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Conserved domains on  [gi|663071126|ref|NP_001284685|]
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helicase POLQ-like isoform 3 [Homo sapiens]

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

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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];
21-390 9.40e-55

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: 194.34  E-value: 9.40e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  21 YVPkVELKEYLKINDTIYevdskaengmtfsrllnykYSDTLKKMDpDHLVALVTEVIP-NYSCLVFCPSKKNCENVAEM 99
Cdd:COG1204  200 WRP-VPLNEGVLYDGVLR-------------------FDDGSRRSK-DPTLALALDLLEeGGQVLVFVSSRRDAESLAKK 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 100 ICKFLsKEYLKHKEKEKC-EVIKNLKNIGNGN-LCPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLA 177
Cdd:COG1204  259 LADEL-KRRLTPEEREELeELAEELLEVSEEThTNEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLA 337

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 178 AGVNLPARRVILRAPY-VAKEFLKRNQYKQMIGRAGRAGIDTIGESILIlqEKDKQQVLELITKPL----ENCYSHLVQE 252
Cdd:COG1204  338 AGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILV--AKSSDEADELFERYIlgepEPIRSKLANE 415

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 253 ftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQkvllKEKSLWEITVESLRYLTEKGLLQKDTIYkseeevqynFH 332
Cdd:COG1204  416 --SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEVVDDALEFLLENGFIEEDGDR---------LR 480

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 663071126 333 ITKLGRASFKGTIDLAYCDILYRDLKKGLEGLVLESLLHLIYLTTpydlvsqcnpDWM 390
Cdd:COG1204  481 ATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----------DWI 528
HHH_5 pfam14520
Helix-hairpin-helix domain;
516-569 2.43e-03

Helix-hairpin-helix domain;


:

Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 36.31  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 663071126  516 LMEVTGVLEGRAKQLYSAGYKSLMHLANANPEVLVRTIDhLSRRQAKQIVSSAK 569
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
21-390 9.40e-55

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 194.34  E-value: 9.40e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  21 YVPkVELKEYLKINDTIYevdskaengmtfsrllnykYSDTLKKMDpDHLVALVTEVIP-NYSCLVFCPSKKNCENVAEM 99
Cdd:COG1204  200 WRP-VPLNEGVLYDGVLR-------------------FDDGSRRSK-DPTLALALDLLEeGGQVLVFVSSRRDAESLAKK 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 100 ICKFLsKEYLKHKEKEKC-EVIKNLKNIGNGN-LCPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLA 177
Cdd:COG1204  259 LADEL-KRRLTPEEREELeELAEELLEVSEEThTNEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLA 337

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 178 AGVNLPARRVILRAPY-VAKEFLKRNQYKQMIGRAGRAGIDTIGESILIlqEKDKQQVLELITKPL----ENCYSHLVQE 252
Cdd:COG1204  338 AGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILV--AKSSDEADELFERYIlgepEPIRSKLANE 415

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 253 ftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQkvllKEKSLWEITVESLRYLTEKGLLQKDTIYkseeevqynFH 332
Cdd:COG1204  416 --SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEVVDDALEFLLENGFIEEDGDR---------LR 480

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 663071126 333 ITKLGRASFKGTIDLAYCDILYRDLKKGLEGLVLESLLHLIYLTTpydlvsqcnpDWM 390
Cdd:COG1204  481 ATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----------DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
25-569 4.02e-48

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 179.38  E-value: 4.02e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  25 VELKEYLKINDTIYEVDSKAEngmtfsrllnykysdtLKKMDPDHLVALVTEVI-PNYSCLVFCPSKKNCENVAEMICKF 103
Cdd:PRK02362 203 IDLREGVFYGGAIHFDDSQRE----------------VEVPSKDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASA 266

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 104 LSKEYLKHKEKEKCEVIKNLKNIGNGNLCPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLP 183
Cdd:PRK02362 267 LKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLP 346

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 184 ARRVILR-----------APYVAKEflkrnqYKQMIGRAGRAGIDTIGESILIlqEKDKQQVLEL----ITKPLENCYSH 248
Cdd:PRK02362 347 ARRVIIRdyrrydggagmQPIPVLE------YHQMAGRAGRPGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSK 418

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 249 LVQEftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQKvllKEKSLWEITVESLRYLTEKGLLQKDtiyksEEEVq 328
Cdd:PRK02362 419 LATE--PALRTHVLSTIASGFARTRDGLLEFLEATFYATQTD---DTGRLERVVDDVLDFLERNGMIEED-----GETL- 487

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 329 ynfHITKLGRasfkgTIDLAYCDILY-RDLKKGLEGLVLES---LLHLIYLTtpydlvsqcnPD-WMIYFRqfsqlSPAE 403
Cdd:PRK02362 488 ---EATELGH-----LVSRLYIDPLSaAEIIDGLEAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDY 544

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 404 QNVAAILGVSES-FIGKKASgqaigkkVDKNVVNRLYLSFVLYTLLKETNIWTVSE-----KFNMPRGYIQN-------L 470
Cdd:PRK02362 545 EWLNEYLYEHEDeLLGDVPS-------EFEDDEFEDFLSAVKTALLLEDWIDEVDEeriteRYGVGPGDIRGkvetaewL 617

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 471 LTGTASFSScvlhfceELEEFWVYRAllVELTKKLTYCVKAELIPLMEVTGVLEGRAKQLYSAGYKSLMHLANANPEVLV 550
Cdd:PRK02362 618 LHAAERLAS-------ELDLDLARAA--RELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVL 688

                        570
                 ....*....|....*....
gi 663071126 551 RTidhLSRRQAKQIVSSAK 569
Cdd:PRK02362 689 AI---LGEKIAENILEQAG 704
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 50-225 2.05e-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: 2.05e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  50 FSRLLNYKYSDTLKKMDPDHLVALVTEVIPNY-SCLVFCPSKKNCENVAEMIckflskeylkhkekekceviknlknign 128
Cdd:cd18795   12 FNGLGIKLRVDVMNKFDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL---------------------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 129 gnlcpvlkrtipFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLPARRVILRAPYVAK----EFLKRNQY 204
Cdd:cd18795   64 ------------AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEY 131

                        170       180
                 ....*....|....*....|.
gi 663071126 205 KQMIGRAGRAGIDTIGESILI 225
Cdd:cd18795  132 LQMIGRAGRPGFDTRGEAIIM 152
HTH_61 pfam20470
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ...
 220-316 1.94e-30

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: 114.57  E-value: 1.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  220 GESILILQEKDKQQVLELITKPLENCYSHLVQEfTKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQKVLLKEKSlw 299
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 663071126  300 eiTVESLRYLTEKGLLQ 316
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
HELICc smart00490
helicase superfamily c-terminal domain;
137-215 7.31e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.16  E-value: 7.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126   137 RTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLP-ARRVILRAPYVAKEflkrnQYKQMIGRAGRAG 215
Cdd:smart00490   8 KELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDLPWSPA-----SYIQRIGRAGRAG 82
HHH_5 pfam14520
Helix-hairpin-helix domain;
516-569 2.43e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 36.31  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 663071126  516 LMEVTGVLEGRAKQLYSAGYKSLMHLANANPEVLVRTIDhLSRRQAKQIVSSAK 569
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
 
Name Accession Description Interval E-value
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
21-390 9.40e-55

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


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 194.34  E-value: 9.40e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  21 YVPkVELKEYLKINDTIYevdskaengmtfsrllnykYSDTLKKMDpDHLVALVTEVIP-NYSCLVFCPSKKNCENVAEM 99
Cdd:COG1204  200 WRP-VPLNEGVLYDGVLR-------------------FDDGSRRSK-DPTLALALDLLEeGGQVLVFVSSRRDAESLAKK 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 100 ICKFLsKEYLKHKEKEKC-EVIKNLKNIGNGN-LCPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLA 177
Cdd:COG1204  259 LADEL-KRRLTPEEREELeELAEELLEVSEEThTNEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLA 337

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 178 AGVNLPARRVILRAPY-VAKEFLKRNQYKQMIGRAGRAGIDTIGESILIlqEKDKQQVLELITKPL----ENCYSHLVQE 252
Cdd:COG1204  338 AGVNLPARRVIIRDTKrGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILV--AKSSDEADELFERYIlgepEPIRSKLANE 415

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 253 ftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQkvllKEKSLWEITVESLRYLTEKGLLQKDTIYkseeevqynFH 332
Cdd:COG1204  416 --SALRTHLLALIASGFANSREELLDFLENTFYAYQY----DKGDLEEVVDDALEFLLENGFIEEDGDR---------LR 480

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 663071126 333 ITKLGRASFKGTIDLAYCDILYRDLKKGLEGLVLESLLHLIYLTTpydlvsqcnpDWM 390
Cdd:COG1204  481 ATKLGKLVSRLYIDPLTAAELVDGLRKADEEFTDLGLLHLILILR----------DWI 528
PRK02362 PRK02362
ATP-dependent DNA helicase;
25-569 4.02e-48

ATP-dependent DNA helicase;


Pssm-ID: 235032 [Multi-domain]  Cd Length: 737  Bit Score: 179.38  E-value: 4.02e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  25 VELKEYLKINDTIYEVDSKAEngmtfsrllnykysdtLKKMDPDHLVALVTEVI-PNYSCLVFCPSKKNCENVAEMICKF 103
Cdd:PRK02362 203 IDLREGVFYGGAIHFDDSQRE----------------VEVPSKDDTLNLVLDTLeEGGQCLVFVSSRRNAEGFAKRAASA 266

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 104 LSKEYLKHKEKEKCEVIKNLKNIGNGNLCPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLP 183
Cdd:PRK02362 267 LKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLP 346

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 184 ARRVILR-----------APYVAKEflkrnqYKQMIGRAGRAGIDTIGESILIlqEKDKQQVLEL----ITKPLENCYSH 248
Cdd:PRK02362 347 ARRVIIRdyrrydggagmQPIPVLE------YHQMAGRAGRPGLDPYGEAVLL--AKSYDELDELferyIWADPEDVRSK 418

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 249 LVQEftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQKvllKEKSLWEITVESLRYLTEKGLLQKDtiyksEEEVq 328
Cdd:PRK02362 419 LATE--PALRTHVLSTIASGFARTRDGLLEFLEATFYATQTD---DTGRLERVVDDVLDFLERNGMIEED-----GETL- 487

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 329 ynfHITKLGRasfkgTIDLAYCDILY-RDLKKGLEGLVLES---LLHLIYLTtpydlvsqcnPD-WMIYFRqfsqlSPAE 403
Cdd:PRK02362 488 ---EATELGH-----LVSRLYIDPLSaAEIIDGLEAAKKPTdlgLLHLVCST----------PDmYELYLR-----SGDY 544

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 404 QNVAAILGVSES-FIGKKASgqaigkkVDKNVVNRLYLSFVLYTLLKETNIWTVSE-----KFNMPRGYIQN-------L 470
Cdd:PRK02362 545 EWLNEYLYEHEDeLLGDVPS-------EFEDDEFEDFLSAVKTALLLEDWIDEVDEeriteRYGVGPGDIRGkvetaewL 617

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 471 LTGTASFSScvlhfceELEEFWVYRAllVELTKKLTYCVKAELIPLMEVTGVLEGRAKQLYSAGYKSLMHLANANPEVLV 550
Cdd:PRK02362 618 LHAAERLAS-------ELDLDLARAA--RELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVL 688

                        570
                 ....*....|....*....
gi 663071126 551 RTidhLSRRQAKQIVSSAK 569
Cdd:PRK02362 689 AI---LGEKIAENILEQAG 704
SF2_C_Ski2 cd18795
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ...
 50-225 2.05e-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: 2.05e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  50 FSRLLNYKYSDTLKKMDPDHLVALVTEVIPNY-SCLVFCPSKKNCENVAEMIckflskeylkhkekekceviknlknign 128
Cdd:cd18795   12 FNGLGIKLRVDVMNKFDSDIIVLLKIETVSEGkPVLVFCSSRKECEKTAKDL---------------------------- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 129 gnlcpvlkrtipFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLPARRVILRAPYVAK----EFLKRNQY 204
Cdd:cd18795   64 ------------AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTVIIKGTQRYDgkgyRELSPLEY 131

                        170       180
                 ....*....|....*....|.
gi 663071126 205 KQMIGRAGRAGIDTIGESILI 225
Cdd:cd18795  132 LQMIGRAGRPGFDTRGEAIIM 152
PRK01172 PRK01172
ATP-dependent DNA helicase;
58-575 1.50e-30

ATP-dependent DNA helicase;


Pssm-ID: 100801 [Multi-domain]  Cd Length: 674  Bit Score: 126.92  E-value: 1.50e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  58 YSDTLKKMDPDHLVALVTEVIPNYSCLVFCPSKKNCENVAEMICKFLSKeylkhkekekcevIKNLK-NIGNGNLCP-VL 135
Cdd:PRK01172 214 ILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPE-------------FNDFKvSSENNNVYDdSL 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 136 KRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLPARRVIL----RAPYVAKEFLKRNQYKQMIGRA 211
Cdd:PRK01172 281 NEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVrditRYGNGGIRYLSNMEIKQMIGRA 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 212 GRAGIDTIGESILILQEKDKQQVL-ELITKPLENCYSHLVQEFTKGIQTlfLSLIGLKIATNLDDIYHFMNGTFFGVQQK 290
Cdd:PRK01172 361 GRPGYDQYGIGYIYAASPASYDAAkKYLSGEPEPVISYMGSQRKVRFNT--LAAISMGLASSMEDLILFYNETLMAIQNG 438

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 291 VLLKEKSLweitVESLRYLTEKGLLQKDTIYKSeeevqynfhiTKLGRAsfkgTIDLaYCDIlyrdlkkgleglvlESLL 370
Cdd:PRK01172 439 VDEIDYYI----ESSLKFLKENGFIKGDVTLRA----------TRLGKL----TSDL-YIDP--------------ESAL 485

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 371 HLI-YLTTPYDLvsqcnpDWMIYFRQFS-QLSPAE-QNVAAILGVSESfIGkkasgqaigkKVDKNvVNRLYLSFVLYTL 447
Cdd:PRK01172 486 ILKsAFDHDYDE------DLALYYISLCrEIIPANtRDDYYAMEFLED-IG----------VIDGD-ISAAKTAMVLRGW 547

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 448 LKETNIWTVSEKFNMPRGYIQNLLTGTASFSSCVLHFCEeleefwVY----RALLVELTKKLTYCVKAELIPLMEVTGVL 523
Cdd:PRK01172 548 ISEASMQKITDTYGIAPGDVQARASSADWISYSLARLSS------IYkpemRRKLEILNIRIKEGIREDLIDLVLIPKVG 621

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|..
gi 663071126 524 EGRAKQLYSAGYKSLMHLANANPEvLVRTIDHLSRRQAKQIVSSAKMLLHEK 575
Cdd:PRK01172 622 RVRARRLYDAGFKTVDDIARSSPE-RIKKIYGFSDTLANAIVNRAMKISSMY 672
HTH_61 pfam20470
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ...
 220-316 1.94e-30

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: 114.57  E-value: 1.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  220 GESILILQEKDKQQVLELITKPLENCYSHLVQEfTKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQKVLLKEKSlw 299
Cdd:pfam20470   1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS-- 77

                          90
                  ....*....|....*..
gi 663071126  300 eiTVESLRYLTEKGLLQ 316
Cdd:pfam20470  78 --IESSLEELVENGLIT 92
PRK00254 PRK00254
ski2-like helicase; Provisional
 84-551 3.70e-29

ski2-like helicase; Provisional


Pssm-ID: 234702 [Multi-domain]  Cd Length: 720  Bit Score: 123.00  E-value: 3.70e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  84 LVFCPSKKNCENVAEMICKFLSKEYLKHKEKEKCEVIKNLK-NIGNGNLcpvlKRTIPFGVAYHHSGLTSDERKLLEEAY 162
Cdd:PRK00254 242 LVFVNTRRSAEKEALELAKKIKRFLTKPELRALKELADSLEeNPTNEKL----KKALRGGVAFHHAGLGRTERVLIEDAF 317

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 163 STGVLCLFTCTSTLAAGVNLPARRVILRAPYVAKEF----LKRNQYKQMIGRAGRAGIDTIGESILILQEKDKQQVLE-- 236
Cdd:PRK00254 318 REGLIKVITATPTLSAGINLPAFRVIIRDTKRYSNFgwedIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMEry 397

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 237 LITKPlENCYSHLVQEftKGIQTLFLSLIGLKIATNLDDIYHFMNGTFFGVQQkvllKEKSLWEITVESLRYLtekgLLQ 316
Cdd:PRK00254 398 IFGKP-EKLFSMLSNE--SAFRSQVLALITNFGVSNFKELVNFLERTFYAHQR----KDLYSLEEKAKEIVYF----LLE 466

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 317 KDTIyksEEEVQYNFHITKLGRASFKGTIDlaycDILYRDLKKGLEGLVLE----SLLHLIYLTtpydlvsqcnPDwmiy 392
Cdd:PRK00254 467 NEFI---DIDLEDRFIPLPLGIRTSQLYID----PLTAKKFKDAFPKIEKNpnplGIFQLIAST----------PD---- 525

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 393 frqFSQLSPAEQNVAAILGVSESFIGK-KASGQAIGKKVDKNVVNRLYLSFVLYTLLKETNIWTVSEKFNMPRGYIQNLL 471
Cdd:PRK00254 526 ---MTPLNYSRKEMEDLLDEAYEMEDRlYFNIPYWEDYKFQKFLRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRIL 602

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 472 tgtasfsscvlhfceELEEFWVYRalLVELTK-----------------KLTYCVKAELIPLMEVTGVLEGRAKQLYSAG 534
Cdd:PRK00254 603 ---------------ELADWLMYS--LIELYKlfepkqevldyletlhlRVKHGVREELLELMRLPMIGRKRARALYNAG 665

                        490
                 ....*....|....*..
gi 663071126 535 YKSLMHLANANPEVLVR 551
Cdd:PRK00254 666 FRSIEDIVNAKPSELLK 682
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
60-243 1.07e-18

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


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 90.38  E-value: 1.07e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  60 DTLKKMDPDHLValvteviPNYsclVFCPSKKNCENVAEMIckfLSKEYLKHKEKEK-CEVIKNLKNIGNGNLCPVLKRT 138
Cdd:COG4581  231 EVIEELDRGGLL-------PAI---VFIFSRRGCDEAAQQL---LSARLTTKEERAEiREAIDEFAEDFSVLFGKTLSRL 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 139 IPFGVAYHHSGLTSDERKLLEEAYSTG---VLClftCTSTLAAGVNLPARRVIL----------RAPYVAKEFLkrnqyk 205
Cdd:COG4581  298 LRRGIAVHHAGMLPKYRRLVEELFQAGllkVVF---ATDTLAVGINMPARTVVFtklskfdgerHRPLTAREFH------ 368

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 663071126 206 QMIGRAGRAGIDTIGESILILQE-KDKQQVLELITKPLE 243
Cdd:COG4581  369 QIAGRAGRRGIDTEGHVVVLAPEhDDPKKFARLASARPE 407
HELICc smart00490
helicase superfamily c-terminal domain;
137-215 7.31e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.16  E-value: 7.31e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126   137 RTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLP-ARRVILRAPYVAKEflkrnQYKQMIGRAGRAG 215
Cdd:smart00490   8 KELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDLPWSPA-----SYIQRIGRAGRAG 82
COG1202 COG1202
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
132-231 1.41e-10

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


Pssm-ID: 440815 [Multi-domain]  Cd Length: 790  Bit Score: 64.14  E-value: 1.41e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 132 CPVLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLPARRVILRAPYVAKEFLKRNQYKQMIGRA 211
Cdd:COG1202  440 CHEIARALGYKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRA 519

                         90       100
                 ....*....|....*....|
gi 663071126 212 GRAGIDTIGEsILILQEKDK 231
Cdd:COG1202  520 GRPDYHDRGK-VYLLVEPGK 538
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 106-215 3.65e-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: 57.22  E-value: 3.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  106 KEYLKHKEKEKCEVIKNLKNIGNGNLcpvLKRTIPFGVAYHHSGLTSDERKLLEEAYSTGVLCLFTCTSTLAAGVNLP-A 184
Cdd:pfam00271   7 LELLKKERGGKVLIFSQTKKTLEAEL---LLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPdV 83

                          90       100       110
                  ....*....|....*....|....*....|..
gi 663071126  185 RRVI-LRAPYvakeflKRNQYKQMIGRAGRAG 215
Cdd:pfam00271  84 DLVInYDLPW------NPASYIQRIGRAGRAG 109
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 82-213 3.87e-06

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: 46.87  E-value: 3.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  82 SCLVFCPSKKNCENVAEmickflskeylkhkekekcevikNLKNigngnLCPvlKRTIPFGVAYHHSGLTSDERKLLEEA 161
Cdd:cd18796   40 STLVFTNTRSQAERLAQ-----------------------RLRE-----LCP--DRVPPDFIALHHGSLSRELREEVEAA 89

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 663071126 162 YSTGVLCLFTCTSTLAAGVNLPA-RRVI-LRAPYVAKEFLKRnqykqmIGRAGR 213
Cdd:cd18796   90 LKRGDLKVVVATSSLELGIDIGDvDLVIqIGSPKSVARLLQR------LGRSGH 137
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 70-228 1.17e-05

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: 48.29  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  70 LVALVTEvipNYSCLVFCPSKKNCENVAEMICKFLSKEYLKHKekekceviknlknigngnlcpvlkrtipfgVAYHHSG 149
Cdd:COG1205  281 LADLVRE---GLRTLVFTRSRRGAELLARYARRALREPDLADR------------------------------VAAYRAG 327

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 150 LTSDERKLLEEAYSTG-VLCLFTcTSTLAAGVNLP---ArrVILRA-PYvakeflKRNQYKQMIGRAGRAGIDtiGESIL 224
Cdd:COG1205  328 YLPEERREIERGLRSGeLLGVVS-TNALELGIDIGgldA--VVLAGyPG------TRASFWQQAGRAGRRGQD--SLVVL 396


                 ....
gi 663071126 225 ILQE 228
Cdd:COG1205  397 VAGD 400
HHH_5 pfam14520
Helix-hairpin-helix domain;
516-569 2.43e-03

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 36.31  E-value: 2.43e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 663071126  516 LMEVTGVLEGRAKQLYSAGYKSLMHLANANPEVLVRTIDhLSRRQAKQIVSSAK 569
Cdd:pfam14520   4 LLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPG-IGEKTAQRIILELR 56
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 68-226 3.79e-03

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: 37.87  E-value: 3.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  68 DHLVALVTEVIPNYSCLVFCPSKKNCENVAEMICKFlskeylkhkeKEKCEVIknlknigngnlcpvlkrtipfgvayhH 147
Cdd:cd18787   15 LLLLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL----------GIKVAAL--------------------------H 58

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126 148 SGLTSDERKLLEEAYSTG-VLCLFtCTSTLAAGVNLPA-RRVI-LRAPYVAKEFLKRnqykqmIGRAGRAGidTIGESIL 224
Cdd:cd18787   59 GDLSQEERERALKKFRSGkVRVLV-ATDVAARGLDIPGvDHVInYDLPRDAEDYVHR------IGRTGRAG--RKGTAIT 129


                 ..
gi 663071126 225 IL 226
Cdd:cd18787  130 FV 131
SF2_C_Hrq cd18797
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...
 83-215 3.98e-03

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: 38.01  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663071126  83 CLVFCPSKKNCENVAEMIckflsKEYLKHKEkekceviknlknigngnlcPVLKRtipfgVAYHHSGLTSDERKLLEEAY 162
Cdd:cd18797   38 TIVFCRSRKLAELLLRYL-----KARLVEEG-------------------PLASK-----VASYRAGYLAEDRREIEAEL 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 663071126 163 STGVLCLFTCTSTLAAGVNLPARRVILRAPY---VAKeflkrnqYKQMIGRAGRAG 215
Cdd:cd18797   89 FNGELLGVVATNALELGIDIGGLDAVVLAGYpgsLAS-------LWQQAGRAGRRG 137
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 155-225 4.40e-03

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: 36.14  E-value: 4.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663071126 155 RKLLEEAYStgVLCLFTCTSTLAAGVNLP-ARRVILRAPYVAKeflkrNQYKQMIGRAGRAGiDTIGESILI 225
Cdd:cd18785   13 IEHAEEIAS--SLEILVATNVLGEGIDVPsLDTVIFFDPPSSA-----ASYIQRVGRAGRGG-KDEGEVILF 76
 
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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