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Conserved domains on  [gi|1907161234|ref|XP_036020801|]
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helicase POLQ-like isoform X10 [Mus musculus]

Protein Classification

SF2_C_Ski2 and HHH_5 domain-containing protein( domain architecture ID 13383144)

SF2_C_Ski2 and HHH_5 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BRR2 super family cl34180
Replicative superfamily II helicase [Replication, recombination and repair];
4-325 4.84e-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: 4.84e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   4 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 80
Cdd:COG1204   226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  81 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 159
Cdd:COG1204   305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 160 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 237
Cdd:COG1204   385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 238 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 317
Cdd:COG1204   459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                  ....*...
gi 1907161234 318 aqsepDWM 325
Cdd:COG1204   526 -----DWI 528
HHH_5 pfam14520
Helix-hairpin-helix domain;
451-504 5.39e-03

Helix-hairpin-helix domain;


:

Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.16  E-value: 5.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907161234 451 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 504
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
4-325 4.84e-56

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 196.65  E-value: 4.84e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   4 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 80
Cdd:COG1204   226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  81 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 159
Cdd:COG1204   305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 160 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 237
Cdd:COG1204   385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 238 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 317
Cdd:COG1204   459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                  ....*...
gi 1907161234 318 aqsepDWM 325
Cdd:COG1204   526 -----DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
3-504 4.18e-51

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 186.70  E-value: 4.18e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   3 PDRLVALVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKdYLNHREKEK-CEVIKSLRNIGNGKVCPVLKRTVPFGIA 80
Cdd:PRK02362  229 KDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASALKK-TLTAAERAElAELAEEIREVSDTETSKDLADCVAKGAA 307

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  81 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILR-----------APyvantfLKRNQYKQMVGRAGR 149
Cdd:PRK02362  308 FHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggagmQP------IPVLEYHQMAGRAGR 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 150 AGIDTAGESILLlqEKDKQQVLEL----ISGPLETCCSHLVEEftkgiQAL---FLSLIGLKIAASLGDIYQFMSGTFFG 222
Cdd:PRK02362  382 PGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSKLATE-----PALrthVLSTIASGFARTRDGLLEFLEATFYA 454

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 223 VQQKillKEKSLWEITVDALEHLTEKGLLQKDscGDneglecHFRITKLGQAsfkgaidlayCDTLYRD------LKKGL 296
Cdd:PRK02362  455 TQTD---DTGRLERVVDDVLDFLERNGMIEED--GE------TLEATELGHL----------VSRLYIDplsaaeIIDGL 513

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 297 EGLVLES---LLHLIYLTtpydlaaqsePD-WMVYFKqfgqlSPTEQNVAALLGVSES-FIGKKAAgqavrkkVDKNVVN 371
Cdd:PRK02362  514 EAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDYEWLNEYLYEHEDeLLGDVPS-------EFEDDEF 571

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 372 RLYLSFVLYSLL-----KETNVWSVSEKFNLPRGYIQNL------LMGAASfsscvlHFCEELEEFWVYKAllVELTKKL 440
Cdd:PRK02362  572 EDFLSAVKTALLledwiDEVDEERITERYGVGPGDIRGKvetaewLLHAAE------RLASELDLDLARAA--RELEKRV 643

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907161234 441 TYCVKAELIPLMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTidhLSRRQARQIVSSAK 504
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 ...
 1-161 1.28e-41

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: 146.93  E-value: 1.28e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   1 MDPDRLVALVTEVIPNY-SCLVFCPSKKNCENVAEMLckflskdylnhrekekcevikslrnigngkvcpvlkrtvpFGI 79
Cdd:cd18795    27 FDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL----------------------------------------AGI 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  80 AYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVAN----TFLKRNQYKQMVGRAGRAGIDTA 155
Cdd:cd18795    67 AFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEYLQMIGRAGRPGFDTR 146


                  ....*.
gi 1907161234 156 GESILL 161
Cdd:cd18795   147 GEAIIM 152
HTH_61 pfam20470
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ...
 156-252 2.60e-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: 102.63  E-value: 2.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 156 GESILLLQEKDKQQVLELISGPLETCCSHLVEEfTKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSlw 235
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 1907161234 236 eiTVDALEHLTEKGLLQ 252
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
HELICc smart00490
helicase superfamily c-terminal domain;
77-151 1.36e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.08  E-value: 1.36e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907161234   77 FGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP-ARRVIlrapyVANTFLKRNQYKQMVGRAGRAG 151
Cdd:smart00490  12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVI-----IYDLPWSPASYIQRIGRAGRAG 82
HHH_5 pfam14520
Helix-hairpin-helix domain;
451-504 5.39e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.16  E-value: 5.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907161234 451 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 504
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
4-325 4.84e-56

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 196.65  E-value: 4.84e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   4 DRLVALVTEVIP-NYSCLVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLRNIGNG-KVCPVLKRTVPFGIA 80
Cdd:COG1204   226 DPTLALALDLLEeGGQVLVFVSSRRDAESLAKKLADEL-KRRLTPEEREELeELAEELLEVSEEtHTNEKLADCLEKGVA 304

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  81 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPY-VANTFLKRNQYKQMVGRAGRAGIDTAGESI 159
Cdd:COG1204   305 FHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAI 384

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 160 LLLQEKD--KQQVLELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQkillKEKSLWEI 237
Cdd:COG1204   385 LVAKSSDeaDELFERYILGEPEPIRSKLANE--SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEV 458

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 238 TVDALEHLTEKGLLQKDSCGdneglechFRITKLGQASFKGAIDLAYCDTLYRDLKKGLEGLVLESLLHLIYLTTpydla 317
Cdd:COG1204   459 VDDALEFLLENGFIEEDGDR--------LRATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----- 525


                  ....*...
gi 1907161234 318 aqsepDWM 325
Cdd:COG1204   526 -----DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
3-504 4.18e-51

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 186.70  E-value: 4.18e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   3 PDRLVALVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKdYLNHREKEK-CEVIKSLRNIGNGKVCPVLKRTVPFGIA 80
Cdd:PRK02362  229 KDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASALKK-TLTAAERAElAELAEEIREVSDTETSKDLADCVAKGAA 307

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  81 YHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILR-----------APyvantfLKRNQYKQMVGRAGR 149
Cdd:PRK02362  308 FHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrrydggagmQP------IPVLEYHQMAGRAGR 381

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 150 AGIDTAGESILLlqEKDKQQVLEL----ISGPLETCCSHLVEEftkgiQAL---FLSLIGLKIAASLGDIYQFMSGTFFG 222
Cdd:PRK02362  382 PGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSKLATE-----PALrthVLSTIASGFARTRDGLLEFLEATFYA 454

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 223 VQQKillKEKSLWEITVDALEHLTEKGLLQKDscGDneglecHFRITKLGQAsfkgaidlayCDTLYRD------LKKGL 296
Cdd:PRK02362  455 TQTD---DTGRLERVVDDVLDFLERNGMIEED--GE------TLEATELGHL----------VSRLYIDplsaaeIIDGL 513

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 297 EGLVLES---LLHLIYLTtpydlaaqsePD-WMVYFKqfgqlSPTEQNVAALLGVSES-FIGKKAAgqavrkkVDKNVVN 371
Cdd:PRK02362  514 EAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDYEWLNEYLYEHEDeLLGDVPS-------EFEDDEF 571

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 372 RLYLSFVLYSLL-----KETNVWSVSEKFNLPRGYIQNL------LMGAASfsscvlHFCEELEEFWVYKAllVELTKKL 440
Cdd:PRK02362  572 EDFLSAVKTALLledwiDEVDEERITERYGVGPGDIRGKvetaewLLHAAE------RLASELDLDLARAA--RELEKRV 643

                         490       500       510       520       530       540
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907161234 441 TYCVKAELIPLMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTidhLSRRQARQIVSSAK 504
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 ...
 1-161 1.28e-41

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: 146.93  E-value: 1.28e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   1 MDPDRLVALVTEVIPNY-SCLVFCPSKKNCENVAEMLckflskdylnhrekekcevikslrnigngkvcpvlkrtvpFGI 79
Cdd:cd18795    27 FDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL----------------------------------------AGI 66

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  80 AYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVAN----TFLKRNQYKQMVGRAGRAGIDTA 155
Cdd:cd18795    67 AFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEYLQMIGRAGRPGFDTR 146


                  ....*.
gi 1907161234 156 GESILL 161
Cdd:cd18795   147 GEAIIM 152
PRK00254 PRK00254
ski2-like helicase; Provisional
 20-486 2.66e-32

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 131.86  E-value: 2.66e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  20 LVFCPSKKNCENVAEMLCKFLsKDYLNHREKEKC-EVIKSLR-NIGNGKvcpvLKRTVPFGIAYHHSGLTSEERKLLEEA 97
Cdd:PRK00254  242 LVFVNTRRSAEKEALELAKKI-KRFLTKPELRALkELADSLEeNPTNEK----LKKALRGGVAFHHAGLGRTERVLIEDA 316

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  98 YSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVANTF----LKRNQYKQMVGRAGRAGIDTAGESILLLQEKDKQQVLE- 172
Cdd:PRK00254  317 FREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFgwedIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMEr 396

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 173 LISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILlkeKSLWEITVDALEHLTEKGLLQ 252
Cdd:PRK00254  397 YIFGKPEKLFSMLSNE--SAFRSQVLALITNFGVSNFKELVNFLERTFYAHQRKDL---YSLEEKAKEIVYFLLENEFID 471

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 253 KDscgdnegLECHFRITKLGQASFKGAIDlAYCDTLYRDLKKGLE------GlvlesLLHLIYLT---TPYDLAAQSEPD 323
Cdd:PRK00254  472 ID-------LEDRFIPLPLGIRTSQLYID-PLTAKKFKDAFPKIEknpnplG-----IFQLIASTpdmTPLNYSRKEMED 538

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 324 WMVYFKQFgqlsptEQNVAALLGVSESFIGKKAAGQAVRKKvdknvvnrlylsfVLYSLLKETNVWSVSEKFNLPRGYIQ 403
Cdd:PRK00254  539 LLDEAYEM------EDRLYFNIPYWEDYKFQKFLRAFKTAK-------------VLLDWINEVPEGEIVETYNIDPGDLY 599

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 404 NLLmgaasfsscvlhfceELEEFWVYKalLVELTK-----------------KLTYCVKAELIPLMEVTGVLEGRAKQLY 466
Cdd:PRK00254  600 RIL---------------ELADWLMYS--LIELYKlfepkqevldyletlhlRVKHGVREELLELMRLPMIGRKRARALY 662

                         490       500
                  ....*....|....*....|
gi 1907161234 467 NAGYRSIMHLANANPEVLVK 486
Cdd:PRK00254  663 NAGFRSIEDIVNAKPSELLK 682
PRK01172 PRK01172
ATP-dependent DNA helicase;
9-510 6.07e-32

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 130.39  E-value: 6.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   9 LVTEVI-PNYSCLVFCPSKKNCENVAEMLCKFLSKDYLNHREKEKCEVIKSLrnigngkvcpvLKRTVPFGIAYHHSGLT 87
Cdd:PRK01172  228 LIKETVnDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDS-----------LNEMLPHGVAFHHAGLS 296

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  88 SEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVIL----RAPYVANTFLKRNQYKQMVGRAGRAGIDTAGESILLLQ 163
Cdd:PRK01172  297 NEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVrditRYGNGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAA 376

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 164 EKDKQQVL-ELISGPLETCCSHLVEEftKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSLWEitvdAL 242
Cdd:PRK01172  377 SPASYDAAkKYLSGEPEPVISYMGSQ--RKVRFNTLAAISMGLASSMEDLILFYNETLMAIQNGVDEIDYYIES----SL 450

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 243 EHLTEKGLLQKDScgdneglecHFRITKLGQASfkgaidlaycDTLYRDlkkgleglvLESLLHLI-YLTTPYDlaaqsE 321
Cdd:PRK01172  451 KFLKENGFIKGDV---------TLRATRLGKLT----------SDLYID---------PESALILKsAFDHDYD-----E 497

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 322 PDWMVYFKQFGQLSP--TEQNVAAL-----LGVSESFIgkKAAGQAVrkkvdknvvnrlylsfVLYSLLKETNVWSVSEK 394
Cdd:PRK01172  498 DLALYYISLCREIIPanTRDDYYAMefledIGVIDGDI--SAAKTAM----------------VLRGWISEASMQKITDT 559

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 395 FNLPRGYIQNLLMGAASFSSCVLHFCEeleefwVYK----ALLVELTKKLTYCVKAELIPLMEVTGVLEGRAKQLYNAGY 470
Cdd:PRK01172  560 YGIAPGDVQARASSADWISYSLARLSS------IYKpemrRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYDAGF 633

                         490       500       510       520
                  ....*....|....*....|....*....|....*....|
gi 1907161234 471 RSIMHLANANPEvLVKTIDHLSRRQARQIVSSAKMLLHEK 510
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 ...
 156-252 2.60e-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: 102.63  E-value: 2.60e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234 156 GESILLLQEKDKQQVLELISGPLETCCSHLVEEfTKGIQALFLSLIGLKIAASLGDIYQFMSGTFFGVQQKILLKEKSlw 235
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 1907161234 236 eiTVDALEHLTEKGLLQ 252
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
19-179 2.25e-21

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 98.09  E-value: 2.25e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  19 CLVFCPSKKNCENVAEMLckfLSKDYLNHREKEK-CEVIKSLR---NIGNGKVcpvLKRTVPFGIAYHHSGLTSEERKLL 94
Cdd:COG4581   244 AIVFIFSRRGCDEAAQQL---LSARLTTKEERAEiREAIDEFAedfSVLFGKT---LSRLLRRGIAVHHAGMLPKYRRLV 317

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  95 EEAYSTGVLCLLTCTSTLAAGVNLPARRVILrapyvanTFL-KRN----------QYKQMVGRAGRAGIDTAGESILLLQ 163
Cdd:COG4581   318 EELFQAGLLKVVFATDTLAVGINMPARTVVF-------TKLsKFDgerhrpltarEFHQIAGRAGRRGIDTEGHVVVLAP 390

                         170
                  ....*....|....*..
gi 1907161234 164 E-KDKQQVLELISGPLE 179
Cdd:COG4581   391 EhDDPKKFARLASARPE 407
HELICc smart00490
helicase superfamily c-terminal domain;
77-151 1.36e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.08  E-value: 1.36e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907161234   77 FGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP-ARRVIlrapyVANTFLKRNQYKQMVGRAGRAG 151
Cdd:smart00490  12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVI-----IYDLPWSPASYIQRIGRAGRAG 82
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 71-151 1.03e-10

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: 1.03e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  71 LKRTVPFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVilrapyVANTFLKRN--QYKQMVGRAG 148
Cdd:pfam00271  33 LLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDL------VINYDLPWNpaSYIQRIGRAG 106


                  ...
gi 1907161234 149 RAG 151
Cdd:pfam00271 107 RAG 109
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
68-149 4.05e-09

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 59.52  E-value: 4.05e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  68 CPVLKRTVPFGIAYHHSGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPARRVILRAPYVANTFLKRNQYKQMVGRA 147
Cdd:COG1202   440 CHEIARALGYKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRA 519


                  ..
gi 1907161234 148 GR 149
Cdd:COG1202   520 GR 521
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 18-149 2.30e-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: 2.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  18 SCLVFCPSKKNCENVAEMLckflskdylnhreKEKCEvikslrnigngkvcpvlKRTVPFGIAYHHSGLTSEERKLLEEA 97
Cdd:cd18796    40 STLVFTNTRSQAERLAQRL-------------RELCP-----------------DRVPPDFIALHHGSLSRELREEVEAA 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907161234  98 YSTGVLCLLTCTSTLAAGVNLPA-RRVI-LRAPYVANTFLKRnqykqmVGRAGR 149
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 ...
 4-162 3.32e-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: 46.35  E-value: 3.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   4 DRLVALVTEVIPNYSCLVFCPSKKNCENVAEMLCKFlskdylnhreKEKCEVIkslrnigngkvcpvlkrtvpfgiayhH 83
Cdd:cd18787    15 LLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL----------GIKVAAL--------------------------H 58

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  84 SGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLPA-RRVI-LRAPYVANTFLKRnqykqmVGRAGRAGidTAGESILL 161
Cdd:cd18787    59 GDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGvDHVInYDLPRDAEDYVHR------IGRTGRAG--RKGTAITF 130


                  .
gi 1907161234 162 L 162
Cdd:cd18787   131 V 131
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 5-151 5.79e-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: 5.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234   5 RLVA-LVTEvipNYSCLVFCPSKKNCENVAEMLCKFLSKDYLNHRekekcevikslrnigngkvcpvlkrtvpfgIAYHH 83
Cdd:COG1205   279 RLLAdLVRE---GLRTLVFTRSRRGAELLARYARRALREPDLADR------------------------------VAAYR 325

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907161234  84 SGLTSEERKLLEEAYSTGVLCLLTCTSTLAAGVNLP---ArrVILRA-PYvantflKRNQYKQMVGRAGRAG 151
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 ...
 19-151 1.83e-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: 1.83e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907161234  19 CLVFCPSKKNCENVAEMLckflskdylnhrekeKCEVIKSLRNIGNgkvcpvlkrtvpfgIAYHHSGLTSEERKLLEEAY 98
Cdd:cd18797    38 TIVFCRSRKLAELLLRYL---------------KARLVEEGPLASK--------------VASYRAGYLAEDRREIEAEL 88

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907161234  99 STGVLCLLTCTSTLAAGVNLPARRVILRAPY---VANtflkrnqYKQMVGRAGRAG 151
Cdd:cd18797    89 FNGELLGVVATNALELGIDIGGLDAVVLAGYpgsLAS-------LWQQAGRAGRRG 137
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 91-161 2.05e-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: 2.05e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907161234  91 RKLLEEAYStgVLCLLTCTSTLAAGVNLP-ARRVILRAPYVAntflkRNQYKQMVGRAGRAGiDTAGESILL 161
Cdd:cd18785    13 IEHAEEIAS--SLEILVATNVLGEGIDVPsLDTVIFFDPPSS-----AASYIQRVGRAGRGG-KDEGEVILF 76
HHH_5 pfam14520
Helix-hairpin-helix domain;
451-504 5.39e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 35.16  E-value: 5.39e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907161234 451 LMEVTGVLEGRAKQLYNAGYRSIMHLANANPEVLVKTIDhLSRRQARQIVSSAK 504
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.
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