|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
44-1208 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1568.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 44 APASARLLVASALARQ--GPLLVVTATGREADDLAAELRGVFGDA-VALLPSWETLPHERLSPGVDTVGTRLMALRRLAH 120
Cdd:COG1197 10 LPGSARALLLAALARAlgRPLLVVTADEREAERLAEDLRFFLPDLpVLLFPAWETLPYDRFSPSPDIVSERLATLRRLAS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 121 PDDaqlgpplGVVVTSVRSLLQPMTP-QLGMMEPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFA 199
Cdd:COG1197 90 GKP-------GIVVTPVRALLQRLPPpELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIFP 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 200 PTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDihTLVAFACRELLLSEDVRARAAQLAArhpaAESTVTGSASDMLAK 279
Cdd:COG1197 163 PGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVD--EVELLPAREFPLDEEAIERFRERLR----ELFGLDPKLDELYEA 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 280 LAEGIAVDGMEAVLPVLWsDGHALLTDQLPDGTPVLVCDPEKVRTRAADLIRTGREFLEAswsvaaLGTAENQAPVDVEQ 359
Cdd:COG1197 237 LSEGIAFAGIEYYLPLFY-EELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEA------RRHDRGRPLLPPEE 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 360 LggsgFVELDQVRAAAARTGHPwwTLSQLS----DESAIELDVRAAPSARGhqrDIDEIFAMLRAHIATGGYAALVAPGT 435
Cdd:COG1197 310 L----FLDPEELFAALKRRPRV--TLSPFAalpeGAGVVNLGARPLPSFAG---QLEALLEELKRLLKDGGRVLLAAESE 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 436 GTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANLVVITETDLTGSRVSAAEGKRLAAKRRNIVDP 515
Cdd:COG1197 381 GRRERLLELLRDHGIPARLVESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSADAFIRDL 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 516 LALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYAsakrgggakNTDKLYVPMDSLDQLSRYVG--GQAPALSRL 593
Cdd:COG1197 461 SELKPGDYVVHVDHGIGRYLGLETLEVGGAERDYLVLEYA---------GGDKLYVPVDQLDLISRYVGseGEAPKLDKL 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 594 GGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRV 673
Cdd:COG1197 532 GGSDWQKAKAKAKKAVRDIAAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRL 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 674 ICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVD 753
Cdd:COG1197 612 VCGDVGFGKTEVALRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVD 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 754 IVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYP 833
Cdd:COG1197 692 IVIGTHRLLSKDVKFKDLGLLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLP 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 834 VLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDIL 913
Cdd:COG1197 772 VKTFVGEYDDALIREAILRELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVL 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 914 VCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQNNELGAGMAV 993
Cdd:COG1197 852 VCTTIIETGIDIPNANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKL 931
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 994 ALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRDAyraaadgqtvRTAEEPKDVRIDLPVDAHLPPDYIAS 1073
Cdd:COG1197 932 AMHDLEIRGAGNLLGEEQSGHIAEVGFDLYLQMLEEAVAALKGG----------KEPEEEWEPEINLGVPALIPEDYIPD 1001
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1074 DRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA-ASAATVRLSPLTLPDSAQ 1152
Cdd:COG1197 1002 VRQRLELYKRIASAESEEELDELQEELIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAgGKGIRIEFSPNTPLDPEK 1081
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*..
gi 489500368 1153 -VRLKRMYPGAHYRATTATVQVPIPRAGglgaprirDVELVQMVADLITALAGKPRQ 1208
Cdd:COG1197 1082 lIRLIQKQPGRYKLDGDDKLVITLDLED--------PEERLEALEELLEALAKLAKE 1130
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
171-1133 |
0e+00 |
|
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: 1371.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 171 LVELAYTRVDMVGRRGEFAVRGGILDIFAPTAEHPVRVEFWGDEITEMRMFSVADQRSIPEIDIHTLVAFACReLLLSED 250
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEF-ILLEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 251 VRARAAQLAARHPAAESTVTGSAsdmlakLAEGIAVDGMEAVLPVLWSDgHALLTDQLPDGTPVLVCDPEKVRTRAADLI 330
Cdd:TIGR00580 80 TIARLKDNAARVEDAKHLETIEA------LSEGTLPAGEEMFLPLFFED-LSSLFDYLPDNTPILLDDPERFHSAARFLQ 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 331 RTGREFLEASWSVAALGTAeNQAPVDVEQLGGSGfveldqvraaaartghPWWTLSQLSDESAI-ELDVRAAPSARG-HQ 408
Cdd:TIGR00580 153 RELEEFYNALEEAKKLINP-PRLDLDPSELAFEA----------------SAISLSRVQLENEHlSLKASEAIEGAQkHS 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 409 R-DIDEIFAMLR---AHIATGGYAALVAPGTGTAHRVVERLSESDTPAGMLDPGQAPKPGVVGVLQGPLRDGVIIPGANL 484
Cdd:TIGR00580 216 RlEFGEILAFKEelfRWLKAGFKITVAAESESQAERLKSLLAEHDIAAQVIDESCIIIPAVRYVMIGALSSGFILPTAGL 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 485 VVITETDLTGSRVSAAEGKRLAAKRRnIVDPLALTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYASAkrgggak 564
Cdd:TIGR00580 296 AVITESELFGSRVLRRPKKSRLKSKP-IESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGE------- 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 565 ntDKLYVPMDSLDQLSRYVGG--QAPALSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELE 642
Cdd:TIGR00580 368 --DKLYVPVEQLHLISRYVGGsgKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFE 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 643 DAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMS 722
Cdd:TIGR00580 446 DSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFA 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 723 GFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTM 802
Cdd:TIGR00580 526 NFPVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTL 605
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 803 SATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVP 882
Cdd:TIGR00580 606 SATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVP 685
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 883 EARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYF 962
Cdd:TIGR00580 686 EARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYL 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 963 LYPPQVPLTETAYDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLVGEALETYRdayraaa 1042
Cdd:TIGR00580 766 LYPHQKALTEDAQKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELK------- 838
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1043 dGQTVRTAEEpkDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRL 1122
Cdd:TIGR00580 839 -GGKPPKLEE--ETDIELPYSAFIPDDYIADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKL 915
|
970
....*....|.
gi 489500368 1123 LCRGSGITDVT 1133
Cdd:TIGR00580 916 LARKLGIRKLK 926
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
46-1134 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 698.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 46 ASARLLVASALAR-QGPLLVVTATGREADDLAAELRGVFGDAVALLPSWETLPHERLSPGVDTVGTRLMALRRLahpdda 124
Cdd:PRK10689 25 AACATEVAEIAERhAGPVVLIAPDMQNALRLHDEIQQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQL------ 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 125 qlgPPL--GVVVTSVRSLLQPMTPQLGMM-EPLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPT 201
Cdd:PRK10689 99 ---PTMqrGVLILPVNTLMQRVCPHSFLHgHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMG 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 202 AEHPVRVEFWGDEITEMRMFSVADQRSIPEID-IHTLVAF------ACRELLLSEdvraraaqlaarhPAAESTVTGSAS 274
Cdd:PRK10689 176 SEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEaINLLPAHefptdkAAIELFRSQ-------------WRDTFEVKRDAE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 275 DMLAKLAEGIAVDGMEAVLPVLWSDGHALLTDQLPDGTPVLVC-DPEKVRTRAADLIRTGREFLEASWSVAALGTAENQA 353
Cdd:PRK10689 243 HIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTgDLETSAERFWADTLARFENRGVDPMRPLLPPESLWL 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 354 PVDveqlggSGFVELDQvraaaartghpwWTLSQLSDEsaiELDVRAAPSARGHQRDID-EIFAMLRAHIAT-------- 424
Cdd:PRK10689 323 RVD------ELFSELKN------------WPRVQLKTE---HLPTKAANTNLGYQKLPDlAVQAQQKAPLDAlrrflesf 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 425 GGYAALVAPGTGTAHRVVERLSESD-TPAGMLDPGQAPKPGVVgVLQGPLRDGVIIPGANLVVITETDLTGSRVSaaegK 503
Cdd:PRK10689 382 DGPVVFSVESEGRREALGELLARIKiAPKRIMRLDEASDRGRY-LMIGAAEHGFIDTVRNLALICESDLLGERVA----R 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 504 RLAAKRRNI-----VDPLA-LTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYAsakrgggakNTDKLYVPMDSLD 577
Cdd:PRK10689 457 RRQDSRRTInpdtlIRNLAeLHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYA---------NDAKLYVPVSSLH 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 578 QLSRYVGG---QAPaLSRLGGSDWANTKTKARRAVREIAGELVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQL 654
Cdd:PRK10689 528 LISRYAGGaeeNAP-LHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQA 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 655 TAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRF 734
Cdd:PRK10689 607 QAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRF 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 735 TDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMS 814
Cdd:PRK10689 687 RSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMA 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 815 LAGIREMSTILTPPEERYPVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMP 894
Cdd:PRK10689 767 MSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMR 846
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 895 EDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETA 974
Cdd:PRK10689 847 ERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDA 926
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 975 YDRLATIAQNNELGAGMAVALKDLEIRGAGNVLGIEQSGHVAGVGFDLYVRLvgeaLETYRDAYRAAADGQTVRTAEEPK 1054
Cdd:PRK10689 927 QKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMEL----LENAVDALKAGREPSLEDLTSQQT 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1055 DVRIDLPvdAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA 1134
Cdd:PRK10689 1003 EVELRMP--SLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEG 1080
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
634-826 |
7.39e-121 |
|
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: 371.52 E-value: 7.39e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 634 DTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQH 713
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 714 LQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSL 793
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 489500368 794 RTHVDVLTMSATPIPRTLEMSLAGIREMSTILT 826
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
616-1013 |
2.42e-111 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 364.37 E-value: 2.42e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 616 LVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQ 695
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 696 DGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVV 775
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 776 VDEEQRFGVEHKEhikSLR---THVDVLTMSATPIPRTLEMSLAG------IREMstiltpPEERYPVLTYVGPHDD-KQ 845
Cdd:COG1200 387 IDEQHRFGVEQRL---ALRekgEAPHVLVMTATPIPRTLAMTLYGdldvsvIDEL------PPGRKPIKTRVVPEERrDE 457
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 846 IAAALRRELLRDGQAFYVHNRVS---SIDAAAA-----RVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTT 917
Cdd:COG1200 458 VYERIREEIAKGRQAYVVCPLIEeseKLDLQAAeetyeELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATT 537
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 918 IVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPqvPLTETAYDRLATIAQNNElgaGMAVALKD 997
Cdd:COG1200 538 VIEVGVDVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDA--PLSETARERLEVMRETND---GFEIAEED 612
|
410
....*....|....*.
gi 489500368 998 LEIRGAGNVLGIEQSG 1013
Cdd:COG1200 613 LELRGPGEFLGTRQSG 628
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
616-1013 |
7.04e-109 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 357.54 E-value: 7.04e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 616 LVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQ 695
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 696 DGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVV 775
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 776 VDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEERYPVLTYVGPHDDK-QIAAALRREL 854
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRdEVYERIREEI 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 855 LRDGQAFYVHNRVS--------SIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDIS 926
Cdd:PRK10917 469 AKGRQAYVVCPLIEesekldlqSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 927 NANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPqvPLTETAYDRLATIAQNNElgaGMAVALKDLEIRGAGNV 1006
Cdd:PRK10917 549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKD--PLSETARERLKIMRETND---GFVIAEKDLELRGPGEL 623
|
....*..
gi 489500368 1007 LGIEQSG 1013
Cdd:PRK10917 624 LGTRQSG 630
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
602-1013 |
6.43e-105 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 345.10 E-value: 6.43e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 602 KTKARRavREIAGELVSL--------YAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRV 673
Cdd:TIGR00643 183 LELARR--RLIFDEFFYLqlamlarrLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRL 260
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 674 ICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVD 753
Cdd:TIGR00643 261 LQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIH 340
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 754 IVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIK---SLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPPEE 830
Cdd:TIGR00643 341 LVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLRekgQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPG 420
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 831 RYPVLTYVGPHDDKQIA-AALRRELLRDGQAFYVHNRVSS---IDAAAA-----RVRELVPEARVVVAHGQMPEDLLETT 901
Cdd:TIGR00643 421 RKPITTVLIKHDEKDIVyEFIEEEIAKGRQAYVVYPLIEEsekLDLKAAealyeRLKKAFPKYNVGLLHGRMKSDEKEAV 500
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 902 VQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPqvPLTETAYDRLATI 981
Cdd:TIGR00643 501 MEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKN--PKSESAKKRLRVM 578
|
410 420 430
....*....|....*....|....*....|..
gi 489500368 982 AQNNElgaGMAVALKDLEIRGAGNVLGIEQSG 1013
Cdd:TIGR00643 579 ADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
833-983 |
1.21e-83 |
|
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: 269.21 E-value: 1.21e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 833 PVLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQRFWNREHDI 912
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489500368 913 LVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQ 983
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
833-983 |
8.56e-70 |
|
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: 230.62 E-value: 8.56e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 833 PVLTYVGPHDDK-QIAAALRRELLRDGQAFYVHNRVS--------SIDAAAARVRELVPEARVVVAHGQMPEDLLETTVQ 903
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEesekldlkSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 904 RFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPQVPLTETAYDRLATIAQ 983
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
616-828 |
1.41e-60 |
|
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: 207.00 E-value: 1.41e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 616 LVSLYAKRQASPGHAFSPDTPWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQ 695
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 696 DGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDAAESRAVIDGLADGSVDIVIGTHRLLQTGVRWKDLGLVV 775
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 489500368 776 VDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIPRTLEMSLAGIREMSTILTPP 828
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
639-824 |
3.96e-50 |
|
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: 175.30 E-value: 3.96e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 639 AELEDAFGFTETVDQLTAIEEVKADMEKPIPMDRVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFG 718
Cdd:cd17918 6 QELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEAR 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 719 ERMSGFPVTIkgLSRFTDAAESRavidgladgSVDIVIGTHRLLQTGVRWKDLGLVVVDEEQRFGVEHKEHIKSLRThVD 798
Cdd:cd17918 86 KFLPFINVEL--VTGGTKAQILS---------GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA-TH 153
|
170 180
....*....|....*....|....*.
gi 489500368 799 VLTMSATPIPRTLEMSLAGIREMSTI 824
Cdd:cd17918 154 FLEATATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
518-621 |
8.68e-38 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Pssm-ID: 215001 [Multi-domain] Cd Length: 99 Bit Score: 136.81 E-value: 8.68e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 518 LTAGDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYAsakrgggakNTDKLYVPMDSLDQLSRYVGGQA---PALSRLG 594
Cdd:smart01058 2 LKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYA---------GGDKLYVPVDNLDLGSRYVGSEGevePVLDKLG 72
|
90 100
....*....|....*....|....*..
gi 489500368 595 GSDWANTKTKARRAVREIAGELVSLYA 621
Cdd:smart01058 73 GGSWSKRKRKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
833-983 |
4.85e-37 |
|
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: 137.09 E-value: 4.85e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 833 PVLTYVGPHDDK-QIAAALRRELLRDGQAFYVHNRVSSID-----AAAARVREL----VPEARVVVAHGQMPEDLLETTV 902
Cdd:cd18811 1 PITTYLIFHTRLdKVYEFVREEIAKGRQAYVIYPLIEESEkldlkAAVAMYEYLkerfRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 903 QRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLHQLRGRVGRSRERGYAYFLYPPqvPLTETAYDRLATIA 982
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKD--PLTETAKQRLRVMT 158
|
.
gi 489500368 983 Q 983
Cdd:cd18811 159 E 159
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1059-1157 |
1.43e-30 |
|
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.
Pssm-ID: 198050 [Multi-domain] Cd Length: 100 Bit Score: 116.03 E-value: 1.43e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1059 DLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA-ASA 1137
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAgGKG 80
|
90 100
....*....|....*....|
gi 489500368 1138 ATVRLSPLTLPDSAQVRLKR 1157
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
518-620 |
5.42e-27 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.
Pssm-ID: 460590 [Multi-domain] Cd Length: 89 Bit Score: 105.61 E-value: 5.42e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 518 LTAGDLVVHDQHGIGRFVEMVERTVggarREYLVLEYAsakrgggakNTDKLYVPMDSLDQLSRYVGGQapALSRLG-GS 596
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLET----KDYYVLEYA---------GGDKLYVPVDNLDLIRKYISKG--ELDKLGdGR 65
|
90 100
....*....|....*....|....
gi 489500368 597 DWANTKTKARRAVREIAGELVSLY 620
Cdd:pfam02559 66 RWRKYKEKLKSGDIEEAAELIKLY 89
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
154-233 |
2.80e-26 |
|
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein.
Pssm-ID: 465486 [Multi-domain] Cd Length: 91 Bit Score: 103.63 E-value: 2.80e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 154 LTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIFAPTAE-HPVRVEFWGDEITEMRMFSVADQRSIPEI 232
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
.
gi 489500368 233 D 233
Cdd:pfam17757 81 D 81
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1060-1153 |
3.60e-26 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 103.27 E-value: 3.60e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1060 LPVDAHLPPDYIASDRLRLEGYRRLAAASSDREVAAVVDELTDRYGALPEPARRLAAVARLRLLCRGSGITDVTA-ASAA 1138
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLkGGGI 80
|
90
....*....|....*
gi 489500368 1139 TVRLSPLTLPDSAQV 1153
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
650-813 |
6.49e-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: 102.32 E-value: 6.49e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 650 TVDQLTAIEEVKADMekpipmDRVICGDVGYGKTEIAVRAAFKAV---QDGKQVAVLVPTTLLADQHLQTFGERMSGFPV 726
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 727 TIkglSRFTDAAESRAVIDGLADgsVDIVIGTH----RLLQTGVRWKDLGLVVVDEEQR-----FGVEHKEHIKSLRTHV 797
Cdd:pfam00270 75 KV---ASLLGGDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 489500368 798 DVLTMSATPiPRTLEM 813
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
641-831 |
1.92e-23 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 99.49 E-value: 1.92e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 641 LEDAFGFTETVDQLTAIEEVKADMekpipMDRVICGDVGYGKTEIAVRAAFKAVQ--DGKQVAVLVPTTLLADQHLQTFG 718
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKrgKGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 719 ERMSGFPVTIKGLsrfTDAAESRAVIDGLADGSVDIVIGT-----HRLLQTGVRWKDLGLVVVDEEQR-----FGVEHKE 788
Cdd:smart00487 76 KLGPSLGLKVVGL---YGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 489500368 789 HIKSLRTHVDVLTMSATP---IPRTLEMSLAGIREMSTILTPPEER 831
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
848-953 |
5.85e-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: 77.64 E-value: 5.85e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 848 AALRREL--LRDGQAFYVHNRVSSIDAAAARVRElvpEARVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDI 925
Cdd:pfam00271 4 EALLELLkkERGGKVLIFSQTKKTLEAELLLEKE---GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDL 80
|
90 100
....*....|....*....|....*...
gi 489500368 926 SNANTLIVERADtFGLSQLHQLRGRVGR 953
Cdd:pfam00271 81 PDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
148-221 |
4.06e-15 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 80.09 E-value: 4.06e-15
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489500368 148 LGMMepLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIF-APTAEHPVRVEFWGDEITEMRMF 221
Cdd:PRK05298 155 LKMV--LSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFpAYYEERAIRIEFFGDEIERISEF 227
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
670-805 |
1.40e-14 |
|
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: 72.05 E-value: 1.40e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 670 MDRVICGDVGYGKTEIAVRAAF-KAVQDGKQVAVLVPTTLLADQHLQTFGERMSGfPVTIKGLSRFTDAAESRAVIDGLA 748
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEEREKNKLGDA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 749 dgsvDIVIGTHRLLQT------GVRWKDLGLVVVDEEQRFGVEHKE-------HIKSLRTHVDVLTMSAT 805
Cdd:cd00046 81 ----DIIIATPDMLLNlllredRLFLKDLKLIIVDEAHALLIDSRGalildlaVRKAGLKNAQVILLSAT 146
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
148-221 |
2.45e-14 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 77.74 E-value: 2.45e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489500368 148 LGMMepLTLTVGDESPFDGVVARLVELAYTRVDMVGRRGEFAVRGGILDIF-APTAEHPVRVEFWGDEITEMRMF 221
Cdd:COG0556 152 LKMV--LSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFpAYSEERAIRIEFFGDEIERISEF 224
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
653-1123 |
1.87e-13 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 74.68 E-value: 1.87e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 653 QLTAIEEVKADMEKPiPMDRVICGDVGYGKTEIAVRAAfKAVQDGKQVAVLVPTTLLADQhlqtfgermsgfpvTIKGLS 732
Cdd:COG1061 85 QQEALEALLAALERG-GGRGLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQ--------------WAEELR 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 733 RFTDAAEsraVIDGLADGSVDIVIGTHRLLQTGVRWKDL----GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMSATPIp 808
Cdd:COG1061 149 RFLGDPL---AGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF- 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 809 RT-----LEMSLAGIR--------------------EMSTILTPPEERYPVLT------YVGPHDDK-QIAAALRRELLR 856
Cdd:COG1061 225 RSdgreiLLFLFDGIVyeyslkeaiedgylappeyyGIRVDLTDERAEYDALSerlreaLAADAERKdKILRELLREHPD 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 857 DGQAFYVHNRVSSIDAAAARVRELVPEARVVvaHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERA 936
Cdd:COG1061 305 DRKTLVFCSSVDHAEALAELLNEAGIRAAVV--TGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRP 382
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 937 dTFGLSQLHQLRGRVGRSRERG-YAYFL--YPPQVPLTETAYDRLatiaqnnELGAGMAVALKDLEIRGAGNVLGIEQSG 1013
Cdd:COG1061 383 -TGSPREFIQRLGRGLRPAPGKeDALVYdfVGNDVPVLEELAKDL-------RDLAGYRVEFLDEEESEELALLIAVKPA 454
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 1014 HVAGVGFDLYVRLVGEALETYRDAYRAAADGQTVRTAEEPKDVRIDLPVDAHLPPDYIASDRLRLEGYRRLAAASSDREV 1093
Cdd:COG1061 455 LEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLL 534
|
490 500 510
....*....|....*....|....*....|
gi 489500368 1094 AAVVDELTDRYGALPEPARRLAAVARLRLL 1123
Cdd:COG1061 535 LLELLELLAALLRLEELAALLLKELLRAAL 564
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
885-953 |
1.55e-12 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 64.16 E-value: 1.55e-12
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489500368 885 RVVVAHGQMPEDLLETTVQRFWNREHDILVCTTIVETGLDISNANTLIVERADtFGLSQLHQLRGRVGR 953
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGR 80
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
653-779 |
4.47e-12 |
|
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: 65.69 E-value: 4.47e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 653 QLTAIEEVKA--DMEKPIpmdrVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMsGFPVTI-- 728
Cdd:cd17929 1 QRKAYEAIVSslGGFKTF----LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRF-GDKVAVlh 75
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 489500368 729 KGLSRFTDAAESRavidGLADGSVDIVIGTHRLLQTGVrwKDLGLVVVDEE 779
Cdd:cd17929 76 SKLSDKERADEWR----KIKRGEAKVVIGARSALFAPF--KNLGLIIVDEE 120
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
679-957 |
2.59e-11 |
|
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: 67.59 E-value: 2.59e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 679 GYGKTEIAVRAAFKAVQDGKQVAVLVPTTllaDQHLQTFgERM-SGFP-VTIKGL-----SRFTDAaesravidgladgs 751
Cdd:COG4098 139 GAGKTEMLFPAIAEALKQGGRVCIATPRV---DVVLELA-PRLqQAFPgVDIAALyggseEKYRYA-------------- 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 752 vDIVIGT-HRLLqtgvRWKD-LGLVVVDE---------EQ-RFGVEhkehiKSLRTHVDVLTMSATPiPRTLEMSLA-GI 818
Cdd:COG4098 201 -QLVIATtHQLL----RFYQaFDLLIIDEvdafpysgdPMlQYAVK-----RARKPDGKLIYLTATP-SKALQRQVKrGK 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 819 REMSTILTppeeRY-------PVLTYVGPHDDK--------QIAAALRRELLRDGQAFYVHNRVSSIDAAAARVRELVPE 883
Cdd:COG4098 270 LKVVKLPA----RYhghplpvPKFKWLGNWKKRlrrgklprKLLKWLKKRLKEGRQLLIFVPTIELLEQLVALLQKLFPE 345
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489500368 884 ARVVVAHGQMPEDllETTVQRFWNREHDILVCTTIVETGLDISNANTLIVErAD--TFGLSQLHQLRGRVGRSRER 957
Cdd:COG4098 346 ERIAGVHAEDPER--KEKVQAFRDGEIPILVTTTILERGVTFPNVDVAVLG-ADhpVFTEAALVQIAGRVGRSADY 418
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
596-958 |
6.91e-10 |
|
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: 63.18 E-value: 6.91e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 596 SDWANT--KTKARRAVREIAGELVSLYAKRQASPGhafSPDTPWQAE-LEDAFGFTETVDQLTAIEevkadmekpIPMdr 672
Cdd:COG1203 91 ADWLDSanFDMARQALDHLLAERLERLLPKKSKPR---TPINPLQNEaLELALEAAEEEPGLFILT---------APT-- 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 673 vicgdvGYGKTEIAVRAAFKAVQDGKQ--VAVLVPTTLLADQHLQTFgERMSGFPVTIKGLSRFTDAAESRAVIDGLADG 750
Cdd:COG1203 157 ------GGGKTEAALLFALRLAAKHGGrrIIYALPFTSIINQTYDRL-RDLFGEDVLLHHSLADLDLLEEEEEYESEARW 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 751 SVD--------IVIGT-----HRLLQTGVRW--KDLGL----VVVDEEQRFGVE-----HK--EHIKSLRTHVdVLtMSA 804
Cdd:COG1203 230 LKLlkelwdapVVVTTidqlfESLFSNRKGQerRLHNLansvIILDEVQAYPPYmlallLRllEWLKNLGGSV-IL-MTA 307
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 805 TpIPRTLEMSLAGIREMSTILTPPEERYP-------VLTYVGPHDDKQIAAALRRELLRDGQAFYVHNRVSSIDAAAARV 877
Cdd:COG1203 308 T-LPPLLREELLEAYELIPDEPEELPEYFrafvrkrVELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDAQELYEAL 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 878 RELVPEARVVVAHGQMP----EDLLETTVQRFWNREHDILVCTTIVETGLDISnANTLIVERAdtfGLSQLHQLRGRVGR 953
Cdd:COG1203 387 KEKLPDEEVYLLHSRFCpadrSEIEKEIKERLERGKPCILVSTQVVEAGVDID-FDVVIRDLA---PLDSLIQRAGRCNR 462
|
....*
gi 489500368 954 SRERG 958
Cdd:COG1203 463 HGRKE 467
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
676-812 |
8.00e-09 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 59.70 E-value: 8.00e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 676 GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMsGFPVTI--KGLSrftdAAESRAVIDGLADGSVD 753
Cdd:TIGR00595 4 GVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRF-GSQVAVlhSGLS----DSEKLQAWRKVKNGEIL 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489500368 754 IVIGTHRLLQTGVrwKDLGLVVVDEEQRFGVE-------HKEHIKSLRTH---VDVLTMSATPiprTLE 812
Cdd:TIGR00595 79 VVIGTRSALFLPF--KNLGLIIVDEEHDSSYKqeegpryHARDVAVYRAKkfnCPVVLGSATP---SLE 142
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
636-779 |
1.31e-08 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 59.36 E-value: 1.31e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 636 PWQAELEDAFGFTETVDQLTAIEEVKADMEKPIPMdrVICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQ 715
Cdd:COG1198 183 PFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQTVE 260
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489500368 716 TFGERmsgFPVTI----KGLSrftdAAESRAVIDGLADGSVDIVIGThrllqtgvR------WKDLGLVVVDEE 779
Cdd:COG1198 261 RFRAR---FGARVavlhSGLS----DGERLDEWRRARRGEARIVIGT--------RsalfapFPNLGLIIVDEE 319
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
673-964 |
9.02e-08 |
|
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: 55.51 E-value: 9.02e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 673 VICGDVGYGKTEIAVRAAFKAVQDGK--QVAVLVPT-TLLADQHLQ---TFGERMSGFpvTIKGLSRFTDAAESRAVI-- 744
Cdd:cd09639 3 VIEAPTGYGKTEAALLWALHSLKSQKadRVIIALPTrATINAMYRRakeAFGETGLYH--SSILSSRIKEMGDSEEFEhl 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 745 -------------DGLADGSVDIVI-------GTHRLLQTGVRwkdLGLVVVDEEQRFGVEHKEHIKSLRTH-----VDV 799
Cdd:cd09639 81 fplyihsndtlflDPITVCTIDQVLksvfgefGHYEFTLASIA---NSLLIFDEVHFYDEYTLALILAVLEVlkdndVPI 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 800 LTMSATpIPRTLEMSLAGI---REMSTILTPPEERYP----VLTYVGphdDKQIAAALRRELLRDGQAFYVHNRVSSIDA 872
Cdd:cd09639 158 LLMSAT-LPKFLKEYAEKIgyvEENEPLDLKPNERAPfikiESDKVG---EISSLERLLEFIKKGGSVAIIVNTVDRAQE 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 873 AAARVRELVPEARVVVAHGQMPE----DLLETTVQRFWNREHDILVCTTIVETGLDISnANTLIVERADtfgLSQLHQLR 948
Cdd:cd09639 234 FYQQLKEKGPEEEIMLIHSRFTEkdraKKEAELLLEFKKSEKFVIVATQVIEASLDIS-VDVMITELAP---IDSLIQRL 309
|
330
....*....|....*.
gi 489500368 949 GRVGRsRERGYAYFLY 964
Cdd:cd09639 310 GRLHR-YGEKNGEEVY 324
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
673-805 |
4.79e-07 |
|
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: 51.11 E-value: 4.79e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 673 VICGDVGYGKTEIAVRAAFKAVQDGKQVAV-LVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTdaaesraVIDGLADGS 751
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLGKNVGLLTGDP-------SVNKLLLAE 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489500368 752 VDIVIGTH-----RLLQTGVRW-KDLGLVVVDEEQRFGVEHK--------EHIKSLRTHVDVLTMSAT 805
Cdd:cd17921 94 ADILVATPekldlLLRNGGERLiQDVRLVVVDEAHLIGDGERgvvlelllSRLLRINKNARFVGLSAT 161
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
676-779 |
1.42e-06 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 52.47 E-value: 1.42e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 676 GDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMsGFPVTI--KGLSrftdAAESRAVIDGLADGSVD 753
Cdd:PRK05580 169 GVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQMLARFRARF-GAPVAVlhSGLS----DGERLDEWRKAKRGEAK 243
|
90 100 110
....*....|....*....|....*....|..
gi 489500368 754 IVIGThrllqtgvR------WKDLGLVVVDEE 779
Cdd:PRK05580 244 VVIGA--------RsalflpFKNLGLIIVDEE 267
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
912-965 |
7.03e-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: 45.00 E-value: 7.03e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 489500368 912 ILVCTTIVETGLDISNANTLIVERADTFgLSQLHQLRGRVGRSRERGYAYFLYP 965
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDEGEVILFV 77
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
521-579 |
1.40e-05 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 46.28 E-value: 1.40e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 489500368 521 GDLVVHDQHGIGRFVEMVERTVGGARREYLVLEYasakrgggAKNTDKLYVPMDSLDQL 579
Cdd:COG1329 4 GDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRF--------PYDDMTIMVPVDKAESV 54
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
681-778 |
1.79e-05 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 48.74 E-value: 1.79e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 681 GKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSRFTDaaesravIDGLADGSVDIVIGT-- 758
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGDYD-------SDDEWLGRYDILVATpe 122
|
90 100
....*....|....*....|...
gi 489500368 759 --HRLLQTGVRW-KDLGLVVVDE 778
Cdd:COG1204 123 klDSLLRNGPSWlRDVDLVVVDE 145
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
673-805 |
3.73e-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: 42.71 E-value: 3.73e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 673 VICGDVGYGKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFG--ERMsGFPVTIK-GLSRFTDaaesraviDGLAD 749
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKklEEI-GLKVGIStGDYDEDD--------EWLGD 91
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489500368 750 gsVDIVIGTHR----LLQTGVRW-KDLGLVVVDEEQRFGVEHK--------EHIKSLRTHVDVLTMSAT 805
Cdd:cd18028 92 --YDIIVATYEkfdsLLRHSPSWlRDVGVVVVDEIHLISDEERgptlesivARLRRLNPNTQIIGLSAT 158
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
876-963 |
7.13e-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: 41.19 E-value: 7.13e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 876 RVRELVPEARVVVAHGQMPEDLLETtVQRFWNREHDILVCTTIVETGLDISNANTLIVERADTFGLSQLhQLRGRVGRSR 955
Cdd:cd18801 58 RATRFIGQASGKSSKGMSQKEQKEV-IEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMI-QRMGRTGRKR 135
|
....*...
gi 489500368 956 ErGYAYFL 963
Cdd:cd18801 136 Q-GRVVVL 142
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
653-806 |
7.47e-04 |
|
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: 41.14 E-value: 7.47e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 653 QLTAIEEVKADMEKpipmDR-VICGDVGYGKTEIAVRAAFKAVQDGkqVAVLVPTTLLADQ---HLQTFGERMSgfpvti 728
Cdd:cd17926 5 QEEALEAWLAHKNN----RRgILVLPTGSGKTLTALALIAYLKELR--TLIVVPTDALLDQwkeRFEDFLGDSS------ 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 729 kgLSRFTdaAESRAVIDGladgsVDIVIGT----HRLLQTGVRWKDL-GLVVVDEEQRFGVEHKEHIKSLRTHVDVLTMS 803
Cdd:cd17926 73 --IGLIG--GGKKKDFDD-----ANVVVATyqslSNLAEEEKDLFDQfGLLIVDEAHHLPAKTFSEILKELNAKYRLGLT 143
|
...
gi 489500368 804 ATP 806
Cdd:cd17926 144 ATP 146
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
877-977 |
1.09e-03 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' 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 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: 350191 [Multi-domain] Cd Length: 238 Bit Score: 42.23 E-value: 1.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 877 VRELVPEARVV------VAHGQMPEDLLEttvqRFWNREHDILVCTTIVETGLDISNANTLIVERAD------------- 937
Cdd:cd18804 110 LKTLFPEARIAridrdtTRKKGALEKLLD----QFERGEIDILIGTQMIAKGLDFPNVTLVGILNADsglnspdfraser 185
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 489500368 938 TFGLsqLHQLRGRVGRSRERGYAYF-LYPPQVPLTETAYDR 977
Cdd:cd18804 186 AFQL--LTQVSGRAGRGDKPGKVIIqTYNPEHPLIQAAKEE 224
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
837-961 |
3.01e-03 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350174 [Multi-domain] Cd Length: 131 Bit Score: 39.03 E-value: 3.01e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 837 YVGPHDDKQIAAALRRELLRDGQA--FyvhnrVSSIDAAAaRVRELVPEARVVVA--HGQMPEDLLETTVQRFWNREHDI 912
Cdd:cd18787 7 VVEEEEKKLLLLLLLLEKLKPGKAiiF-----VNTKKRVD-RLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRV 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 489500368 913 LVCTTIVETGLDISNANtLIV-----ERADTFglsqLHqlR-GRVGRSRERGYAY 961
Cdd:cd18787 81 LVATDVAARGLDIPGVD-HVInydlpRDAEDY----VH--RiGRTGRAGRKGTAI 128
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
681-778 |
7.05e-03 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 40.71 E-value: 7.05e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 681 GKTEIAVRAAFKAVQDGKQVAVLVPTTLLADQHLQTFgERMSGFPVTIkGLSrfTDAAESRAviDGLadGSVDIVIGTHR 760
Cdd:PRK02362 51 GKTLIAELAMLKAIARGGKALYIVPLRALASEKFEEF-ERFEELGVRV-GIS--TGDYDSRD--EWL--GDNDIIVATSE 122
|
90 100
....*....|....*....|...
gi 489500368 761 ----LLQTGVRW-KDLGLVVVDE 778
Cdd:PRK02362 123 kvdsLLRNGAPWlDDITCVVVDE 145
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
679-778 |
8.00e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain] Cd Length: 200 Bit Score: 39.07 E-value: 8.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 679 GYGKTEIAVRAAFKAVQ--DGKQVAVLVPTTLLADQHLQT-FGERMSGFPVT-IKGLSrftdaaESRAVIDGLADGSvDI 754
Cdd:cd18075 27 GAGKTRAAVYVARRHLEtkRGAKVAVLVNKVHLVDQHLEKeFHVLLDKYTVTaISGDS------SHKCFFGQLARGS-DV 99
|
90 100 110
....*....|....*....|....*....|...
gi 489500368 755 VIGTHRLLQTG---------VRWKDLGLVVVDE 778
Cdd:cd18075 100 VICTAQILQNAllsgeeeahVELTDFSLLVIDE 132
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
673-806 |
8.36e-03 |
|
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: 38.95 E-value: 8.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489500368 673 VICGDVGYGKTEIAVRAA------FKAVQDGKqVAVLVPTTLLADQHLQTFGERMSGFPVTIKGLSrftdAAESRAVIDG 746
Cdd:cd17927 21 IICLPTGSGKTFVAVLICehhlkkFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS----GDTSENVSVE 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489500368 747 LADGSVDIVIGTHRLLQ------TGVRWKDLGLVVVDEEQRFGVEH----------KEHIKSLRTHVDVLTMSATP 806
Cdd:cd17927 96 QIVESSDVIIVTPQILVndlksgTIVSLSDFSLLVFDECHNTTKNHpyneimfrylDQKLGSSGPLPQILGLTASP 171
|
|
| |
