|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
14-1115 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1360.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 14 PLSVRGAKTTFASYLVSRIFGDMAGPLLVVVPNESEVLPLQGDLALF--GVESIALPSWGTSAYAEPSSRSSAWGERMRA 91
Cdd:COG1197 4 RLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFlpDLPVLLFPAWETLPYDRFSPSPDIVSERLAT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 92 MVEMNRGARRVVIAPMRAIMMRTASPGDLLEQVITLETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFLP 171
Cdd:COG1197 84 LRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIFPP 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 172 GWDFPCRAVFDFDEISGIRLFDAVTQASREKISTLQVYPLRESLWTREERDLLFQEALQWPEMRAVKNQVLDLAERETAP 251
Cdd:COG1197 164 GSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALSEGIAF 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 252 P---YWTAAFsqeFRQSATVFDYLHRHGRVIWIDPQRTIALGESFRKEYESIFAE--EHFRRPLPRPERVFLSCQDLMER 326
Cdd:COG1197 244 AgieYYLPLF---YEELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEArrHDRGRPLLPPEELFLDPEELFAA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 327 VQNSS-VHFDSLASAREAGG-IRFSCDPPRSFFGNINYLKEELSTLTGSGHRVIVVADTEAQQKRIEFLLRDYAVD---- 400
Cdd:COG1197 321 LKRRPrVTLSPFAALPEGAGvVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRRERLLELLRDHGIParlv 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 401 ------------VVLGHITGGFALPEQRLVVIQENEIFGRR-RRAPASLRKTESAPIDTFVELDEGDYVVHMNYGIGRFC 467
Cdd:COG1197 401 eslaelspggvaITVGPLEHGFELPDAKLAVITESELFGERvKRRRRKKKRSADAFIRDLSELKPGDYVVHVDHGIGRYL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 468 GIKRMTAAGNERDYIQLEYADEESVFTPIEQVNLIQRYIGSGGTPPRLDKIGGKSWEKRKGAVRKNVEDLADRLIALYSR 547
Cdd:COG1197 481 GLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIAAELLKLYAE 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 548 RKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVASGKQVAF 627
Cdd:COG1197 561 RAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKAVMDGKQVAV 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 628 LAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLIIVDEEQRF 707
Cdd:COG1197 641 LVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGLLIIDEEQRF 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 708 GVKDKERLKELKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPPHNRQPVETVIAEFSDETIARAIRAEVERGGQVFF 787
Cdd:COG1197 721 GVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRELLRGGQVFY 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 788 LHNRVETLENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADMYGIS 867
Cdd:COG1197 801 VHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIIIERADRFGLA 880
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 868 QLYQLRGRVGRSDRTSFAYLFYPDQRALSELAMKRLEIINDFTELGSGFKIAMKDLEVRGAGNLLGSQQSGDIGSIGFDL 947
Cdd:COG1197 881 QLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSGHIAEVGFDL 960
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 948 YLKLLDDAIRS--AEKPaasgDDQGEEVYLELEYTGFIPDQYIEEPMEKMEVYKKIASVTTDAQFEELIGEIEDRFGPMP 1025
Cdd:COG1197 961 YLQMLEEAVAAlkGGKE----PEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELIDRFGPLP 1036
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 1026 EEIQSLLALAEIRILARRLHVASLRERQGRLAVEFGKVASVSVDRVLSLIKNSGGAVSLDPQRPNVIIMETgrVGLKEKS 1105
Cdd:COG1197 1037 EEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDL--EDPEERL 1114
|
1130
....*....|
gi 1339315144 1106 EFIRGRLAQL 1115
Cdd:COG1197 1115 EALEELLEAL 1124
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
142-1049 |
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: 1092.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 142 LIQMGYWRVPKVSVHGEFALRGEVLDIFLPGWDFPCRAVFDFDEISGIRLFDAVTQASREKISTLQVYPLRES-LWTREE 220
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFiLLEEET 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 221 RDLLFQEALQWPEMRAVKNqvLDLAERETAPPYWTAAFSQEFRQSATVFDYLHRHGRVIWIDPQRTIALGESFRKEYESI 300
Cdd:TIGR00580 81 IARLKDNAARVEDAKHLET--IEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILLDDPERFHSAARFLQRELEEF 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 301 FAEEHFRRPLPRPERVFLSCQDLMERVQNSSVHFDSLAS------AREAggIRFSCDPPRSFFGNINYLKEELSTLTGSG 374
Cdd:TIGR00580 159 YNALEEAKKLINPPRLDLDPSELAFEASAISLSRVQLENehlslkASEA--IEGAQKHSRLEFGEILAFKEELFRWLKAG 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 375 HRVIVVADTEAQQKRIEFLL--RDYAVDV----------VLGHITG----GFALPEQRLVVIQENEIFGRRRRAPASLRK 438
Cdd:TIGR00580 237 FKITVAAESESQAERLKSLLaeHDIAAQVidesciiipaVRYVMIGalssGFILPTAGLAVITESELFGSRVLRRPKKSR 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 439 TESAPIDTFVELDEGDYVVHMNYGIGRFCGIKRMTAAGNERDYIQLEYADEESVFTPIEQVNLIQRYIGSGGTPPRLDKI 518
Cdd:TIGR00580 317 LKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPALDKL 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 519 GGKSWEKRKGAVRKNVEDLADRLIALYSRRKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRL 598
Cdd:TIGR00580 397 GGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRL 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 599 VCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSID 678
Cdd:TIGR00580 477 VCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASGKID 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 679 AVIGTHSILQKTVEFQNLGLIIVDEEQRFGVKDKERLKELKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPPHNRQP 758
Cdd:TIGR00580 557 ILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPEDRLP 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 759 VETVIAEFSDETIARAIRAEVERGGQVFFLHNRVETLENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVL 838
Cdd:TIGR00580 637 VRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVL 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 839 VATTIIENGIDIPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQRALSELAMKRLEIINDFTELGSGFKI 918
Cdd:TIGR00580 717 VCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAGFKI 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 919 AMKDLEVRGAGNLLGSQQSGDIGSIGFDLYLKLLDDAIrsAEKPAASGDDQGEEVYLELEYTGFIPDQYIEEPMEKMEVY 998
Cdd:TIGR00580 797 ALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAI--EELKGGKPPKLEEETDIELPYSAFIPDDYIADDSLRLEFY 874
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|.
gi 1339315144 999 KKIASVTTDAQFEELIGEIEDRFGPMPEEIQSLLALAEIRILARRLHVASL 1049
Cdd:TIGR00580 875 KRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKL 925
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
37-1115 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 654.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 37 AGPLLVVVPNESEVLPLQGDLALFGVESI-ALPSWGTSAYAEPSSRSSAWGERMRAMVEMNRGARRVVIAPMRAIMMRTA 115
Cdd:PRK10689 39 AGPVVLIAPDMQNALRLHDEIQQFTDQMVmNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLILPVNTLMQRVC 118
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 116 SPGDLLEQVITLETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFLPGWDFPCRAVFDFDEISGIRLFDAV 195
Cdd:PRK10689 119 PHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVD 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 196 TQASREKISTLQVYPLREsLWTREERDLLFQEalQWPEMRAVK---NQVLDLAERETAPP---YWTAAFsqeFRQS-ATV 268
Cdd:PRK10689 199 SQRTLEEVEAINLLPAHE-FPTDKAAIELFRS--QWRDTFEVKrdaEHIYQQVSKGTLPAgieYWQPLF---FSEPlPPL 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 269 FDYLHRHGRVI------------W-----------IDPQRTIALGESFRKEYESIFAEehfrrpLPRPERVFLSCQDLME 325
Cdd:PRK10689 273 FSYFPANTLLVntgdletsaerfWadtlarfenrgVDPMRPLLPPESLWLRVDELFSE------LKNWPRVQLKTEHLPT 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 326 RVQNSSVHFDSLASAREAGGIRFSCDPPRSFfgninylkeeLSTLTGsghRVIVVADTEAQQKRIEFLLRDYAVD----- 400
Cdd:PRK10689 347 KAANTNLGYQKLPDLAVQAQQKAPLDALRRF----------LESFDG---PVVFSVESEGRREALGELLARIKIApkrim 413
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 401 -----------VVLGHITGGFALPEQRLVVIQENEIFGRR--RRAPASlRKTESAP--IDTFVELDEGDYVVHMNYGIGR 465
Cdd:PRK10689 414 rldeasdrgryLMIGAAEHGFIDTVRNLALICESDLLGERvaRRRQDS-RRTINPDtlIRNLAELHPGQPVVHLEHGVGR 492
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 466 FCGIKRMTAAGNERDYIQLEYADEESVFTPIEQVNLIQRYIGSGGTPPRLDKIGGKSWEKRKGAVRKNVEDLADRLIALY 545
Cdd:PRK10689 493 YAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIY 572
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 546 SRRKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVASGKQV 625
Cdd:PRK10689 573 AQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQV 652
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 626 AFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLIIVDEEQ 705
Cdd:PRK10689 653 AVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEH 732
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 706 RFGVKDKERLKELKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPPHNRQPVETVIAEFSDETIARAIRAEVERGGQV 785
Cdd:PRK10689 733 RFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQV 812
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 786 FFLHNRVETLENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADMYG 865
Cdd:PRK10689 813 YYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFG 892
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 866 ISQLYQLRGRVGRSDRTSFAYLFYPDQRALSELAMKRLEIINDFTELGSGFKIAMKDLEVRGAGNLLGSQQSGDIGSIGF 945
Cdd:PRK10689 893 LAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGF 972
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 946 DLYLKLLD---DAIRSAEKPAASgDDQGEEVYLELEYTGFIPDQYIEEPMEKMEVYKKIASVTTDAQFEELIGEIEDRFG 1022
Cdd:PRK10689 973 SLYMELLEnavDALKAGREPSLE-DLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFG 1051
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 1023 PMPEEIQSLLALAEIRILARRLHVASLRERQGRLAVEFGKVASVSVDRVLSLIKNSGGAVSLD-PQRPNVIIMETGRvgl 1101
Cdd:PRK10689 1052 LLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDgPTRLKFIQDLSER--- 1128
|
1130
....*....|....
gi 1339315144 1102 KEKSEFIRGRLAQL 1115
Cdd:PRK10689 1129 KTRIEWVRQFMREL 1142
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
541-953 |
2.00e-134 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 423.31 E-value: 2.00e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 541 LIALYSRRKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVA 620
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 621 SGKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLII 700
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 701 VDEEQRFGVKDKERLKELKHSVDCLTLTATPIPRTLHMSL---LkirDMSLLRTPPHNRQPVETVIaeFSDETIARA--- 774
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLygdL---DVSVIDELPPGRKPIKTRV--VPEERRDEVyer 461
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 775 IRAEVERGGQVFF------------LHNRVETLENVQQFLeqlvPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATT 842
Cdd:COG1200 462 IREEIAKGRQAYVvcplieesekldLQAAEETYEELREAF----PGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATT 537
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 843 IIENGIDIPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQraLSELAMKRLEII---NDftelgsGFKIA 919
Cdd:COG1200 538 VIEVGVDVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMretND------GFEIA 609
|
410 420 430
....*....|....*....|....*....|....
gi 1339315144 920 MKDLEVRGAGNLLGSQQSGDIGsigfdlyLKLLD 953
Cdd:COG1200 610 EEDLELRGPGEFLGTRQSGLPD-------LRIAD 636
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
540-938 |
1.50e-129 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 410.70 E-value: 1.50e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 540 RLIALYSRRKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAV 619
Cdd:PRK10917 228 SLLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAI 307
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 620 ASGKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLI 699
Cdd:PRK10917 308 EAGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLV 387
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 700 IVDEEQRFGVKDKERLKELKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPPHNRQPVETVIA--EFSDETIARaIRA 777
Cdd:PRK10917 388 IIDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIpdSRRDEVYER-IRE 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 778 EVERGGQVFFLHNRVE--------TLENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGID 849
Cdd:PRK10917 467 EIAKGRQAYVVCPLIEesekldlqSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVD 546
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 850 IPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQraLSELAMKRLEII---NDftelgsGFKIAMKDLEVR 926
Cdd:PRK10917 547 VPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP--LSETARERLKIMretND------GFVIAEKDLELR 618
|
410
....*....|..
gi 1339315144 927 GAGNLLGSQQSG 938
Cdd:PRK10917 619 GPGELLGTRQSG 630
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
559-751 |
1.10e-120 |
|
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: 368.82 E-value: 1.10e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 559 DTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQH 638
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 639 YENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLIIVDEEQRFGVKDKERLKEL 718
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1339315144 719 KHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRT 751
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
546-938 |
1.56e-116 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 374.37 E-value: 1.56e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 546 SRRKKVQGYGFP--PDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVASGK 623
Cdd:TIGR00643 206 RLGEKQQFSAPPanPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGY 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 624 QVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLIIVDE 703
Cdd:TIGR00643 286 QVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDE 365
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 704 EQRFGVKDKERLKE---LKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPPHNRQPVETVIAEFSDETIA-RAIRAEV 779
Cdd:TIGR00643 366 QHRFGVEQRKKLREkgqGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVyEFIEEEI 445
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 780 ERGGQVFFLHNRVE-----TLENVQQFLEQL---VPEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIP 851
Cdd:TIGR00643 446 AKGRQAYVVYPLIEeseklDLKAAEALYERLkkaFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 852 NVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQraLSELAMKRLEIINDFTElgsGFKIAMKDLEVRGAGNL 931
Cdd:TIGR00643 526 NATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNP--KSESAKKRLRVMADTLD---GFVIAEEDLELRGPGDL 600
|
....*..
gi 1339315144 932 LGSQQSG 938
Cdd:TIGR00643 601 LGTKQSG 607
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
540-753 |
2.06e-74 |
|
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: 245.52 E-value: 2.06e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 540 RLIALYSRRKKVQGYGFPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAV 619
Cdd:cd17992 12 ALLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 620 ASGKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVIGTHSILQKTVEFQNLGLI 699
Cdd:cd17992 92 ENGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLV 171
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1339315144 700 IVDEEQRFGVKDKERLKELKHSVDCLTLTATPIPRTLHMSLLKIRDMSLLRTPP 753
Cdd:cd17992 172 IIDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
758-906 |
1.40e-64 |
|
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: 214.90 E-value: 1.40e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 758 PVETVIAEFSDETIARAIRAEVERGGQVFFLHNRVETLENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMHRFVSGAFHV 837
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 838 LVATTIIENGIDIPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQRALSELAMKRLEII 906
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAI 149
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
565-750 |
2.32e-57 |
|
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: 195.71 E-value: 2.32e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 565 EFESTFPYEETEDQLRCLAEIKQDMERPQPMDRLVCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQHYENMLE 644
Cdd:cd17918 7 ELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARK 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 645 RFDRFPVklAMLSRFVKNKekkeVLQGlasgsIDAVIGTHSILQKTVEFQNLGLIIVDEEQRFGVKDKERLKELKhSVDC 724
Cdd:cd17918 87 FLPFINV--ELVTGGTKAQ----ILSG-----ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLG-ATHF 154
|
170 180
....*....|....*....|....*.
gi 1339315144 725 LTLTATPIPRTLHMSLLKIRDMSLLR 750
Cdd:cd17918 155 LEATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
758-906 |
1.13e-56 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 192.87 E-value: 1.13e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 758 PVETVIAEFSDET-IARAIRAEVERGGQVFFLHNRVET--------LENVQQFLEQLVPEVIVESAHGQMGGRQLEDIMH 828
Cdd:cd18792 1 PIRTYVIPHDDLDlVYEAIERELARGGQVYYVYPRIEEsekldlksIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1339315144 829 RFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQRALSELAMKRLEII 906
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAI 158
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
449-546 |
2.83e-35 |
|
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: 129.50 E-value: 2.83e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 449 ELDEGDYVVHMNYGIGRFCGIKRMTAAGNERDYIQLEYADEESVFTPIEQVNLIQRYIGSGGT-PPRLDKIGGKSWEKRK 527
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEvEPVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1339315144 528 GAVRKNVEDLADRLIALYS 546
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
758-908 |
3.81e-32 |
|
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: 122.84 E-value: 3.81e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 758 PVETVIAEFSD-ETIARAIRAEVERGGQVFFLHNRVET-----LENVQQFLEQL----VPEVIVESAHGQMGGRQLEDIM 827
Cdd:cd18811 1 PITTYLIFHTRlDKVYEFVREEIAKGRQAYVIYPLIEEsekldLKAAVAMYEYLkerfRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 828 HRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADMYGISQLYQLRGRVGRSDRTSFAYLFYPDQraLSELAMKRLEIIN 907
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVMT 158
|
.
gi 1339315144 908 D 908
Cdd:cd18811 159 E 159
|
|
| TRCF |
pfam03461 |
TRCF domain; |
977-1071 |
2.42e-29 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 112.52 E-value: 2.42e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 977 LEYTGFIPDQYIEEPMEKMEVYKKIASVTTDAQFEELIGEIEDRFGPMPEEIQSLLALAEIRILARRLHVASLRERQGRL 1056
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 1339315144 1057 AVEFGKVASVSVDRV 1071
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
976-1075 |
1.75e-27 |
|
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: 107.17 E-value: 1.75e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 976 ELEYTGFIPDQYIEEPMEKMEVYKKIASVTTDAQFEELIGEIEDRFGPMPEEIQSLLALAEIRILARRLHVASLRERQGR 1055
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 1339315144 1056 LAVEFGKVASVSVDRVLSLI 1075
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
450-545 |
3.28e-26 |
|
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: 103.29 E-value: 3.28e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 450 LDEGDYVVHMNYGIGRFCGIKRMTaagnERDYIQLEYADEESVFTPIEQVNLIQRYIGSGgtppRLDKIG-GKSWEKRKG 528
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 1339315144 529 AVRKNVEDLADRLIALY 545
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
575-738 |
6.61e-26 |
|
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: 105.02 E-value: 6.61e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 575 TEDQLRCLAEIKQDMerpqpmDRLVCGDVGYGKTELALRAAFKAVA---SGKQVAFLAPTTILAEQHYENMLERFDRFPV 651
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 652 KlamLSRFVKNKEKKEVLQGLASGSIdaVIGTH----SILQKTVEFQNLGLIIVDEEQRFGVKD-----KERLKELKHSV 722
Cdd:pfam00270 75 K---VASLLGGDSRKEQLEKLKGPDI--LVGTPgrllDLLQERKLLKNLKLLVLDEAHRLLDMGfgpdlEEILRRLPKKR 149
|
170
....*....|....*.
gi 1339315144 723 DCLTLTATPiPRTLHM 738
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
566-757 |
2.84e-24 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 101.80 E-value: 2.84e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 566 FESTFPYEETEDQLRCLAEIKQDMerpqpMDRLVCGDVGYGKTELALRAAFKAVASG--KQVAFLAPTTILAEQHYENML 643
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 644 ERFDRFPVKLAMLsrfVKNKEKKEVLQGLASGSIDAVIGT-----HSILQKTVEFQNLGLIIVDEEQRFGVKD-----KE 713
Cdd:smart00487 76 KLGPSLGLKVVGL---YGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDGGfgdqlEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1339315144 714 RLKELKHSVDCLTLTATP---IPRTLHMSLLKIRDMSLLRTPPHNRQ 757
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPIE 199
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
125-213 |
1.69e-21 |
|
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: 89.76 E-value: 1.69e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 125 ITLETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFLPG-WDFPCRAVFDFDEISGIRLFDAVTQASREKI 203
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYsEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|
gi 1339315144 204 STLQVYPLRE 213
Cdd:pfam17757 81 DEVTIYPASH 90
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
578-704 |
1.50e-19 |
|
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: 87.26 E-value: 1.50e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 578 QLRCLAEIKQDMERPQPMdrLVCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQhyenMLERF-DRFPVKLAML 656
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQ----LIKRFkKRFGDKVAVL 74
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1339315144 657 SRFVKNKEKKEVLQGLASGSIDAVIGTHSILqkTVEFQNLGLIIVDEE 704
Cdd:cd17929 75 HSKLSDKERADEWRKIKRGEAKVVIGARSAL--FAPFKNLGLIIVDEE 120
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
778-878 |
2.49e-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: 84.18 E-value: 2.49e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 778 EVERGGQVFFLHNRVETLEnVQQFLEQLvpEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTII 857
Cdd:pfam00271 11 KKERGGKVLIFSQTKKTLE-AELLLEKE--GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI 87
|
90 100
....*....|....*....|.
gi 1339315144 858 IDRADmYGISQLYQLRGRVGR 878
Cdd:pfam00271 88 NYDLP-WNPASYIQRIGRAGR 107
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
598-881 |
1.41e-17 |
|
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: 87.44 E-value: 1.41e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQhyenMLERF-DRFPVKLAMLSRFVKNKEKKEVLQGLASGS 676
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQ----MIQRFkYRFGSQVAVLHSGLSDSEKLQAWRKVKNGE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 677 IDAVIGTHSILqkTVEFQNLGLIIVDEEQ----------RFGVKDKERLKELKHSVDCLTLTATPIPRTLH-MSLLKIRD 745
Cdd:TIGR00595 77 ILVVIGTRSAL--FLPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHnAKQKAYRL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 746 MSLLRTPPHNRQPVETVI--------AEFSDETIaRAIRAEVERGGQV--FF---------------------------- 787
Cdd:TIGR00595 155 LVLTRRVSGRKPPEVKLIdmrkeprqSFLSPELI-TAIEQTLAAGEQSilFLnrrgysknllcrscgyilccpncdvslt 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 788 LHNRVETL------------------------------ENVQQFLEQLVPEV---IVESAHGQMGGrQLEDIMHRFVSGA 834
Cdd:TIGR00595 234 YHKKEGKLrchycgyqepipktcpqcgsedlvykgygtEQVEEELAKLFPGAriaRIDSDTTSRKG-AHEALLNQFANGK 312
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 1339315144 835 FHVLVATTIIENGIDIPNVNTIIIDRAD--MY---------GISQLYQLRGRVGRSDR 881
Cdd:TIGR00595 313 ADILIGTQMIAKGHHFPNVTLVGVLDADsgLHspdfraaerGFQLLTQVAGRAGRAED 370
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
595-730 |
7.86e-16 |
|
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: 75.52 E-value: 7.86e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 595 MDRLVCGDVGYGKTELALRAAFKAVAS-GKQVAFLAPTTILAEQHYENMLERFDRfPVKLAMLSRFVKNKEKKEVLQGLA 673
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEEREKNKLGDA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 674 sgsiDAVIGTHSILQKTVE------FQNLGLIIVDEEQRFGVKDKERL-------KELKHSVDCLTLTAT 730
Cdd:cd00046 81 ----DIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
525-704 |
1.80e-15 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 81.32 E-value: 1.80e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 525 KRKGAVRKNVEDLADR-LIALYSRRkkvqgygfPPDTEWQMEFESTFPYEETEDQLRCLAEIKQDMERPQPMdrLVCGDV 603
Cdd:COG1198 154 KEAGVSRSVLKALVKKgLLEIEERE--------VDRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVT 223
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKAVASGKQVAFLAPTTILAEQhyenMLERF-DRFPVKLAML-SRfVKNKEKKEVLQGLASGSIDAVI 681
Cdd:COG1198 224 GSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQ----TVERFrARFGARVAVLhSG-LSDGERLDEWRRARRGEARIVI 298
|
170 180
....*....|....*....|....
gi 1339315144 682 GTHS-ILqktVEFQNLGLIIVDEE 704
Cdd:COG1198 299 GTRSaLF---APFPNLGLIIVDEE 319
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
796-878 |
3.37e-15 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 71.47 E-value: 3.37e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 796 ENVQQFLEQLvpEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADmYGISQLYQLRGR 875
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGR 77
|
...
gi 1339315144 876 VGR 878
Cdd:smart00490 78 AGR 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
578-1021 |
3.14e-14 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 76.99 E-value: 3.14e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 578 QLRCLAEIKQDMERPQpmDR-LVCGDVGYGKTELALRAAfKAVASGKQVAFLAPTTILAEQHYENMLERFDRFPVKlaml 656
Cdd:COG1061 85 QQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLGDPLAG---- 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 657 srfvknkekkevlQGLASGSIDAVIGTHSILQKTVEFQNL----GLIIVDEEQRFGVKDKERLKELKHSVDCLTLTATPI 732
Cdd:COG1061 158 -------------GGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPF 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 733 pRT-----LHMSLLKIR-DMSLLR-------TPPH-----------------NRQPVETVIAEFSDET--IARAIRAEVE 780
Cdd:COG1061 225 -RSdgreiLLFLFDGIVyEYSLKEaiedgylAPPEyygirvdltderaeydaLSERLREALAADAERKdkILRELLREHP 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 781 RGGQVFFLHNRVETLENVQQFLEQLVPEVIVesAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDR 860
Cdd:COG1061 304 DDRKTLVFCSSVDHAEALAELLNEAGIRAAV--VTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLR 381
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 861 admyGIS---QLYQLRGRVGR-SDRTSFAYLF------YPDQRALSE----LAMKRLEIINDFTELGSGFKIAMKDLEVR 926
Cdd:COG1061 382 ----PTGsprEFIQRLGRGLRpAPGKEDALVYdfvgndVPVLEELAKdlrdLAGYRVEFLDEEESEELALLIAVKPALEV 457
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 927 GAGN------LLGSQQSGDIGSIGFDLYLKLLDDAIRSAEKPAASGDDQGEEVYLELEYTGFIPDQYIEEPMEKMEVYKK 1000
Cdd:COG1061 458 KGELeeelleELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLE 537
|
490 500
....*....|....*....|.
gi 1339315144 1001 IASVTTDAQFEELIGEIEDRF 1021
Cdd:COG1061 538 LLELLAALLRLEELAALLLKE 558
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
601-704 |
1.30e-13 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 75.19 E-value: 1.30e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 601 GDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQhyenMLERF-DRFPVKLAML-SRfVKNKEKKEVLQGLASGSID 678
Cdd:PRK05580 169 GVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQ----MLARFrARFGAPVAVLhSG-LSDGERLDEWRKAKRGEAK 243
|
90 100
....*....|....*....|....*....
gi 1339315144 679 AVIGTHSILqktveF---QNLGLIIVDEE 704
Cdd:PRK05580 244 VVIGARSAL-----FlpfKNLGLIIVDEE 267
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
561-880 |
1.51e-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: 71.06 E-value: 1.51e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 561 EWQMEFestfpyeeTEDQLRCLAEIKQDMERPQPMdrL---VCGDvgyGKTELALRAAFKAVASGKQVAFLAPTTilaeq 637
Cdd:COG4098 106 TWEGTL--------TPAQQKASDELLEAIKKKEEH--LvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRV----- 167
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 638 hyENMLERFDR----FP-VKLAMLSRFVKNKEKKEVLqglasgsidaVIGT-HSILQktveF-QNLGLIIVDE------- 703
Cdd:COG4098 168 --DVVLELAPRlqqaFPgVDIAALYGGSEEKYRYAQL----------VIATtHQLLR----FyQAFDLLIIDEvdafpys 231
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 704 --EQ-RFGVKdkerlKELKHSVDCLTLTATPiPRTLhMSLLKIRDMSLLRTP--PHNRQ-PVETVIAEFS---------- 767
Cdd:COG4098 232 gdPMlQYAVK-----RARKPDGKLIYLTATP-SKAL-QRQVKRGKLKVVKLParYHGHPlPVPKFKWLGNwkkrlrrgkl 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 768 DETIARAIRAEVERGGQVF-FLHNrVETLENVQQFLEQLVPEVIVESAHGQMGGRQlEDIMhRFVSGAFHVLVATTIIEN 846
Cdd:COG4098 305 PRKLLKWLKKRLKEGRQLLiFVPT-IELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILER 381
|
330 340 350
....*....|....*....|....*....|....*.
gi 1339315144 847 GIDIPNVNTIIIDrAD--MYGISQLYQLRGRVGRSD 880
Cdd:COG4098 382 GVTFPNVDVAVLG-ADhpVFTEAALVQIAGRVGRSA 416
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
785-889 |
3.79e-10 |
|
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: 58.67 E-value: 3.79e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 785 VFFlhNRVETLENVQQFLEQLvpEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidradmy 864
Cdd:cd18787 32 IFV--NTKKRVDRLAELLEEL--GIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVI------- 100
|
90 100 110
....*....|....*....|....*....|....*
gi 1339315144 865 gisqLYQL---------R-GRVGRSDRTSFAYLFY 889
Cdd:cd18787 101 ----NYDLprdaedyvhRiGRTGRAGRKGTAITFV 131
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
116-210 |
8.50e-10 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 62.76 E-value: 8.50e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 116 SPGDLLEQVITLETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFlPGW--DFPCRAVFDFDEISGIRLFD 193
Cdd:PRK05298 150 SPEEYLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIF-PAYyeERAIRIEFFGDEIERISEFD 228
|
90
....*....|....*..
gi 1339315144 194 AVTQASREKISTLQVYP 210
Cdd:PRK05298 229 PLTGEVLGELDRVTIYP 245
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
604-912 |
2.03e-09 |
|
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: 61.64 E-value: 2.03e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFK-AVASGKQ-VAFLAPTTILAEQhyenMLERF-DRFPVKLAML--SRFVKNKEKKEVLQG------L 672
Cdd:COG1203 157 GGGKTEAALLFALRlAAKHGGRrIIYALPFTSIINQ----TYDRLrDLFGEDVLLHhsLADLDLLEEEEEYESearwlkL 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 673 ASGSIDA--VIGT-----HSILQK----TVEFQNLG--LIIVDEEQRFGVKD----KERLKELKH---SVdCLtLTATpI 732
Cdd:COG1203 233 LKELWDApvVVTTidqlfESLFSNrkgqERRLHNLAnsVIILDEVQAYPPYMlallLRLLEWLKNlggSV-IL-MTAT-L 309
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 733 PRTLHMSLLKIRDM---------SLLRTPPHNRqpVETVIAEFSDETIARAIRAEVERGGQVFFLHNRVETLENVQQFLE 803
Cdd:COG1203 310 PPLLREELLEAYELipdepeelpEYFRAFVRKR--VELKEGPLSDEELAELILEALHKGKSVLVIVNTVKDAQELYEALK 387
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 804 QLVPEVIVESAHGQMGG----RQLEDIMHRFVSGAFHVLVATTIIENGIDIpNVNTIIIDRAdmyGISQLYQLRGRV--- 876
Cdd:COG1203 388 EKLPDEEVYLLHSRFCPadrsEIEKEIKERLERGKPCILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQRAGRCnrh 463
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 1339315144 877 GRSDRTSFAYLFYPDQRALS-----ELAMKRLEIINDFTEL 912
Cdd:COG1203 464 GRKEEEGNVYVFDPEDEGGGyvydkPLLERTRELLREHDEI 504
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
116-210 |
2.45e-09 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 61.56 E-value: 2.45e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 116 SPGDLLEQVITLETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFLPGW-DFPCRAVFDFDEISGIRLFDA 194
Cdd:COG0556 147 SPEEYLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFDP 226
|
90
....*....|....*.
gi 1339315144 195 VTQASREKISTLQVYP 210
Cdd:COG0556 227 LTGEVLGELDRVTIYP 242
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
604-881 |
1.59e-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: 57.82 E-value: 1.59e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKAVASGK--QVAFLAPTTILAEQHYENMLERF-DRFPVKLAMLSRFVKNKEKKEVLQG---LASGSI 677
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFgETGLYHSSILSSRIKEMGDSEEFEHlfpLYIHSN 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 678 DAV------IGTHSILQKTV-------EFQNLGL----IIVDE-------EQRFGVKDKERLKELKHSVdcLTLTATpIP 733
Cdd:cd09639 89 DTLfldpitVCTIDQVLKSVfgefghyEFTLASIanslLIFDEvhfydeyTLALILAVLEVLKDNDVPI--LLMSAT-LP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 734 RTLHMSLLKI---RDMSLLRTPPHNRQPVETVIAEF-SDETIARAIRAEVERGGQVFFLHNRVETLENVQQFLEQLVPEV 809
Cdd:cd09639 166 KFLKEYAEKIgyvEENEPLDLKPNERAPFIKIESDKvGEISSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEE 245
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339315144 810 IVESAHGQMG----GRQLEDIMHRFVSGAFHVLVATTIIENGIDIpNVNTIIIDRADmygISQLYQLRGRVGRSDR 881
Cdd:cd09639 246 EIMLIHSRFTekdrAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYGE 317
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
604-881 |
2.39e-07 |
|
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: 54.38 E-value: 2.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKAVASGK--QVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKK-----EVLQGLASGS 676
Cdd:TIGR01587 9 GYGKTEAALLWALHSIKSQKadRVIIALPTRATINAMYRRAKELFGSELVGLHHSSSFSRIKEMGdseefEHLFPLYIHS 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 677 IDAV------IGTHSILQKTV-------EFQNLGL----IIVDE-------EQRFGVKDKERLKELKHSVdcLTLTATpI 732
Cdd:TIGR01587 89 NDKLfldpitVCTIDQVLKSVfgefghyEFTLASIanslLIFDEvhfydeyTLALILAVLEVLKDNDVPI--LLMSAT-L 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 733 PRTLHMSLLKIRDMSLLRTPP------HNRQPVETVIAE-FSDETIARAIRAEVERGGQVFFLHNRVETLENVQQFLEQL 805
Cdd:TIGR01587 166 PKFLKEYAEKIGYVEFNEPLDlkeerrFENHRFILIESDkVGEISSLERLLEFIKKGGSIAIIVNTVDRAQEFYQQLKEK 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 806 VPEVIVESAHGQMG-----GRQLEDIMHRFVSGAFHVLVATTIIENGIDIpNVNTIIIDRADmygISQLYQLRGRVGRSD 880
Cdd:TIGR01587 246 APEEEIILYHSRFTekdraKKEAELLREMKKSNEKFVIVATQVIEASLDI-SADVMITELAP---IDSLIQRLGRLHRYG 321
|
.
gi 1339315144 881 R 881
Cdd:TIGR01587 322 R 322
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
793-878 |
3.90e-07 |
|
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: 50.43 E-value: 3.90e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 793 ETLENVQQFLEQLVPEVIVESAHGQ--------MGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRADMY 864
Cdd:cd18801 41 DSAEEIVNFLSKIRPGIRATRFIGQasgksskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPS 120
|
90
....*....|....
gi 1339315144 865 GIsQLYQLRGRVGR 878
Cdd:cd18801 121 PI-RMIQRMGRTGR 133
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
604-732 |
3.39e-06 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 48.44 E-value: 3.39e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKAVASG--KQVAFLAPTTILAEQhyenMLERFDRFPVKLAMLSRFVKNKEKKEvlqglASGSIDAVI 681
Cdd:pfam04851 33 GSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQ----ALEEFKKFLPNYVEIGEIISGDKKDE-----SVDDNKIVV 103
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 682 GTHSILQKTVEFQNL-------GLIIVDEEQRFGVKDKERLKE-LKHSVdCLTLTATPI 732
Cdd:pfam04851 104 TTIQSLYKALELASLellpdffDVIIIDEAHRSGASSYRNILEyFKPAF-LLGLTATPE 161
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
598-731 |
1.18e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 49.34 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAAFKAVAS-GKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKNKEKKEVlqgLASGS 676
Cdd:COG1111 21 LVVLPTGLGKTAVALLVIAERLHKkGGKVLFLAPTKPLVEQHAEFFKEALNIPEDEIVVFTGEVSPEKRKEL---WEKAR 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339315144 677 IdaVIGT-----HSILQKTVEFQNLGLIIVDEEQRfGVKD------KERLKELKHSVDCLTLTATP 731
Cdd:COG1111 98 I--IVATpqvieNDLIAGRIDLDDVSLLIFDEAHR-AVGNyayvyiAERYHEDAKDPLILGMTASP 160
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
604-731 |
2.14e-05 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 45.76 E-value: 2.14e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKavASGKQVAFLAPTTILAEQhyenMLERFDRFpVKLAMLSRFVKNKEKkevlqglASGSIDAVIGT 683
Cdd:cd17926 28 GSGKTLTALALIAY--LKELRTLIVVPTDALLDQ----WKERFEDF-LGDSSIGLIGGGKKK-------DFDDANVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1339315144 684 HSILQKTVE-----FQNLGLIIVDEEQRFGVKDKER-LKELKHSVDcLTLTATP 731
Cdd:cd17926 94 YQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTFSEiLKELNAKYR-LGLTATP 146
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
744-881 |
3.97e-05 |
|
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: 44.95 E-value: 3.97e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 744 RDMSLLRTPPHnrQPVETVIAEFSDETIARAIRAEVERGGQVFFLHN---RVETL-ENVQQFLEQLVPEVIVESAHGQMG 819
Cdd:cd18796 2 KKLDIKVILPV--APEIFPWAGESGADAYAEVIFLLERHKSTLVFTNtrsQAERLaQRLRELCPDRVPPDFIALHHGSLS 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1339315144 820 GRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTII-IDRAdmYGISQLYQlrgRVGRSDR 881
Cdd:cd18796 80 RELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIqIGSP--KSVARLLQ---RLGRSGH 137
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
837-878 |
4.82e-05 |
|
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: 42.69 E-value: 4.82e-05
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1339315144 837 VLVATTIIENGIDIPNVNTIIIDRADMYgISQLYQLRGRVGR 878
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGR 65
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
604-702 |
8.34e-05 |
|
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: 44.63 E-value: 8.34e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 604 GYGKTELALRAAFKAVASGKQVAFLAPTTILAEQHYE--NMLERFDRFPVKLAMLSRFVKNKEKKEVLQGLASGSIDAVI 681
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYErlSKYAEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
90 100
....*....|....*....|....
gi 1339315144 682 GTHSILQKTVEF---QNLGLIIVD 702
Cdd:cd17924 122 TTNQFLSKNFDLlsnKKFDFVFVD 145
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
598-714 |
9.82e-05 |
|
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: 44.17 E-value: 9.82e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAAFKAVASGKQVA-FLAPTTILAEQHYENMLERFDRFPVKLAMLSRFVKnkekkevLQGLASGS 676
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAvYIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPS-------VNKLLLAE 93
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 1339315144 677 IDAVIGTHSILQ------KTVEFQNLGLIIVDEEQRFGvkDKER 714
Cdd:cd17921 94 ADILVATPEKLDlllrngGERLIQDVRLVVVDEAHLIG--DGER 135
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
602-732 |
1.15e-04 |
|
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: 44.59 E-value: 1.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 602 DVGYGKT--------ELALRAAfkavasGKQVAFLAPTTiLAEQHYENMLERF-DRFPVKL-AMLSRFVKNKEKKEVLQG 671
Cdd:cd18011 25 EVGLGKTieagliikELLLRGD------AKRVLILCPAS-LVEQWQDELQDKFgLPFLILDrETAAQLRRLIGNPFEEFP 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 672 LASGSIDaVIGTHSILQKTVEFQNLGLIIVDEEQRF----GVKDKER---LKELKHSVD-CLTLTATPI 732
Cdd:cd18011 98 IVIVSLD-LLKRSEERRGLLLSEEWDLVVVDEAHKLrnsgGGKETKRyklGRLLAKRARhVLLLTATPH 165
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
598-706 |
1.51e-04 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 43.66 E-value: 1.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELA-LRAAFKAVASGKQVAFLAPTTILAEQHYENmLERFDRFPVKLAMLSRFVKNKEKKEVlqgLASGS 676
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAEN-LKRVLNIPDKITSLTGEVKPEERAER---WDASK 95
|
90 100 110
....*....|....*....|....*....|....*
gi 1339315144 677 IdaVIGT-----HSILQKTVEFQNLGLIIVDEEQR 706
Cdd:cd18035 96 I--IVATpqvieNDLLAGRITLDDVSLLIFDEAHH 128
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
796-880 |
1.55e-04 |
|
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: 44.54 E-value: 1.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 796 ENVQQFLEQLVPEV---IVESAHGQMGGrQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIDRAD--MY------ 864
Cdd:cd18804 104 ERVEEELKTLFPEAriaRIDRDTTRKKG-ALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADsgLNspdfra 182
|
90
....*....|....*....
gi 1339315144 865 ---GISQLYQLRGRVGRSD 880
Cdd:cd18804 183 serAFQLLTQVSGRAGRGD 201
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
915-947 |
1.56e-04 |
|
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: 41.69 E-value: 1.56e-04
10 20 30
....*....|....*....|....*....|...
gi 1339315144 915 GFKIAMKDLEVRGAGNLLGSQQSGdigsIGFDL 947
Cdd:pfam19833 4 GFEIAEADLKLRGPGDLEGTQQSG----IAFDL 32
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
606-878 |
2.58e-04 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 44.89 E-value: 2.58e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 606 GKTELALRAAFKAVASGKQVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSR-FVKNKEKkevlqglaSGSIDAVIGT- 683
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGdYDSDDEW--------LGRYDILVATp 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 684 ---HSILQKTVEF-QNLGLIIVDEEQRFGvkDKER----------LKELKHSVDCLTLTAT------------------- 730
Cdd:COG1204 122 eklDSLLRNGPSWlRDVDLVVVDEAHLID--DESRgptlevllarLRRLNPEAQIVALSATignaeeiaewldaelvksd 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 731 --PIPrtLHMSLLKIRDMSLLRTPPHNRQPVETVIAEFSD---------------ETIARAIRAEVERGGQvffLHNRVE 793
Cdd:COG1204 200 wrPVP--LNEGVLYDGVLRFDDGSRRSKDPTLALALDLLEeggqvlvfvssrrdaESLAKKLADELKRRLT---PEEREE 274
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 794 TLENVQQFLEqlVPEVIVESA-------------HGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPnVNTIIID- 859
Cdd:COG1204 275 LEELAEELLE--VSEETHTNEkladclekgvafhHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIIRd 351
|
330 340
....*....|....*....|...
gi 1339315144 860 --RADMYGISQL--YQLRGRVGR 878
Cdd:COG1204 352 tkRGGMVPIPVLefKQMAGRAGR 374
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
598-736 |
5.20e-04 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 42.42 E-value: 5.20e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAA------FKAVASGKqVAFLAPTTILAEQHYENMLERFDRFPVKLAMLSrfvkNKEKKEVLQG 671
Cdd:cd17927 21 IICLPTGSGKTFVAVLICehhlkkFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS----GDTSENVSVE 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1339315144 672 LASGSIDAVIGTHSILQ------KTVEFQNLGLIIVDEEQRfGVKDKERLKELKHSVDCLTLTATPIPRTL 736
Cdd:cd17927 96 QIVESSDVIIVTPQILVndlksgTIVSLSDFSLLVFDECHN-TTKNHPYNEIMFRYLDQKLGSSGPLPQIL 165
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
663-911 |
5.20e-04 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 43.98 E-value: 5.20e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 663 KEKKEVLQGLASGSIDAVI---------GTHSILQKtvefQNLGLIIVDE-------------EQRfgvkdkeRLKELKH 720
Cdd:COG0514 94 EERREVLRALRAGELKLLYvaperllnpRFLELLRR----LKISLFAIDEahcisqwghdfrpDYR-------RLGELRE 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 721 S---VDCLTLTATPIPRTLH--MSLLKIRDMSLLRTPPhNRqP-----VETVIAEFSDETIARAIRAEVERGGQVFFLhN 790
Cdd:COG0514 163 RlpnVPVLALTATATPRVRAdiAEQLGLEDPRVFVGSF-DR-PnlrleVVPKPPDDKLAQLLDFLKEHPGGSGIVYCL-S 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 791 RVETlENVQQFLEQLvpEVIVESAHGQMGGRQLEDIMHRFVSGAFHVLVATtiieN----GIDIPNVNTIIidRADM--- 863
Cdd:COG0514 240 RKKV-EELAEWLREA--GIRAAAYHAGLDAEEREANQDRFLRDEVDVIVAT----IafgmGIDKPDVRFVI--HYDLpks 310
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339315144 864 ---YgisqlYQLRGRVGRSDRTSFAYLFY---------------PDQRALSELAMKRLEIINDFTE 911
Cdd:COG0514 311 ieaY-----YQEIGRAGRDGLPAEALLLYgpedvaiqrffieqsPPDEERKRVERAKLDAMLAYAE 371
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
821-875 |
6.91e-04 |
|
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: 41.04 E-value: 6.91e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1339315144 821 RQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidRADMYG-ISQLYQLRGR 875
Cdd:cd18802 77 RKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI--RFDLPKtLRSYIQSRGR 130
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
127-190 |
7.19e-04 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 39.46 E-value: 7.19e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1339315144 127 LETGAPLDPAGIAQQLIQMGYWRVPKVSVHGEFALRGEVLDIFLPGWDFP--------CRAVFDFDEISGIR 190
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELYRRGFDFPdgaeparrVRLRFAGGRVARLQ 72
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
815-889 |
1.15e-03 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 40.27 E-value: 1.15e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 815 HGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidradMYGISQ----LYQLRGRVGRSDRTSFAYLFY 889
Cdd:cd18794 61 HAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVI-----HYSLPKsmesYYQESGRAGRDGLPSECILFY 134
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
811-892 |
1.83e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 42.12 E-value: 1.83e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 811 VESAHGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidRADMYGISQLYQLR-GRVGRSDRTSFAYLFY 889
Cdd:PTZ00424 294 VSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVI--NYDLPASPENYIHRiGRSGRFGRKGVAINFV 371
|
...
gi 1339315144 890 PDQ 892
Cdd:PTZ00424 372 TPD 374
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
598-737 |
2.16e-03 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 41.51 E-value: 2.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKT--ELALRAAFKAVASGKQVAFL--APTTILaeQHYENMLERFDRFPV--KLAMLSrfVKNKEKKEVLQG 671
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVDKNWGGPTLivVPLSLL--HNWMNEFERWVSPPAlrVVVLHG--NKRPQERWKNDP 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1339315144 672 LASGSIDAVIGTHSILQKTVEF---QNLGLIIVDEEQRF-GVKDK--ERLKELKhSVDCLTLTATPIPRTLH 737
Cdd:pfam00176 97 NFLADFDVVITTYETLRKHKELlkkVHWHRIVLDEGHRLkNSKSKlsKALKSLK-TRNRWILTGTPLQNNLE 167
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
821-879 |
2.29e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 42.17 E-value: 2.29e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 821 RQLEdIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidradmygisqLY----------QLRGRVGRS 879
Cdd:PRK13766 411 EQIE-ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-----------FYepvpseirsiQRKGRTGRQ 467
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
822-880 |
3.16e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 41.64 E-value: 3.16e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1339315144 822 QLEdIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIidradmygisqLY----------QLRGRVGRSD 880
Cdd:COG1111 400 QIE-ILERFRAGEFNVLVATSVAEEGLDIPEVDLVI-----------FYepvpseirsiQRKGRTGRKR 456
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
598-730 |
3.27e-03 |
|
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: 39.62 E-value: 3.27e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAAFKAVASGKQVAFLAPTTILAEQHYENmLERFDRFPVKLAMlsRFVKNKEKKEVLqglasGSI 677
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEE-FKKLEEIGLKVGI--STGDYDEDDEWL-----GDY 92
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1339315144 678 DAVIGTH----SIL-QKTVEFQNLGLIIVDE------EQRFGVKDK--ERLKELKHSVDCLTLTAT 730
Cdd:cd18028 93 DIIVATYekfdSLLrHSPSWLRDVGVVVVDEihlisdEERGPTLESivARLRRLNPNTQIIGLSAT 158
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
815-889 |
7.23e-03 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 38.38 E-value: 7.23e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 815 HGQMGGRQLEDIMHRFVSGAFHVLVATTIIENGIDIPNVNTIIIdradmygISQLY-------QLRGRVGR-SDRTSFAY 886
Cdd:cd18789 75 TGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ-------ISGHGgsrrqeaQRLGRILRpKKGGGKNA 147
|
...
gi 1339315144 887 LFY 889
Cdd:cd18789 148 FFY 150
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
598-703 |
8.87e-03 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain] Cd Length: 204 Bit Score: 39.00 E-value: 8.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1339315144 598 LVCGDVGYGKTELALRAA------FKAVASGKQVAFLAPTTILAEQHyenmLERFDRFPVKLAMLSRFVKNKEKKEVLQG 671
Cdd:cd18036 21 IICAPTGSGKTRVAVYICrhhlekRRSAGEKGRVVVLVNKVPLVEQQ----LEKFFKYFRKGYKVTGLSGDSSHKVSFGQ 96
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1339315144 672 LASGSiDAVIGTHSILQ---------KTVEFQNLGLIIVDE 703
Cdd:cd18036 97 IVKAS-DVIICTPQILInnllsgreeERVYLSDFSLLIFDE 136
|
|
| |
