860135 433 IDEI 436
Cdd:COG1373   84 LDEI 87
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 367-437 2.86e-05

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN 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: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 45.41  E-value: 2.86e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167860135 367 KVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASddrsaELFQKRIDTATQMKSVL--GANEKPNCLI-IDEID 437
Cdd:cd19502   38 KGVLLYGPPGTGKTLLAKAVANHTDATFIRVVGS-----ELVQKYIGEGARLVRELfeMAREKAPSIIfIDEID 106
PRK13341 PRK13341
AAA family ATPase;
369-436 6.17e-05

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 46.97  E-value: 6.17e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 167860135 369 ALLSGPPGLGKTTLAHIIAKHAGYNVVEINA-----SDDRSAelfqkrIDTATQMksvLGANEKPNCLIIDEI 436
Cdd:PRK13341  55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAvlagvKDLRAE------VDRAKER---LERHGKRTILFIDEV 118
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 330-568 1.05e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 45.64  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 330 NFTNAQNQNQAQRFKT---KSQMTEEILEAELDQYKRPKFkvaLLSGPPGLGKTTLAHIIAK------------HAGYNV 394
Cdd:PRK14970   3 NFVVSARKYRPQTFDDvvgQSHITNTLLNAIENNHLAQAL---LFCGPRGVGKTTCARILARkinqpgyddpneDFSFNI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 395 VEINASDDRSAELFQKRIDTATQMKSVlganEKPNCLIIDEIDGAPAAAINILLATLnrkdskdgEETGVNALKKKKKKQ 474
Cdd:PRK14970  80 FELDAASNNSVDDIRNLIDQVRIPPQT----GKYKIYIIDEVHMLSSAAFNAFLKTL--------EEPPAHAIFILATTE 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 475 SVLLRPIICIcndlyvpalrplRQQAFllVFPQTLPSRLAQRLAEISRRQGMKADTGTLMALCEKTDNDIRSCINTLQFL 554
Cdd:PRK14970 148 KHKIIPTILS------------RCQIF--DFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRV 213

                        250
                 ....*....|....
gi 167860135 555 HSRGQKHLDQRSVS 568
Cdd:PRK14970 214 VTFCGKNITRQAVT 227
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 335-558 1.22e-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: 45.72  E-value: 1.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  335 QNQNQAQRFKTKSQMTEEILEAelDQYKRPKFKVALLSGPPGLGKTTLAHIIAKHAGYNVVE-INA------SDDRSAEL 407
Cdd:TIGR00602  81 ETQHELAVHKKKIEEVETWLKA--QVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEwSNPtlpdfqKNDHKVTL 158

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  408 F--------------------------QKRIDTATQMKSVLGANEKPNCLIIDeidgaPAAAINILLATLNRKDS----- 456
Cdd:TIGR00602 159 SlescfsnfqsqievfsefllratnklQMLGDDLMTDKKIILVEDLPNQFYRD-----TRALHEILRWKYVSIGRcplvf 233

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  457 --KDGEEtGVNalkkkkkKQSVLLRPIICICND--LYVPALRPLRqqafllvFPQTLPSRLAQRLAEISRRQGMK----- 527
Cdd:TIGR00602 234 iiTESLE-GDN-------NQRRLLFPAETIMNKeiLEEPRVSNIS-------FNPIAPTIMKKFLNRIVTIEAKKngeki 298

                         250       260       270
                  ....*....|....*....|....*....|...
gi 167860135  528 --ADTGTLMALCEKTDNDIRSCINTLQFLHSRG 558
Cdd:TIGR00602 299 kvPKKTSVELLCQGCSGDIRSAINSLQFSSSKS 331
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 370-437 1.81e-04

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 43.04  E-value: 1.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINAsddrsAELFQKRIDTATQMKSVL---GANEKPNCLIIDEID 437
Cdd:cd19511   31 LLYGPPGCGKTLLAKALASEAGLNFISVKG-----PELFSKYVGESERAVREIfqkARQAAPCIIFFDEID 96
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 370-439 2.23e-04

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. 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: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 42.72  E-value: 2.23e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDdrsaelfqkRIDTATQMKSVLGANEKPNCLIIDEIDGA 439
Cdd:cd19510   27 LLYGPPGTGKSSFIAALAGELDYDICDLNLSE---------VVLTDDRLNHLLNTAPKQSIILLEDIDAA 87
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 370-437 4.36e-04

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. 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: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 42.03  E-value: 4.36e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASD--DRSAELFQKRIDTATQMKSVLganeKPNCLIIDEID 437
Cdd:cd19520   39 LLYGPPGCGKTMLAKATAKEAGARFINLQVSSltDKWYGESQKLVAAVFSLASKL----QPSIIFIDEID 104
AAA_22 pfam13401
AAA domain;
368-452 6.94e-04

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.79  E-value: 6.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  368 VALLSGPPGLGKTTLA-HIIAKHAGYN--VVEINASDDRSAELFQKRIDTATQMKSVLGANEKP---------------N 429
Cdd:pfam13401   7 ILVLTGESGTGKTTLLrRLLEQLPEVRdsVVFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEEllaalqqlllalavaV 86

                          90       100
                  ....*....|....*....|...
gi 167860135  430 CLIIDEIDGAPAAAINILLATLN 452
Cdd:pfam13401  87 VLIIDEAQHLSLEALEELRDLLN 109
ftsH CHL00176
cell division protein; Validated
 366-437 1.61e-03

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 42.34  E-value: 1.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 366 FKVALLSGPPGLGKTTLAHIIAKHAG---YNV---------VEINASddRSAELFQKridtatqmksvlgANEKPNCLI- 432
Cdd:CHL00176 216 PKGVLLVGPPGTGKTLLAKAIAGEAEvpfFSIsgsefvemfVGVGAA--RVRDLFKK-------------AKENSPCIVf 280


                 ....*
gi 167860135 433 IDEID 437
Cdd:CHL00176 281 IDEID 285
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 367-440 1.67e-03

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 42.20  E-value: 1.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  367 KVALLSGPPGLGKTTLAHIIAKHAGYNVVEINA----------SDDRSAELFQKRIDTAtqmksvlganekPNCLIIDEI 436
Cdd:TIGR01243 213 KGVLLYGPPGTGKTLLAKAVANEAGAYFISINGpeimskyygeSEERLREIFKEAEENA------------PSIIFIDEI 280


                  ....*
gi 167860135  437 DG-AP 440
Cdd:TIGR01243 281 DAiAP 285
AAA_14 pfam13173
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 365-436 1.82e-03

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 463799 [Multi-domain]  Cd Length: 128  Bit Score: 39.49  E-value: 1.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 167860135  365 KFKVALLSGPPGLGKTTLAHIIAKH--AGYNVVEINASDDRSAELFQKRIDTATQMKsvlgANEKPNCLIIDEI 436
Cdd:pfam13173   1 SRKILVITGPRQVGKTTLLLQLIKEllPPENILYINLDDPRLLKLADFELLELFLEL----LYPGKTYLFLDEI 70
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 362-437 2.15e-03

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. 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: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 39.85  E-value: 2.15e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167860135 362 KRPKFKVALLSGPPGLGKTTLAHIIAKHAGYNVVEINASDdrsaeLFQKRIDTATQMKSVLGA---NEKPNCLIIDEID 437
Cdd:cd19521   36 NRKPWSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSD-----LVSKWMGESEKLVKQLFAmarENKPSIIFIDEVD 109
ADK cd01428
Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine ...
 368-459 2.26e-03

Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.


Pssm-ID: 238713 [Multi-domain]  Cd Length: 194  Bit Score: 40.30  E-value: 2.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135 368 VALLSGPPGLGKTTLAHIIAKHagYNVVEINASDdrsaeLFQKRIDTAT----QMKSVLGANEkpncLIIDEIdgapaaA 443
Cdd:cd01428    1 RILLLGPPGSGKGTQAERLAKK--YGLPHISTGD-----LLREEIASGTelgkKAKEYIDSGK----LVPDEI------V 63

                         90
                 ....*....|....*.
gi 167860135 444 INILLATLNRKDSKDG 459
Cdd:cd01428   64 IKLLKERLKKPDCKKG 79
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 370-437 2.65e-03

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). 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: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 39.64  E-value: 2.65e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASDdrsaeLFQKRIDTATQMKSVL---GANEKPNCLIIDEID 437
Cdd:cd19509   36 LLYGPPGTGKTLLARAVASESGSTFFSISASS-----LVSKWVGESEKIVRALfalARELQPSIIFIDEID 101
CMPK cd02020
Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine ...
 371-395 3.42e-03

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


Pssm-ID: 238978 [Multi-domain]  Cd Length: 147  Bit Score: 39.01  E-value: 3.42e-03
                         10        20
                 ....*....|....*....|....*
gi 167860135 371 LSGPPGLGKTTLAHIIAKHAGYNVV 395
Cdd:cd02020    4 IDGPAGSGKSTVAKLLAKKLGLPYL 28
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 370-440 4.85e-03

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. 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: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 38.56  E-value: 4.85e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEInasddRSAELFQKRIDTATQMKSVL---GANEKPNCLIIDEIDG-AP 440
Cdd:cd19526   31 LLYGPPGCGKTLLASAIASECGLNFISV-----KGPELLNKYIGASEQNVRDLfsrAQSAKPCILFFDEFDSiAP 100
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 370-437 5.37e-03

second 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: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 38.62  E-value: 5.37e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEInasddRSAELFQKRI-DTATQMKSVL--GANEKPNCLIIDEID 437
Cdd:cd19530   34 LLYGPPGCGKTLLAKAVANESGANFISV-----KGPELLNKYVgESERAVRQVFqrARASAPCVIFFDEVD 99
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 370-440 6.06e-03

first of two ATPase domains of CDC48 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. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like 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: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 38.57  E-value: 6.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNVVEINASddrsaELFQKRI-DTATQMKSVLGANEK--PNCLIIDEIDG-AP 440
Cdd:cd19519   38 LLYGPPGTGKTLIARAVANETGAFFFLINGP-----EIMSKLAgESESNLRKAFEEAEKnaPAIIFIDEIDAiAP 107
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
370-407 6.58e-03

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 39.95  E-value: 6.58e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 167860135 370 LLSGPPGLGKTTLAHIIAKHAGYNV--VEINASDDRSAEL 407
Cdd:COG1224   68 LIVGPPGTGKTALAVAIARELGEDTpfVAISGSEIYSAEL 107
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
370-388 6.80e-03

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 39.79  E-value: 6.80e-03
                         10
                 ....*....|....*....
gi 167860135 370 LLSGPPGLGKTTLAHIIAK 388
Cdd:COG2812   36 LFTGPRGVGKTTLARILAK 54
PRK04182 PRK04182
cytidylate kinase; Provisional
 371-395 7.77e-03

cytidylate kinase; Provisional


Pssm-ID: 235244 [Multi-domain]  Cd Length: 180  Bit Score: 38.63  E-value: 7.77e-03
                         10        20
                 ....*....|....*....|....*
gi 167860135 371 LSGPPGLGKTTLAHIIAKHAGYNVV 395
Cdd:PRK04182   5 ISGPPGSGKTTVARLLAEKLGLKHV 29
AAA_18 pfam13238
AAA domain;
370-457 9.16e-03

AAA domain;


Pssm-ID: 433052 [Multi-domain]  Cd Length: 128  Bit Score: 37.41  E-value: 9.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167860135  370 LLSGPPGLGKTTLAHIIAKHAGYnvveinasddrsaelFQKRIDTATQMKSVLG-ANEKPNCLIIDEidGAPAAAINILL 448
Cdd:pfam13238   2 LITGTPGVGKTTLAKELSKRLGF---------------GDNVRDLALENGLVLGdDPETRESKRLDE--DKLDRLLDLLE 64


                  ....*....
gi 167860135  449 ATLNRKDSK 457
Cdd:pfam13238  65 ENAALEEGG 73
 
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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