NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|568935403|ref|XP_006534892|]
View 

helicase POLQ-like isoform X9 [Mus musculus]

Protein Classification

helix-hairpin-helix domain-containing protein( domain architecture ID 13383144)

helix-hairpin-helix (HhH) domain-containing protein binds DNA in the major groove; similar to Arabidopsis thaliana protein PARTING DANCERS

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
21-342 7.21e-56

Replicative superfamily II helicase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG1204:

Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 196.65  E-value: 7.21e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  21 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 97
Cdd:COG1204  226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  98 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 176
Cdd:COG1204  305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 177 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 254
Cdd:COG1204  385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 255 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 334
Cdd:COG1204  459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                 ....*...
gi 568935403 335 aqsepDWM 342
Cdd:COG1204  526 -----DWI 528
HHH_5 pfam14520
Helix-hairpin-helix domain;
468-521 5.46e-03

Helix-hairpin-helix domain;


:

Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.54  E-value: 5.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568935403  468 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 521
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
21-342 7.21e-56

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 196.65  E-value: 7.21e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  21 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 97
Cdd:COG1204  226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  98 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 176
Cdd:COG1204  305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 177 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 254
Cdd:COG1204  385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 255 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 334
Cdd:COG1204  459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                 ....*...
gi 568935403 335 aqsepDWM 342
Cdd:COG1204  526 -----DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
20-521 5.52e-51

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 186.70  E-value: 5.52e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  20 PDRLVALVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKdYLNHREKEK-CEVIKSLRNIGNGKVCPVLKRTVPFGIA 97
Cdd:PRK02362 229 KDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASALKK-TLTAAERAElAELAEEIREVSDTETSKDLADCVAKGAA 307

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  98 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILR-----------APyvantfLKRNQYKQMVGRAGR 166
Cdd:PRK02362 308 FHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggagmQP------IPVLEYHQMAGRAGR 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 167 AGIDTAGESILLlqEKDKQQVLEL----ISGPLETCCSHLVEEftkgiQAL---FLSLIGLKIAASLGDIYQFMSGTFFG 239
Cdd:PRK02362 382 PGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSKLATE-----PALrthVLSTIASGFARTRDGLLEFLEATFYA 454

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 240 VQQKillKEKSLWEITVDALEHLTEKGLLQKDscGDneglecHFRITKLGQAsfkgaidlayCDTLYRD------LKKGL 313
Cdd:PRK02362 455 TQTD---DTGRLERVVDDVLDFLERNGMIEED--GE------TLEATELGHL----------VSRLYIDplsaaeIIDGL 513

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 314 EGLVLES---LLHLIYLTtpydlaaqsePD-WMVYFKqfgqlSPTEQNVAALLGVSES-FIGKKAAgqavrkkVDKNVVN 388
Cdd:PRK02362 514 EAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDYEWLNEYLYEHEDeLLGDVPS-------EFEDDEF 571

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 389 RLYLSFVLYSLL-----KETNVWSVSEKFNLPRGYIQNL------LMGAASfsscvlHFCEELEEFWVYKAllVELTKKL 457
Cdd:PRK02362 572 EDFLSAVKTALLledwiDEVDEERITERYGVGPGDIRGKvetaewLLHAAE------RLASELDLDLARAA--RELEKRV 643

                        490       500       510       520       530       540
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568935403 458 TYCVKAELIPLMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTidhLSRRQARQIVSSAK 521
Cdd:PRK02362 644 EYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI---LGEKIAENILEQAG 704
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 14-178 4.09e-42

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 148.47  E-value: 4.09e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  14 ALKKMDPDRLVALVTEVIPNY-SCLVFCPSKKNCENVAEMLckflskdylnhrekekcevikslrnigngkvcpvlkrtv 92
Cdd:cd18795   23 VMNKFDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL--------------------------------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  93 pFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVAN----TFLKRNQYKQMVGRAGRAG 168
Cdd:cd18795   64 -AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEYLQMIGRAGRPG 142

                        170
                 ....*....|
gi 568935403 169 IDTAGESILL 178
Cdd:cd18795  143 FDTRGEAIIM 152
HTH_61 pfam20470
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ...
 173-269 2.99e-26

Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.


Pssm-ID: 466619 [Multi-domain]  Cd Length: 92  Bit Score: 102.24  E-value: 2.99e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  173 GESILLLQEKDKQQVLELISGPLETCCSHLVEEfTKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSlw 252
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 568935403  253 eiTVDALEHLTEKGLLQ 269
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
HELICc smart00490
helicase superfamily c-terminal domain;
94-168 1.41e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.08  E-value: 1.41e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568935403    94 FGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP-ARRVIlrapyVANTFLKRNQYKQMVGRAGRAG 168
Cdd:smart00490  12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVI-----IYDLPWSPASYIQRIGRAGRAG 82
HHH_5 pfam14520
Helix-hairpin-helix domain;
468-521 5.46e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.54  E-value: 5.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568935403  468 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 521
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
21-342 7.21e-56

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 196.65  E-value: 7.21e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  21 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 97
Cdd:COG1204  226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  98 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 176
Cdd:COG1204  305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 177 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 254
Cdd:COG1204  385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 255 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 334
Cdd:COG1204  459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                 ....*...
gi 568935403 335 aqsepDWM 342
Cdd:COG1204  526 -----DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
20-521 5.52e-51

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 186.70  E-value: 5.52e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  20 PDRLVALVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKdYLNHREKEK-CEVIKSLRNIGNGKVCPVLKRTVPFGIA 97
Cdd:PRK02362 229 KDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASALKK-TLTAAERAElAELAEEIREVSDTETSKDLADCVAKGAA 307

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  98 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILR-----------APyvantfLKRNQYKQMVGRAGR 166
Cdd:PRK02362 308 FHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggagmQP------IPVLEYHQMAGRAGR 381

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 167 AGIDTAGESILLlqEKDKQQVLEL----ISGPLETCCSHLVEEftkgiQAL---FLSLIGLKIAASLGDIYQFMSGTFFG 239
Cdd:PRK02362 382 PGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSKLATE-----PALrthVLSTIASGFARTRDGLLEFLEATFYA 454

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 240 VQQKillKEKSLWEITVDALEHLTEKGLLQKDscGDneglecHFRITKLGQAsfkgaidlayCDTLYRD------LKKGL 313
Cdd:PRK02362 455 TQTD---DTGRLERVVDDVLDFLERNGMIEED--GE------TLEATELGHL----------VSRLYIDplsaaeIIDGL 513

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 314 EGLVLES---LLHLIYLTtpydlaaqsePD-WMVYFKqfgqlSPTEQNVAALLGVSES-FIGKKAAgqavrkkVDKNVVN 388
Cdd:PRK02362 514 EAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDYEWLNEYLYEHEDeLLGDVPS-------EFEDDEF 571

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 389 RLYLSFVLYSLL-----KETNVWSVSEKFNLPRGYIQNL------LMGAASfsscvlHFCEELEEFWVYKAllVELTKKL 457
Cdd:PRK02362 572 EDFLSAVKTALLledwiDEVDEERITERYGVGPGDIRGKvetaewLLHAAE------RLASELDLDLARAA--RELEKRV 643

                        490       500       510       520       530       540
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568935403 458 TYCVKAELIPLMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTidhLSRRQARQIVSSAK 521
Cdd:PRK02362 644 EYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI---LGEKIAENILEQAG 704
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 14-178 4.09e-42

C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350182 [Multi-domain]  Cd Length: 154  Bit Score: 148.47  E-value: 4.09e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  14 ALKKMDPDRLVALVTEVIPNY-SCLVFCPSKKNCENVAEMLckflskdylnhrekekcevikslrnigngkvcpvlkrtv 92
Cdd:cd18795   23 VMNKFDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL--------------------------------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  93 pFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVAN----TFLKRNQYKQMVGRAGRAG 168
Cdd:cd18795   64 -AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEYLQMIGRAGRPG 142

                        170
                 ....*....|
gi 568935403 169 IDTAGESILL 178
Cdd:cd18795  143 FDTRGEAIIM 152
PRK00254 PRK00254
ski2-like helicase; Provisional
 37-503 4.34e-32

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 131.48  E-value: 4.34e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  37 LVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLR-NIGNGKvcpvLKRTVPFGIAYHHSGLTSEERKLLEEA 114
Cdd:PRK00254 242 LVFVNTRRSAEKEALELAKKI-KRFLTKPELRALkELADSLEeNPTNEK----LKKALRGGVAFHHAGLGRTERVLIEDA 316

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 115 YSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVANTF----LKRNQYKQMVGRAGRAGIDTAGESILLLQEKDKQQVLE- 189
Cdd:PRK00254 317 FREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFgwedIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMEr 396

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 190 LISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILlkeKSLWEITVDALEHLTEKGLLQ 269
Cdd:PRK00254 397 YIFGKPEKLFSMLSNE--SAFRSQVLALITNFGVSNFKELVNFLERTFYAHQRKDL---YSLEEKAKEIVYFLLENEFID 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 270 KDscgdnegLECHFRITKLGQASFKGAIDlAYCDTLYRDLKKGLE------GlvlesLLHLIYLT---TPYDLAAQSEPD 340
Cdd:PRK00254 472 ID-------LEDRFIPLPLGIRTSQLYID-PLTAKKFKDAFPKIEknpnplG-----IFQLIASTpdmTPLNYSRKEMED 538

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 341 WMVYFKQFgqlsptEQNVAALLGVSESFIGKKAAGQAVRKKvdknvvnrlylsfVLYSLLKETNVWSVSEKFNLPRGYIQ 420
Cdd:PRK00254 539 LLDEAYEM------EDRLYFNIPYWEDYKFQKFLRAFKTAK-------------VLLDWINEVPEGEIVETYNIDPGDLY 599

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 421 NLLmgaasfsscvlhfceELEEFWVYKalLVELTK-----------------KLTYCVKAELIPLMEVTGVLEGRAKQLY 483
Cdd:PRK00254 600 RIL---------------ELADWLMYS--LIELYKlfepkqevldyletlhlRVKHGVREELLELMRLPMIGRKRARALY 662

                        490       500
                 ....*....|....*....|
gi 568935403 484 NAGYRSIMHLANANPEVLVK 503
Cdd:PRK00254 663 NAGFRSIEDIVNAKPSELLK 682
PRK01172 PRK01172
ATP-dependent DNA helicase;
26-527 7.27e-32

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 130.39  E-value: 7.27e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  26 LVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKDYLNHREKEKCEVIKSLrnigngkvcpvLKRTVPFGIAYHHSGLT 104
Cdd:PRK01172 228 LIKETVnDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDS-----------LNEMLPHGVAFHHAGLS 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 105 SEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVIL----RAPYVANTFLKRNQYKQMVGRAGRAGIDTAGESILLLQ 180
Cdd:PRK01172 297 NEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVrditRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAA 376

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 181 EKDKQQVL-ELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSLWEitvdAL 259
Cdd:PRK01172 377 SPASYDAAkKYLSGEPEPVISYMGSQ--RKVRFNTLAAISMGLASSMEDLILFYNETLMAIQNGVDEIDYYIES----SL 450

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 260 EHLTEKGLLQKDScgdneglecHFRITKLGQASfkgaidlaycDTLYRDlkkgleglvLESLLHLI-YLTTPYDlaaqsE 338
Cdd:PRK01172 451 KFLKENGFIKGDV---------TLRATRLGKLT----------SDLYID---------PESALILKsAFDHDYD-----E 497

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 339 PDWMVYFKQFGQLSP--TEQNVAAL-----LGVSESFIgkKAAGQAVrkkvdknvvnrlylsfVLYSLLKETNVWSVSEK 411
Cdd:PRK01172 498 DLALYYISLCREIIPanTRDDYYAMefledIGVIDGDI--SAAKTAM----------------VLRGWISEASMQKITDT 559

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 412 FNLPRGYIQNLLMGAASFSSCVLHFCEeleefwVYK----ALLVELTKKLTYCVKAELIPLMEVTGVLEGRAKQLYNAGY 487
Cdd:PRK01172 560 YGIAPGDVQARASSADWISYSLARLSS------IYKpemrRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDAGF 633

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|
gi 568935403 488 RSIMHLANANPEvLVKTIDHLSRRQARQIVSSAKMLLHEK 527
Cdd:PRK01172 634 KTVDDIARSSPE-RIKKIYGFSDTLANAIVNRAMKISSMY 672
HTH_61 pfam20470
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ...
 173-269 2.99e-26

Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.


Pssm-ID: 466619 [Multi-domain]  Cd Length: 92  Bit Score: 102.24  E-value: 2.99e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  173 GESILLLQEKDKQQVLELISGPLETCCSHLVEEfTKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSlw 252
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 568935403  253 eiTVDALEHLTEKGLLQ 269
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
36-196 2.29e-21

Superfamily II RNA helicase [Replication, recombination and repair];


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 98.47  E-value: 2.29e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  36 CLVFCPSKKNCENVAEMLckfLSKDYLNHREKEK-CEVIKSLR---NIGNGKVcpvLKRTVPFGIAYHHSGLTSEERKLL 111
Cdd:COG4581  244 AIVFIFSRRGCDEAAQQL---LSARLTTKEERAEiREAIDEFAedfSVLFGKT---LSRLLRRGIAVHHAGMLPKYRRLV 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 112 EEAYSTGVLCLLTCTSTLAAGVNLPARRVILrapyvanTFL-KRN----------QYKQMVGRAGRAGIDTAGESILLLQ 180
Cdd:COG4581  318 EELFQAGLLKVVFATDTLAVGINMPARTVVF-------TKLsKFDgerhrpltarEFHQIAGRAGRRGIDTEGHVVVLAP 390

                        170
                 ....*....|....*..
gi 568935403 181 E-KDKQQVLELISGPLE 196
Cdd:COG4581  391 EhDDPKKFARLASARPE 407
HELICc smart00490
helicase superfamily c-terminal domain;
94-168 1.41e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.08  E-value: 1.41e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568935403    94 FGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP-ARRVIlrapyVANTFLKRNQYKQMVGRAGRAG 168
Cdd:smart00490  12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVI-----IYDLPWSPASYIQRIGRAGRAG 82
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 88-168 9.97e-11

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 58.76  E-value: 9.97e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403   88 LKRTVPFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVilrapyVANTFLKRN--QYKQMVGRAG 165
Cdd:pfam00271  33 LLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDL------VINYDLPWNpaSYIQRIGRAG 106


                  ...
gi 568935403  166 RAG 168
Cdd:pfam00271 107 RAG 109
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
85-166 4.39e-09

Superfamily II helicase, archaea-specific [Replication, recombination and repair];


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 59.52  E-value: 4.39e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  85 CPVLKRTVPFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVANTFLKRNQYKQMVGRA 164
Cdd:COG1202  440 CHEIARALGYKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRA 519


                 ..
gi 568935403 165 GR 166
Cdd:COG1202  520 GR 521
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 35-166 2.28e-07

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350183 [Multi-domain]  Cd Length: 150  Bit Score: 50.34  E-value: 2.28e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  35 SCLVFCPSKKNCENVAEMLckflskdylnhreKEKCEvikslrnigngkvcpvlKRTVPFGIAYHHSGLTSEERKLLEEA 114
Cdd:cd18796   40 STLVFTNTRSQAERLAQRL-------------RELCP-----------------DRVPPDFIALHHGSLSRELREEVEAA 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568935403 115 YSTGVLCLLTCTSTLAAGVNLPA-RRVI-LRAPYVANTFLKRnqykqmVGRAGR 166
Cdd:cd18796   90 LKRGDLKVVVATSSLELGIDIGDvDLVIqIGSPKSVARLLQR------LGRSGH 137
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 21-179 3.41e-06

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 46.73  E-value: 3.41e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  21 DRLVALVTEVIPNYSCLVFCPSKKNCENVAEMLCKFlskdylnhreKEKCEVIkslrnigngkvcpvlkrtvpfgiayhH 100
Cdd:cd18787   15 LLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL----------GIKVAAL--------------------------H 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403 101 SGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPA-RRVI-LRAPYVANTFLKRnqykqmVGRAGRAGidTAGESILL 178
Cdd:cd18787   59 GDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGvDHVInYDLPRDAEDYVHR------IGRTGRAG--RKGTAITF 130


                 .
gi 568935403 179 L 179
Cdd:cd18787  131 V 131
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 22-168 6.06e-06

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];


Pssm-ID: 440818 [Multi-domain]  Cd Length: 758  Bit Score: 49.06  E-value: 6.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  22 RLVA-LVTEvipNYSCLVFCPSKKNCENVAEMLCKFLSKDYLNHRekekcevikslrnigngkvcpvlkrtvpfgIAYHH 100
Cdd:COG1205  279 RLLAdLVRE---GLRTLVFTRSRRGAELLARYARRALREPDLADR------------------------------VAAYR 325

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568935403 101 SGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP---ArrVILRA-PYvantflKRNQYKQMVGRAGRAG 168
Cdd:COG1205  326 AGYLPEERREIERGLRSGELLGVVSTNALELGIDIGgldA--VVLAGyPG------TRASFWQQAGRAGRRG 389
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 36-168 1.82e-04

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350184 [Multi-domain]  Cd Length: 146  Bit Score: 41.86  E-value: 1.82e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568935403  36 CLVFCPSKKNCENVAEMLckflskdylnhrekeKCEVIKSLRNIGNgkvcpvlkrtvpfgIAYHHSGLTSEERKLLEEAY 115
Cdd:cd18797   38 TIVFCRSRKLAELLLRYL---------------KARLVEEGPLASK--------------VASYRAGYLAEDRREIEAEL 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 568935403 116 STGVLCLLTCTSTLAAGVNLPARRVILRAPY---VANtflkrnqYKQMVGRAGRAG 168
Cdd:cd18797   89 FNGELLGVVATNALELGIDIGGLDAVVLAGYpgsLAS-------LWQQAGRAGRRG 137
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 108-178 2.12e-04

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 39.99  E-value: 2.12e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568935403 108 RKLLEEAYStgVLCLLTCTSTLAAGVNLP-ARRVILRAPYVAntflkRNQYKQMVGRAGRAGiDTAGESILL 178
Cdd:cd18785   13 IEHAEEIAS--SLEILVATNVLGEGIDVPsLDTVIFFDPPSS-----AASYIQRVGRAGRGG-KDEGEVILF 76
HHH_5 pfam14520
Helix-hairpin-helix domain;
468-521 5.46e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.54  E-value: 5.46e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 568935403  468 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 521
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH