|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
107-785 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 921.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 107 STPIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGY-TIISAVV 185
Cdd:COG1200 5 DTPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRRRRRrRILEVTL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 186 SDGFGQLLLKWFNQDYILQKLKRDREYLIHGLAKGTpFGPMEMNSPEIEEIQGEVP---REILPVYSLTSGISMKMMRKI 262
Cdd:COG1200 85 SDGTGSLTLVFFNQPYLKKQLKPGTRVLVSGKVERF-RGGLQMVHPEYELLDEEEAelaGRLTPVYPLTEGLSQKTLRKL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 263 VKRNLGLVRS-LDDLVPSSITIERGLLPRKHAFTAIHFPKSLYEISKAREALAYEEFFLFETTILFRRRQIRKEyQGLQK 341
Cdd:COG1200 164 IRQALDLLAPdLPEPLPEELRARYGLPSLAEALRNIHFPPSDEDLHPARRRLAFEELLALQLALLLRRARRRKR-KGPAL 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 342 EISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAM 421
Cdd:COG1200 243 PGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPTEILAE 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 422 QHYEKIKRELSPIGIETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLT 501
Cdd:COG1200 323 QHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVEQRLALR 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 502 AKGKLLDSLVMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILTRKRLKDLYSYISDELKMGHQAFFIYPLIEES 581
Cdd:COG1200 403 EKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIAKGRQAYVVCPLIEES 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 582 EQIDLKNATDEATRLReEVFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGM 661
Cdd:COG1200 483 EKLDLQAAEETYEELR-EAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIENAERFGL 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 662 AQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDR 741
Cdd:COG1200 562 SQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPDLRIADLVRDA 641
|
650 660 670 680
....*....|....*....|....*....|....*....|....
gi 1275696812 742 DLLFKAREDAKKLMEEDPELLEHGALRIEMERVYsERARLIEVG 785
Cdd:COG1200 642 DLLEAAREDAEELLEEDPELASHPALRRWLGLRF-RDEDYLEVG 684
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
107-779 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 879.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 107 STPIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGyTIISAVVS 186
Cdd:PRK10917 8 DAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVFGKR-RRLTVTVS 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 187 DGFGQLLLKWF--NQDYILQKLKRDREYLIHGLAKGTPFGpMEMNSPEIEEIQGE---VPREILPVYSLTSGISMKMMRK 261
Cdd:PRK10917 87 DGTGNLTLRFFnfNQPYLKKQLKVGKRVAVYGKVKRGKYG-LEMVHPEYEVLEEEspeLEGRLTPVYPLTEGLKQKTLRK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 262 IVKRNLGLVRSLDDLVPSSITIERGLLPRKHAFTAIHFPKSLYEISKAREALAYEEFFLFETTILFRRRQIRKEYQGLQK 341
Cdd:PRK10917 166 LIKQALELLDALPELLPEELLEKYGLLSLAEALRAIHFPPSDEDLHPARRRLKFEELFALQLSLLLLRAGRRSKKAGPLP 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 342 eISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAM 421
Cdd:PRK10917 246 -YDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAE 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 422 QHYEKIKRELSPIGIETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLT 501
Cdd:PRK10917 325 QHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 502 AKGKLLDSLVMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILTRKRLKDLYSYISDELKMGHQAFFIYPLIEES 581
Cdd:PRK10917 405 EKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEES 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 582 EQIDLKNATDEATRLREEvFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGM 661
Cdd:PRK10917 485 EKLDLQSAEETYEELQEA-FPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGL 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 662 AQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDR 741
Cdd:PRK10917 564 AQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRDE 643
|
650 660 670
....*....|....*....|....*....|....*...
gi 1275696812 742 DLLFKAREDAKKLMEEDPELLEHGALRIEMERVYSERA 779
Cdd:PRK10917 644 ELLEEARKDARELLERDPELAEALLERWLGERERYDKA 681
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
129-751 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 712.96 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 129 IETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGYTIISAVVSDGFGQLL-LKWFNQDYILQKLK 207
Cdd:TIGR00643 3 IHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLeLRFFNRAFLKKKFK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 208 RDREYLIHGLAKGTPFGPMEMNSP-EIEEIQGEVPREILPVYSLTSGISMKMMRKIVKRNLG-LVRSLDDLVPSSITIER 285
Cdd:TIGR00643 83 VGSKVVVYGKVKSSKFKAYLIHPEfISEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDqLDKSLEDPLPEELREKY 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 286 GLLPRKHAFTAIHFPKSLYEISKAREALAYEEFFLFETTILFRRRQIRKEYQGLQKEISGVLSKRLIESLPFELTKDQVT 365
Cdd:TIGR00643 163 GLLSLEDALRAIHFPKTLSLLELARRRLIFDEFFYLQLAMLARRLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKR 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 366 AFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSM 445
Cdd:TIGR00643 243 VVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 446 KKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKLL---DSLVMTATPIPRTLA 522
Cdd:TIGR00643 323 KGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGQGGftpHVLVMSATPIPRTLA 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 523 LTVYGDLDISTILTLPKGRSPVRTIILTRKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATRLReEVFP 602
Cdd:TIGR00643 403 LTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLK-KAFP 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVM 682
Cdd:TIGR00643 482 KYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLL 561
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1275696812 683 VMNKAISDDALSRLREFASTSSGFDVAELDLRLRGPGEFLGLRQHGMPQFLIGDIVNDRDLLFKAREDA 751
Cdd:TIGR00643 562 VYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAREDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
313-538 |
3.11e-115 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 347.98 E-value: 3.11e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 313 LAYEEFFLFETTILFRRRQIRKEyQGLQKEISGVLSKRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGK 392
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEEL-KGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 393 TLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALI 472
Cdd:cd17992 80 TVVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALI 159
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1275696812 473 QDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKLLDSLVMTATPIPRTLALTVYGDLDISTILTLP 538
Cdd:cd17992 160 QEDVEFHNLGLVIIDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
353-728 |
3.68e-107 |
|
transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273152 [Multi-domain] Cd Length: 926 Bit Score: 349.35 E-value: 3.68e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELS 432
Cdd:TIGR00580 446 DSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFA 525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 433 PIGIETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKLLDSLVM 512
Cdd:TIGR00580 526 NFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTL 605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 513 TATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIIL--TRKRLKDLysyISDELKMGHQAFFIYPLIEESEQIdlknat 590
Cdd:TIGR00580 606 SATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMeyDPELVREA---IRRELLRGGQVFYVHNRIESIEKL------ 676
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 591 deATRLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGR 670
Cdd:TIGR00580 677 --ATQLRELV-PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGR 753
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1275696812 671 VGRSNLKSICVMVM--NKAISDDALSRLR---EFASTSSGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:TIGR00580 754 VGRSKKKAYAYLLYphQKALTEDAQKRLEaiqEFSELGAGFKIALHDLEIRGAGNLLGEEQSG 816
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
109-270 |
3.89e-92 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 285.49 E-value: 3.89e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 109 PIKYAYSVGEARSKILKRMDIETIGDLIQYFPRDYEDRRIIMPISSIVPDQKVSVKGRLLNFSAKKASGYTIISAVVSDG 188
Cdd:pfam17191 1 PIKYAKGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETKKIGSLVIISAVLSDG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 189 FGQLLLKWFNQDYILQKLKRDREYLIHGLAKGTPFGPMEMNSPEIEEIQGEVPREILPVYSLTSGISMKMMRKIVKRNLG 268
Cdd:pfam17191 81 IGQVLLKWFNQEYIKKFLQKGKEVYITGTVKEGPFGPIEMNNPEIEEITGEQEREILPVYPLTEGISQKNMRKIVKENIS 160
|
..
gi 1275696812 269 LV 270
Cdd:pfam17191 161 YV 162
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
353-728 |
5.26e-92 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 312.00 E-value: 5.26e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTlvaELAM------VDNyeaGYQSALMVPTSVLAMQHYEK 426
Cdd:COG1197 581 AAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKT---EVALraafkaVMD---GKQVAVLVPTTLLAQQHYET 654
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 427 IKRELSPIGIETGLL----TgsmkKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTA 502
Cdd:COG1197 655 FKERFAGFPVRVEVLsrfrT----AKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHKEKLKA 730
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 503 KGKLLDSLVMTATPIPRTL--ALTvyGDLDISTILTLPKGRSPVRTIILTR--KRLKDLysyISDELKMGHQAFFIYPLI 578
Cdd:COG1197 731 LRANVDVLTLTATPIPRTLqmSLS--GIRDLSIIATPPEDRLPVKTFVGEYddALIREA---ILRELLRGGQVFYVHNRV 805
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 579 EESEQIdlknatdeATRLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPER 658
Cdd:COG1197 806 EDIEKV--------AARLQELV-PEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERADR 876
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1275696812 659 FGMAQLHQLRGRVGRSNLKSICVMVM--NKAISDDALSRL---REFASTSSGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:COG1197 877 FGLAQLYQLRGRVGRSHRRAYAYLLYppDKVLTEDAEKRLeaiQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSG 951
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
353-728 |
7.18e-72 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 255.44 E-value: 7.18e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 353 ESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELS 432
Cdd:PRK10689 595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA 674
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 433 --PIGIEtgLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKLLDSL 510
Cdd:PRK10689 675 nwPVRIE--MLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDIL 752
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 511 VMTATPIPRTLALTVYGDLDISTILTLPKGRSPVRTIILTRKRLKdLYSYISDELKMGHQAFFIYPlieeseqiDLKNAT 590
Cdd:PRK10689 753 TLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLV-VREAILREILRGGQVYYLYN--------DVENIQ 823
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 591 DEATRLrEEVFPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGR 670
Cdd:PRK10689 824 KAAERL-AELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGR 902
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1275696812 671 VGRSNLKSICVMVM--NKAISDDALSRLREFASTS---SGFDVAELDLRLRGPGEFLGLRQHG 728
Cdd:PRK10689 903 VGRSHHQAYAWLLTphPKAMTTDAQKRLEAIASLEdlgAGFALATHDLEIRGAGELLGEEQSG 965
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
349-536 |
8.72e-68 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 222.06 E-value: 8.72e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 349 KRLIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:cd17991 6 EEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 429 RELSPIGIETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKLLD 508
Cdd:cd17991 86 ERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKELRPNVD 165
|
170 180
....*....|....*....|....*...
gi 1275696812 509 SLVMTATPIPRTLALTVYGDLDISTILT 536
Cdd:cd17991 166 VLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
351-534 |
2.02e-65 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 215.36 E-value: 2.02e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 351 LIESLPFELTKDQVTAFEEIRDDMRAASPMNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRE 430
Cdd:cd17918 8 LCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKF 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 431 LSPIGIEtgLLTGSMKknEQDfvrmrlkKGEIDVVVGTHALIQDGVEFRNLGLVVVDEQHRFGVKQRETLTAKGKlLDSL 510
Cdd:cd17918 88 LPFINVE--LVTGGTK--AQI-------LSGISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA-THFL 155
|
170 180
....*....|....*....|....
gi 1275696812 511 VMTATPIPRTLALTVYGDLDISTI 534
Cdd:cd17918 156 EATATPIPRTLALALSGLLDLSVI 179
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
543-701 |
3.55e-63 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 208.74 E-value: 3.55e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 543 PVRTIILTRKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATRLREEVFPGVGVELLHGRLNDNEKQEIM 622
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1275696812 623 QRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVMNKAISDDALSRLREFAS 701
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
543-701 |
1.47e-56 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They 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: 350179 [Multi-domain] Cd Length: 160 Bit Score: 190.56 E-value: 1.47e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 543 PVRTIILTRKRLKDLYSYISDELKMGHQAFFIYPLIEESEQIDLKNATDEATRLREeVFPGVGVELLHGRLNDNEKQEIM 622
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKE-LVPEARVALLHGKMTEDEKEAVM 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 623 QRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVMN--KAISDDALSRLREFA 700
Cdd:cd18792 80 LEFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPdpKKLTETAKKRLRAIA 159
|
.
gi 1275696812 701 S 701
Cdd:cd18792 160 E 160
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
561-697 |
6.54e-31 |
|
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 118.60 E-value: 6.54e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 561 ISDELKMGHQAFFIYPLIEESEQIdlknatdeATRLREEVfPGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVE 640
Cdd:cd18810 18 IERELLRGGQVFYVHNRIESIEKL--------ATQLRQLV-PEARIAIAHGQMTENELEEVMLEFAKGEYDILVCTTIIE 88
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1275696812 641 VGIDIPTATVMVIEHPERFGMAQLHQLRGRVGRSNLKSICVMVM--NKAISDDALSRLR 697
Cdd:cd18810 89 SGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYpdQKKLTEDALKRLE 147
|
|
| RecG_N |
pfam17190 |
RecG N-terminal helical domain; This four helical bundle domain is found at the N-terminus of ... |
2-89 |
1.43e-29 |
|
RecG N-terminal helical domain; This four helical bundle domain is found at the N-terminus of bacterial RecG proteins.
Pssm-ID: 407315 Cd Length: 89 Bit Score: 112.50 E-value: 1.43e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 2 LLEQFLEECERLLEAHLSGKREDNVL-PELKRFLSLLDRSELSYFSSLGEYLSKFISYLSRVDEFPHDRKVKRLKNGLEM 80
Cdd:pfam17190 1 LLEEFLDECEQLLKKVLNGKLKTNELiEEIKDNLSLLDDPLLENEEGLKEKLGQFLEYYKPIANLPPERAIKRLKNGLEM 80
|
....*....
gi 1275696812 81 IAKLRIFFL 89
Cdd:pfam17190 81 IEKLRYWFL 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
351-541 |
2.04e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 107.19 E-value: 2.04e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 351 LIESLPFELTKDQVTAFEEIRDDMRaaspmNRLLQGDVGSGKTLVAELAMVDNY--EAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 429 RELSPIGIETGLLTGSMKKNEQdfvRMRLKKGEIDVVVGT-----HALIQDGVEFRNLGLVVVDEQHRFGVK-QRETLTA 502
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGgFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1275696812 503 KGKLLDS----LVMTATP---IPRTLALTVYGDLDISTILTLPKGR 541
Cdd:smart00487 153 LLKLLPKnvqlLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
360-522 |
1.88e-25 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 103.48 E-value: 1.88e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 360 TKDQVTAFEEIRddmraaSPMNRLLQGDVGSGKTLVAELAM---VDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGI 436
Cdd:pfam00270 1 TPIQAEAIPAIL------EGRDVLVQAPTGSGKTLAFLLPAleaLDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 437 ETGLLTGSMKKNEQdfvRMRLKKgeIDVVVGTH----ALIQDGVEFRNLGLVVVDEQHRFGVK-QRETLTAKGKLLDS-- 509
Cdd:pfam00270 75 KVASLLGGDSRKEQ---LEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMgFGPDLEEILRRLPKkr 149
|
170
....*....|....*
gi 1275696812 510 --LVMTATPiPRTLA 522
Cdd:pfam00270 150 qiLLLSATL-PRNLE 163
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
380-515 |
1.23e-19 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 85.92 E-value: 1.23e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 380 MNRLLQGDVGSGKTLVAELAMVDNY-EAGYQSALMVPTSVLAMQHYEKIKRELSPiGIETGLLTGSMKKNEqdfvRMRLK 458
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLlKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEE----REKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 459 KGEIDVVVGTHALIQ------DGVEFRNLGLVVVDEQHRFGVKQRETLT-------AKGKLLDSLVMTAT 515
Cdd:cd00046 77 LGDADIIIATPDMLLnlllreDRLFLKDLKLIIVDEAHALLIDSRGALIldlavrkAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
603-675 |
9.67e-17 |
|
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: 76.48 E-value: 9.67e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1275696812 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPErFGMAQLHQLRGRVGRSN 675
Cdd:pfam00271 38 GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
389-673 |
1.78e-16 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 83.41 E-value: 1.78e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGsmkkneqDFVRMRLKKGEIDVVVGT 468
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTG-------DYDSDDEWLGRYDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 469 ----HALIQDGVEF-RNLGLVVVDEQHRFGVKQR----ETLTAK-----------------------GKLLDSLVMTAT- 515
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlEVLLARlrrlnpeaqivalsatignaeeiAEWLDAELVKSDw 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 516 -PIPRTLAL------------TVYGDLDISTIL-TLPKGRSpvrTIIL--TRKRLKDLYSYISDELKMGHQAFFIYPLIE 579
Cdd:COG1204 201 rPVPLNEGVlydgvlrfddgsRRSKDPTLALALdLLEEGGQ---VLVFvsSRRDAESLAKKLADELKRRLTPEEREELEE 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 580 ESEQI-DLKNATDEATRLREEVFPGVGVEllHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVIEHPER 658
Cdd:COG1204 278 LAEELlEVSEETHTNEKLADCLEKGVAFH--HAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRV-IIRDTKR 354
|
330 340
....*....|....*....|
gi 1275696812 659 FGMAQL-----HQLRGRVGR 673
Cdd:COG1204 355 GGMVPIpvlefKQMAGRAGR 374
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
603-673 |
2.11e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 2.11e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1275696812 603 GVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVIEHPeRFGMAQLHQLRGRVGR 673
Cdd:smart00490 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
279-653 |
6.29e-14 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 75.45 E-value: 6.29e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 279 SSITIERGLLPRKHAFTAIHFPKSLYEISKAREALAYEEFFLFETTILFRRRQIRKEYQGLQKEISGVLSKRLIESLPFE 358
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 359 LTKDQVTAFEEIRDDMRAASPMNrLLQGDVGSGKTLVAELAMVDNYEAgyQSAL-MVPTSVLAMQHYEKIKRELSPIGIE 437
Cdd:COG1061 81 LRPYQQEALEALLAALERGGGRG-LVVAPTGTGKTVLALALAAELLRG--KRVLvLVPRRELLEQWAEELRRFLGDPLAG 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 438 TGlltgsmkKNEQDFvrmrlkkgeiDVVVGTHALIQDGVEFRNL----GLVVVDEQHRFGVKQ-RETLTA-KGKLLdsLV 511
Cdd:COG1061 158 GG-------KKDSDA----------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSyRRILEAfPAAYR--LG 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 512 MTATPI---PRTLALTVYGDL---------------------DISTILTLPKGRSPV------RTIILTRKRLKDLYSYI 561
Cdd:COG1061 219 LTATPFrsdGREILLFLFDGIvyeyslkeaiedgylappeyyGIRVDLTDERAEYDAlserlrEALAADAERKDKILREL 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 562 SDELKMGHQAFFIYPLIEESEQIdlknatdeATRLREEvfpGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEV 641
Cdd:COG1061 299 LREHPDDRKTLVFCSSVDHAEAL--------AELLNEA---GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNE 367
|
410
....*....|..
gi 1275696812 642 GIDIPTATVMVI 653
Cdd:COG1061 368 GVDVPRLDVAIL 379
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
351-673 |
1.60e-12 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 71.07 E-value: 1.60e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 351 LIESLPFELTKDQVTAFEEIRDDMraaspmNRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRe 430
Cdd:PRK01172 15 LFTGNDFELYDHQRMAIEQLRKGE------NVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAMEKYEELSR- 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 431 LSPIGIETGLLTGSMkKNEQDFVRmrlkkgEIDVVVGTHA-----LIQDGVEFRNLGLVVVDEQHRFGVKQRetltakGK 505
Cdd:PRK01172 88 LRSLGMRVKISIGDY-DDPPDFIK------RYDVVILTSEkadslIHHDPYIINDVGLIVADEIHIIGDEDR------GP 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 506 LLDSLVMTA---TPIPRTLAL--TVYGDLDISTILTLPKGRS-----PVRTIILTRKRL---------KDLYSYISDELK 566
Cdd:PRK01172 155 TLETVLSSAryvNPDARILALsaTVSNANELAQWLNASLIKSnfrpvPLKLGILYRKRLildgyersqVDINSLIKETVN 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 567 MGHQAFFIYPLIEESEQI------------DLKNATDEATRLRE---EVFPGvGVELLHGRLNDNEKQEIMQRFRSRQSM 631
Cdd:PRK01172 235 DGGQVLVFVSSRKNAEDYaemliqhfpefnDFKVSSENNNVYDDslnEMLPH-GVAFHHAGLSNEQRRFIEEMFRNRYIK 313
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|
gi 1275696812 632 ILVSTTVVEVGIDIPtATVMVIEHPERFGMA--------QLHQLRGRVGR 673
Cdd:PRK01172 314 VIVATPTLAAGVNLP-ARLVIVRDITRYGNGgirylsnmEIKQMIGRAGR 362
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
483-674 |
5.80e-12 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 68.75 E-value: 5.80e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 483 LVVVDE----------QHRFGVKQreTLTAKGKLLdslVMTATPiPRTL-ALTVYGDLDISTILTLPKGRS-PV-RTII- 548
Cdd:COG4098 219 LLIIDEvdafpysgdpMLQYAVKR--ARKPDGKLI---YLTATP-SKALqRQVKRGKLKVVKLPARYHGHPlPVpKFKWl 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 549 ------LTRKRLKD-LYSYISDELKMGHQAFFIYPLIEESEQidlknatdeATRLREEVFPGVGVELLHGRlnDNEKQEI 621
Cdd:COG4098 293 gnwkkrLRRGKLPRkLLKWLKKRLKEGRQLLIFVPTIELLEQ---------LVALLQKLFPEERIAGVHAE--DPERKEK 361
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1275696812 622 MQRFRSRQSMILVSTTVVEVGIDIPTATVMVI--EHPeRFGMAQLHQLRGRVGRS 674
Cdd:COG4098 362 VQAFRDGEIPILVTTTILERGVTFPNVDVAVLgaDHP-VFTEAALVQIAGRVGRS 415
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
389-497 |
1.33e-11 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 63.82 E-value: 1.33e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNeqdfvrmRLKKGEIDVVVG 467
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVN-------KLLLAEADILVA 99
|
90 100 110
....*....|....*....|....*....|....*.
gi 1275696812 468 T----HALIQDGVE--FRNLGLVVVDEQHRFGVKQR 497
Cdd:cd17921 100 TpeklDLLLRNGGErlIQDVRLVVVDEAHLIGDGER 135
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
702-761 |
2.19e-11 |
|
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 60.56 E-value: 2.19e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1275696812 702 TSSGFDVAELDLRLRGPGEFLGLRQHGMPQFL-IGDIVNDRDLLFKAREDAKKLMEEDPEL 761
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAFDLkIADIARDGQLLQLARTEAEEIIDNDPEC 61
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
381-507 |
5.03e-11 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 62.35 E-value: 5.03e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 381 NRLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKReLSPIGIETGLLTGsmkkneqDFVRMRLKKG 460
Cdd:cd18028 19 NLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-LEEIGLKVGISTG-------DYDEDDEWLG 90
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 1275696812 461 EIDVVVGTH----ALIQDGVEF-RNLGLVVVDEQHRFGVKQR----ETLTAKGKLL 507
Cdd:cd18028 91 DYDIIVATYekfdSLLRHSPSWlRDVGVVVVDEIHLISDEERgptlESIVARLRRL 146
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
363-516 |
2.07e-10 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 60.30 E-value: 2.07e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 363 QVTAFEEIRDDMRAASPMnrLLQGDVGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRElspIGIETGLLT 442
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKR---FGDKVAVLH 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 443 GSMKKNEQDFVRMRLKKGEIDVVVGTH-ALIqdgVEFRNLGLVVVDEQHRFGVKQ--------RETLTAKGKLLD-SLVM 512
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEHDSSYKQdsgpryhaRDVAIYRAKLENaPVVL 152
|
....*
gi 1275696812 513 -TATP 516
Cdd:cd17929 153 gSATP 157
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
383-673 |
1.77e-08 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 57.46 E-value: 1.77e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 383 LLQG-DV------GSGKT---LVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNEQd 451
Cdd:COG0513 36 ILAGrDVlgqaqtGTGKTaafLLPLLQRLDPSRPRAPQALiLAPTRELALQVAEELRKLAKYLGLRVATVYGGVSIGRQ- 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 452 fvRMRLKKGeIDVVVGT----HALIQDG-VEFRNLGLVVVDEqhrfgvkqretltAkgkllDslvmtatpipRTLaltvy 526
Cdd:COG0513 115 --IRALKRG-VDIVVATpgrlLDLIERGaLDLSGVETLVLDE-------------A-----D----------RML----- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 527 gDL----DISTILT-LPKGR----------SPVRTiiLTRKRLKD--LYSYISDEL---KMGHQAFFIYP---------L 577
Cdd:COG0513 159 -DMgfieDIERILKlLPKERqtllfsatmpPEIRK--LAKRYLKNpvRIEVAPENAtaeTIEQRYYLVDKrdklellrrL 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 578 IEEsEQIDL-------KNATDE-ATRLREEvfpGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTAT 649
Cdd:COG0513 236 LRD-EDPERaivfcntKRGADRlAEKLQKR---GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVS 311
|
330 340 350
....*....|....*....|....*....|
gi 1275696812 650 vMVI-----EHPERFgmaqLHqlR-GRVGR 673
Cdd:COG0513 312 -HVInydlpEDPEDY----VH--RiGRTGR 334
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
363-490 |
2.05e-08 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 54.97 E-value: 2.05e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 363 QVTAFEEIRDDmraaspmNRLLQGDVGSGKTLVAELAM----VDNYEAGY---QSALMVPTSVLAMQHYEKIKRELspiG 435
Cdd:cd18034 7 QLELFEAALKR-------NTIVVLPTGSGKTLIAVMLIkemgELNRKEKNpkkRAVFLVPTVPLVAQQAEAIRSHT---D 76
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 436 IETGLLTGSMKKNEQDFVRMRLKKGEIDVVVGT-----HALIQDGVEFRNLGLVVVDEQH 490
Cdd:cd18034 77 LKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTaqillDALRHGFLSLSDINLLIFDECH 136
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
389-645 |
3.62e-07 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 53.55 E-value: 3.62e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQS----ALmvPTSVLAMQHYEKIKRELSP-IGIETGLLTGSMKKNEQDF------VRMRL 457
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGRriiyAL--PFTSIINQTYDRLRDLFGEdVLLHHSLADLDLLEEEEEYesearwLKLLK 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 458 KKGEIDVVVGT--HALiqDGVEFRN-------LGL----VVVDEQHRFGVkqrETLTAKGKLLDSL--------VMTATp 516
Cdd:COG1203 235 ELWDAPVVVTTidQLF--ESLFSNRkgqerrlHNLansvIILDEVQAYPP---YMLALLLRLLEWLknlggsviLMTAT- 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 517 IPrtlALTVYGDLDISTILTLPKGRSPVRTIILTRKRLK---------DLYSYISDELKMGHQAFFIYPLIEESEQIdlk 587
Cdd:COG1203 309 LP---PLLREELLEAYELIPDEPEELPEYFRAFVRKRVElkegplsdeELAELILEALHKGKSVLVIVNTVKDAQEL--- 382
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1275696812 588 natdeATRLREEvFPGVGVELLHGRLNDNEK----QEIMQRFRSRQSMILVSTTVVEVGIDI 645
Cdd:COG1203 383 -----YEALKEK-LPDEEVYLLHSRFCPADRseieKEIKERLERGKPCILVSTQVVEAGVDI 438
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
383-488 |
6.15e-07 |
|
DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 50.52 E-value: 6.15e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 383 LLQG-DV------GSGKTL------VAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKN 448
Cdd:cd00268 24 ILSGrDVigqaqtGSGKTLafllpiLEKLLPEPKKKGRGPQALvLAPTRELAMQIAEVARKLGKGTGLKVAAIYGGAPIK 103
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1275696812 449 EQdfvRMRLKKGeIDVVVGT----HALIQDG-VEFRNLGLVVVDE 488
Cdd:cd00268 104 KQ---IEALKKG-PDIVVGTpgrlLDLIERGkLDLSNVKYLVLDE 144
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
356-516 |
6.17e-07 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 52.85 E-value: 6.17e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 356 PFELTKDQVTAFEEIRDDMR-AASpmnrLLQGDVGSGKT-----LVAE-LAmvdnyeAGYQSALMVPTSVLAMQHYEKIK 428
Cdd:PRK05580 142 PPTLNPEQAAAVEAIRAAAGfSPF----LLDGVTGSGKTevylqAIAEvLA------QGKQALVLVPEIALTPQMLARFR 211
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 429 REL-SPIGIETGLLTGSMKKNeqdfVRMRLKKGEIDVVVGTH-ALIqdgVEFRNLGLVVVDEQHRFGVKQRETLT----- 501
Cdd:PRK05580 212 ARFgAPVAVLHSGLSDGERLD----EWRKAKRGEAKVVIGARsALF---LPFKNLGLIIVDEEHDSSYKQQEGPRyhard 284
|
170 180
....*....|....*....|
gi 1275696812 502 ---AKGKLLDS-LVM-TATP 516
Cdd:PRK05580 285 lavVRAKLENIpVVLgSATP 304
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
308-490 |
6.99e-07 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 52.81 E-value: 6.99e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 308 KAREALAYeeffLFETTILFRRRQIRKEY-------QGLQKEisGVLSKRLIESL------------PFELTKDQVTAFE 368
Cdd:COG1198 132 KQRRVLEA----LREHGGPLTLSELAKEAgvsrsvlKALVKK--GLLEIEEREVDrdpfapdvpaepPPTLNEEQQAAVE 205
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 369 EIRDDMRAASPMnrLLQGDVGSGKT-----LVAE-LAmvdnyeAGYQSALMVPTSVLAMQHYEKIKRELspiGIETGLLT 442
Cdd:COG1198 206 AIRAAAGGFSVF--LLHGVTGSGKTevylqAIAEvLA------QGKQALVLVPEIALTPQTVERFRARF---GARVAVLH 274
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1275696812 443 GSMKKNEQDFVRMRLKKGEIDVVVGTH-ALIqdgVEFRNLGLVVVDEQH 490
Cdd:COG1198 275 SGLSDGERLDEWRRARRGEARIVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
390-490 |
8.20e-07 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 52.59 E-value: 8.20e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 390 SGKTLVAELAMVDNYEAGYQSAL-MVPTSVLAMQHYEKIKRELSPiGIETGLLTGSmkkneqdfVRMRLKKGE----IDV 464
Cdd:COG1202 236 TGKTLIGELAGIKNALEGKGKMLfLVPLVALANQKYEDFKDRYGD-GLDVSIRVGA--------SRIRDDGTRfdpnADI 306
|
90 100 110
....*....|....*....|....*....|
gi 1275696812 465 VVGTHA----LIQDGVEFRNLGLVVVDEQH 490
Cdd:COG1202 307 IVGTYEgidhALRTGRDLGDIGTVVIDEVH 336
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
163-234 |
8.73e-07 |
|
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.
Pssm-ID: 239934 [Multi-domain] Cd Length: 75 Bit Score: 47.19 E-value: 8.73e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1275696812 163 VKGRLLNFSAKKASGYTIISAVVSDGFGQLLLKWFN-QDYILQKLKRDREYLIHGLAKGTPFGPmEMNSPEIE 234
Cdd:cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNfQPYLKKQLPPGTRVRVSGKVKRFRGGL-QIVHPEYE 73
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
390-490 |
1.08e-06 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 52.27 E-value: 1.08e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 390 SGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKReLSPIGIETGLLTGsmkkneqDFVRMRLKKGEIDVVVGTH 469
Cdd:PRK02362 50 SGKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEFER-FEELGVRVGISTG-------DYDSRDEWLGDNDIIVATS 121
|
90 100
....*....|....*....|....*.
gi 1275696812 470 ----ALIQDGVEF-RNLGLVVVDEQH 490
Cdd:PRK02362 122 ekvdSLLRNGAPWlDDITCVVVDEVH 147
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
632-673 |
3.42e-06 |
|
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: 45.39 E-value: 3.42e-06
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1275696812 632 ILVSTTVVEVGIDIPTATVMVIEHPERFgMAQLHQLRGRVGR 673
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGR 65
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
381-673 |
5.24e-06 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 50.20 E-value: 5.24e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 381 NRLLQGDVGSGKTLVAELAMVDN-YEAGYQSALMVPTSVLAMQHYEKIKrELSPIGIETGLLTGSMKKNEQDFvrmrlkk 459
Cdd:PRK00254 41 NLVLAIPTASGKTLVAEIVMVNKlLREGGKAVYLVPLKALAEEKYREFK-DWEKLGLRVAMTTGDYDSTDEWL------- 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 460 GEIDVVVGT----HALIQDGVEF-RNLGLVVVDEQHRFGVKQRetltakGKLLDSLVMTATPIPRTLAL--TVYGDLDIS 532
Cdd:PRK00254 113 GKYDIIIATaekfDSLLRHGSSWiKDVKLVVADEIHLIGSYDR------GATLEMILTHMLGRAQILGLsaTVGNAEELA 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 533 TILTLPKGRSPVRTIILTR----------------KRLKDLYSYISDELKMGHQAFF------------------IYPLI 578
Cdd:PRK00254 187 EWLNAELVVSDWRPVKLRKgvfyqgflfwedgkieRFPNSWESLVYDAVKKGKGALVfvntrrsaekealelakkIKRFL 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 579 EESEQIDLKNATD--EATRLREEVFPGV--GVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMV-- 652
Cdd:PRK00254 267 TKPELRALKELADslEENPTNEKLKKALrgGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIrd 346
|
330 340
....*....|....*....|....*.
gi 1275696812 653 IEHPERFGMA-----QLHQLRGRVGR 673
Cdd:PRK00254 347 TKRYSNFGWEdipvlEIQQMMGRAGR 372
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
382-540 |
6.04e-06 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 47.71 E-value: 6.04e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 382 RLLQGD-------VGSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLT--GSMKKNEQDF 452
Cdd:cd17924 28 RLLRGKsfaiiapTGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILVyhSRLKKKEKEE 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 453 VRMRLKKGEIDVVVGTHALIQDGVEF---RNLGLVVVDEqhrfgvkqretltakgklLDSLVMTATPIPRTLALTVYGDL 529
Cdd:cd17924 108 LLEKIEKGDFDILVTTNQFLSKNFDLlsnKKFDFVFVDD------------------VDAVLKSSKNIDRLLKLLGFGQL 169
|
170
....*....|.
gi 1275696812 530 DISTILTLPKG 540
Cdd:cd17924 170 VVSSATGRPRG 180
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
587-673 |
8.92e-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: 45.96 E-value: 8.92e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 587 KNATDE-ATRLREEvfpGVGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVI-----EHPERFg 660
Cdd:cd18787 37 KKRVDRlAELLEEL---GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDH-VInydlpRDAEDY- 111
|
90
....*....|....
gi 1275696812 661 maqLHqlR-GRVGR 673
Cdd:cd18787 112 ---VH--RiGRTGR 120
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
337-693 |
1.50e-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: 48.68 E-value: 1.50e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 337 QGLQKEISGVLSKRLIEslpfELTKDQVTAFEEIRD--DMRAASPmnrllqgdVGSGKTLVAELAMVDNYEAGYQS-ALM 413
Cdd:COG1205 39 DWLPPELRAALKKRGIE----RLYSHQAEAIEAARAgkNVVIATP--------TASGKSLAYLLPVLEALLEDPGAtALY 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 414 V-PTSVLAMQHYEKIKR--ELSPIGIETGLLTGSMKKNEQDFVRmrlKKGeiDVVVGT----HALIQDGVE-----FRNL 481
Cdd:COG1205 107 LyPTKALARDQLRRLRElaEALGLGVRVATYDGDTPPEERRWIR---EHP--DIVLTNpdmlHYGLLPHHTrwarfFRNL 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 482 GLVVVDEQHR----FG--VKQretltakgkLLDSL--------------VMTATpI--PRTLALTVYG------DLDISt 533
Cdd:COG1205 182 RYVVIDEAHTyrgvFGshVAN---------VLRRLrricrhygsdpqfiLASAT-IgnPAEHAERLTGrpvtvvDEDGS- 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 534 iltlPKGRspvRTIILTRKRLKDLYSY----------ISDELKMGHQ--AFFiyplieES----EQIdlknatdeATRLR 597
Cdd:COG1205 251 ----PRGE---RTFVLWNPPLVDDGIRrsalaeaarlLADLVREGLRtlVFT------RSrrgaELL--------ARYAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 598 EEVF-PGVGVELL--HGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPT--ATVMViehperfG----MAQLHQLR 668
Cdd:COG1205 310 RALRePDLADRVAayRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGldAVVLA-------GypgtRASFWQQA 382
|
410 420
....*....|....*....|....*
gi 1275696812 669 GRVGRSNLKSICVMVMnkaiSDDAL 693
Cdd:COG1205 383 GRAGRRGQDSLVVLVA----GDDPL 403
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
389-516 |
1.60e-05 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 45.37 E-value: 1.60e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGyqSALMVPTSVLAMQHYEKIKRELSPIGIetGLLTGSMKKneqdfvrmrlKKGEIDVVVGT 468
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFEDFLGDSSI--GLIGGGKKK----------DFDDANVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1275696812 469 -HALIQDGVEFRNL----GLVVVDEQHRFGVKQ-RETLT-AKGKLLdsLVMTATP 516
Cdd:cd17926 94 yQSLSNLAEEEKDLfdqfGLLIVDEAHHLPAKTfSEILKeLNAKYR--LGLTATP 146
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
611-683 |
2.17e-05 |
|
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: 44.94 E-value: 2.17e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1275696812 611 GRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPT--ATVMViEHPerFGMAQLHQLRGRVGRSNLKSICVMV 683
Cdd:cd18797 74 AGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGldAVVLA-GYP--GSLASLWQQAGRAGRRGKDSLVILV 145
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
389-503 |
2.48e-05 |
|
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region.
Pssm-ID: 350784 [Multi-domain] Cd Length: 202 Bit Score: 46.05 E-value: 2.48e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQSALMVPTSVLAMQhyEKIkRELSPIGIETGLLTGSMKKNEQDFVRMRlkKGEIDVVVGT 468
Cdd:cd18026 43 SGGKTLVAEILMLKRLLERRKKALFVLPYVSIVQ--EKV-DALSPLFEELGFRVEGYAGNKGRSPPKR--RKSLSVAVCT 117
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1275696812 469 ----HALIQDGVEFR---NLGLVVVDEQHRFGVKQR----ETLTAK 503
Cdd:cd18026 118 iekaNSLVNSLIEEGrldELGLVVVDELHMLGDGHRgallELLLTK 163
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
389-516 |
2.61e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 47.80 E-value: 2.61e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQSALMV-PTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNEqdfvRMRLKKgEIDVVVG 467
Cdd:COG1111 27 GLGKTAVALLVIAERLHKKGGKVLFLaPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEK----RKELWE-KARIIVA 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1275696812 468 T-----HALIQDGVEFRNLGLVVVDEQHR-------FGVKQRETLTAKGKLldSLVMTATP 516
Cdd:COG1111 102 TpqvieNDLIAGRIDLDDVSLLIFDEAHRavgnyayVYIAERYHEDAKDPL--ILGMTASP 160
|
|
| tRNA_anti-codon |
pfam01336 |
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ... |
161-236 |
9.94e-05 |
|
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Pssm-ID: 460164 [Multi-domain] Cd Length: 75 Bit Score: 41.07 E-value: 9.94e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1275696812 161 VSVKGRLLNfsaKKASGYTIISAVVSDGFGQLLLKWFNQDY--ILQKLKRDREYLIHGLAKGTPFGPMEMNSPEIEEI 236
Cdd:pfam01336 1 VTVAGRVTS---IRRSGGKLLFLTLRDGTGSIQVVVFKEEAekLAKKLKEGDVVRVTGKVKKRKGGELELVVEEIELL 75
|
|
| DEADc_DDX23 |
cd17945 |
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ... |
389-491 |
2.51e-04 |
|
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350703 [Multi-domain] Cd Length: 220 Bit Score: 43.08 E-value: 2.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTL---------VAELAMVDNY--EAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNEQDFvrmRL 457
Cdd:cd17945 37 GSGKTAaflipllvyISRLPPLDEEtkDDGPYALILAPTRELAQQIEEETQKFAKPLGIRVVSIVGGHSIEEQAF---SL 113
|
90 100 110
....*....|....*....|....*....|....*....
gi 1275696812 458 KKGeIDVVVGTHALIQDGVEFRNLGL-----VVVDEQHR 491
Cdd:cd17945 114 RNG-CEILIATPGRLLDCLERRLLVLnqctyVVLDEADR 151
|
|
| DEADc_DDX1 |
cd17938 |
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
386-492 |
5.89e-04 |
|
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350696 [Multi-domain] Cd Length: 204 Bit Score: 41.92 E-value: 5.89e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 386 GDV------GSGKTLVAELAMVDNYeagyQSALMVPTSVLAMQHYEKI---KRELSPIGIETGLLTGSMKKNEQdfvrMR 456
Cdd:cd17938 37 GDVlmaaetGSGKTGAFCLPVLQIV----VALILEPSRELAEQTYNCIenfKKYLDNPKLRVALLIGGVKAREQ----LK 108
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1275696812 457 LKKGEIDVVVGT----HALIQDG-VEFRNLGLVVVDEQHRF 492
Cdd:cd17938 109 RLESGVDIVVGTpgrlEDLIKTGkLDLSSVRFFVLDEADRL 149
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
389-524 |
9.90e-04 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 41.26 E-value: 9.90e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAM---VDNYEAGYQS--ALMVPTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNeqdfVRMRLKKGEID 463
Cdd:cd17927 27 GSGKTFVAVLICehhLKKFPAGRKGkvVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSEN----VSVEQIVESSD 102
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1275696812 464 VVVGTHALIQD------GVEFRNLGLVVVDEQHRfGVKQRETLTAKGKLLDSLVMTATPIPRTLALT 524
Cdd:cd17927 103 VIIVTPQILVNdlksgtIVSLSDFSLLVFDECHN-TTKNHPYNEIMFRYLDQKLGSSGPLPQILGLT 168
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
389-443 |
1.06e-03 |
|
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350781 [Multi-domain] Cd Length: 206 Bit Score: 41.19 E-value: 1.06e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1275696812 389 GSGKTLVAELAMV-------DNYEAGYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLTG 443
Cdd:cd18023 27 GSGKTVLFELAILrllkernPLPWGNRKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTG 88
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
613-684 |
1.13e-03 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 39.88 E-value: 1.13e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1275696812 613 LNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMViehpeRFG----MAQLHQLRGRVGRSNlkSICVMVM 684
Cdd:cd18802 74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDlpktLRSYIQSRGRARAPN--SKYILMV 142
|
|
| DEADc_DDX24 |
cd17946 |
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ... |
389-491 |
2.34e-03 |
|
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
Pssm-ID: 350704 [Multi-domain] Cd Length: 235 Bit Score: 40.30 E-value: 2.34e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMV-----------DNYEAGYQSALMV-PTSVLAMQHYEKIKRELSPIGIETGLLTGSMKKNEQDfvRMR 456
Cdd:cd17946 38 GSGKTLAFGIPILerllsqkssngVGGKQKPLRALILtPTRELAVQVKDHLKAIAKYTNIKIASIVGGLAVQKQE--RLL 115
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1275696812 457 LKKGEIdvVVGTH----ALIQDG----VEFRNLGLVVVDEQHR 491
Cdd:cd17946 116 KKRPEI--VVATPgrlwELIQEGnehlANLKSLRFLVLDEADR 156
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
483-679 |
2.39e-03 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 40.88 E-value: 2.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 483 LVVVDEQHRFGVKQRETLTAKGKLLDS-----LVMTATpIP---RTLALTVygDLDISTILTLPKGRSPVRTIILTRKRL 554
Cdd:cd09639 126 LLIFDEVHFYDEYTLALILAVLEVLKDndvpiLLMSAT-LPkflKEYAEKI--GYVEENEPLDLKPNERAPFIKIESDKV 202
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 555 KDLYSY--ISDELKMGHQAFFIYPLIEESEQIDLknatdeatRLREEVfPGVGVELLHGR--LNDNEKQE--IMQRFRSR 628
Cdd:cd09639 203 GEISSLerLLEFIKKGGSVAIIVNTVDRAQEFYQ--------QLKEKG-PEEEIMLIHSRftEKDRAKKEaeLLLEFKKS 273
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1275696812 629 QSMILVSTTVVEVGIDIpTATVMVIEHperfgmAQLHQLRGRVGRSNLKSI 679
Cdd:cd09639 274 EKFVIVATQVIEASLDI-SVDVMITEL------APIDSLIQRLGRLHRYGE 317
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
605-653 |
2.47e-03 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 39.15 E-value: 2.47e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1275696812 605 GVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVMVI 653
Cdd:cd18789 70 LKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
305-518 |
2.64e-03 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 41.36 E-value: 2.64e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 305 EISKAREALAYEEFFLFETTILFRRRQIRKEYQGLQKEISGVLskrliesLPFeltkdQVTAFEEIRDDMRAAspMNRLL 384
Cdd:COG0553 200 ELLLLLELLLELELLAEAAVDAFRLRRLREALESLPAGLKATL-------RPY-----QLEGAAWLLFLRRLG--LGGLL 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 385 QGDVGSGKTLVAELAMVDNYEAGYQS-ALMV-PTSVLamqhyEKIKRELS---PiGIETGLLTGSMKkneqdfvRMRLKK 459
Cdd:COG0553 266 ADDMGLGKTIQALALLLELKERGLARpVLIVaPTSLV-----GNWQRELAkfaP-GLRVLVLDGTRE-------RAKGAN 332
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1275696812 460 --GEIDVVVGTHALIQDGVEF---RNLGLVVVDEQHRfgVKQRETLTAK-GKLLDS---LVMTATPIP 518
Cdd:COG0553 333 pfEDADLVITSYGLLRRDIELlaaVDWDLVILDEAQH--IKNPATKRAKaVRALKArhrLALTGTPVE 398
|
|
| DEADc_DDX54 |
cd17959 |
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ... |
375-522 |
4.53e-03 |
|
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350717 [Multi-domain] Cd Length: 205 Bit Score: 39.21 E-value: 4.53e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 375 RAASPMnrLLQG-DV------GSGKTLVAELAMVDNYEA-----GYQSALMVPTSVLAMQHYEKIKRELSPIGIETGLLT 442
Cdd:cd17959 29 RKTIPL--ILDGrDVvamartGSGKTAAFLIPMIEKLKAhsptvGARALILSPTRELALQTLKVTKELGKFTDLRTALLV 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 443 G--SMkknEQDFVRMrlkKGEIDVVVGT-----HALIQDGVEFRNLGLVVVDEQHR-----FGVKQRETLTAKGKLLDSL 510
Cdd:cd17959 107 GgdSL---EEQFEAL---ASNPDIIIATpgrllHLLVEMNLKLSSVEYVVFDEADRlfemgFAEQLHEILSRLPENRQTL 180
|
170
....*....|..
gi 1275696812 511 VMTATpIPRTLA 522
Cdd:cd17959 181 LFSAT-LPKLLV 191
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
385-698 |
4.57e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 40.19 E-value: 4.57e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 385 QGDVGSGKT---LVAELAMVDNYEAGYQSALMVPTSVLAMQhyekIKRELSPIGIETGL-----LTGSMKKNEQDfvrmR 456
Cdd:PTZ00424 71 QAQSGTGKTatfVIAALQLIDYDLNACQALILAPTRELAQQ----IQKVVLALGDYLKVrchacVGGTVVRDDIN----K 142
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 457 LKKGeIDVVVGTHALIQDGVEFRNLGlvvVDEQHRFGVKQRETLTAKGkLLDSLVMTATPIPRTLALTVYGDLDISTILT 536
Cdd:PTZ00424 143 LKAG-VHMVVGTPGRVYDMIDKRHLR---VDDLKLFILDEADEMLSRG-FKGQIYDVFKKLPPDVQVALFSATMPNEILE 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 537 LPKG--RSPVRTII----LTRKRLKDLYSYI-SDELKMgHQAFFIYPLIEESEQIDLKNATDEATRLREEVFPG-VGVEL 608
Cdd:PTZ00424 218 LTTKfmRDPKRILVkkdeLTLEGIRQFYVAVeKEEWKF-DTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERdFTVSC 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 609 LHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATvMVIEH-----PERFgmaqLHQLrGRVGRSNLKSICVmv 683
Cdd:PTZ00424 297 MHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVS-LVINYdlpasPENY----IHRI-GRSGRFGRKGVAI-- 368
|
330
....*....|....*
gi 1275696812 684 mnKAISDDALSRLRE 698
Cdd:PTZ00424 369 --NFVTPDDIEQLKE 381
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
357-517 |
6.30e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 38.04 E-value: 6.30e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 357 FELTKDQVTAFEEIRDdMRAASPMNRLLQGDVGSGKTLVAeLAMVDNY--EAGYQSALM-VPTSVLAMQHYEKIKRELSP 433
Cdd:pfam04851 2 LELRPYQIEAIENLLE-SIKNGQKRGLIVMATGSGKTLTA-AKLIARLfkKGPIKKVLFlVPRKDLLEQALEEFKKFLPN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 434 IGIETGLLTGsmkkNEQDFvrmrlKKGEIDVVVGT-HALIQDGVEFRNL------GLVVVDEQHRFGVKQRETLTAKGK- 505
Cdd:pfam04851 80 YVEIGEIISG----DKKDE-----SVDDNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGASSYRNILEYFKp 150
|
170
....*....|....
gi 1275696812 506 --LLDslvMTATPI 517
Cdd:pfam04851 151 afLLG---LTATPE 161
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
604-673 |
7.42e-03 |
|
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: 37.92 E-value: 7.42e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1275696812 604 VGVELLHGRLNDNEKQEIMQRFRSRQSMILVSTTVVEVGIDIPTATVmVIEHPERFG--------MAQLHQLRGRVGR 673
Cdd:cd18795 64 AGIAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNLPARTV-IIKGTQRYDgkgyrelsPLEYLQMIGRAGR 140
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
389-491 |
8.08e-03 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 38.26 E-value: 8.08e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275696812 389 GSGKTLVAELAMVDNYEAGYQSALMV-PTSVLAMQHYEKIKRELSpIGIETGLLTGSMKKNEQDfvrMRLKKGEIDVV-- 465
Cdd:cd18035 26 GLGKTIIAILVAADRLTKKGGKVLILaPSRPLVEQHAENLKRVLN-IPDKITSLTGEVKPEERA---ERWDASKIIVAtp 101
|
90 100
....*....|....*....|....*..
gi 1275696812 466 -VGTHALIQDGVEFRNLGLVVVDEQHR 491
Cdd:cd18035 102 qVIENDLLAGRITLDDVSLLIFDEAHH 128
|
|
| |
