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Conserved domains on  [gi|27501458|ref|NP_071375|]
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chromosome transmission fidelity protein 18 homolog [Homo sapiens]

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
 366-594 8.76e-31

replication factor C large subunit; Provisional


The actual alignment was detected with superfamily member PRK04195:

Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 127.34  E-value: 8.76e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  366 KQKVALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVFRTRIEAATQMESVLGAGGKpncLVI-DEIDG----- 439
Cdd:PRK04195  38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRK---LILlDEVDGihgne 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  440 --APVAAINVLLsilnRKGPQevgpqgpavpsgggrrrraeggllmrPIICICNDQFAPSLRQLKQQAFLLHFPPtLPSR 517
Cdd:PRK04195 115 drGGARAILELI----KKAKQ--------------------------PIILTANDPYDPSLRELRNACLMIEFKR-LSTR 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27501458  518 -LVQRLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFLySRGQRELSVRDVQAtrVGLKDQRRGLFSVWQEVF 594
Cdd:PRK04195 164 sIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LGRRDREESIFDALDAVF 238
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 366-594 8.76e-31

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 127.34  E-value: 8.76e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  366 KQKVALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVFRTRIEAATQMESVLGAGGKpncLVI-DEIDG----- 439
Cdd:PRK04195  38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRK---LILlDEVDGihgne 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  440 --APVAAINVLLsilnRKGPQevgpqgpavpsgggrrrraeggllmrPIICICNDQFAPSLRQLKQQAFLLHFPPtLPSR 517
Cdd:PRK04195 115 drGGARAILELI----KKAKQ--------------------------PIILTANDPYDPSLRELRNACLMIEFKR-LSTR 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27501458  518 -LVQRLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFLySRGQRELSVRDVQAtrVGLKDQRRGLFSVWQEVF 594
Cdd:PRK04195 164 sIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LGRRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 352-522 4.72e-17

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: 79.11  E-value: 4.72e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 352 EEMLEAGLDPSQRPKQKVALLCGPPGLGKTTLAHVIARHA---GYSVVEMNASDDRSPEVFRTRIEA-ATQMESVLGAGG 427
Cdd:cd00009   4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKA 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 428 KPNCLVIDEIDGAPVAAINVLLSILNRKGPQEVGPQGpavpsgggrrrraeggllmRPIICICNDqfapslrqlkqqAFL 507
Cdd:cd00009  84 KPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN-------------------VRVIGATNR------------PLL 132

                       170
                ....*....|....*
gi 27501458 508 LHFPPTLPSRLVQRL 522
Cdd:cd00009 133 GDLDRALYDRLDIRI 147
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 371-454 1.44e-11

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: 62.61  E-value: 1.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   371 LLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVfrtrIEAATQMESVLGAGGKPNC--LVIDEID---------- 438
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYV----GESEKRLRELFEAAKKLAPcvIFIDEIDalagsrgsgg 77

                          90
                  ....*....|....*..
gi 27501458   439 -GAPVAAINVLLSILNR 454
Cdd:pfam00004  78 dSESRRVVNQLLTELDG 94
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 339-437 7.62e-08

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 55.83  E-value: 7.62e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 339 TAPGKWksheqvLEEMLEAGLDPSqrpkqkvALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVfRTRIEAATQ 418
Cdd:COG2256  34 LGPGKP------LRRAIEAGRLSS-------MILWGPPGTGKTTLARLIANATDAEFVALSAVTSGVKDI-REVIEEARE 99

                        90
                ....*....|....*....
gi 27501458 419 mesvLGAGGKPNCLVIDEI 437
Cdd:COG2256 100 ----RRAYGRRTILFVDEI 114
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 366-454 1.45e-07

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 1.45e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458    366 KQKVALLCGPPGLGKTTLAHVIARHA---GYSVVEMNASDDRSPEVFRTRIEAATQMESVLGAG------------GKPN 430
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGElrlrlalalarkLKPD 80

                           90       100
                   ....*....|....*....|....
gi 27501458    431 CLVIDEIDGAPVAAINVLLSILNR 454
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEE 104
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 345-563 9.90e-06

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: 49.57  E-value: 9.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   345 KSHEQVLEEMLEAGLDPSQrpKQKVALLCGPPGLGKTTLAHVIARHAGYSVVE-MNASDDRSP----------------- 406
Cdd:TIGR00602  90 KKKIEEVETWLKAQVLENA--PKRILLITGPSGCGKSTTIKILSKELGIQVQEwSNPTLPDFQkndhkvtlslescfsnf 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   407 ----EVFRTRIEAATQMESVLG--AGGKPNCLVIDEIDGAPVAAINVLLSILNRKGPQEvgpqgPAVP-----SGGGRRR 475
Cdd:TIGR00602 168 qsqiEVFSEFLLRATNKLQMLGddLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSI-----GRCPlvfiiTESLEGD 242

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   476 RAEGGLLMRPIICICND-QFAPSLRQLKqqafllhFPPTLPSRLVQRLQEVSLRQGMRADPGVLAA-------LCEKTDN 547
Cdd:TIGR00602 243 NNQRRLLFPAETIMNKEiLEEPRVSNIS-------FNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPkktsvelLCQGCSG 315

                         250
                  ....*....|....*.
gi 27501458   548 DIRACINTLQFLYSRG 563
Cdd:TIGR00602 316 DIRSAINSLQFSSSKS 331
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 366-594 8.76e-31

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 127.34  E-value: 8.76e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  366 KQKVALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVFRTRIEAATQMESVLGAGGKpncLVI-DEIDG----- 439
Cdd:PRK04195  38 PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRK---LILlDEVDGihgne 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  440 --APVAAINVLLsilnRKGPQevgpqgpavpsgggrrrraeggllmrPIICICNDQFAPSLRQLKQQAFLLHFPPtLPSR 517
Cdd:PRK04195 115 drGGARAILELI----KKAKQ--------------------------PIILTANDPYDPSLRELRNACLMIEFKR-LSTR 163

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27501458  518 -LVQRLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFLySRGQRELSVRDVQAtrVGLKDQRRGLFSVWQEVF 594
Cdd:PRK04195 164 sIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAI-AEGYGKLTLEDVKT--LGRRDREESIFDALDAVF 238
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 352-522 4.72e-17

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: 79.11  E-value: 4.72e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 352 EEMLEAGLDPSQRPKQKVALLCGPPGLGKTTLAHVIARHA---GYSVVEMNASDDRSPEVFRTRIEA-ATQMESVLGAGG 427
Cdd:cd00009   4 EEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHfLVRLLFELAEKA 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 428 KPNCLVIDEIDGAPVAAINVLLSILNRKGPQEVGPQGpavpsgggrrrraeggllmRPIICICNDqfapslrqlkqqAFL 507
Cdd:cd00009  84 KPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDREN-------------------VRVIGATNR------------PLL 132

                       170
                ....*....|....*
gi 27501458 508 LHFPPTLPSRLVQRL 522
Cdd:cd00009 133 GDLDRALYDRLDIRI 147
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 515-575 6.11e-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: 67.17  E-value: 6.11e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 27501458 515 PSRLVQRLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFLySRGQRELSVRDVQAT 575
Cdd:cd18140   3 KEQIVKRLREICKKEGVKIDEEALEAIAEKSEGDMRKAINDLQAA-AAGGGVITEEDVYEV 62
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 371-454 1.44e-11

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: 62.61  E-value: 1.44e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   371 LLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVfrtrIEAATQMESVLGAGGKPNC--LVIDEID---------- 438
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYV----GESEKRLRELFEAAKKLAPcvIFIDEIDalagsrgsgg 77

                          90
                  ....*....|....*..
gi 27501458   439 -GAPVAAINVLLSILNR 454
Cdd:pfam00004  78 dSESRRVVNQLLTELDG 94
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 339-437 3.33e-09

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 60.10  E-value: 3.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  339 TAPGKwksheqVLEEMLEAGLDPSqrpkqkvALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVfRTRIEAATQ 418
Cdd:PRK13342  21 LGPGK------PLRRMIEAGRLSS-------MILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGVKDL-REVIEEARQ 86

                         90
                 ....*....|....*....
gi 27501458  419 MESvlgAGGKPnCLVIDEI 437
Cdd:PRK13342  87 RRS---AGRRT-ILFIDEI 101
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 371-455 7.75e-09

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: 54.99  E-value: 7.75e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   371 LLCGPPGLGKTTLAHVIARH-AGYSVVEMNASDDRSPEVFRTRIEAATQM----ESVLG-AGGKPNCLVIDEIDGAPVAA 444
Cdd:pfam07728   3 LLVGPPGTGKTELAERLAAAlSNRPVFYVQLTRDTTEEDLFGRRNIDPGGaswvDGPLVrAAREGEIAVLDEINRANPDV 82

                          90
                  ....*....|.
gi 27501458   445 INVLLSILNRK 455
Cdd:pfam07728  83 LNSLLSLLDER 93
PLN03025 PLN03025
replication factor C subunit; Provisional
 371-444 4.77e-08

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 55.89  E-value: 4.77e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 27501458  371 LLCGPPGLGKTTLAHVIARH---AGYS--VVEMNASDDRSPEVFRTRIEAATQMESVLgAGGKPNCLVIDEIDGAPVAA 444
Cdd:PLN03025  38 ILSGPPGTGKTTSILALAHEllgPNYKeaVLELNASDDRGIDVVRNKIKMFAQKKVTL-PPGRHKIVILDEADSMTSGA 115
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 339-437 7.62e-08

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 55.83  E-value: 7.62e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 339 TAPGKWksheqvLEEMLEAGLDPSqrpkqkvALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVfRTRIEAATQ 418
Cdd:COG2256  34 LGPGKP------LRRAIEAGRLSS-------MILWGPPGTGKTTLARLIANATDAEFVALSAVTSGVKDI-REVIEEARE 99

                        90
                ....*....|....*....
gi 27501458 419 mesvLGAGGKPNCLVIDEI 437
Cdd:COG2256 100 ----RRAYGRRTILFVDEI 114
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 366-454 1.45e-07

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 51.61  E-value: 1.45e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458    366 KQKVALLCGPPGLGKTTLAHVIARHA---GYSVVEMNASDDRSPEVFRTRIEAATQMESVLGAG------------GKPN 430
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGElrlrlalalarkLKPD 80

                           90       100
                   ....*....|....*....|....
gi 27501458    431 CLVIDEIDGAPVAAINVLLSILNR 454
Cdd:smart00382  81 VLILDEITSLLDAEQEALLLLLEE 104
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 371-438 1.73e-07

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


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 51.90  E-value: 1.73e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 371 LLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSPEVFrtriEAATQMESVL-GAGGKPNCLV-IDEID 438
Cdd:cd19481  30 LLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVG----ESEKNLRKIFeRARRLAPCILfIDEID 95
AAA_22 pfam13401
AAA domain;
363-453 7.95e-07

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 49.26  E-value: 7.95e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   363 QRPKQKVALLCGPPGLGKTTLAHVIARH---AGYSVVEMNASDDRSPEVFRTRIEAAT---------------QMESVLG 424
Cdd:pfam13401   1 IRFGAGILVLTGESGTGKTTLLRRLLEQlpeVRDSVVFVDLPSGTSPKDLLRALLRALglplsgrlskeellaALQQLLL 80

                          90       100
                  ....*....|....*....|....*....
gi 27501458   425 AGGKPNCLVIDEIDGAPVAAINVLLSILN 453
Cdd:pfam13401  81 ALAVAVVLIIDEAQHLSLEALEELRDLLN 109
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 371-401 2.19e-06

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 50.85  E-value: 2.19e-06
                        10        20        30
                ....*....|....*....|....*....|.
gi 27501458 371 LLCGPPGLGKTTLAHVIARhagysvvEMNAS 401
Cdd:COG2255  58 LLYGPPGLGKTTLAHIIAN-------EMGVN 81
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 371-437 3.50e-06

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 47.88  E-value: 3.50e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 27501458   371 LLCGPPGLGKTTLAHVIARhagysvvEMNASddrspevFRTR----IEAATQMESVLGAGGKPNCLVIDEI 437
Cdd:pfam05496  37 LLYGPPGLGKTTLANIIAN-------EMGVN-------IRITsgpaIERPGDLAAILTNLEPGDVLFIDEI 93
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 347-438 3.93e-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: 50.29  E-value: 3.93e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 347 HEQVLEEMLEAGLDPSQRPKQ---------KVALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSP----------E 407
Cdd:COG0464 162 LEEVKEELRELVALPLKRPELreeyglpppRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKyvgeteknlrE 241

                        90       100       110
                ....*....|....*....|....*....|.
gi 27501458 408 VFRTrieaATQMESVLgaggkpncLVIDEID 438
Cdd:COG0464 242 VFDK----ARGLAPCV--------LFIDEAD 260
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
371-401 4.85e-06

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 49.74  E-value: 4.85e-06
                         10        20        30
                 ....*....|....*....|....*....|.
gi 27501458  371 LLCGPPGLGKTTLAHVIARhagysvvEMNAS 401
Cdd:PRK00080  55 LLYGPPGLGKTTLANIIAN-------EMGVN 78
rfc PRK00440
replication factor C small subunit; Reviewed
 371-413 7.25e-06

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 49.10  E-value: 7.25e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 27501458  371 LLCGPPGLGKTTLAHVIARHAgY------SVVEMNASDDRSPEVFRTRI 413
Cdd:PRK00440  42 LFAGPPGTGKTTAALALAREL-YgedwreNFLELNASDERGIDVIRNKI 89
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 345-563 9.90e-06

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: 49.57  E-value: 9.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   345 KSHEQVLEEMLEAGLDPSQrpKQKVALLCGPPGLGKTTLAHVIARHAGYSVVE-MNASDDRSP----------------- 406
Cdd:TIGR00602  90 KKKIEEVETWLKAQVLENA--PKRILLITGPSGCGKSTTIKILSKELGIQVQEwSNPTLPDFQkndhkvtlslescfsnf 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   407 ----EVFRTRIEAATQMESVLG--AGGKPNCLVIDEIDGAPVAAINVLLSILNRKGPQEvgpqgPAVP-----SGGGRRR 475
Cdd:TIGR00602 168 qsqiEVFSEFLLRATNKLQMLGddLMTDKKIILVEDLPNQFYRDTRALHEILRWKYVSI-----GRCPlvfiiTESLEGD 242

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   476 RAEGGLLMRPIICICND-QFAPSLRQLKqqafllhFPPTLPSRLVQRLQEVSLRQGMRADPGVLAA-------LCEKTDN 547
Cdd:TIGR00602 243 NNQRRLLFPAETIMNKEiLEEPRVSNIS-------FNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPkktsvelLCQGCSG 315

                         250
                  ....*....|....*.
gi 27501458   548 DIRACINTLQFLYSRG 563
Cdd:TIGR00602 316 DIRSAINSLQFSSSKS 331
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 348-439 1.80e-05

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 48.08  E-value: 1.80e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 348 EQVLEEMLEAGLDPSQRPKQ---------KVALLCGPPGLGKTTLAHVIARHAGYSVVEMNASDDRSP----------EV 408
Cdd:COG1222  84 DEQIEEIREAVELPLKNPELfrkygieppKGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKyigegarnvrEV 163

                        90       100       110
                ....*....|....*....|....*....|.
gi 27501458 409 FrtriEAATQMesvlgaggKPNCLVIDEIDG 439
Cdd:COG1222 164 F----ELAREK--------APSIIFIDEIDA 182
44 PHA02544
clamp loader, small subunit; Provisional
 371-563 2.87e-05

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 47.29  E-value: 2.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  371 LLCGP-PGLGKTTLAHVIARHAGYSVVEMNASDDRSpEVFRTRIeaaTQMESVLGAGGKPNCLVIDEIDGAPVAAINVLL 449
Cdd:PHA02544  46 LLHSPsPGTGKTTVAKALCNEVGAEVLFVNGSDCRI-DFVRNRL---TRFASTVSLTGGGKVIIIDEFDRLGLADAQRHL 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  450 silnrKGPQEvgpqgpAVPSGGGrrrraeggllmrpIICICNDQ---FAPSLRQLKQQAFLLhfpPT------LPSRLVQ 520
Cdd:PHA02544 122 -----RSFME------AYSKNCS-------------FIITANNKngiIEPLRSRCRVIDFGV---PTkeeqieMMKQMIV 174

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 27501458  521 RLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFLYSRG 563
Cdd:PHA02544 175 RCKGILEAEGVEVDMKVLAALVKKNFPDFRRTINELQRYASTG 217
Rad17 pfam03215
Rad17 P-loop domain;
345-406 3.37e-04

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 42.64  E-value: 3.37e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27501458   345 KSHEQVLEEMLEAGLDPSQrpKQKVALLCGPPGLGKTTLAHVIARHAGYSVVE-MNASDDRSP 406
Cdd:pfam03215  25 KRKIKDVQEWLDAMFLENA--KHRILLISGPSGCGKSTVIKELSKELGPKYREwSNPTSFRSP 85
AAA_18 pfam13238
AAA domain;
371-435 3.47e-04

AAA domain;


Pssm-ID: 433052 [Multi-domain]  Cd Length: 128  Bit Score: 41.65  E-value: 3.47e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 27501458   371 LLCGPPGLGKTTLAHVIARHAGYSVV------EMNASDDRSPEVFRTRIEAATQMESVLGA------GGKPNCLVID 435
Cdd:pfam13238   2 LITGTPGVGKTTLAKELSKRLGFGDNvrdlalENGLVLGDDPETRESKRLDEDKLDRLLDLleenaaLEEGGNLIID 78
PRK13341 PRK13341
AAA family ATPase;
370-437 3.62e-04

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 44.28  E-value: 3.62e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27501458  370 ALLCGPPGLGKTTLAHVIARHAGYSVVEMNA-----SDdrspevFRTRIEAATQMesvLGAGGKPNCLVIDEI 437
Cdd:PRK13341  55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAvlagvKD------LRAEVDRAKER---LERHGKRTILFIDEV 118
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 371-441 3.98e-04

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 41.89  E-value: 3.98e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 27501458 371 LLCGPPGLGKTTLAHVIARHAGYSVVEMNAsddrsPEVFRTRI-EAATQMESVLGAGGK--PNCLVIDEIDG-AP 441
Cdd:cd19503  38 LLHGPPGTGKTLLARAVANEAGANFLSISG-----PSIVSKYLgESEKNLREIFEEARShaPSIIFIDEIDAlAP 107
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
371-564 6.94e-04

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 42.65  E-value: 6.94e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 371 LLCGPPGLGKTTLAHVIARHAGYS-----------------------VVEMNA---SDDRSPEVFRTRIEAATQmeSVLG 424
Cdd:COG0470  22 LLHGPPGIGKTTLALALARDLLCEnpeggkacgqchsrlmaagnhpdLLELNPeekSDQIGIDQIRELGEFLSL--TPLE 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 425 AGGKpnCLVIDEIDGAPVAAINVLLSILNRkgpqevgPQGPAvpsgggrrrraeggllmrPIICICNDQFA--PSLRQLK 502
Cdd:COG0470 100 GGRK--VVIIDEADAMNEAAANALLKTLEE-------PPKNT------------------PFILIANDPSRllPTIRSRC 152

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 27501458 503 QQaflLHFPPTLPSRLVQRLQEvslrQGmrADPGVLAALCEKTDNDIRACINTLQFLYSRGQ 564
Cdd:COG0470 153 QV---IRFRPPSEEEALAWLRE----EG--VDEDALEAILRLAGGDPRAAINLLQALAGRKE 205
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 371-388 7.43e-04

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: 42.67  E-value: 7.43e-04
                          10
                  ....*....|....*...
gi 27501458   371 LLCGPPGLGKTTLAHVIA 388
Cdd:TIGR00635  34 LLYGPPGLGKTTLAHIIA 51
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
349-438 1.21e-03

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 41.79  E-value: 1.21e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 349 QVLEEMLEAGLDPSQRpkqkvALLCGPPGLGKTTLAHVIARHAGYSVVEMNASddrspEVFRTRI-EAATQMESVL-GAG 426
Cdd:COG1223  22 RRRENLRKFGLWPPRK-----ILFYGPPGTGKTMLAEALAGELKLPLLTVRLD-----SLIGSYLgETARNLRKLFdFAR 91

                        90
                ....*....|..
gi 27501458 427 GKPNCLVIDEID 438
Cdd:COG1223  92 RAPCVIFFDEFD 103
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 371-452 1.69e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 41.78  E-value: 1.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458  371 LLCGPPGLGKTTLAHVIAR------------HAGYSVVEMNASDDRSPEVFRTRIEAATQMESVlgagGKPNCLVIDEID 438
Cdd:PRK14970  43 LFCGPRGVGKTTCARILARkinqpgyddpneDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQT----GKYKIYIIDEVH 118

                         90
                 ....*....|....
gi 27501458  439 GAPVAAINVLLSIL 452
Cdd:PRK14970 119 MLSSAAFNAFLKTL 132
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 330-441 1.78e-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: 1.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458   330 EPARVSKEATAP-------GKWKSHEQVLEEMLEAgldPSQRPK---------QKVALLCGPPGLGKTTLAHVIARHAGY 393
Cdd:TIGR01243 162 KPVREEIERKVPkvtyediGGLKEAKEKIREMVEL---PMKHPElfehlgiepPKGVLLYGPPGTGKTLLAKAVANEAGA 238

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 27501458   394 SVVEMNA----------SDDRSPEVFRTRIEAAtqmesvlgaggkPNCLVIDEIDG-AP 441
Cdd:TIGR01243 239 YFISINGpeimskyygeSEERLREIFKEAEENA------------PSIIFIDEIDAiAP 285
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 348-438 1.99e-03

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 40.29  E-value: 1.99e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 348 EQVLEEMLEAgLDPSQRPKQ---------KVALLCGPPGLGKTTLAHVIARHAG---YSV-----VEM----NASddRSP 406
Cdd:cd19501  10 EEAKEELKEV-VEFLKNPEKftklgakipKGVLLVGPPGTGKTLLAKAVAGEAGvpfFSIsgsdfVEMfvgvGAS--RVR 86

                        90       100       110
                ....*....|....*....|....*....|...
gi 27501458 407 EVFRTrieaatqmesvlgAGGKPNCLV-IDEID 438
Cdd:cd19501  87 DLFEQ-------------AKKNAPCIVfIDEID 106
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 349-441 2.51e-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: 39.72  E-value: 2.51e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 349 QVLEEMLEAgldPSQRPK---------QKVALLCGPPGLGKTTLAHVIARHAGYSVVEMnasddRSPEVFRTRIEAATQM 419
Cdd:cd19526   3 KALEETIEW---PSKYPKifassplrlRSGILLYGPPGCGKTLLASAIASECGLNFISV-----KGPELLNKYIGASEQN 74

                        90       100
                ....*....|....*....|....*.
gi 27501458 420 ESVL---GAGGKPNCLVIDEIDG-AP 441
Cdd:cd19526  75 VRDLfsrAQSAKPCILFFDEFDSiAP 100
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 348-401 3.26e-03

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: 39.33  E-value: 3.26e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27501458 348 EQVLEEMLEAGLDPSQRPK----------QKVALLCGPPGLGKTTLAHVIARHAGYSVVEMNAS 401
Cdd:cd19520   6 DEVITELKELVILPLQRPElfdnsrllqpPKGVLLYGPPGCGKTMLAKATAKEAGARFINLQVS 69
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 371-438 4.15e-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: 4.15e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27501458 371 LLCGPPGLGKTTLAHVIARHAGYSVVEMNA----------SDDRSPEVFRTRIEAAtqmesvlgaggkPNCLVIDEID 438
Cdd:cd19518  38 LLHGPPGCGKTMLANAIAGELKVPFLKISAteivsgvsgeSEEKIRELFDQAISNA------------PCIVFIDEID 103
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 358-389 4.59e-03

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 39.06  E-value: 4.59e-03
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 27501458 358 GLDPSQR------PKQKVALLCGPPGLGKTTLAHVIAR 389
Cdd:cd17936   1 TLDPSQLealkhaLTSELALIQGPPGTGKTFLGVKLVR 38
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 350-418 6.61e-03

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 39.99  E-value: 6.61e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 27501458   350 VLEEMLEAGldpsqRPKQKVALLCGPPGLGKTTLAHVIARHAGYSV--VEMNASDDRSPEVFRTriEAATQ 418
Cdd:pfam06068  38 VIVEMIKEG-----KIAGRAVLIAGPPGTGKTALAIAISKELGEDTpfTSISGSEVYSLEMKKT--EALTQ 101
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
371-413 7.02e-03

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 39.95  E-value: 7.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 27501458 371 LLCGPPGLGKTTLAHVIARHAGYSV--VEMNASDDRSPEVFRTRI 413
Cdd:COG1224  68 LIVGPPGTGKTALAVAIARELGEDTpfVAISGSEIYSAELKKTEF 112
ADK cd01428
Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine ...
 369-437 7.45e-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: 38.76  E-value: 7.45e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27501458 369 VALLCGPPGLGKTTLAHVIARHagYSVVEMNASDdrspeVFRTRIEAAT----QMESVLGAGGkpncLVIDEI 437
Cdd:cd01428   1 RILLLGPPGSGKGTQAERLAKK--YGLPHISTGD-----LLREEIASGTelgkKAKEYIDSGK----LVPDEI 62
DNA_pol3_delta pfam06144
DNA polymerase III, delta subunit; DNA polymerase III, delta subunit (EC 2.7.7.7) is required ...
 497-559 8.37e-03

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


Pssm-ID: 428788 [Multi-domain]  Cd Length: 174  Bit Score: 38.42  E-value: 8.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27501458   497 SLRQLKQQAFLLH-FPPTLpSRLVQRLQEVSLRQGMRADPGVLAALCEKTDNDIRACINTLQFL 559
Cdd:pfam06144 110 LTKLLKKKATVVEcFTLKE-EELIQWIQSRAQELGLQIEPEAIELLCELVENNLSALAQELEKL 172
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
371-454 8.43e-03

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 38.99  E-value: 8.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27501458 371 LLCGPPGLGKTTLAHVIARHA---GYSVVEMNASDdrspevFRTRIEAA---TQMESVLGAGGKPNCLVIDEIDGAPVAA 444
Cdd:COG1484 103 ILLGPPGTGKTHLAIALGHEAcraGYRVRFTTAPD------LVNELKEAradGRLERLLKRLAKVDLLILDELGYLPLDA 176

                        90
                ....*....|..
gi 27501458 445 I--NVLLSILNR 454
Cdd:COG1484 177 EgaELLFELISD 188
 
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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