|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
38-1176 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1815.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 38 AKDQLRAGQLYGSAQGLLLAKAAQQHDGPLLVVTDDVASAHRLELEIRFYLGnaELPILHFPDWETLPYDSFSPHQDIVS 117
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLP--DLPVLLFPAWETLPYDRFSPSPDIVS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 118 ERLQTLHHLPDFNHGILLVPIATLMQRIAPRSFLDGNHLELKIGDQFDIEQWRLKLEKSGYRNVAQVIEHGEFAVRGAII 197
Cdd:COG1197 79 ERLATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGIL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 198 DLFPMGSRQPYRIDLFDDEIDTLRTFDPETQRSIDNIDQIQLLPAREFPVNDDSIALFRKQFRQFFDGDPQRSLIYREVS 277
Cdd:COG1197 159 DIFPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFGLDPKLDELYEALS 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 278 AGNMPGGIEFYLPLFFEQTARLTDYLPDNTLLVQL--NDTFHAAEQFWQEIQIRYRQHSVDPERPLLPPINVFVPVEELF 355
Cdd:COG1197 239 EGIAFAGIEYYLPLFYEELATLFDYLPEDALVVLDepERIEEAAEEFWEEIEERYEARRHDRGRPLLPPEELFLDPEELF 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 356 SQFKQWQRLQCQNF-ELDGSAGNSNYATVIPPSLplNSKQDRPCEALHQFIDKfAGRILIAAESAGRRETLLDLLRKNQL 434
Cdd:COG1197 319 AALKRRPRVTLSPFaALPEGAGVVNLGARPLPSF--AGQLEALLEELKRLLKD-GGRVLLAAESEGRRERLLELLRDHGI 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 435 QPKVVDNWDAFinDSAPLCITVAPLEQGLLLQIENIAVVAETQLFGQQVMQRRRRSRKKRDsdAIIRNLAELTIGDAVVH 514
Cdd:COG1197 396 PARLVESLAEL--SPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSAD--AFIRDLSELKPGDYVVH 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 515 EDHGVGRYLGLQTLDVGDVATEYVTLEYAKGDKLYVPVASLDLISRYSGSAPELAPLHQLGTTQWEKARRRAAEKVRDVA 594
Cdd:COG1197 472 VDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDIA 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 595 AELLDIYAKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAAFLA 674
Cdd:COG1197 552 AELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFKA 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 675 VQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDIDPKRLGL 754
Cdd:COG1197 632 VMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLGL 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 755 FVLDEEHRFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATAPARRLAIKTFVLQWNADKIREGMLRE 834
Cdd:COG1197 712 LIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILRE 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 835 IKRGGQVYFLHNKVEDIDRVARELETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFI 914
Cdd:COG1197 792 LLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTIII 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 915 DRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQQAMTADAIKRLEAIESIEDLGAGFTLATHDMEIRGAGELLGDEQSG 994
Cdd:COG1197 872 ERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQSG 951
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 995 QMQEIGFTLYNELLERAVNALKSGKTPDLDnmarHTVEIDLHVPALIPSDYLPDVHTRLVLYKRIAAAADKEALRELQVE 1074
Cdd:COG1197 952 HIAEVGFDLYLQMLEEAVAALKGGKEPEEE----WEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEE 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 1075 MIDRFGLLPEPVQTLFAVHELRLKAKTIGIRKIDVYDQGGRLLFDKEPQVEPMTIIQLIQKQPSRFKLDGQDKLRFTDNM 1154
Cdd:COG1197 1028 LIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTPLDPEKLIRLIQKQPGRYKLDGDDKLVITLDL 1107
|
1130 1140
....*....|....*....|..
gi 2535554553 1155 PDAESRILAIDSLLDNLLKPAA 1176
Cdd:COG1197 1108 EDPEERLEALEELLEALAKLAK 1129
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
34-1171 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 1430.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 34 LPVSAKDQLRAGQLYGSAQGLLLAKAAQQHDGPLLVVTDDVASAHRLELEIRFYlgnAELPILHFPDWETLPYDSFSPHQ 113
Cdd:PRK10689 9 LPVKAGDQRQLGELTGAACATEVAEIAERHAGPVVLIAPDMQNALRLHDEIQQF---TDQMVMNLADWETLPYDSFSPHQ 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 114 DIVSERLQTLHHLPDFNHGILLVPIATLMQRIAPRSFLDGNHLELKIGDQFDIEQWRLKLEKSGYRNVAQVIEHGEFAVR 193
Cdd:PRK10689 86 DIISSRLSTLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATR 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 194 GAIIDLFPMGSRQPYRIDLFDDEIDTLRTFDPETQRSIDNIDQIQLLPAREFPVNDDSIALFRKQFRQFFDGDPQRSLIY 273
Cdd:PRK10689 166 GALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDAEHIY 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 274 REVSAGNMPGGIEFYLPLFFEQT-ARLTDYLPDNTLLVQLNDTFHAAEQFWQEIQIRYRQHSVDPERPLLPPINVFVPVE 352
Cdd:PRK10689 246 QQVSKGTLPAGIEYWQPLFFSEPlPPLFSYFPANTLLVNTGDLETSAERFWADTLARFENRGVDPMRPLLPPESLWLRVD 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 353 ELFSQFKQWQRLQCQNFELDGSAGNSNYATVIPPSLPLNSKQDRPCEALHQFIDKFAGRILIAAESAGRRETLLDLLRKN 432
Cdd:PRK10689 326 ELFSELKNWPRVQLKTEHLPTKAANTNLGYQKLPDLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGELLARI 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 433 QLQPKVVDNwdaFINDSAPLC-ITVAPLEQGLLLQIENIAVVAETQLFGQQVMQRRRRSRKKRDSDAIIRNLAELTIGDA 511
Cdd:PRK10689 406 KIAPKRIMR---LDEASDRGRyLMIGAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHPGQP 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 512 VVHEDHGVGRYLGLQTLDVGDVATEYVTLEYAKGDKLYVPVASLDLISRYSGSAPELAPLHQLGTTQWEKARRRAAEKVR 591
Cdd:PRK10689 483 VVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVR 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 592 DVAAELLDIYAKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAA 671
Cdd:PRK10689 563 DVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAA 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 672 FLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDIDPKR 751
Cdd:PRK10689 643 FLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKD 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 752 LGLFVLDEEHRFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATAPARRLAIKTFVLQWNADKIREGM 831
Cdd:PRK10689 723 LGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAI 802
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 832 LREIKRGGQVYFLHNKVEDIDRVARELETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANT 911
Cdd:PRK10689 803 LREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANT 882
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 912 IFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQQAMTADAIKRLEAIESIEDLGAGFTLATHDMEIRGAGELLGDE 991
Cdd:PRK10689 883 IIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEE 962
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 992 QSGQMQEIGFTLYNELLERAVNALKSGKTPDLDNMARHTVEIDLHVPALIPSDYLPDVHTRLVLYKRIAAAADKEALREL 1071
Cdd:PRK10689 963 QSGQMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEI 1042
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 1072 QVEMIDRFGLLPEPVQTLFAVHELRLKAKTIGIRKIDVYDQGGRLLFDKEPQVEPMTIIQLIQKQPSRFKLDGQDKLRFT 1151
Cdd:PRK10689 1043 KVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVDPAWLIGLLQKQPQHYRLDGPTRLKFI 1122
|
1130 1140
....*....|....*....|
gi 2535554553 1152 DNMPDAESRILAIDSLLDNL 1171
Cdd:PRK10689 1123 QDLSERKTRIEWVRQFMREL 1142
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
177-1108 |
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: 1088.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 177 GYRNVAQVIEHGEFAVRGAIIDLFPMGSRQPYRIDLFDDEIDTLRTFDPETQRSIDNIDQIQLLPAREFPVnDDSIALFR 256
Cdd:TIGR00580 5 GYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFIL-LEEETIAR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 257 KQFRQFFDGDPQRSLIYREVSAGNMPGGIEFYLPLFFEQTARLTDYLPDNTL-LVQLNDTFHAAEQFWQEIQIRYRQHSV 335
Cdd:TIGR00580 84 LKDNAARVEDAKHLETIEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPiLLDDPERFHSAARFLQRELEEFYNALE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 336 DPERpLLPPINVFVPVEELFSQFK--QWQRLQCQN--FELDGSAGNSNyaTVIPPSLPLNSKQDRPCEALHQFIDKFAgr 411
Cdd:TIGR00580 164 EAKK-LINPPRLDLDPSELAFEASaiSLSRVQLENehLSLKASEAIEG--AQKHSRLEFGEILAFKEELFRWLKAGFK-- 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 412 ILIAAESAGRRETLLDLLRKNQLQPKVVDNWDAFIndSAPLCITVAPLEQGLLLQIENIAVVAETQLFGQQVmqrRRRSR 491
Cdd:TIGR00580 239 ITVAAESESQAERLKSLLAEHDIAAQVIDESCIII--PAVRYVMIGALSSGFILPTAGLAVITESELFGSRV---LRRPK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 492 KKRDSDAIIRNLAELTIGDAVVHEDHGVGRYLGLQTLDVGDVATEYVTLEYAKGDKLYVPVASLDLISRYSGSAPELAPL 571
Cdd:TIGR00580 314 KSRLKSKPIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNPAL 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 572 HQLGTTQWEKARRRAAEKVRDVAAELLDIYAKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPM 651
Cdd:TIGR00580 394 DKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPRPM 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 652 DRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEG 731
Cdd:TIGR00580 474 DRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELASG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 732 TADIVIGTHKLLQQDIDPKRLGLFVLDEEHRFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATAPAR 811
Cdd:TIGR00580 554 KIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPED 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 812 RLAIKTFVLQWNADKIREGMLREIKRGGQVYFLHNKVEDIDRVARELETLMPEARIAVAHGQMRERELEQVMLDFYHQRF 891
Cdd:TIGR00580 634 RLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEF 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 892 NVLVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQQAMTADAIKRLEAIESIEDLGAG 971
Cdd:TIGR00580 714 QVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELGAG 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 972 FTLATHDMEIRGAGELLGDEQSGQMQEIGFTLYNELLERAVNALKSGKTPDLdnmaRHTVEIDLHVPALIPSDYLPDVHT 1051
Cdd:TIGR00580 794 FKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKL----EEETDIELPYSAFIPDDYIADDSL 869
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*..
gi 2535554553 1052 RLVLYKRIAAAADKEALRELQVEMIDRFGLLPEPVQTLFAVHELRLKAKTIGIRKID 1108
Cdd:TIGR00580 870 RLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
577-997 |
9.24e-120 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 385.94 E-value: 9.24e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 577 TQWEKARRR-AAEkvrdvaaELL-------DIYAKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSE 648
Cdd:COG1200 206 EDLHPARRRlAFE-------ELLalqlallLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASP 278
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 649 TPMDRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAI 728
Cdd:COG1200 279 HPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAAL 358
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 729 TEGTADIVIGTHKLLQQDIDPKRLGLFVLDEEHRFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATA 808
Cdd:COG1200 359 ASGEADIVVGTHALIQDDVEFKNLGLVVIDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDEL 438
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 809 PARRLAIKTFVL-QWNADKIREGMLREIKRGGQVYF------------LHNkVEDidrVARELETLMPEARIAVAHGQMR 875
Cdd:COG1200 439 PPGRKPIKTRVVpEERRDEVYERIREEIAKGRQAYVvcplieesekldLQA-AEE---TYEELREAFPGLRVGLLHGRMK 514
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 876 ERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQqaMTADA 955
Cdd:COG1200 515 PAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETA 592
|
410 420 430 440
....*....|....*....|....*....|....*....|..
gi 2535554553 956 IKRLEAIESIEDlgaGFTLATHDMEIRGAGELLGDEQSGQMQ 997
Cdd:COG1200 593 RERLEVMRETND---GFEIAEEDLELRGPGEFLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
602-1011 |
7.08e-118 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 380.65 E-value: 7.08e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 602 AKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAAFLAVQSGKQV 681
Cdd:PRK10917 234 AGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQA 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 682 LVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDIDPKRLGLFVLDEEH 761
Cdd:PRK10917 314 ALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQH 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 762 RFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATAPARRLAIKTFVLQWN-ADKIREGMLREIKRGGQ 840
Cdd:PRK10917 394 RFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSrRDEVYERIREEIAKGRQ 473
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 841 VYF---LhnkVEDIDR--------VARELETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTA 909
Cdd:PRK10917 474 AYVvcpL---IEESEKldlqsaeeTYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNA 550
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 910 NTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQqaMTADAIKRLEAIESIEDlgaGFTLATHDMEIRGAGELLG 989
Cdd:PRK10917 551 TVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP--LSETARERLKIMRETND---GFVIAEKDLELRGPGELLG 625
|
410 420
....*....|....*....|....*..
gi 2535554553 990 DEQSGqmqEIGFTLYN-----ELLERA 1011
Cdd:PRK10917 626 TRQSG---LPEFKVADlvrdeELLEEA 649
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
580-994 |
1.68e-112 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 364.74 E-value: 1.68e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 580 EKARRRAaekvrdVAAEL----LDIYAKRAANKK----PPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPM 651
Cdd:TIGR00643 184 ELARRRL------IFDEFfylqLAMLARRLGEKQqfsaPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPM 257
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 652 DRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEG 731
Cdd:TIGR00643 258 NRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASG 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 732 TADIVIGTHKLLQQDIDPKRLGLFVLDEEHRFGVTQKEQL-KKYRAQI--DVLTLTATPIPRTLNMSISGIRDLSIIATA 808
Cdd:TIGR00643 338 QIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLrEKGQGGFtpHVLVMSATPIPRTLALTVYGDLDTSIIDEL 417
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 809 PARRLAIKTFVLQWN-ADKIREGMLREIKRGGQVYFLHNKVEDIDR--------VARELETLMPEARIAVAHGQMREREL 879
Cdd:TIGR00643 418 PPGRKPITTVLIKHDeKDIVYEFIEEEIAKGRQAYVVYPLIEESEKldlkaaeaLYERLKKAFPKYNVGLLHGRMKSDEK 497
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 880 EQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQqaMTADAIKRL 959
Cdd:TIGR00643 498 EAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNP--KSESAKKRL 575
|
410 420 430
....*....|....*....|....*....|....*
gi 2535554553 960 EAIESIEDlgaGFTLATHDMEIRGAGELLGDEQSG 994
Cdd:TIGR00643 576 RVMADTLD---GFVIAEEDLELRGPGDLLGTKQSG 607
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
615-807 |
7.36e-112 |
|
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: 346.48 E-value: 7.36e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 615 PDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQH 694
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 695 YENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDIDPKRLGLFVLDEEHRFGVTQKEQLKKY 774
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 2535554553 775 RAQIDVLTLTATPIPRTLNMSISGIRDLSIIAT 807
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
814-964 |
1.22e-73 |
|
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: 240.71 E-value: 1.22e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 814 AIKTFVLQWNADKIREGMLREIKRGGQVYFLHNKVEDIDRVARELETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNV 893
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2535554553 894 LVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQQAMTADAIKRLEAIES 964
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
617-806 |
2.72e-65 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 218.44 E-value: 2.72e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 617 EQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYE 696
Cdd:cd17918 3 ALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 697 NFKDRFAdwPIRVEVLSRFRSKKqlddvksaITEGtADIVIGTHKLLQQDIDPKRLGLFVLDEEHRFGVTQKEQLKKYRA 776
Cdd:cd17918 83 EARKFLP--FINVELVTGGTKAQ--------ILSG-ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA 151
|
170 180 190
....*....|....*....|....*....|
gi 2535554553 777 qIDVLTLTATPIPRTLNMSISGIRDLSIIA 806
Cdd:cd17918 152 -THFLEATATPIPRTLALALSGLLDLSVID 180
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
597-809 |
3.12e-64 |
|
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: 217.40 E-value: 3.12e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 597 LLDIYAKRAANKKPPMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMDRLVCGDVGFGKTEVAMRAAFLAVQ 676
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 677 SGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDIDPKRLGLFV 756
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2535554553 757 LDEEHRFGVTQKEQLKKYRAQIDVLTLTATPIPRTLNMSISGIRDLSIIATAP 809
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
814-964 |
5.74e-63 |
|
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: 210.97 E-value: 5.74e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 814 AIKTFVLQWN-ADKIREGMLREIKRGGQVYFLHNKVE--------DIDRVARELETLMPEARIAVAHGQMRERELEQVML 884
Cdd:cd18792 1 PIRTYVIPHDdLDLVYEAIERELARGGQVYYVYPRIEesekldlkSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 885 DFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQQAMTADAIKRLEAIES 964
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
505-602 |
1.40e-43 |
|
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: 153.38 E-value: 1.40e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 505 ELTIGDAVVHEDHGVGRYLGLQTLDVGDVATEYVTLEYAKGDKLYVPVASLDLISRYSGSAPEL-APLHQLGTTQWEKAR 583
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEVePVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 2535554553 584 RRAAEKVRDVAAELLDIYA 602
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1034-1133 |
8.85e-41 |
|
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: 145.30 E-value: 8.85e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 1034 DLHVPALIPSDYLPDVHTRLVLYKRIAAAADKEALRELQVEMIDRFGLLPEPVQTLFAVHELRLKAKTIGIRKIDVYDQG 1113
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 2535554553 1114 GRLLFDKEPQVEPMTIIQLI 1133
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1035-1129 |
7.59e-37 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 133.70 E-value: 7.59e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 1035 LHVPALIPSDYLPDVHTRLVLYKRIAAAADKEALRELQVEMIDRFGLLPEPVQTLFAVHELRLKAKTIGIRKIDVYDQGG 1114
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....*
gi 2535554553 1115 RLLFDKEPQVEPMTI 1129
Cdd:pfam03461 81 RITFSEDAKIDPEKL 95
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
823-964 |
1.54e-36 |
|
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: 135.55 E-value: 1.54e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 823 NADKIREGMLREIKRGGQVYFLHNKVEDIDR--------VAREL-ETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNV 893
Cdd:cd18811 11 RLDKVYEFVREEIAKGRQAYVIYPLIEESEKldlkaavaMYEYLkERFRPELNVGLLHGRLKSDEKDAVMAEFREGEVDI 90
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2535554553 894 LVCTTIIETGIDVPTANTIFIDRADKLGLAQLYQIRGRVGRSHHRAYAYLITPPQqaMTADAIKRLEAIES 964
Cdd:cd18811 91 LVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVMTE 159
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
156-245 |
1.39e-34 |
|
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: 127.13 E-value: 1.39e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 156 LELKIGDQFDIEQWRLKLEKSGYRNVAQVIEHGEFAVRGAIIDLFPMGSR-QPYRIDLFDDEIDTLRTFDPETQRSIDNI 234
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 2535554553 235 DQIQLLPAREF 245
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
506-601 |
6.08e-29 |
|
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: 111.00 E-value: 6.08e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 506 LTIGDAVVHEDHGVGRYLGLQTLDVgdvaTEYVTLEYAKGDKLYVPVASLDLISRYSGSapelAPLHQLGTTQ-WEKARR 584
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLET----KDYYVLEYAGGDKLYVPVDNLDLIRKYISK----GELDKLGDGRrWRKYKE 72
|
90
....*....|....*..
gi 2535554553 585 RAAEKVRDVAAELLDIY 601
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
631-794 |
5.47e-28 |
|
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: 111.18 E-value: 5.47e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 631 TPDQQDAIDAVIADMqsetpmDRLVCGDVGFGKTEVAMRAAFLAV---QSGKQVLVLVPTTLLAQQHYENFKDRFADWPI 707
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 708 RVE-VLSRFRSKKQLDDVKsaitegTADIVIGTHKLLQQDIDP----KRLGLFVLDEEHRFGV-TQKEQLKKYRAQID-- 779
Cdd:pfam00270 75 KVAsLLGGDSRKEQLEKLK------GPDILVGTPGRLLDLLQErkllKNLKLLVLDEAHRLLDmGFGPDLEEILRRLPkk 148
|
170
....*....|....*..
gi 2535554553 780 --VLTLTATPiPRTLNM 794
Cdd:pfam00270 149 rqILLLSATL-PRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
622-809 |
1.42e-26 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 108.35 E-value: 1.42e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 622 FSAAFPFETTPDQQDAIDAVIADMQsetpmDRLVCGDVGFGKTEVAMRAAFLAVQSG--KQVLVLVPTTLLAQQHYENFK 699
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 700 DRFADWPIR-VEVLSRFRSKKQLDDVKSaiteGTADIVIGT-----HKLLQQDIDPKRLGLFVLDEEHRFGV-TQKEQLK 772
Cdd:smart00487 76 KLGPSLGLKvVGLYGGDSKREQLRKLES----GKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRLLDgGFGDQLE 151
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 2535554553 773 KY----RAQIDVLTLTATP---IPRTLNMSISGIRDLSIIATAP 809
Cdd:smart00487 152 KLlkllPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPL 195
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
651-786 |
1.44e-24 |
|
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: 100.56 E-value: 1.44e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 651 MDRLVCGDVGFGKTEVAMRAAF-LAVQSGKQVLVLVPTTLLAQQHYENFKDRFaDWPIRVEVLSRFRSKKQlddvKSAIT 729
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEE----REKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 730 EGTADIVIGTHKLLQQDIDP------KRLGLFVLDEEHRFGVTQKEQL-------KKYRAQIDVLTLTAT 786
Cdd:cd00046 77 LGDADIIIATPDMLLNLLLRedrlflKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
552-936 |
9.42e-20 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 94.71 E-value: 9.42e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 552 VASLDLISRYSGSAPELAPLHQLGTTQWEKARRRAAEKVRDVAAELLDIYAKRAANKKPPMQSPDEQYEAFSAAFPFETT 631
Cdd:COG1061 1 VLLRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGTSFE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 632 --PDQQDAIDAVIADMQSETpmDR-LVCGDVGFGKTEVAMRAAfLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADwpir 708
Cdd:COG1061 81 lrPYQQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLGD---- 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 709 vevlsrfrskkqlDDVKSAITEGTADIVIGTHKLLQQDIDPKRL----GLFVLDEEHRFGVTQKEQLKKYRAQIDVLTLT 784
Cdd:COG1061 154 -------------PLAGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLT 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 785 ATPIpRTLNMSISGIRDLSIIATAPARRLAIKTFV---------------------------------LQWNADKIREgM 831
Cdd:COG1061 221 ATPF-RSDGREILLFLFDGIVYEYSLKEAIEDGYLappeyygirvdltderaeydalserlrealaadAERKDKILRE-L 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 832 LREIKRGGQVYFLHNKVEDIDRVARELETLmpEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANT 911
Cdd:COG1061 299 LREHPDDRKTLVFCSSVDHAEALAELLNEA--GIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDV 376
|
410 420
....*....|....*....|....*
gi 2535554553 912 IFIDRADKlGLAQLYQIRGRVGRSH 936
Cdd:COG1061 377 AILLRPTG-SPREFIQRLGRGLRPA 400
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
654-936 |
1.10e-16 |
|
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: 84.74 E-value: 1.10e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADwpiRVEVLSRFRSKKQLDDVKSAITEGTA 733
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 734 DIVIGTHKLLQQDIdpKRLGLFVLDEEHRFGVTQKE-------QLKKYRA---QIDVLTLTATPIPRTL-NMSISGIRDL 802
Cdd:TIGR00595 78 LVVIGTRSALFLPF--KNLGLIIVDEEHDSSYKQEEgpryharDVAVYRAkkfNCPVVLGSATPSLESYhNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 803 SIIATAPARRLAIKTFV------------------LQWNADKIREGMLREIKRG----------GQV---------YFLH 845
Cdd:TIGR00595 156 VLTRRVSGRKPPEVKLIdmrkeprqsflspelitaIEQTLAAGEQSILFLNRRGysknllcrscGYIlccpncdvsLTYH 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 846 NK-----------------------VEDI-------DRVARELETLMPEARIAVAHGQM--RERELEQVMLDFYHQRFNV 893
Cdd:TIGR00595 236 KKegklrchycgyqepipktcpqcgSEDLvykgygtEQVEEELAKLFPGARIARIDSDTtsRKGAHEALLNQFANGKADI 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 2535554553 894 LVCTTIIETGIDVPTANTIFIDRADKL-----------GLAQLYQIRGRVGRSH 936
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADSGlhspdfraaerGFQLLTQVAGRAGRAE 369
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
832-934 |
1.20e-16 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 76.87 E-value: 1.20e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 832 LREIKRGGQVYFLHNKVEDIDRvarELETLMPEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANT 911
Cdd:pfam00271 9 LLKKERGGKVLIFSQTKKTLEA---ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDL 85
|
90 100
....*....|....*....|...
gi 2535554553 912 IFIDRADKlGLAQLYQIRGRVGR 934
Cdd:pfam00271 86 VINYDLPW-NPASYIQRIGRAGR 107
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
627-938 |
1.27e-15 |
|
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: 81.07 E-value: 1.27e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 627 PFETTPDQQDAIDAVIADMQSETPMdrL---VCGDvgfGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFA 703
Cdd:COG4098 108 EGTLTPAQQKASDELLEAIKKKEEH--LvwaVCGA---GKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFP 182
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 704 DwpIRVEVLSRfrskkqlddvKSAITEGTADIVIGT-HKLLQ--QDIDpkrlgLFVLDEEHRFGVTQKEQLKK--YRA-Q 777
Cdd:COG4098 183 G--VDIAALYG----------GSEEKYRYAQLVIATtHQLLRfyQAFD-----LLIIDEVDAFPYSGDPMLQYavKRArK 245
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 778 IDVLT--LTATPiPRTLNMSI-SGIRDLSIIataPAR----RLAIKTFVLQWN-ADKIREG---------MLREIKRGGQ 840
Cdd:COG4098 246 PDGKLiyLTATP-SKALQRQVkRGKLKVVKL---PARyhghPLPVPKFKWLGNwKKRLRRGklprkllkwLKKRLKEGRQ 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 841 VY-FLHNkVEDIDRVARELETLMPEARIAVAHGQMRERElEQVMlDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADK 919
Cdd:COG4098 322 LLiFVPT-IELLEQLVALLQKLFPEERIAGVHAEDPERK-EKVQ-AFRDGEIPILVTTTILERGVTFPNVDVAVLGADHP 398
|
330 340
....*....|....*....|
gi 2535554553 920 L-GLAQLYQIRGRVGRSHHR 938
Cdd:COG4098 399 VfTEAALVQIAGRVGRSADY 418
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
634-761 |
1.64e-14 |
|
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: 73.01 E-value: 1.64e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 634 QQDAIDAVI-ADMQSETpmdRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFADwpiRVEVL 712
Cdd:cd17929 1 QRKAYEAIVsSLGGFKT---FLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGD---KVAVL 74
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 2535554553 713 SRFRSKKQLDDVKSAITEGTADIVIGTHKLLqqdIDP-KRLGLFVLDEEH 761
Cdd:cd17929 75 HSKLSDKERADEWRKIKRGEAKVVIGARSAL---FAPfKNLGLIIVDEEH 121
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
852-934 |
2.73e-14 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 69.16 E-value: 2.73e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 852 DRVARELETLmpEARIAVAHGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADKlGLAQLYQIRGR 931
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPW-SPASYIQRIGR 77
|
...
gi 2535554553 932 VGR 934
Cdd:smart00490 78 AGR 80
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
147-252 |
6.32e-14 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 76.24 E-value: 6.32e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 147 PRSFLDgNHLELKIGDQFDIEQWRLKLEKSGY-RNvAQVIEHGEFAVRGAIIDLFPMGS-RQPYRIDLFDDEIDTLRTFD 224
Cdd:PRK05298 151 PEEYLK-MVLSLRVGQEIDRRELLRRLVDLQYeRN-DIDFQRGTFRVRGDVIEIFPAYYeERAIRIEFFGDEIERISEFD 228
|
90 100
....*....|....*....|....*...
gi 2535554553 225 PETQRSIDNIDQIQLLPAREFPVNDDSI 252
Cdd:PRK05298 229 PLTGEVLGELDRVTIYPASHYVTPRERL 256
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
614-761 |
1.41e-13 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 75.15 E-value: 1.41e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 614 SPDEQYEAFSAAFPFETTPDQQDAIDAVIADMQSETPMdrLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQ 693
Cdd:COG1198 180 DRDPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQ 257
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2535554553 694 HYENFKDRFADwpiRVEVL-SRFRSKKQLdDVKSAITEGTADIVIGTHK--LLqqdidP-KRLGLFVLDEEH 761
Cdd:COG1198 258 TVERFRARFGA---RVAVLhSGLSDGERL-DEWRRARRGEARIVIGTRSalFA-----PfPNLGLIIVDEEH 320
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
593-761 |
1.41e-12 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 72.11 E-value: 1.41e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 593 VAAELLDIYAKRAANKKPPMQSPDEqyeafsaafPFETTPDQQDAIDAVIADMQSETPmdrLVCGDVGFGKTEVAMRAAF 672
Cdd:PRK05580 117 VKKGLIELEEVEVLRLRPPPDPAFE---------PPTLNPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVYLQAIA 184
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 673 LAVQSGKQVLVLVPTTLLAQQHYENFKDRFADwpiRVEVL-SRFrSKKQLDDVKSAITEGTADIVIGThkllqqdidpkR 751
Cdd:PRK05580 185 EVLAQGKQALVLVPEIALTPQMLARFRARFGA---PVAVLhSGL-SDGERLDEWRKAKRGEAKVVIGA-----------R 249
|
170
....*....|....*....
gi 2535554553 752 ---------LGLFVLDEEH 761
Cdd:PRK05580 250 salflpfknLGLIIVDEEH 268
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
634-787 |
1.45e-12 |
|
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: 66.18 E-value: 1.45e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 634 QQDAIDAVIADMQSETPMDRLVCGdvgFGKTEVAMRAAFLAVQsgKQVLVLVPTTLLAQQHYENFKDRFADWPIRvevls 713
Cdd:cd17926 5 QEEALEAWLAHKNNRRGILVLPTG---SGKTLTALALIAYLKE--LRTLIVVPTDALLDQWKERFEDFLGDSSIG----- 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535554553 714 RFRSKKQLDDVKSAITEGTADIVIGTHKLLQQDidPKRLGLFVLDEEHRFGVTQKEQLKKYRAQIDVLTLTATP 787
Cdd:cd17926 75 LIGGGKKKDFDDANVVVATYQSLSNLAEEEKDL--FDQFGLLIVDEAHHLPAKTFSEILKELNAKYRLGLTATP 146
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
147-245 |
3.00e-12 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 70.81 E-value: 3.00e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 147 PRSFLDgNHLELKIGDQFDIEQWRLKLEKSGY-RNVAQvIEHGEFAVRGAIIDLFPMGS-RQPYRIDLFDDEIDTLRTFD 224
Cdd:COG0556 148 PEEYLK-MVLSLRVGEEIDRDELLRRLVELQYeRNDID-FTRGTFRVRGDVIEIFPAYSeERAIRIEFFGDEIERISEFD 225
|
90 100
....*....|....*....|.
gi 2535554553 225 PETQRSIDNIDQIQLLPAREF 245
Cdd:COG0556 226 PLTGEVLGELDRVTIYPASHY 246
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
620-977 |
1.58e-11 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 68.38 E-value: 1.58e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 620 EAFSAAFPFETTPDQQDAIDAVIADMQSetpmdRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFK 699
Cdd:COG1204 13 EFLKERGIEELYPPQAEALEAGLLEGKN-----LVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 700 DRFADWPIRVEVLSRfrskkqldDVKSAITE-GTADIVIGT----HKLLQQDIDP-KRLGLFVLDEEHRFGVTQK----- 768
Cdd:COG1204 88 RDFEELGIKVGVSTG--------DYDSDDEWlGRYDILVATpeklDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptle 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 769 ---EQLKKYRAQIDVLTLTAT---------------------PIP----------------------RTLNMSISGIRDL 802
Cdd:COG1204 160 vllARLRRLNPEAQIVALSATignaeeiaewldaelvksdwrPVPlnegvlydgvlrfddgsrrskdPTLALALDLLEEG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 803 -SIIATAPARRLAIKTfvlqwnADKIREGmLREIKRGGQVYFLHNKVEDIDRVARELETLMPEAR-----IAVAHGQMRe 876
Cdd:COG1204 240 gQVLVFVSSRRDAESL------AKKLADE-LKRRLTPEEREELEELAEELLEVSEETHTNEKLADclekgVAFHHAGLP- 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 877 RELEQVMLDFYHQR-FNVLVCTTIIETGIDVPtANTIFIDRADKLGLAQL-----YQIRGRVGRSHHRAY--AYLITPPQ 948
Cdd:COG1204 312 SELRRLVEDAFREGlIKVLVATPTLAAGVNLP-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYDPYgeAILVAKSS 390
|
410 420 430
....*....|....*....|....*....|...
gi 2535554553 949 QAMTADAIKRL----EAIESIedLGAGFTLATH 977
Cdd:COG1204 391 DEADELFERYIlgepEPIRSK--LANESALRTH 421
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
628-788 |
1.34e-10 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 61.15 E-value: 1.34e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 628 FETTPDQQDAIDAVIADMQSEtpmDRLVC--GDVGFGKTEVAMRAAFLAVQSG--KQVLVLVPTTLLAQQHYENFKDRFA 703
Cdd:pfam04851 2 LELRPYQIEAIENLLESIKNG---QKRGLivMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 704 DWPIRVEVLSrfrskkqldDVKSAITEGTADIVIGT-HKLL------QQDIDPKRLGLFVLDEEHRFGVTQKEQLKKYRA 776
Cdd:pfam04851 79 NYVEIGEIIS---------GDKKDESVDDNKIVVTTiQSLYkalelaSLELLPDFFDVIIIDEAHRSGASSYRNILEYFK 149
|
170
....*....|..
gi 2535554553 777 QIDVLTLTATPI 788
Cdd:pfam04851 150 PAFLLGLTATPE 161
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
654-764 |
8.35e-08 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 53.42 E-value: 8.35e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVAMRAAFLAV-QSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRfrskkqlDDVKSAITEGT 732
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALaTSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLLTG-------DPSVNKLLLAE 93
|
90 100 110
....*....|....*....|....*....|....*...
gi 2535554553 733 ADIVIGT----HKLLQQDIDP--KRLGLFVLDEEHRFG 764
Cdd:cd17921 94 ADILVATpeklDLLLRNGGERliQDVRLVVVDEAHLIG 131
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
875-942 |
2.47e-07 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 49.24 E-value: 2.47e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2535554553 875 RERELEQVMldfyhQRFNVLVCTTIIETGIDVPTANTIFIDRADKlGLAQLYQIRGRVGRSHHRAYAY 942
Cdd:cd18785 12 SIEHAEEIA-----SSLEILVATNVLGEGIDVPSLDTVIFFDPPS-SAASYIQRVGRAGRGGKDEGEV 73
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
628-907 |
5.24e-07 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 53.61 E-value: 5.24e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 628 FET-TPDQQDAIDAVIA--DM--QSETpmdrlvcgdvGFGKTevamrAAF-------LAVQSGK--QVLVLVPTTLLAQQ 693
Cdd:COG0513 22 YTTpTPIQAQAIPLILAgrDVlgQAQT----------GTGKT-----AAFllpllqrLDPSRPRapQALILAPTRELALQ 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 694 HYENFKDRFADWPIRVEVLSRFRS-KKQLDdvksAITEGtADIVIGT------HkLLQQDIDPKRLGLFVLDEEHR---- 762
Cdd:COG0513 87 VAEELRKLAKYLGLRVATVYGGVSiGRQIR----ALKRG-VDIVVATpgrlldL-IERGALDLSGVETLVLDEADRmldm 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 763 -FgvtqKEQLKKyraqIdvltLTATPIPR-------TLNmsiSGIRDLS--------IIATAPARRLA--IKTFVLQWNA 824
Cdd:COG0513 161 gF----IEDIER----I----LKLLPKERqtllfsaTMP---PEIRKLAkrylknpvRIEVAPENATAetIEQRYYLVDK 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 825 DKIREgMLREIKRGGQVY----FLHNKvEDIDRVARELEtlmpEARIAVA--HGQMRERELEQVMLDFYHQRFNVLVCTT 898
Cdd:COG0513 226 RDKLE-LLRRLLRDEDPEraivFCNTK-RGADRLAEKLQ----KRGISAAalHGDLSQGQRERALDAFRNGKIRVLVATD 299
|
....*....
gi 2535554553 899 IIETGIDVP 907
Cdd:COG0513 300 VAARGIDID 308
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
654-787 |
6.33e-07 |
|
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: 51.28 E-value: 6.33e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVAMRAA------FLAVQSGKqVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSrfrskkqlDDVKSA 727
Cdd:cd17927 21 IICLPTGSGKTFVAVLICehhlkkFPAGRKGK-VVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS--------GDTSEN 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 728 ITEG----TADIVIGTHKLLQQDI------DPKRLGLFVLDEEHRfgvTQKE----------QLKKYRAQID---VLTLT 784
Cdd:cd17927 92 VSVEqiveSSDVIIVTPQILVNDLksgtivSLSDFSLLVFDECHN---TTKNhpyneimfryLDQKLGSSGPlpqILGLT 168
|
...
gi 2535554553 785 ATP 787
Cdd:cd17927 169 ASP 171
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
658-788 |
1.39e-06 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 50.37 E-value: 1.39e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 658 DVGFGKT-EVAMRAAFLAVQS-GKQVLVLVPTTLLAQQHYEnFKDRFAdwpIRVEVLSRFRSKKQLDDVKSaiTEGTADI 735
Cdd:cd18011 25 EVGLGKTiEAGLIIKELLLRGdAKRVLILCPASLVEQWQDE-LQDKFG---LPFLILDRETAAQLRRLIGN--PFEEFPI 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2535554553 736 VIGTHKLLQQDID------PKRLGLFVLDEEHRFGVTQ-KEQLKKYR-----AQID--VLTLTATPI 788
Cdd:cd18011 99 VIVSLDLLKRSEErrglllSEEWDLVVVDEAHKLRNSGgGKETKRYKlgrllAKRArhVLLLTATPH 165
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
654-787 |
1.62e-06 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 52.42 E-value: 1.62e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVAMR--AAFLAVQSGKqVLVLVPTTLLAQQHYENFKDRFADWPIRVEVlsrFRSKKQLDDVKSAitEG 731
Cdd:COG1111 21 LVVLPTGLGKTAVALLviAERLHKKGGK-VLFLAPTKPLVEQHAEFFKEALNIPEDEIVV---FTGEVSPEKRKEL--WE 94
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2535554553 732 TADIVIGTHKLLQQDIDPKRL-----GLFVLDEEHR-FG----VTQKEQLKKYRAQIDVLTLTATP 787
Cdd:COG1111 95 KARIIVATPQVIENDLIAGRIdlddvSLLIFDEAHRaVGnyayVYIAERYHEDAKDPLILGMTASP 160
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
654-793 |
2.05e-06 |
|
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: 50.76 E-value: 2.05e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKT--EVAMRAAFLAV--QSGKQVLVLVPTTLLaqqhyENFKDRFADW----PIRVEVLSRfRSKKQLDDVK 725
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVdkNWGGPTLIVVPLSLL-----HNWMNEFERWvsppALRVVVLHG-NKRPQERWKN 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2535554553 726 SAITEGTADIVIGTHKLLQQD------IDPKRLglfVLDEEHRFGVTQ---KEQLKKYRAQIDVLtLTATPIPRTLN 793
Cdd:pfam00176 95 DPNFLADFDVVITTYETLRKHkellkkVHWHRI---VLDEGHRLKNSKsklSKALKSLKTRNRWI-LTGTPLQNNLE 167
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
660-946 |
2.76e-06 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 50.89 E-value: 2.76e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 660 GFGKTEVAMRAAFLAVQSGK--QVLVLVPTTLLAQQHYENFKDRFADWPI--RVEVLSRFRSKKQLDDVK---------- 725
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGETGLyhSSILSSRIKEMGDSEEFEhlfplyihsn 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 726 -----SAITEGTADIVI-------GTHKLLQQDIDPKRLglfVLDEEHRFG-------VTQKEQLKKYRAQIDVLTLTAT 786
Cdd:cd09639 89 dtlflDPITVCTIDQVLksvfgefGHYEFTLASIANSLL---IFDEVHFYDeytlaliLAVLEVLKDNDVPILLMSATLP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 787 PIPRTLNMSISGIRDLSIIATAPARRLAIKTFVLQWNAD-KIREGMLREIKRGGQVYFLHNKVEDIDRVARELETLMPEA 865
Cdd:cd09639 166 KFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEiSSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 866 RIAVAHGQM----RERELEQVMLDFYHQRFNVLVCTTIIETGIDVpTANTIFIDRADklgLAQLYQIRGRVGRsHHRAYA 941
Cdd:cd09639 246 EIMLIHSRFtekdRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHR-YGEKNG 320
|
....*...
gi 2535554553 942 ---YLITP 946
Cdd:cd09639 321 eevYIITD 328
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
660-816 |
4.59e-06 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 48.48 E-value: 4.59e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 660 GFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKD--RFADWPIRVEVLSRFRSKKQLDDVKSAITEGTADIVI 737
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKyaEKAGVEVKILVYHSRLKKKEKEELLEKIEKGDFDILV 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 738 GTHKLLQQDID---PKRLGLFVLDEehrfgvtqkeqlkkyraqIDVLTLTATPIPRTLNMsiSGIRDLsIIATAPARRLA 814
Cdd:cd17924 122 TTNQFLSKNFDllsNKKFDFVFVDD------------------VDAVLKSSKNIDRLLKL--LGFGQL-VVSSATGRPRG 180
|
..
gi 2535554553 815 IK 816
Cdd:cd17924 181 IR 182
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
654-787 |
1.12e-05 |
|
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: 47.12 E-value: 1.12e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVA-MRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKdRFADWPIRVEVLSrfrSKKQLDdvKSAITEGT 732
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAENLK-RVLNIPDKITSLT---GEVKPE--ERAERWDA 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2535554553 733 ADIVIGTHKLLQQDIDPKRL-----GLFVLDEEHRFGVTQKEQL--KKYRAQID---VLTLTATP 787
Cdd:cd18035 94 SKIIVATPQVIENDLLAGRItlddvSLLIFDEAHHAVGNYAYVYiaHRYKREANnplILGLTASP 158
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
851-945 |
7.79e-05 |
|
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: 45.70 E-value: 7.79e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 851 IDRVARELETLMPEARIAVahgqM------RERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRADKL---- 920
Cdd:cd18804 103 TERVEEELKTLFPEARIAR----IdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGlnsp 178
|
90 100 110
....*....|....*....|....*....|..
gi 2535554553 921 -------GLAQLYQIRGRVGRSHHRAYAYLIT 945
Cdd:cd18804 179 dfraserAFQLLTQVSGRAGRGDKPGKVIIQT 210
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
628-759 |
1.05e-04 |
|
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 44.74 E-value: 1.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 628 FET-TPDQQDAIDAVIAD----MQSETpmdrlvcgdvGFGKTevamrAAFL------------AVQSGKQVLVLVPTTLL 690
Cdd:cd00268 10 FEKpTPIQAQAIPLILSGrdviGQAQT----------GSGKT-----LAFLlpilekllpepkKKGRGPQALVLAPTREL 74
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2535554553 691 AQQHYENFKDRFADWPIRVEVL----SRfrsKKQLDDVKsaiteGTADIVIGT----HKLLQQ-DIDPKRLGLFVLDE 759
Cdd:cd00268 75 AMQIAEVARKLGKGTGLKVAAIyggaPI---KKQIEALK-----KGPDIVVGTpgrlLDLIERgKLDLSNVKYLVLDE 144
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
852-931 |
1.42e-04 |
|
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 42.55 E-value: 1.42e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 852 DRVARELETLMPEARIAVAHGQMRERELEQVMLDFYHQ-RFNVLVCTTIIETGIDVPTANTIFIDRADKlGLAQLYQIRG 930
Cdd:cd18799 20 EFMAEAFNEAGIDAVALNSDYSDRERGDEALILLFFGElKPPILVTVDLLTTGVDIPEVDNVVFLRPTE-SRTLFLQMLG 98
|
.
gi 2535554553 931 R 931
Cdd:cd18799 99 R 99
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
632-761 |
1.64e-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: 43.86 E-value: 1.64e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 632 PDQQDAIDAVIADMQSetpmdRLVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRFadwPIRVEV 711
Cdd:cd18028 4 PPQAEAVRAGLLKGEN-----LLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLE---EIGLKV 75
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 2535554553 712 LSR---FRSK-KQLDDvksaitegtADIVIGTHK----LLQQDIDPKR-LGLFVLDEEH 761
Cdd:cd18028 76 GIStgdYDEDdEWLGD---------YDIIVATYEkfdsLLRHSPSWLRdVGVVVVDEIH 125
|
|
| DEAD-like_helicase_N |
cd17912 |
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ... |
654-695 |
2.64e-04 |
|
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.
Pssm-ID: 350670 [Multi-domain] Cd Length: 81 Bit Score: 40.97 E-value: 2.64e-04
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 2535554553 654 LVCGDVGFGKTEVAMRAAFLAVQSGKQVLVLVPTTLLAQQHY 695
Cdd:cd17912 3 LHLGPTGSGKTLVAIQKIASAMSSGKSVLVVTPTKLLAHEIL 44
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
658-789 |
4.53e-04 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins 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: 350677 [Multi-domain] Cd Length: 182 Bit Score: 42.55 E-value: 4.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 658 DVGFGKTevAMRAAFLAV--QSGKQ---VLVLVPTTLLaqQHYENFKDRFADWPIRVEVLSRFRSKKQLDDVKSaitEGT 732
Cdd:cd17919 27 EMGLGKT--LQAIAFLAYllKEGKErgpVLVVCPLSVL--ENWEREFEKWTPDLRVVVYHGSQRERAQIRAKEK---LDK 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2535554553 733 ADIVIGTHKLLQQDIDpkRLGLF-----VLDEEHRF---GVTQKEQLKKYRAQIDVLtLTATPIP 789
Cdd:cd17919 100 FDVVLTTYETLRRDKA--SLRKFrwdlvVVDEAHRLknpKSQLSKALKALRAKRRLL-LTGTPLQ 161
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
662-761 |
6.37e-04 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 44.11 E-value: 6.37e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 662 GKTEVAMRAAFLAVQSGK-QVLVLVPTTLLAQQHYENFKDR---FADWPIRVEVlSRFRSKKQLDDVKsaitegtADIVI 737
Cdd:COG1202 237 GKTLIGELAGIKNALEGKgKMLFLVPLVALANQKYEDFKDRygdGLDVSIRVGA-SRIRDDGTRFDPN-------ADIIV 308
|
90 100
....*....|....*....|....*...
gi 2535554553 738 GTHK----LLQQDIDPKRLGLFVLDEEH 761
Cdd:COG1202 309 GTYEgidhALRTGRDLGDIGTVVIDEVH 336
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
508-558 |
6.76e-04 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 41.27 E-value: 6.76e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 2535554553 508 IGDAVVHEDHGVGRYLGLQTLDVGDVATEYVTLEYAKGD-KLYVPVASLDLI 558
Cdd:COG1329 3 VGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDmTIMVPVDKAESV 54
|
|
| DEXQc_arch_SWI2_SNF2 |
cd18012 |
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ... |
658-788 |
7.81e-04 |
|
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350770 [Multi-domain] Cd Length: 218 Bit Score: 42.17 E-value: 7.81e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 658 DVGFGKTeVAMRAAFLAV-QSG--KQVLVLVPTTLLAqqhyeNFKD---RFAdwP-IRVEVLS-RFRSKKQLDDVKSAit 729
Cdd:cd18012 31 DMGLGKT-LQTLALLLSRkEEGrkGPSLVVAPTSLIY-----NWEEeaaKFA--PeLKVLVIHgTKRKREKLRALEDY-- 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2535554553 730 egtaDIVIGTHKLLQQDID---PKRLGLFVLDEEHrfgVTQKEQLKKYRA--QIDV---LTLTATPI 788
Cdd:cd18012 101 ----DLVITSYGLLRRDIEllkEVKFHYLVLDEAQ---NIKNPQTKTAKAvkALKAdhrLALTGTPI 160
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
654-762 |
7.92e-04 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 43.71 E-value: 7.92e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 654 LVCGDVGFGKTEVAM--RAAFLAVQSGKqVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLS-RFRSKKqlddvKSAITE 730
Cdd:PRK13766 33 LVVLPTGLGKTAIALlvIAERLHKKGGK-VLILAPTKPLVEQHAEFFRKFLNIPEEKIVVFTgEVSPEK-----RAELWE 106
|
90 100 110
....*....|....*....|....*....|....*..
gi 2535554553 731 gTADIVIGTHKLLQQDIDPKRLGL--FVL---DEEHR 762
Cdd:PRK13766 107 -KAKVIVATPQVIENDLIAGRISLedVSLlifDEAHR 142
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
406-789 |
1.03e-03 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 43.29 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 406 DKFAGRILIAAESAGRRETLLDLLRKNQLQPKVVDNWDAFINDSAPLCITVAPLEQGLLLQIENIAVVAETQLFGQQVMQ 485
Cdd:COG0553 20 LLLLLRLGALLLELVLARELLLLLLAADALLLLALLLLLELLLLLAALLLLALLLLALSALALLLLRLLLALLLLALLLL 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 486 RRRRSRKKRDSDAIIRNLAELTIGDAVVHEDHGVGRYLGLQTLDVGDVATEYVTLEYAKGDKLYVPVASLDLISRYSGSA 565
Cdd:COG0553 100 LAGLLALALLLLALLGLLLSLALLLLLLLLLLLLLLALLLVLLAALLLLLLLLLLLALLLGRLLLLALLLLALEALLLLG 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 566 PELAPLHQLGTTQWEKARRRAAEKVRDVAAELLDIYAKRAANKKppMQSPDEQYEAFSAAFPFETTPDQQDAIDAVIAdm 645
Cdd:COG0553 180 LLLALALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFR--LRRLREALESLPAGLKATLRPYQLEGAAWLLF-- 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 646 qsetpMDRLVCG-----DVGFGKT-EVAMRAAFLAVQSGKQ-VLVLVPTTLLAQQHYEnfKDRFADwPIRVEVLSRFRSK 718
Cdd:COG0553 256 -----LRRLGLGglladDMGLGKTiQALALLLELKERGLARpVLIVAPTSLVGNWQRE--LAKFAP-GLRVLVLDGTRER 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 719 KQLDDVKSaitegTADIVIGTHKLLQQDID---PKRLGLFVLDEEHRFgvtqKEQLKK-YRA--QID---VLTLTATPIP 789
Cdd:COG0553 328 AKGANPFE-----DADLVITSYGLLRRDIEllaAVDWDLVILDEAQHI----KNPATKrAKAvrALKarhRLALTGTPVE 398
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
634-799 |
1.05e-03 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs 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: 350790 [Multi-domain] Cd Length: 163 Bit Score: 41.01 E-value: 1.05e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 634 QQDAIDAVIADMQSETpmDR-LVCGDVGFGKTEVA--MRAAFLAVQSGKQVLVLVPTTLLAQQHYENFKDRF-ADWPIRV 709
Cdd:cd18032 5 QQEAIEALEEAREKGQ--RRaLLVMATGTGKTYTAafLIKRLLEANRKKRILFLAHREELLEQAERSFKEVLpDGSFGNL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 710 EVLsrfrsKKQLDDvksaitegtADIVIGT-----HKLLQQDIDPKRLGLFVLDEEHRfGVTqkeqlKKYRAQID----- 779
Cdd:cd18032 83 KGG-----KKKPDD---------ARVVFATvqtlnKRKRLEKFPPDYFDLIIIDEAHH-AIA-----SSYRKILEyfepa 142
|
170 180
....*....|....*....|.
gi 2535554553 780 -VLTLTATPIpRTLNMSISGI 799
Cdd:cd18032 143 fLLGLTATPE-RTDGLDTYEL 162
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
873-931 |
1.13e-03 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 40.65 E-value: 1.13e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 873 QMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFidRADKLG-LAQLYQIRGR 931
Cdd:cd18802 73 LMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVI--RFDLPKtLRSYIQSRGR 130
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
846-907 |
1.45e-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: 39.80 E-value: 1.45e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2535554553 846 NKVEDIDRVARELEtlmpEARIAVA--HGQMRERELEQVMLDFYHQRFNVLVCTTIIETGIDVP 907
Cdd:cd18787 35 NTKKRVDRLAELLE----ELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIP 94
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
707-897 |
1.50e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 42.44 E-value: 1.50e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 707 IRVEVLSRFRSKKQLDDVKSAITEGTADIVI---------GTHKLLQQDidpkRLGLFVLDEEH-------------Rfg 764
Cdd:COG0514 82 IRAAFLNSSLSAEERREVLRALRAGELKLLYvaperllnpRFLELLRRL----KISLFAIDEAHcisqwghdfrpdyR-- 155
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 765 vtqkeQLKKYRAQID---VLTLTATPIPRT-------LnmsisGIRDLSIIATAPAR---RLAIKTFvlqWNADKIRE-- 829
Cdd:COG0514 156 -----RLGELRERLPnvpVLALTATATPRVradiaeqL-----GLEDPRVFVGSFDRpnlRLEVVPK---PPDDKLAQll 222
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2535554553 830 GMLREIKRG-GQVYFL-HNKVEDidrVARELEtlmpEARIAVA--HGQMRERELEQVMLDFYHQRFNVLVCT 897
Cdd:COG0514 223 DFLKEHPGGsGIVYCLsRKKVEE---LAEWLR----EAGIRAAayHAGLDAEEREANQDRFLRDEVDVIVAT 287
|
|
| DEADc_DDX54 |
cd17959 |
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ... |
631-792 |
1.93e-03 |
|
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350717 [Multi-domain] Cd Length: 205 Bit Score: 40.75 E-value: 1.93e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 631 TPDQQDAIDAVIAdmqsetPMDRLVCGDVGFGKTevamrAAFL----------AVQSGKQVLVLVPTTLLAQQHYENFKD 700
Cdd:cd17959 25 TPIQRKTIPLILD------GRDVVAMARTGSGKT-----AAFLipmieklkahSPTVGARALILSPTRELALQTLKVTKE 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 701 --RFADwpIRVEVLSRFRSkkqLDDVKSAITEGtADIVIGT-----HKLLQQDIDPKRLGLFVLDEEHR-FGVTQKEQLK 772
Cdd:cd17959 94 lgKFTD--LRTALLVGGDS---LEEQFEALASN-PDIIIATpgrllHLLVEMNLKLSSVEYVVFDEADRlFEMGFAEQLH 167
|
170 180
....*....|....*....|....
gi 2535554553 773 KYRAQI----DVLTLTATpIPRTL 792
Cdd:cd17959 168 EILSRLpenrQTLLFSAT-LPKLL 190
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
846-934 |
2.80e-03 |
|
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: 39.26 E-value: 2.80e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 846 NKVEDIdrvARELETLMPEARIAVAHGQ--------MRERELEQVMLDFYHQRFNVLVCTTIIETGIDVPTANTIFIDRA 917
Cdd:cd18801 41 DSAEEI---VNFLSKIRPGIRATRFIGQasgksskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDA 117
|
90
....*....|....*..
gi 2535554553 918 DKLGLaQLYQIRGRVGR 934
Cdd:cd18801 118 SPSPI-RMIQRMGRTGR 133
|
|
| DEADc_DDX52 |
cd17957 |
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ... |
652-759 |
4.75e-03 |
|
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350715 [Multi-domain] Cd Length: 198 Bit Score: 39.49 E-value: 4.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 652 DRLVCGDVGFGKTevamrAAFL----------AVQSGKQVLVLVPTTLLAQQHYENFKDRFADWPIRVEVLSRFRSKKQl 721
Cdd:cd17957 29 DLLACAPTGSGKT-----LAFLipilqklgkpRKKKGLRALILAPTRELASQIYRELLKLSKGTGLRIVLLSKSLEAKA- 102
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 2535554553 722 DDVKSAITegTADIVIGTHK----LLQQD-IDPKRLGLFVLDE 759
Cdd:cd17957 103 KDGPKSIT--KYDILVSTPLrlvfLLKQGpIDLSSVEYLVLDE 143
|
|
| DEADc_DDX1 |
cd17938 |
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ... |
644-763 |
6.04e-03 |
|
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350696 [Multi-domain] Cd Length: 204 Bit Score: 39.23 E-value: 6.04e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 644 DMQSET-PM-----DRLVCGDVGFGKTevamrAAF-LAVQSGKQVLVLVPTTLLAQQHY---ENFKDRFADWPIRVEVL- 712
Cdd:cd17938 24 DIQAEAiPLilgggDVLMAAETGSGKT-----GAFcLPVLQIVVALILEPSRELAEQTYnciENFKKYLDNPKLRVALLi 98
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 2535554553 713 SRFRSKKQLddvksAITEGTADIVIGT-HKLL----QQDIDPKRLGLFVLDEEHRF 763
Cdd:cd17938 99 GGVKAREQL-----KRLESGVDIVVGTpGRLEdlikTGKLDLSSVRFFVLDEADRL 149
|
|
| DEADc_DDX56 |
cd17961 |
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
660-759 |
9.74e-03 |
|
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350719 [Multi-domain] Cd Length: 206 Bit Score: 38.72 E-value: 9.74e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2535554553 660 GFGKTevamrAAFL--------------AVQSGKQVLVLVPTTLLAQQHYENFKD--RFADWPIRVEVLSRFRSkkqlDD 723
Cdd:cd17961 41 GSGKT-----AAYAlpiiqkilkakaesGEEQGTRALILVPTRELAQQVSKVLEQltAYCRKDVRVVNLSASSS----DS 111
|
90 100 110 120
....*....|....*....|....*....|....*....|..
gi 2535554553 724 VKSAITEGTADIVIGT-HKLLQQ-----DIDPKRLGLFVLDE 759
Cdd:cd17961 112 VQRALLAEKPDIVVSTpARLLSHlesgsLLLLSTLKYLVIDE 153
|
|
| |
