|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
100-774 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 982.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 100 MPLATDIKFIKGVGNKRAKILREFGINSIEDTFYFFPRDYEDRREIKRIIDCYHGQNCLVVGNIVNFEEKNI-GSLRILS 178
Cdd:COG1200 2 APLDTPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRTRLTPIAELRPGETVTVEGTVVSVEVVRRrRRRRILE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 179 YALEDKDGSvLILTWFNQDYIKKFIQVGLKVAAYGTVEVEFGRKTIKNPDFQIITSEQEVQTG-ILPVYPLKRGIYQNNM 257
Cdd:COG1200 82 VTLSDGTGS-LTLVFFNQPYLKKQLKPGTRVLVSGKVERFRGGLQMVHPEYELLDEEEAELAGrLTPVYPLTEGLSQKTL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 258 RNIFSETIPYVNYK-EEFIPEEIKNKYKLISLSRRIKGIHFPKSFFHYEKAKEALKYEEIFLFEFSVLMKKRLIKEKIGI 336
Cdd:COG1200 161 RKLIRQALDLLAPDlPEPLPEELRARYGLPSLAEALRNIHFPPSDEDLHPARRRLAFEELLALQLALLLRRARRRKRKGP 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 337 SKKNEGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVL 416
Cdd:COG1200 241 ALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPTEIL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 417 AKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQRLS 496
Cdd:COG1200 321 AEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVEQRLA 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 497 LINKGVMPDILFMTATPIPRTLAMTLYGDLDVSIIDEMPSGRKKVKTVYATEEKINEIYKFIEDELKQKHQVFFIYPLIE 576
Cdd:COG1200 401 LREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIAKGRQAYVVCPLIE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 577 ESEAIDLKAATEMYEVLNKRFKKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFG 656
Cdd:COG1200 481 ESEKLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIENAERFG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 657 LSQLHQLRGRVGRSNKQAYCFLVVSKKTTSETRERLRKFAQTTNGFEVSEMDLQWRGPGKFFGTEQHGLPDFKFPDILSN 736
Cdd:COG1200 561 LSQLHQLRGRVGRGSAQSYCLLLYDAPLSETARERLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPDLRIADLVRD 640
|
650 660 670
....*....|....*....|....*....|....*...
gi 504061724 737 PELINTARKDANEILSKDPDLIKYPALREEIYKRYGKK 774
Cdd:COG1200 641 ADLLEAAREDAEELLEEDPELASHPALRRWLGLRFRDE 678
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
100-764 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 938.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 100 MPLATDIKFIKGVGNKRAKILREFGINSIEDTFYFFPRDYEDRREIKRIIDCYHGQNCLVVGNIVNFEEKNiGSLRILSY 179
Cdd:PRK10917 5 LLLDAPLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRTRLKPIAELRPGEKVTVEGEVLSAEVVF-GKRRRLTV 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 180 ALEDKDGSvLILTWF--NQDYIKKFIQVGLKVAAYGTVEVEFGRKTIKNPDFQIITSEQEVQTG-ILPVYPLKRGIYQNN 256
Cdd:PRK10917 84 TVSDGTGN-LTLRFFnfNQPYLKKQLKVGKRVAVYGKVKRGKYGLEMVHPEYEVLEEESPELEGrLTPVYPLTEGLKQKT 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 257 MRNIFSETIPYVNYKEEFIPEEIKNKYKLISLSRRIKGIHFPKSFFHYEKAKEALKYEEIFLFEFSVLMKKRLIKEKIGI 336
Cdd:PRK10917 163 LRKLIKQALELLDALPELLPEELLEKYGLLSLAEALRAIHFPPSDEDLHPARRRLKFEELFALQLSLLLLRAGRRSKKAG 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 337 SKKNEGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVL 416
Cdd:PRK10917 243 PLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEIL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 417 AKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQRLS 496
Cdd:PRK10917 323 AEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLA 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 497 LINKGVMPDILFMTATPIPRTLAMTLYGDLDVSIIDEMPSGRKKVKTVYATEEKINEIYKFIEDELKQKHQVFFIYPLIE 576
Cdd:PRK10917 403 LREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIE 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 577 ESEAIDLKAATEMYEVLNKRFKKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFG 656
Cdd:PRK10917 483 ESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFG 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 657 LSQLHQLRGRVGRSNKQAYCFLVVSKKTTSETRERLRKFAQTTNGFEVSEMDLQWRGPGKFFGTEQHGLPDFKFPDILSN 736
Cdd:PRK10917 563 LAQLHQLRGRVGRGAAQSYCVLLYKDPLSETARERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRD 642
|
650 660
....*....|....*....|....*...
gi 504061724 737 PELINTARKDANEILSKDPDLIKYPALR 764
Cdd:PRK10917 643 EELLEEARKDARELLERDPELAEALLER 670
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
123-747 |
0e+00 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 710.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 123 FGINSIEDTFYFFPRDYEDRREIKRIIDCYHGQNCLVVGNIVNFEEKNIGSLRILSYALEDKDGSVLILTWFNQDYIKKF 202
Cdd:TIGR00643 1 LGIHTVQDLLFYFPRRYEDRTLLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 203 IQVGLKVAAYGTVEVEFGRKTIKNPDFQIITSEQEVQTGILPVYPLKRGIYQNNMRNIFSETIPYV-NYKEEFIPEEIKN 281
Cdd:TIGR00643 81 FKVGSKVVVYGKVKSSKFKAYLIHPEFISEKDGVEFELKILPVYPLTEGLTQKKLRKLIQQALDQLdKSLEDPLPEELRE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 282 KYKLISLSRRIKGIHFPKSFFHYEKAKEALKYEEIFLFEFSVLMKKRLIKEKI-GISKKNEGKLIEEFKKILSFKLTNAQ 360
Cdd:TIGR00643 161 KYGLLSLEDALRAIHFPKTLSLLELARRRLIFDEFFYLQLAMLARRLGEKQQFsAPPANPSEELLTKFLASLPFKLTRAQ 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 361 NKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKHMENFGINVELLLG 440
Cdd:TIGR00643 241 KRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTG 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 441 ETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQRLSLINKG---VMPDILFMTATPIPRT 517
Cdd:TIGR00643 321 SLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKGqggFTPHVLVMSATPIPRT 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 518 LAMTLYGDLDVSIIDEMPSGRKKVKTVYATEEKINEIYKFIEDELKQKHQVFFIYPLIEESEAIDLKAATEMYEVLNKRF 597
Cdd:TIGR00643 401 LALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAF 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 598 KKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFGLSQLHQLRGRVGRSNKQAYCF 677
Cdd:TIGR00643 481 PKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCL 560
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 678 LVVSKKTTSETRERLRKFAQTTNGFEVSEMDLQWRGPGKFFGTEQHGLPDFKFPDILSNPELINTARKDA 747
Cdd:TIGR00643 561 LVYKNPKSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAREDA 630
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
311-535 |
3.53e-121 |
|
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: 363.01 E-value: 3.53e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 311 LKYEEIFLFEFSVLMKKRLIKEKIGISKKNEGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKT 390
Cdd:cd17992 1 LAFEELFALQLALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 391 VVSEMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQ 470
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504061724 471 EDVEFKNLGLVVIDEQHRFGVKQRLSLINKGVMPDILFMTATPIPRTLAMTLYGDLDVSIIDEMP 535
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
331-724 |
3.56e-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: 3.56e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 331 KEKIGISKKNEGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVM 410
Cdd:TIGR00580 427 KAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVL 506
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 411 VPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFG 490
Cdd:TIGR00580 507 VPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFG 586
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 491 VKQRLSL--INKGVmpDILFMTATPIPRTLAMTLYGDLDVSIIDEMPSGRKKVKTvYATEEKINEIYKFIEDELKQKHQV 568
Cdd:TIGR00580 587 VKQKEKLkeLRTSV--DVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRT-FVMEYDPELVREAIRRELLRGGQV 663
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 569 FFIYPLIEESEaidlKAATEMYEVLNKrfKKYGVelLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIV 648
Cdd:TIGR00580 664 FYVHNRIESIE----KLATQLRELVPE--ARIAI--AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTII 735
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 649 IEHAERFGLSQLHQLRGRVGRSNKQAYCFLVV--SKKTTSETRERLR---KFAQTTNGFEVSEMDLQWRGPGKFFGTEQH 723
Cdd:TIGR00580 736 IERADKFGLAQLYQLRGRVGRSKKKAYAYLLYphQKALTEDAQKRLEaiqEFSELGAGFKIALHDLEIRGAGNLLGEEQS 815
|
.
gi 504061724 724 G 724
Cdd:TIGR00580 816 G 816
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
365-724 |
7.55e-88 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 300.44 E-value: 7.55e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 365 NEIRKDMDSKEPMNRLLQGDVGSGKTvvsEMAL-------LynyeSGFQGAVMVPTSVLAKQQFLKIKKHMENFGINVEL 437
Cdd:COG1197 596 EEVKADMESPRPMDRLVCGDVGFGKT---EVALraafkavM----DGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEV 668
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 438 L------------LGETKNsekkiikeklknGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQ--RLSLINKGVm 503
Cdd:COG1197 669 LsrfrtakeqketLEGLAD------------GKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHkeKLKALRANV- 735
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 504 pDILFMTATPIPRTLAMTLYG--DLdvSIIDEMPSGRKKVKTvYATE---EKINEIykfIEDELKQKHQVFFIYPLIE-- 576
Cdd:COG1197 736 -DVLTLTATPIPRTLQMSLSGirDL--SIIATPPEDRLPVKT-FVGEyddALIREA---ILRELLRGGQVFYVHNRVEdi 808
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 577 ESEAIDLKaatemyevlnkrfkkygvELL--------HGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIV 648
Cdd:COG1197 809 EKVAARLQ------------------ELVpeariavaHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTII 870
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 649 IEHAERFGLSQLHQLRGRVGRSNKQAYCFLVV-SKKTTSET-RERLRKFAQTTN---GFEVSEMDLQWRGPGKFFGTEQH 723
Cdd:COG1197 871 IERADRFGLAQLYQLRGRVGRSHRRAYAYLLYpPDKVLTEDaEKRLEAIQEFTElgaGFKLAMHDLEIRGAGNLLGEEQS 950
|
.
gi 504061724 724 G 724
Cdd:COG1197 951 G 951
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
105-268 |
9.97e-78 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 247.35 E-value: 9.97e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 105 DIKFIKGVGNKRAKILREFGINSIEDTFYFFPRDYEDRREIKRIIDCYHGQNCLVVGNIVNFEEKNIGSLRILSYALEDK 184
Cdd:pfam17191 1 PIKYAKGVGPKREKILKKLGIETIGDLIWYFPRDYEDRRKIIPISDIRHDEKVTTKGKIVNFETKKIGSLVIISAVLSDG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 185 DGSVLiLTWFNQDYIKKFIQVGLKVAAYGTV-EVEFGRKTIKNPDFQIITSEQEVQtgILPVYPLKRGIYQNNMRNIFSE 263
Cdd:pfam17191 81 IGQVL-LKWFNQEYIKKFLQKGKEVYITGTVkEGPFGPIEMNNPEIEEITGEQERE--ILPVYPLTEGISQKNMRKIVKE 157
|
....*
gi 504061724 264 TIPYV 268
Cdd:pfam17191 158 NISYV 162
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
333-724 |
5.41e-74 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 261.60 E-value: 5.41e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 333 KIGISKKNEGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVP 412
Cdd:PRK10689 578 KEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVP 657
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 413 TSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGV- 491
Cdd:PRK10689 658 TTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVr 737
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 492 -KQRLSLINKGVmpDILFMTATPIPRTLAMTLYGDLDVSIIDEMPSGRKKVKTvYATEEKINEIYKFIEDELKQKHQVFF 570
Cdd:PRK10689 738 hKERIKAMRADV--DILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKT-FVREYDSLVVREAILREILRGGQVYY 814
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 571 IYPLIEESEaidlKAATEMYEVLNKRFKKYGvellHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIE 650
Cdd:PRK10689 815 LYNDVENIQ----KAAERLAELVPEARIAIG----HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIE 886
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504061724 651 HAERFGLSQLHQLRGRVGRSNKQAYCFLVV--SKKTTSETRERLRKFAQTTN---GFEVSEMDLQWRGPGKFFGTEQHG 724
Cdd:PRK10689 887 RADHFGLAQLHQLRGRVGRSHHQAYAWLLTphPKAMTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSG 965
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
541-697 |
8.10e-72 |
|
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: 231.46 E-value: 8.10e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 541 VKTVYATEEKINEIYKFIEDELKQKHQVFFIYPLIEESEAIDLKAATEMYEVLNKRFK-KYGVELLHGKMKSQEKNDIME 619
Cdd:cd18811 2 ITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEKLDLKAAVAMYEYLKERFRpELNVGLLHGRLKSDEKDAVMA 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504061724 620 RFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFGLSQLHQLRGRVGRSNKQAYCFLVVSKKTTSETRERLRKFAQ 697
Cdd:cd18811 82 EFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDPLTETAKQRLRVMTE 159
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
341-532 |
6.69e-70 |
|
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: 227.30 E-value: 6.69e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 341 EGKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQ 420
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 421 FLKIKKHMENfgINVELLLGETKNSEKKiikeklkngEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQRLSLINK 500
Cdd:cd17918 81 YEEARKFLPF--INVELVTGGTKAQILS---------GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNL 149
|
170 180 190
....*....|....*....|....*....|..
gi 504061724 501 GvMPDILFMTATPIPRTLAMTLYGDLDVSIID 532
Cdd:cd17918 150 G-ATHFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
540-697 |
5.16e-65 |
|
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: 213.28 E-value: 5.16e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 540 KVKTVYATEEKINEIYKFIEDELKQKHQVFFIYPLIEESEAIDLKAATEMYEVLNKRFKKYGVELLHGKMKSQEKNDIME 619
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESEKLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 620 RFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFGLSQLHQLRGRVGRSNKQAYCFLVV--SKKTTSETRERLRKFAQ 697
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYpdPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
342-532 |
3.64e-64 |
|
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: 212.43 E-value: 3.64e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 342 GKLIEEFKKILSFKLTNAQNKVFNEIRKDMDSKEPMNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQF 421
Cdd:cd17991 2 GEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHY 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 422 LKIKKHMENFGINVELLLGETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEFKNLGLVVIDEQHRFGVKQ--RLSLIN 499
Cdd:cd17991 82 ETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQkeKLKELR 161
|
170 180 190
....*....|....*....|....*....|...
gi 504061724 500 KGVmpDILFMTATPIPRTLAMTLYGDLDVSIID 532
Cdd:cd17991 162 PNV--DVLTLSATPIPRTLHMALSGIRDLSVIA 192
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
558-697 |
3.66e-35 |
|
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: 130.54 E-value: 3.66e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 558 IEDELKQKHQVFFIYPLIEESEaidlKAATEMYEVLNKrfKKYGVelLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEV 637
Cdd:cd18810 18 IERELLRGGQVFYVHNRIESIE----KLATQLRQLVPE--ARIAI--AHGQMTENELEEVMLEFAKGEYDILVCTTIIES 89
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504061724 638 GVDIPDATVIVIEHAERFGLSQLHQLRGRVGRSNKQAYCFLVV--SKKTTSETRERLRKFAQ 697
Cdd:cd18810 90 GIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYpdQKKLTEDALKRLEAIQE 151
|
|
| RecG_N |
pfam17190 |
RecG N-terminal helical domain; This four helical bundle domain is found at the N-terminus of ... |
2-89 |
2.42e-28 |
|
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: 109.03 E-value: 2.42e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 2 NIEDFFNGLEAKLKDALKEKLKWEYLFKELYK-YSANYINIIEQEKGLKEKIGSFLGYYKPIANLSDERRIKRALNGLEL 80
Cdd:pfam17190 1 LLEEFLDECEQLLKKVLNGKLKTNELIEEIKDnLSLLDDPLLENEEGLKEKLGQFLEYYKPIANLPPERAIKRLKNGLEM 80
|
....*....
gi 504061724 81 IEKLKYEYL 89
Cdd:pfam17190 81 IEKLRYWFL 89
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
348-539 |
5.04e-23 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 97.56 E-value: 5.04e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 348 FKKILSFKLTNAQNKVFNEIRKDMdskepMNRLLQGDVGSGKTVVSEMALLYNY--ESGFQGAVMVPTSVLAKQQFLKIK 425
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALkrGKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 426 KHMENFGINVELLLGETKnseKKIIKEKLKNGEIDILIGT-----HALIQEDVEFKNLGLVVIDEQHRFGVKQRLSLINK 500
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDS---KREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 504061724 501 -----GVMPDILFMTATP---IPRTLAMTLYGDLDVSIIDEMPSGRK 539
Cdd:smart00487 153 llkllPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
357-521 |
1.29e-22 |
|
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: 95.00 E-value: 1.29e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 357 TNAQNKVFNEIRKDMDskepMnrLLQGDVGSGKTVVSEMALLYN---YESGFQGAVMVPTSVLAKQQFLKIKKHMENFGI 433
Cdd:pfam00270 1 TPIQAEAIPAILEGRD----V--LVQAPTGSGKTLAFLLPALEAldkLDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 434 NVELLLGETKnsekkIIKEKLKNGEIDILIGTH----ALIQEDVEFKNLGLVVIDEQHRFGVKQRLSLINKGV--MPD-- 505
Cdd:pfam00270 75 KVASLLGGDS-----RKEQLEKLKGPDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILrrLPKkr 149
|
170
....*....|....*..
gi 504061724 506 -ILFMTATPiPRTLAMT 521
Cdd:pfam00270 150 qILLLSATL-PRNLEDL 165
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
549-671 |
5.67e-19 |
|
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: 83.03 E-value: 5.67e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 549 EKINEIYKFIEdeLKQKHQVFFIYPLIEESEAidlkaatemyEVLNKRfKKYGVELLHGKMKSQEKNDIMERFSKKEFLI 628
Cdd:pfam00271 1 EKLEALLELLK--KERGGKVLIFSQTKKTLEA----------ELLLEK-EGIKVARLHGDLSQEEREEILEDFRKGKIDV 67
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 504061724 629 LVSTTVVEVGVDIPDATVIVIEHAErFGLSQLHQLRGRVGRSN 671
Cdd:pfam00271 68 LVATDVAERGLDLPDVDLVINYDLP-WNPASYIQRIGRAGRAG 109
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
588-669 |
4.80e-18 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 79.18 E-value: 4.80e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 588 EMYEVLNKRfkKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAeRFGLSQLHQLRGRV 667
Cdd:smart00490 2 ELAELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRA 78
|
..
gi 504061724 668 GR 669
Cdd:smart00490 79 GR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
286-771 |
1.12e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 83.92 E-value: 1.12e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 286 ISLSRRIKGIHFPKSFFHYEKAKEALKYEEIFLFEFSVLMKKRLIKEKIGISKKNEGKLIEEFKKILS---------FKL 356
Cdd:COG1061 2 LLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEagdeasgtsFEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 357 TNAQNKVFNEIRKDMDSKEPMNrLLQGDVGSGKTVVSeMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKHMENFGINve 436
Cdd:COG1061 82 RPYQQEALEALLAALERGGGRG-LVVAPTGTGKTVLA-LALAAELLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG-- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 437 lllGETKNSEKkiikeklkngeiDILIGTHALIQEDVEFKNL----GLVVIDEQHRFGVKQRLSLINKGVMPDILFMTAT 512
Cdd:COG1061 158 ---GGKKDSDA------------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTAT 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 513 PI---PRTLAMTLYGDL--DVSIID------------------------EMPSGRKKVKTVYATEEKIN-EIYKFIEDEL 562
Cdd:COG1061 223 PFrsdGREILLFLFDGIvyEYSLKEaiedgylappeyygirvdltderaEYDALSERLREALAADAERKdKILRELLREH 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 563 KQKHQVFFIYPLIEESEaidlkaatEMYEVLNKRfkKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIP 642
Cdd:COG1061 303 PDDRKTLVFCSSVDHAE--------ALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVP 372
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 643 DATVIVIeHAERFGLSQLHQLRGRV--GRSNKQ-AYCFLVVSKKTtsETRERLRKFAQTTNGFEVSEMDLQWRGPGKFFG 719
Cdd:COG1061 373 RLDVAIL-LRPTGSPREFIQRLGRGlrPAPGKEdALVYDFVGNDV--PVLEELAKDLRDLAGYRVEFLDEEESEELALLI 449
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....
gi 504061724 720 TEQHGLPDFK--FPDILSNPELINTARKDANEILSKDPDLIKYPALREEIYKRY 771
Cdd:COG1061 450 AVKPALEVKGelEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEG 503
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
377-512 |
5.49e-15 |
|
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: 72.82 E-value: 5.49e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 377 MNRLLQGDVGSGKTVVSEMALLYNYES-GFQGAVMVPTSVLAKQQFLKIKKhMENFGINVELLLGETKnsekKIIKEKLK 455
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRE-LFGPGIRVAVLVGGSS----AEEREKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 456 NGEIDILIGTHALIQEDVE------FKNLGLVVIDEQHRFGVKQR-----LSLINKGVMPD--ILFMTAT 512
Cdd:cd00046 77 LGDADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRgalilDLAVRKAGLKNaqVILLSAT 146
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
698-759 |
2.67e-12 |
|
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: 63.26 E-value: 2.67e-12
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504061724 698 TTNGFEVSEMDLQWRGPGKFFGTEQHGLP-DFKFPDILSNPELINTARKDANEILSKDPDLIK 759
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEEIIDNDPECSL 63
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
480-673 |
3.43e-12 |
|
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: 69.73 E-value: 3.43e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 480 LVVIDEQHRFGVKqrlslinkgvmpdILFMTATpIPRTLAMTLYGDLDvsIIDEMPS---------GRKKVKtVYATEEK 550
Cdd:COG1203 289 LRLLEWLKNLGGS-------------VILMTAT-LPPLLREELLEAYE--LIPDEPEelpeyfrafVRKRVE-LKEGPLS 351
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 551 INEIYKFIEDELKQKHQVFFIYPLIeeseaidlKAATEMYEVLNKRFKKYGVELLHGKM----KSQEKNDIMERFSKKEF 626
Cdd:COG1203 352 DEELAELILEALHKGKSVLVIVNTV--------KDAQELYEALKEKLPDEEVYLLHSRFcpadRSEIEKEIKERLERGKP 423
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 504061724 627 LILVSTTVVEVGVDIpDATVIVIEHAerfGLSQLHQLRGRVGRSNKQ 673
Cdd:COG1203 424 CILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQRAGRCNRHGRK 466
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
351-670 |
8.09e-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: 67.98 E-value: 8.09e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 351 ILSFKLTNAQNKVFNEIRKDMDSKEPMnrLLQGDVGSGKTvvsEM-------ALlynyESGFQGAVMVP-TSV---LA-- 417
Cdd:COG4098 106 TWEGTLTPAQQKASDELLEAIKKKEEH--LVWAVCGAGKT---EMlfpaiaeAL----KQGGRVCIATPrVDVvleLApr 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 418 -KQQFLkikkhmenfGINVELLLGETKNSEKKIikeklkngeiDILIGT-HALIQedveFKN-LGLVVIDE--------- 485
Cdd:COG4098 177 lQQAFP---------GVDIAALYGGSEEKYRYA----------QLVIATtHQLLR----FYQaFDLLIIDEvdafpysgd 233
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 486 -QHRFGVKqrlslinKGVMPD--ILFMTATPiPRTL-AMTLYGDLDVSIIDEMPSGR----------KKVKTVYATEEKI 551
Cdd:COG4098 234 pMLQYAVK-------RARKPDgkLIYLTATP-SKALqRQVKRGKLKVVKLPARYHGHplpvpkfkwlGNWKKRLRRGKLP 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 552 NEIYKFIEDELKQKHQVFFIYPLIEESEAIdlkaatemYEVLNKRFKKYGVELLHGKmkSQEKNDIMERFSKKEFLILVS 631
Cdd:COG4098 306 RKLLKWLKKRLKEGRQLLIFVPTIELLEQL--------VALLQKLFPEERIAGVHAE--DPERKEKVQAFRDGEIPILVT 375
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 504061724 632 TTVVEVGVDIPDATVIVI--EHaERFGLSQLHQLRGRVGRS 670
Cdd:COG4098 376 TTILERGVTFPNVDVAVLgaDH-PVFTEAALVQIAGRVGRS 415
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
360-494 |
2.40e-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: 2.40e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 360 QNKVFNEIRKDMDSKEPMnrLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKHmenFGINVELLL 439
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKR---FGDKVAVLH 75
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 504061724 440 GETKNSEKKIIKEKLKNGEIDILIGTH-ALIqedVEFKNLGLVVIDEQHRFGVKQR 494
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARsALF---APFKNLGLIIVDEEHDSSYKQD 128
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
386-695 |
2.42e-10 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 63.76 E-value: 2.42e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 386 GSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIikeklknGEIDILIGT 465
Cdd:COG1204 48 ASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGDYDSDDEWL-------GRYDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 466 ----HALIQEDVEF-KNLGLVVIDEQHRFGVKQR----------LSLINKGvmPDILFMTAT------------------ 512
Cdd:COG1204 121 peklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevllarLRRLNPE--AQIVALSATignaeeiaewldaelvks 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 513 ---PIPRTLAmTLYGDlDVSIIDEmpSGRKKVKTVYATEEKINE-----IY----KFIEDELKQKHQVFFIYPLIEESEA 580
Cdd:COG1204 199 dwrPVPLNEG-VLYDG-VLRFDDG--SRRSKDPTLALALDLLEEggqvlVFvssrRDAESLAKKLADELKRRLTPEEREE 274
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 581 ID--------LKAATEMYEVLNKRFKKyGVELLHGKMKSQEKnDIMER-FSKKEFLILVSTTVVEVGVDIPdATVIVIEH 651
Cdd:COG1204 275 LEelaeelleVSEETHTNEKLADCLEK-GVAFHHAGLPSELR-RLVEDaFREGLIKVLVATPTLAAGVNLP-ARRVIIRD 351
|
330 340 350 360
....*....|....*....|....*....|....*....|....*....
gi 504061724 652 AERFGLSQL-----HQLRGRVGRSNKQAYCFLVVSKKTTSETRERLRKF 695
Cdd:COG1204 352 TKRGGMVPIpvlefKQMAGRAGRPGYDPYGEAILVAKSSDEADELFERY 400
|
|
| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
159-232 |
1.74e-09 |
|
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: 54.51 E-value: 1.74e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504061724 159 VVGNIVNFEEKNIGSLRILSYALEDkDGSVLILTWFN-QDYIKKFIQVGLKVAAYGTVEVEFGRKTIKNPDFQII 232
Cdd:cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSD-GTGTLTLVFFNfQPYLKKQLPPGTRVRVSGKVKRFRGGLQIVHPEYELL 75
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
386-512 |
1.38e-08 |
|
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: 54.96 E-value: 1.38e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 386 GSGKTVVSEMALLYNYESGFQGAV-MVPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIikeklknGEIDILIG 464
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLL-------AEADILVA 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504061724 465 T----HALIQ--EDVEFKNLGLVVIDEQHRFGVKQR--------LSLINKGVMPDILFMTAT 512
Cdd:cd17921 100 TpeklDLLLRngGERLIQDVRLVVVDEAHLIGDGERgvvlelllSRLLRINKNARFVGLSAT 161
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
475-679 |
4.86e-08 |
|
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: 56.77 E-value: 4.86e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 475 FKNLGLVVIDEQHR----FG-----VKQRLSLINK--GVMPDILFMTATpI--PRTLAMTLYGdLDVSIIDE--MPSGRK 539
Cdd:COG1205 178 FRNLRYVVIDEAHTyrgvFGshvanVLRRLRRICRhyGSDPQFILASAT-IgnPAEHAERLTG-RPVTVVDEdgSPRGER 255
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 540 KVktvyateekineiykfiedelkqkhqVFFIYPLIEE-------SEAIDL-KAATE-------------MYEVLNKRFK 598
Cdd:COG1205 256 TF--------------------------VLWNPPLVDDgirrsalAEAARLlADLVReglrtlvftrsrrGAELLARYAR 309
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 599 KYGVELLHGK--------MKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIP--DATVIViehaerfG----LSQLHQLR 664
Cdd:COG1205 310 RALREPDLADrvaayragYLPEERREIERGLRSGELLGVVSTNALELGIDIGglDAVVLA-------GypgtRASFWQQA 382
|
250
....*....|....*
gi 504061724 665 GRVGRSNKQAYCFLV 679
Cdd:COG1205 383 GRAGRRGQDSLVVLV 397
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
551-678 |
7.19e-08 |
|
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: 51.74 E-value: 7.19e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 551 INEIYKFIEDELKQKHQVFFIYPLIEESEAI----DLKAATEMYEVLNKrfKKYGVELLHGKMKSQEKNDIMERFSKKEF 626
Cdd:cd18787 1 IKQLYVVVEEEEKKLLLLLLLLEKLKPGKAIifvnTKKRVDRLAELLEE--LGIKVAALHGDLSQEERERALKKFRSGKV 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 627 LILVSTTVVEVGVDIPDATViVI-----EHAERFglsqLHqlR-GRVGRSNKQ--AYCFL 678
Cdd:cd18787 79 RVLVATDVAARGLDIPGVDH-VInydlpRDAEDY----VH--RiGRTGRAGRKgtAITFV 131
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
623-680 |
7.90e-07 |
|
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: 47.31 E-value: 7.90e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 504061724 623 KKEFLILVSTTVVEVGVDIPDATVIVIEHAERFgLSQLHQLRGRVGR-SNKQAYCFLVV 680
Cdd:cd18785 20 ASSLEILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRgGKDEGEVILFV 77
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
360-514 |
7.51e-06 |
|
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: 47.65 E-value: 7.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 360 QNKVFNEIRKDmdskepmNRLLQGDVGSGKTVVSEMALLYNYESGFQGAV-------MVPTSVLAKQQFLKIKKHmenFG 432
Cdd:cd18034 7 QLELFEAALKR-------NTIVVLPTGSGKTLIAVMLIKEMGELNRKEKNpkkravfLVPTVPLVAQQAEAIRSH---TD 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 433 INVELLLGETKNSEKKIIKEKLKNGEIDILIGT-----HALIQEDVEFKNLGLVVIDEQHRFG--------VKQRLSLIN 499
Cdd:cd18034 77 LKVGEYSGEMGVDKWTKERWKEELEKYDVLVMTaqillDALRHGFLSLSDINLLIFDECHHATgdhpyariMKEFYHLEG 156
|
170
....*....|....*
gi 504061724 500 KGVMPDILFMTATPI 514
Cdd:cd18034 157 RTSRPRILGLTASPV 171
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
506-669 |
7.97e-06 |
|
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: 48.97 E-value: 7.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 506 ILFMTATpIPRTLaMTLYGDLDVSIIDEMPsgrkkvktvyatEEKINEIYKFIEDELKQKHQVFFIYPLIEESEAI---- 581
Cdd:cd09639 157 ILLMSAT-LPKFL-KEYAEKIGYVEENEPL------------DLKPNERAPFIKIESDKVGEISSLERLLEFIKKGgsva 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 582 ----DLKAATEMYEVLNKRFKKYGVELLHGKMKSQEK----NDIMERFSKKEFLILVSTTVVEVGVDIpDATVIVIEHAE 653
Cdd:cd09639 223 iivnTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRakkeAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP 301
|
170
....*....|....*.
gi 504061724 654 rfgLSQLHQLRGRVGR 669
Cdd:cd09639 302 ---IDSLIQRLGRLHR 314
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
378-514 |
8.60e-06 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA 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: 350769 [Multi-domain] Cd Length: 207 Bit Score: 47.28 E-value: 8.60e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 378 NRLLQGD-VGSGKTVvsEMALLYNY--ESGFQGAVMV--PTSVLAKQQFLKIKKhmenFGINVELLLGETKNSEKKIIKE 452
Cdd:cd18011 18 VRLLLADeVGLGKTI--EAGLIIKEllLRGDAKRVLIlcPASLVEQWQDELQDK----FGLPFLILDRETAAQLRRLIGN 91
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504061724 453 KlkNGEIDILIGTHALI------QEDVEFKNLGLVVIDEQHRFGVK------QRLSLINK--GVMPDILFMTATPI 514
Cdd:cd18011 92 P--FEEFPIVIVSLDLLkrseerRGLLLSEEWDLVVVDEAHKLRNSgggketKRYKLGRLlaKRARHVLLLTATPH 165
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
386-513 |
9.67e-06 |
|
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: 46.14 E-value: 9.67e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 386 GSGKTVVSEMALLYNYESGFqgAVMVPTSVLAKQqflkIKKHMENFGINVEL-LLGETKNsekkiikekLKNGEIDILIG 464
Cdd:cd17926 28 GSGKTLTALALIAYLKELRT--LIVVPTDALLDQ----WKERFEDFLGDSSIgLIGGGKK---------KDFDDANVVVA 92
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 504061724 465 THALIQEDVE-----FKNLGLVVIDEQHRFGVKQ-RLSLINKGVMPdILFMTATP 513
Cdd:cd17926 93 TYQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTfSEILKELNAKY-RLGLTATP 146
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
380-700 |
1.95e-05 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 47.83 E-value: 1.95e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 380 LLQG-DV------GSGKTvvseMA--------LLYNYESGFQGAVMVPTSVLAKQ---QFLKIKKHMenfGINVELLLGE 441
Cdd:COG0513 36 ILAGrDVlgqaqtGTGKT----AAfllpllqrLDPSRPRAPQALILAPTRELALQvaeELRKLAKYL---GLRVATVYGG 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 442 TKnsekkiikeklKNGEI-------DILIGT------HaLIQEDVEFKNLGLVVIDEQHRfgvkqrlsLINKGVMPDILF 508
Cdd:COG0513 109 VS-----------IGRQIralkrgvDIVVATpgrlldL-IERGALDLSGVETLVLDEADR--------MLDMGFIEDIER 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 509 -MTATPIPRTLAM---TLYGDLDvSIIDEM---PSgRKKVKTVYATEEKINEIYKFIEDELKQKhqvfFIYPLIEEsEAI 581
Cdd:COG0513 169 iLKLLPKERQTLLfsaTMPPEIR-KLAKRYlknPV-RIEVAPENATAETIEQRYYLVDKRDKLE----LLRRLLRD-EDP 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 582 DL--------KAATEMYEVLNKRfkKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATViVI---- 649
Cdd:COG0513 242 ERaivfcntkRGADRLAEKLQKR--GISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSH-VInydl 318
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 504061724 650 -EHAERFglsqLHqlR-GRVGRSNKQ--AYCFLvvskktTSETRERLRKFAQTTN 700
Cdd:COG0513 319 pEDPEDY----VH--RiGRTGRAGAEgtAISLV------TPDERRLLRAIEKLIG 361
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
598-656 |
2.38e-05 |
|
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: 44.93 E-value: 2.38e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504061724 598 KKYGVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVI---------EHAERFG 656
Cdd:cd18789 67 KRLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQisghggsrrQEAQRLG 134
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
386-513 |
6.08e-05 |
|
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: 44.73 E-value: 6.08e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 386 GSGKTVVSEMA---LLYNYESGFQG--AVMVPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKKIIKEKLKngeiD 460
Cdd:cd17927 27 GSGKTFVAVLIcehHLKKFPAGRKGkvVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENVSVEQIVESS----D 102
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 504061724 461 ILIGTHALIQED------VEFKNLGLVVIDEQHRFG------------VKQRLSLINKgvMPDILFMTATP 513
Cdd:cd17927 103 VIIVTPQILVNDlksgtiVSLSDFSLLVFDECHNTTknhpyneimfryLDQKLGSSGP--LPQILGLTASP 171
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
378-669 |
7.23e-05 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 46.35 E-value: 7.23e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 378 NRLLQGDVGSGKTVVSEMALLYN-YESGFQGAVMVPTSVLAKQQFLKIKKhMENFGINVELLLGETKNSEKKIikeklkn 456
Cdd:PRK00254 41 NLVLAIPTASGKTLVAEIVMVNKlLREGGKAVYLVPLKALAEEKYREFKD-WEKLGLRVAMTTGDYDSTDEWL------- 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 457 GEIDILIGT----HALIQEDVEF-KNLGLVVIDEQHRFGVKQR---LSLINKGVM--PDILFMTAT-PIPRTLAMTLYGD 525
Cdd:PRK00254 113 GKYDIIIATaekfDSLLRHGSSWiKDVKLVVADEIHLIGSYDRgatLEMILTHMLgrAQILGLSATvGNAEELAEWLNAE 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 526 LDVSiiDEMPSG-RKKV---KTVYATEEKI----NEIYKFIEDELKQKHQ--VFFIYPLIEESEAIDL------------ 583
Cdd:PRK00254 193 LVVS--DWRPVKlRKGVfyqGFLFWEDGKIerfpNSWESLVYDAVKKGKGalVFVNTRRSAEKEALELakkikrfltkpe 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 584 -KAATEMYEVL-----NKRFKKY---GVELLHGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIV--IEHA 652
Cdd:PRK00254 271 lRALKELADSLeenptNEKLKKAlrgGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIrdTKRY 350
|
330 340
....*....|....*....|..
gi 504061724 653 ERFGLS-----QLHQLRGRVGR 669
Cdd:PRK00254 351 SNFGWEdipvlEIQQMMGRAGR 372
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
355-493 |
7.92e-05 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 46.30 E-value: 7.92e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 355 KLTNAQNKVFNEIRKDmDSKEPMnrLLQGDVGSGKT-----VVSEmALlynyESGFQGAVMVP----TsvlakQQFLK-I 424
Cdd:PRK05580 144 TLNPEQAAAVEAIRAA-AGFSPF--LLDGVTGSGKTevylqAIAE-VL----AQGKQALVLVPeialT-----PQMLArF 210
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504061724 425 KKHmenFGINVELL---LGETKnseKKIIKEKLKNGEIDILIGTH-ALIqedVEFKNLGLVVIDEQHRFGVKQ 493
Cdd:PRK05580 211 RAR---FGAPVAVLhsgLSDGE---RLDEWRKAKRGEAKVVIGARsALF---LPFKNLGLIIVDEEHDSSYKQ 274
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
344-484 |
1.29e-04 |
|
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: 43.47 E-value: 1.29e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 344 LIEEFKKILSFKLTNAQnkvfneirkdmdsKEPMNRLLQGD-------VGSGKTVVSEMALLYNYESGFQGAVMVPTSVL 416
Cdd:cd17924 6 FEEFFKKKTGFPPWGAQ-------------RTWAKRLLRGKsfaiiapTGVGKTTFGLATSLYLASKGKRSYLIFPTKSL 72
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504061724 417 AKQQFLKIKKHMENFGINVELLL--GETKNSEKKIIKEKLKNGEIDILIGTHALIQEDVEF---KNLGLVVID 484
Cdd:cd17924 73 VKQAYERLSKYAEKAGVEVKILVyhSRLKKKEKEELLEKIEKGDFDILVTTNQFLSKNFDLlsnKKFDFVFVD 145
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
506-672 |
1.32e-04 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 45.14 E-value: 1.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 506 ILFMTATpIPRTLaMTLYGDLDVSIIDEMPSgrkkvktvyATEEKINEIYKFIEDELKQKHQVFFIYPLIEESEAI---- 581
Cdd:TIGR01587 158 ILLMSAT-LPKFL-KEYAEKIGYVEFNEPLD---------LKEERRFENHRFILIESDKVGEISSLERLLEFIKKGgsia 226
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 582 ----DLKAATEMYEVLNKRFKKYGVELLHGKMKSQEK----NDIMERFSK-KEFLILVSTTVVEVGVDIpDATVIVIEHA 652
Cdd:TIGR01587 227 iivnTVDRAQEFYQQLKEKAPEEEIILYHSRFTEKDRakkeAELLREMKKsNEKFVIVATQVIEASLDI-SADVMITELA 305
|
170 180
....*....|....*....|
gi 504061724 653 ErfgLSQLHQLRGRVGRSNK 672
Cdd:TIGR01587 306 P---IDSLIQRLGRLHRYGR 322
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
587-649 |
1.79e-04 |
|
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. 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: 350180 [Multi-domain] Cd Length: 135 Bit Score: 42.08 E-value: 1.79e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504061724 587 TEMYEVLNKRFKKYGVE--LLHGKMKSQEKNDIMERFSK--KEFLILVSTTVVEVGVDIPDATVIVI 649
Cdd:cd18793 37 TDTLDILEEALRERGIKylRLDGSTSSKERQKLVDRFNEdpDIRVFLLSTKAGGVGLNLTAANRVIL 103
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
384-515 |
1.88e-04 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 44.83 E-value: 1.88e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 384 DVGSGKTVVSEMALLYNYESGFQGAVMV--PTSVLakQQFLK-IKKHmeNFGINVELLLGETKNSEKKIIKeklknGEID 460
Cdd:COG0553 268 DMGLGKTIQALALLLELKERGLARPVLIvaPTSLV--GNWQReLAKF--APGLRVLVLDGTRERAKGANPF-----EDAD 338
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504061724 461 ILIGTHALIQEDVE-FKNL--GLVVIDEQHRfgVKQRLSLINKGVM----PDILFMTATPIP 515
Cdd:COG0553 339 LVITSYGLLRRDIElLAAVdwDLVILDEAQH--IKNPATKRAKAVRalkaRHRLALTGTPVE 398
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
609-672 |
3.07e-04 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is 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. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain] Cd Length: 143 Bit Score: 41.57 E-value: 3.07e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504061724 609 MKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIVIEHAERFGLSQLhQLRGRVGRSNK 672
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRKRQ 136
|
|
| DEXQc_arch_SWI2_SNF2 |
cd18012 |
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
384-514 |
4.15e-04 |
|
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members 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: 350770 [Multi-domain] Cd Length: 218 Bit Score: 42.55 E-value: 4.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 384 DVGSGKTVVSEMALLYNYESGFQGAVMV--PTSVLA--KQQFLKikkhmenFGINVELLLGETKNSEKKIIKEKLKNgei 459
Cdd:cd18012 31 DMGLGKTLQTLALLLSRKEEGRKGPSLVvaPTSLIYnwEEEAAK-------FAPELKVLVIHGTKRKREKLRALEDY--- 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504061724 460 DILIGTHALIQEDVEF---KNLGLVVIDE-QHrfgVKQRLSLINKGVMpDI-----LFMTATPI 514
Cdd:cd18012 101 DLVITSYGLLRRDIELlkeVKFHYLVLDEaQN---IKNPQTKTAKAVK-ALkadhrLALTGTPI 160
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
367-487 |
4.32e-04 |
|
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: 41.94 E-value: 4.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 367 IRKDMDSKEpmNRLLQGDVGSGKTVVSEMALLYNYESGFQGAVMVPTSVLAKQQFLKIKKhMENFGINVELLLGETKNSE 446
Cdd:cd18028 10 VRAGLLKGE--NLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKK-LEEIGLKVGISTGDYDEDD 86
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 504061724 447 KKIikeklknGEIDILIGTH----ALIQEDVEF-KNLGLVVIDEQH 487
Cdd:cd18028 87 EWL-------GDYDIIVATYekfdSLLRHSPSWlRDVGVVVVDEIH 125
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
324-487 |
5.27e-04 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 43.57 E-value: 5.27e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 324 LMKKRLIK-EKIGISKKNEGKLIEEFKKIlsfKLTNAQNKVFNEIRKDMDSKEPMnrLLQGDVGSGKT-----VVSEmAL 397
Cdd:COG1198 166 LVKKGLLEiEEREVDRDPFAPDVPAEPPP---TLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTevylqAIAE-VL 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 398 lynyESGFQGAVMVP----TSvlakqQFLK-IKKHmenFGINVELL---LGET---------KNsekkiikeklknGEID 460
Cdd:COG1198 240 ----AQGKQALVLVPeialTP-----QTVErFRAR---FGARVAVLhsgLSDGerldewrraRR------------GEAR 295
|
170 180
....*....|....*....|....*...
gi 504061724 461 ILIGTH-ALIqedVEFKNLGLVVIDEQH 487
Cdd:COG1198 296 IVIGTRsALF---APFPNLGLIIVDEEH 320
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
611-680 |
7.85e-04 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350184 [Multi-domain] Cd Length: 146 Bit Score: 40.70 E-value: 7.85e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504061724 611 SQEKNDIMERFSKKEFLILVSTTVVEVGVDIP--DATVIViehAERFGLSQLHQLRGRVGRSNKQAYCFLVV 680
Cdd:cd18797 78 AEDRREIEAELFNGELLGVVATNALELGIDIGglDAVVLA---GYPGSLASLWQQAGRAGRRGKDSLVILVA 146
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
547-681 |
1.59e-03 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 42.19 E-value: 1.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 547 TEEKINEIYKFIedelKQKH--QVFFIYPLieesEAIDLKAATEMYEVLNKRFKKYgvellHGKMKSQEKNDIMERFSKK 624
Cdd:PLN03137 663 TKKCLEDIDKFI----KENHfdECGIIYCL----SRMDCEKVAERLQEFGHKAAFY-----HGSMDPAQRAFVQKQWSKD 729
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 504061724 625 EFLILVSTTVVEVGVDIPDATvIVIEHAERFGLSQLHQLRGRVGRSNKQAYCFLVVS 681
Cdd:PLN03137 730 EINIICATVAFGMGINKPDVR-FVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYS 785
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
380-514 |
2.81e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 39.19 E-value: 2.81e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 380 LLQGDVGSGKTVVS-EMALLYNYESGFQGAVM-VPTSVLAKQQFLKIKKHMENFGINVELLLGETKNSEKkiikeklknG 457
Cdd:pfam04851 27 LIVMATGSGKTLTAaKLIARLFKKGPIKKVLFlVPRKDLLEQALEEFKKFLPNYVEIGEIISGDKKDESV---------D 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 504061724 458 EIDILIGT-HALIQEDVEFKNL------GLVVIDEQHRFGVKQRLSLINKGVMPDILFMTATPI 514
Cdd:pfam04851 98 DNKIVVTTiQSLYKALELASLEllpdffDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTATPE 161
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
609-780 |
3.37e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 41.01 E-value: 3.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 609 MKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIV----IEHAERFglsqlHQLRGRVGRSNKqAYCFLVVSKKT 684
Cdd:PRK13766 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIfyepVPSEIRS-----IQRKGRTGRQEE-GRVVVLIAKGT 480
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 685 TSET-------RER-----LRKFAQTTNGFEVSEMDLQwrGPGKFFGTEQHGLPDFKFPDIlSNPELINTARKDANEILS 752
Cdd:PRK13766 481 RDEAyywssrrKEKkmkeeLKNLKGILNKKLQELDEEQ--KGEEEEKDEQLSLDDFVKSKG-KEEEEEEEKEEKDKETEE 557
|
170 180
....*....|....*....|....*...
gi 504061724 753 KDPDLIKYPALREEIYKRYGKKLKMLEA 780
Cdd:PRK13766 558 DEPEGPKIIVDSRELRSNVARHLKRLGA 585
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
609-680 |
4.98e-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: 37.96 E-value: 4.98e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504061724 609 MKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDATVIViehaeRFGLS----QLHQLRGRVGRSNkqAYCFLVV 680
Cdd:cd18802 74 MTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI-----RFDLPktlrSYIQSRGRARAPN--SKYILMV 142
|
|
| DEXHc_Brr2_2 |
cd18021 |
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
354-442 |
6.31e-03 |
|
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350779 [Multi-domain] Cd Length: 191 Bit Score: 38.78 E-value: 6.31e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504061724 354 FKLTNA-QNKVFNEIrkdMDSKEpmNRLLQGDVGSGKTVVSEMALLYNYESGFQG-AV-MVPTSVLAKQQFLK-IKKHME 429
Cdd:cd18021 1 FKFFNPiQTQVFNSL---YNTDD--NVFVGAPTGSGKTVCAELALLRHWRQNPKGrAVyIAPMQELVDARYKDwRAKFGP 75
|
90
....*....|...
gi 504061724 430 NFGINVELLLGET 442
Cdd:cd18021 76 LLGKKVVKLTGET 88
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
584-673 |
9.07e-03 |
|
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: 37.63 E-value: 9.07e-03
10 20 30 40 50 60 70 80
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gi 504061724 584 KAATEMYEVLNKRFKKYGVELL----HGKMKSQEKNDIMERFSKKEFLILVSTTVVEVGVDIPDA-TVIVIEHAerFGLS 658
Cdd:cd18796 49 SQAERLAQRLRELCPDRVPPDFialhHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVdLVIQIGSP--KSVA 126
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90
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gi 504061724 659 QLHQlrgRVGRSNKQ 673
Cdd:cd18796 127 RLLQ---RLGRSGHR 138
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