|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
26-1169 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1610.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 26 RQLITGLAGSAKTLLFARAFKKTNKNMIILMPNLYYANQLAEDLQHVIPQDQIHLFPVDEVLSAEMAFSSPEARGERVAT 105
Cdd:COG1197 4 RLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSERLAT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 106 LNALQEKKAGIYLLPVASLHKRLPNKKTWLQAQLNWHIGDEIDVENLPRQLTLMGYVREEMVAKPGEFSIRGSIIDIYPL 185
Cdd:COG1197 84 LRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDIFPP 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 186 TTTYPVRVELFDVEIDSMRYFEAETQRSIEKTEEIWVSPTSEQVYGPEDLEHGIEQMQKMLEkrlaatTEEADREFLQDy 265
Cdd:COG1197 164 GSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFG------LDPKLDELYEA- 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 266 fgqltssWQAGVPTEEAKFYSDLLYQESVTILDYFPSNSLLVVDDYQRIMETNREIEREAAEWQTQKISELR--VFSEQT 343
Cdd:COG1197 237 -------LSEGIAFAGIEYYLPLFYEELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEARRHDRGrpLLPPEE 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 344 FSADIQKIVQK-EKFTTTFFSLFQkgmGNLRFQAIHNFQYRTMQQFFGQMPLLKTEMDRWRKQKQTVVIFIPTKDRIRKA 422
Cdd:COG1197 310 LFLDPEELFAAlKRRPRVTLSPFA---ALPEGAGVVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRRERL 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 423 EQMLRDEDILVVETEK-NALIRGQVQLVEGALQAGFELPQEKIVAITEKEIFQKTTKKQTRRQTVTNAERLKSYNELKAG 501
Cdd:COG1197 387 LELLRDHGIPARLVESlAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSADAFIRDLSELKPG 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 502 DYVVHANHGIGKYIGMETLEVDGVHQDYMTILYQNDDKLFIPVTQLNLIQKYVASEAKAPRINKLGGSEWTKTKRKVSSK 581
Cdd:COG1197 467 DYVVHVDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKA 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 582 IEDIADDLIKLYAARESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALR 661
Cdd:COG1197 547 VRDIAAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALR 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 662 AAFKAIKESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEF 741
Cdd:COG1197 627 AAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKF 706
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 742 SDLGLLIIDEEQRFGVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRYPIQTYVMEKNPGAIRE 821
Cdd:COG1197 707 KDLGLLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIRE 786
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 822 AIHREMGRGGQVFYLYNRVETIEQKVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNA 901
Cdd:COG1197 787 AILRELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNA 866
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 902 NTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQKILNEVSEKRLQAIKDFTELGSGFKIAMRDLSIRGAGNLLG 981
Cdd:COG1197 867 NTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLG 946
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 982 AQQHGFIDAVGFDMYSQMLSEAVSRKQGKNSQVEKTTVEIDLGVDAYLPETYVADQRQKIEIYKRIRELDSQEMLDELED 1061
Cdd:COG1197 947 EEQSGHIAEVGFDLYLQMLEEAVAALKGGKEPEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQE 1026
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 1062 DLLDRFGEYPEEVAHLLTIGQIKMDGDRALLETIRKQEAHIVFTLSKVgtKRYSVEQLFEALTATKLKASLGVEKeQMVI 1141
Cdd:COG1197 1027 ELIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPN--TPLDPEKLIRLIQKQPGRYKLDGDD-KLVI 1103
|
1130 1140
....*....|....*....|....*...
gi 1080572589 1142 RLTIPNQMEeavWLQEIQKFVKALREQK 1169
Cdd:COG1197 1104 TLDLEDPEE---RLEALEELLEALAKLA 1128
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
159-1086 |
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: 1094.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 159 MGYVREEMVAKPGEFSIRGSIIDIYPLTTTYPVRVELFDVEIDSMRYFEAETQRSIEKTEEIWVSPTSEQVYGPEDLEHG 238
Cdd:TIGR00580 4 LGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEETIAR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 239 IEQMQKMLEKRLAATTEEADREFLQdyfgqltsswqagvPTEEAKFYSdLLYQESVTILDYFPSNSLLVVDDYQRIMETN 318
Cdd:TIGR00580 84 LKDNAARVEDAKHLETIEALSEGTL--------------PAGEEMFLP-LFFEDLSSLFDYLPDNTPILLDDPERFHSAA 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 319 REIEREAAEWQTQKISELRVFSEQTFSADIQKIVqkekFTTTFFSLF--QKGMGNLRFQAIHNFQYRTMQQFFGQMPLLK 396
Cdd:TIGR00580 149 RFLQRELEEFYNALEEAKKLINPPRLDLDPSELA----FEASAISLSrvQLENEHLSLKASEAIEGAQKHSRLEFGEILA 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 397 TEMD--RWRKQKQTVVIFIPTKDRIRKAEQMLRDEDILV-VETEKNALIRGQVQLVEGALQAGFELPQEKIVAITEKEIF 473
Cdd:TIGR00580 225 FKEElfRWLKAGFKITVAAESESQAERLKSLLAEHDIAAqVIDESCIIIPAVRYVMIGALSSGFILPTAGLAVITESELF 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 474 QKTTKKQTRRQTVTNAeRLKSYNELKAGDYVVHANHGIGKYIGMETLEVDGVHQDYMTILYQNDDKLFIPVTQLNLIQKY 553
Cdd:TIGR00580 305 GSRVLRRPKKSRLKSK-PIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRY 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 554 VASEAKAPRINKLGGSEWTKTKRKVSSKIEDIADDLIKLYAARESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEI 633
Cdd:TIGR00580 384 VGGSGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEI 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 634 KRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQ 713
Cdd:TIGR00580 464 KADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQ 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 714 KETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLIIDEEQRFGVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRD 793
Cdd:TIGR00580 544 NEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRD 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 794 LSVIETPPANRYPIQTYVMEKNPGAIREAIHREMGRGGQVFYLYNRVETIEQKVEEIQELVPEARIGYAHGQMTEAQLEN 873
Cdd:TIGR00580 624 LSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEE 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 874 TLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQKILNEVSEKRLQA 953
Cdd:TIGR00580 704 VMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEA 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 954 IKDFTELGSGFKIAMRDLSIRGAGNLLGAQQHGFIDAVGFDMYSQMLSEAVSRKQGKNSQVEKTTVEIDLGVDAYLPETY 1033
Cdd:TIGR00580 784 IQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEETDIELPYSAFIPDDY 863
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 1034 VADQRQKIEIYKRIRELDSQEMLDELEDDLLDRFGEYPEEVAHLLTIGQIKMD 1086
Cdd:TIGR00580 864 IADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLL 916
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
65-1101 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 681.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 65 LAEDLQHVIP-QDQIHLF---PVDEVLSAEM----AFSS-PEARGERVATLNALQEKKAGIYLLPVASLHKRL-PNkkTW 134
Cdd:PRK10689 45 IAPDMQNALRlHDEIQQFtdqMVMNLADWETlpydSFSPhQDIISSRLSTLYQLPTMQRGVLILPVNTLMQRVcPH--SF 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 135 LQAQ-LNWHIGDEIDVENLPRQLTLMGYVREEMVAKPGEFSIRGSIIDIYPLTTTYPVRVELFDVEIDSMRYFEAETQRS 213
Cdd:PRK10689 123 LHGHaLVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHGEYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRT 202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 214 IEKTEEIWVSPTSEQVYGPEDLEHGIEQMQKMLEKRlaattEEADREFLQDYFGqltsSWQAGVPTEEAKFYSDLLyqes 293
Cdd:PRK10689 203 LEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVK-----RDAEHIYQQVSKG----TLPAGIEYWQPLFFSEPL---- 269
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 294 VTILDYFPSNSLLV-VDDYQRIMEtnREIEREAAEWQTQKISELR-VFSEQTFSADIQKIVQKEK------FTTTffSLF 365
Cdd:PRK10689 270 PPLFSYFPANTLLVnTGDLETSAE--RFWADTLARFENRGVDPMRpLLPPESLWLRVDELFSELKnwprvqLKTE--HLP 345
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 366 QK-GMGNLRFQAIHNFQYRTMQqffgqmpllKTEMDRWRK---QKQTVVIFIPTKDRIRKAEQMLRDEdILVVETEKNAL 441
Cdd:PRK10689 346 TKaANTNLGYQKLPDLAVQAQQ---------KAPLDALRRfleSFDGPVVFSVESEGRREALGELLAR-IKIAPKRIMRL 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 442 IRGQVQ---LVEGALQAGFELPQEKIVAITEKEIFQK--TTKKQTRRQTVTNAERLKSYNELKAGDYVVHANHGIGKYIG 516
Cdd:PRK10689 416 DEASDRgryLMIGAAEHGFIDTVRNLALICESDLLGErvARRRQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAG 495
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 517 METLEVDGVHQDYMTILYQNDDKLFIPVTQLNLIQKYVA-SEAKAPrINKLGGSEWTKTKRKVSSKIEDIADDLIKLYAA 595
Cdd:PRK10689 496 MTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGgAEENAP-LHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQ 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 596 RESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIKESKQVAF 675
Cdd:PRK10689 575 RAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAV 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 676 LVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLIIDEEQRF 755
Cdd:PRK10689 655 LVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRF 734
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 756 GVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRYPIQTYVMEKNPGAIREAIHREMGRGGQVFY 835
Cdd:PRK10689 735 GVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYY 814
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 836 LYNRVETIEQKVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYMGLS 915
Cdd:PRK10689 815 LYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLA 894
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 916 TLYQLRGRVGRSSRVAYAYFMYEQQKILNEVSEKRLQAIKDFTELGSGFKIAMRDLSIRGAGNLLGAQQHGFIDAVGFDM 995
Cdd:PRK10689 895 QLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSL 974
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 996 YSQMLSEAV-SRKQGKNSQVEKTT---VEIDLGVDAYLPETYVADQRQKIEIYKRIRELDSQEMLDELEDDLLDRFGEYP 1071
Cdd:PRK10689 975 YMELLENAVdALKAGREPSLEDLTsqqTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLP 1054
|
1050 1060 1070
....*....|....*....|....*....|
gi 1080572589 1072 EEVAHLLTIGQIKMdgdRALLETIRKQEAH 1101
Cdd:PRK10689 1055 DPARNLLDIARLRQ---QAQKLGIRKLEGN 1081
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
589-989 |
3.30e-128 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 408.28 E-value: 3.30e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 589 LIKLYAARESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIK 668
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 669 ESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLI 748
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 749 IDEEQRFGVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRYPIQTYV--MEKNPGAIrEAIHRE 826
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVvpEERRDEVY-ERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 827 MGRGGQVFYLYNRVE--------TIEQKVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDI 898
Cdd:COG1200 466 IAKGRQAYVVCPLIEesekldlqAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 899 PNANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQkiLNEVSEKRLQAIKDFTelgSGFKIAMRDLSIRGAGN 978
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETN---DGFEIAEEDLELRGPGE 620
|
410
....*....|.
gi 1080572589 979 LLGAQQHGFID 989
Cdd:COG1200 621 FLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
589-989 |
1.37e-122 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 393.36 E-value: 1.37e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 589 LIKLYAARESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIK 668
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 669 ESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLI 748
Cdd:PRK10917 309 AGYQAALMAPTEILAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 749 IDEEQRFGVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRYPIQTYVM-EKNPGAIREAIHREM 827
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIpDSRRDEVYERIREEI 468
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 828 GRGGQVFYLYNRVE--------TIEQKVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIP 899
Cdd:PRK10917 469 AKGRQAYVVCPLIEesekldlqSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 900 NANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQkiLNEVSEKRLQAIKDFTelgSGFKIAMRDLSIRGAGNL 979
Cdd:PRK10917 549 NATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP--LSETARERLKIMRETN---DGFVIAEKDLELRGPGEL 623
|
410
....*....|
gi 1080572589 980 LGAQQHGFID 989
Cdd:PRK10917 624 LGTRQSGLPE 633
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
607-799 |
2.51e-120 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 369.21 E-value: 2.51e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 607 DDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQH 686
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 687 YETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLIIDEEQRFGVKHKERLKQL 766
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 1080572589 767 RAQVDVLTLTATPIPRTLHMSMLGVRDLSVIET 799
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
612-989 |
6.25e-107 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 349.72 E-value: 6.25e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 612 KEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETML 691
Cdd:TIGR00643 226 TKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLR 305
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 692 ERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLIIDEEQRFGVKHKERLK---QLRA 768
Cdd:TIGR00643 306 NLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVEQRKKLRekgQGGF 385
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 769 QVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPANRYPIQTYVM-EKNPGAIREAIHREMGRGGQVFYLYNRVETIEQ-- 845
Cdd:TIGR00643 386 TPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIkHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESEKld 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 846 ------KVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYMGLSTLYQ 919
Cdd:TIGR00643 466 lkaaeaLYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQ 545
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 920 LRGRVGRSSRVAYAYFMYEQQKilNEVSEKRLQAIKDFTElgsGFKIAMRDLSIRGAGNLLGAQQHGFID 989
Cdd:TIGR00643 546 LRGRVGRGDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSGYPE 610
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
589-801 |
3.89e-73 |
|
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: 242.44 E-value: 3.89e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 589 LIKLYAARESEKGYAFGPDDAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIK 668
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 669 ESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQVDIVVGTHRILSKDIEFSDLGLLI 748
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 749 IDEEQRFGVKHKERLKQLRAQVDVLTLTATPIPRTLHMSMLGVRDLSVIETPP 801
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
806-955 |
7.21e-71 |
|
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: 233.00 E-value: 7.21e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 806 PIQTYVMEKNPGAIREAIHREMGRGGQVFYLYNRVETIEQKVEEIQELVPEARIGYAHGQMTEAQLENTLFEFIEGQYDV 885
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 886 LVTTTIIETGVDIPNANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQKILNEVSEKRLQAIK 955
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQ 150
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
806-956 |
6.15e-61 |
|
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: 205.19 E-value: 6.15e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 806 PIQTYVMEKNPGA-IREAIHREMGRGGQVFYLYNRVET--------IEQKVEEIQELVPEARIGYAHGQMTEAQLENTLF 876
Cdd:cd18792 1 PIRTYVIPHDDLDlVYEAIERELARGGQVYYVYPRIEEsekldlksIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 877 EFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQKILNEVSEKRLQAIKD 956
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
613-797 |
4.51e-57 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 194.94 E-value: 4.51e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 613 EFENAFPYSETDDQLRSAAEIKRDMEKEKPMDRLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETMLE 692
Cdd:cd17918 7 ELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARK 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 693 RFEgfPVNIGLLSRFRtrkqqKETIEQlrtgQVDIVVGTHRILSKDIEFSDLGLLIIDEEQRFGVKHKERLKQLRAqVDV 772
Cdd:cd17918 87 FLP--FINVELVTGGT-----KAQILS----GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGA-THF 154
|
170 180
....*....|....*....|....*
gi 1080572589 773 LTLTATPIPRTLHMSMLGVRDLSVI 797
Cdd:cd17918 155 LEATATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
497-594 |
5.21e-44 |
|
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: 154.53 E-value: 5.21e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 497 ELKAGDYVVHANHGIGKYIGMETLEVDGVHQDYMTILYQNDDKLFIPVTQLNLIQKYVASEAKA-PRINKLGGSEWTKTK 575
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEVePVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 1080572589 576 RKVSSKIEDIADDLIKLYA 594
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
806-956 |
4.98e-34 |
|
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: 128.23 E-value: 4.98e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 806 PIQTYVM-EKNPGAIREAIHREMGRGGQVFYLYNRVETIE----QKVEEIQE-----LVPEARIGYAHGQMTEAQLENTL 875
Cdd:cd18811 1 PITTYLIfHTRLDKVYEFVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 876 FEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYMGLSTLYQLRGRVGRSSRVAYAYFMYEQQkiLNEVSEKRLQAIK 955
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVMT 158
|
.
gi 1080572589 956 D 956
Cdd:cd18811 159 E 159
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
498-593 |
3.01e-30 |
|
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: 114.85 E-value: 3.01e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 498 LKAGDYVVHANHGIGKYIGMETLEvdgvHQDYMTILYQNDDKLFIPVTQLNLIQKYVASEakapRINKLG-GSEWTKTKR 576
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 1080572589 577 KVSSKIEDIADDLIKLY 593
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
139-227 |
1.23e-29 |
|
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: 113.26 E-value: 1.23e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 139 LNWHIGDEIDVENLPRQLTLMGYVREEMVAKPGEFSIRGSIIDIYPLTT-TYPVRVELFDVEIDSMRYFEAETQRSIEKT 217
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSeDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|
gi 1080572589 218 EEIWVSPTSE 227
Cdd:pfam17757 81 DEVTIYPASH 90
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
614-801 |
2.96e-25 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 104.50 E-value: 2.96e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 614 FENAFPYSETDDQLRSAAEIKRDMekekpMDRLLVGDVGYGKTEVALRAAFKAIKES--KQVAFLVPTTILAQQHYETML 691
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGL-----RDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 692 ERFEGFPVNIGLLsrfRTRKQQKETIEQLRTGQVDIVVGT-----HRILSKDIEFSDLGLLIIDEEQR-----FGVKHKE 761
Cdd:smart00487 76 KLGPSLGLKVVGL---YGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1080572589 762 RLKQLRAQVDVLTLTATP---IPRTLHMSMLGVRDLSVIETPP 801
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPL 195
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
623-786 |
6.08e-25 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 102.32 E-value: 6.08e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 623 TDDQLRSAAEI--KRDMekekpmdrLLVGDVGYGKTEVALRAAFKAIKESK---QVAFLVPTTILAQQHYETMLERFEGF 697
Cdd:pfam00270 1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTLAFLLPALEALDKLDngpQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 698 PVNIgllSRFRTRKQQKETIEQLRTgqVDIVVGTH----RILSKDIEFSDLGLLIIDEEQR-----FGVKHKERLKQLRA 768
Cdd:pfam00270 73 GLKV---ASLLGGDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPK 147
|
170
....*....|....*...
gi 1080572589 769 QVDVLTLTATPiPRTLHM 786
Cdd:pfam00270 148 KRQILLLSATL-PRNLED 164
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1022-1120 |
5.71e-22 |
|
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: 91.76 E-value: 5.71e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 1022 DLGVDAYLPETYVADQRQKIEIYKRIRELDSQEMLDELEDDLLDRFGEYPEEVAHLLTIGQIKMDGDRALLETIRKQEAH 1101
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90
....*....|....*....
gi 1080572589 1102 IVFTLSKVGTKRYSVEQLF 1120
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILL 99
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
132-309 |
6.95e-20 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 95.50 E-value: 6.95e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 132 KTWLQAQLNWHIGDEIDVENLPRQLTLMGYVREEMVAKPGEFSIRGSIIDIYP-LTTTYPVRVELFDVEIDSMRYFEAET 210
Cdd:PRK05298 152 EEYLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPaYYEERAIRIEFFGDEIERISEFDPLT 231
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 211 QRSIEKTEEIWVSPTSEQVYGPEDLEHGIEQMQKMLEKRLAATTE-----EADR---------EFLQ---------DYfg 267
Cdd:PRK05298 232 GEVLGELDRVTIYPASHYVTPRERLERAIESIKEELEERLKELEKegkllEAQRleqrtrydlEMLRelgycsgieNY-- 309
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1080572589 268 qltSSWQAGVPTEEAKFysdllyqesvTILDYFPSNSLLVVD 309
Cdd:PRK05298 310 ---SRHLDGRKPGEPPY----------TLLDYFPDDFLLFID 338
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1023-1108 |
1.71e-18 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 81.32 E-value: 1.71e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 1023 LGVDAYLPETYVADQRQKIEIYKRIRELDSQEMLDELEDDLLDRFGEYPEEVAHLLTIGQIKMDGDRALLETIRKQEAHI 1102
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
....*.
gi 1080572589 1103 VFTLSK 1108
Cdd:pfam03461 81 RITFSE 86
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
643-778 |
1.19e-17 |
|
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: 80.91 E-value: 1.19e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 643 MDRLLVGDVGYGKTEVALRAAFKAIKES-KQVAFLVPTTILAQQHYETMLERFeGFPVNIGLLSRFRTRKQQKEtieqLR 721
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKKgKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEEREK----NK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 722 TGQVDIVVGTHRILSKDIE------FSDLGLLIIDEEQRFGVKHKERL-------KQLRAQVDVLTLTAT 778
Cdd:cd00046 77 LGDADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALildlavrKAGLKNAQVILLSAT 146
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
646-929 |
2.29e-17 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 86.67 E-value: 2.29e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQhyetMLERFEG-FPVNIGLLSRFRTRKQQKETIEQLRTGQ 724
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQ----MIQRFKYrFGSQVAVLHSGLSDSEKLQAWRKVKNGE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 725 VDIVVGTHRILSkdIEFSDLGLLIIDEEQRFGVK-------HKERLKQLRA---QVDVLTLTATPIPRTLHMSMLGVRDL 794
Cdd:TIGR00595 77 ILVVIGTRSALF--LPFKNLGLIIVDEEHDSSYKqeegpryHARDVAVYRAkkfNCPVVLGSATPSLESYHNAKQKAYRL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 795 SVIETPPANRYP--IQTYVMEKNPG------AIREAIHREMGRGGQ-----------------------------VFYLY 837
Cdd:TIGR00595 155 LVLTRRVSGRKPpeVKLIDMRKEPRqsflspELITAIEQTLAAGEQsilflnrrgysknllcrscgyilccpncdVSLTY 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 838 NRVET-------------------------------IEQKVEEIQELVPEARIGYAHGQMT--EAQLENTLFEFIEGQYD 884
Cdd:TIGR00595 235 HKKEGklrchycgyqepipktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTTsrKGAHEALLNQFANGKAD 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1080572589 885 VLVTTTIIETGVDIPNANTLFVENADYM-----------GLSTLYQLRGRVGRSSR 929
Cdd:TIGR00595 315 ILIGTQMIAKGHHFPNVTLVGVLDADSGlhspdfraaerGFQLLTQVAGRAGRAED 370
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
142-309 |
3.22e-17 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 86.99 E-value: 3.22e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 142 HIGDEIDVENLPRQLTLMGYVREEMVAKPGEFSIRGSIIDIYPL-TTTYPVRVELFDVEIDSMRYFEAETQRSIEKTEEI 220
Cdd:COG0556 159 RVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPAySEERAIRIEFFGDEIERISEFDPLTGEVLGELDRV 238
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 221 WVSPTSEQVYGPEDLEHGIEQMQKMLEKRLAATTE-----EADR---------EFLQ---------DYfgqltSSWQAGV 277
Cdd:COG0556 239 TIYPASHYVTPRERLERAIESIKEELEERLAEFESegkllEAQRleqrtrydlEMLRelgycsgieNY-----SRHLDGR 313
|
170 180 190
....*....|....*....|....*....|..
gi 1080572589 278 PTEEAKFysdllyqesvTILDYFPSNSLLVVD 309
Cdd:COG0556 314 KPGEPPP----------TLLDYFPDDFLLFID 335
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
818-926 |
2.87e-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: 75.71 E-value: 2.87e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 818 AIREAIHREmgRGGQVFYLYNRVETIEQKVEEIQElvpEARIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVD 897
Cdd:pfam00271 5 ALLELLKKE--RGGKVLIFSQTKKTLEAELLLEKE---GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLD 79
|
90 100
....*....|....*....|....*....
gi 1080572589 898 IPNANTLFVENADYmGLSTLYQLRGRVGR 926
Cdd:pfam00271 80 LPDVDLVINYDLPW-NPASYIQRIGRAGR 107
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
646-752 |
4.68e-16 |
|
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: 77.25 E-value: 4.68e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQhyetMLERFEG-FPVNIGLLSRFRTRKQQKETIEQLRTGQ 724
Cdd:cd17929 19 LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQ----LIKRFKKrFGDKVAVLHSKLSDKERADEWRKIKRGE 94
|
90 100
....*....|....*....|....*...
gi 1080572589 725 VDIVVGTHRILSkdIEFSDLGLLIIDEE 752
Cdd:cd17929 95 AKVVIGARSALF--APFKNLGLIIVDEE 120
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
624-924 |
7.89e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 82.38 E-value: 7.89e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 624 DDQLRSAAEIKRDMEKEKpmDR-LLVGDVGYGKTEVALRAAfKAIKESKQVAFLVPTTILAQQHYETmLERFEGFPVNIG 702
Cdd:COG1061 83 PYQQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEE-LRRFLGDPLAGG 158
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 703 llsrfrTRKQQKEtieqlrtgqvDIVVGTHRILSKDIEFSDL----GLLIIDEEQRFGVK-HKERLKQLRAQVdVLTLTA 777
Cdd:COG1061 159 ------GKKDSDA----------PITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPsYRRILEAFPAAY-RLGLTA 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 778 TPI---PRTLHMSMLG----------------VRDLSVIE-----TPPANRY-----PIQTYVMEKNPGAIR--EAIHRE 826
Cdd:COG1061 222 TPFrsdGREILLFLFDgivyeyslkeaiedgyLAPPEYYGirvdlTDERAEYdalseRLREALAADAERKDKilRELLRE 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 827 MGRGGQVFYLYNRVETieqkVEEIQELVPEA--RIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTL 904
Cdd:COG1061 302 HPDDRKTLVFCSSVDH----AEALAELLNEAgiRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVA 377
|
330 340
....*....|....*....|.
gi 1080572589 905 FVenADYMG-LSTLYQLRGRV 924
Cdd:COG1061 378 IL--LRPTGsPREFIQRLGRG 396
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
623-927 |
7.15e-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: 78.38 E-value: 7.15e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 623 TDDQLRSAAEIKRDMEKEKPMdrlLVGDV-GYGKTEVALRAAFKAIKESKQVAFLVPTTilaqqhyETMLE---RF-EGF 697
Cdd:COG4098 112 TPAQQKASDELLEAIKKKEEH---LVWAVcGAGKTEMLFPAIAEALKQGGRVCIATPRV-------DVVLElapRLqQAF 181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 698 P-VNIGLLSrfrtrkqqKETIEQLRTGQVdIVVGTHRILskdiEFSD-LGLLIIDE---------EQ-RFGVKhkerlKQ 765
Cdd:COG4098 182 PgVDIAALY--------GGSEEKYRYAQL-VIATTHQLL----RFYQaFDLLIIDEvdafpysgdPMlQYAVK-----RA 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 766 LRAQVDVLTLTATPiPRTLHMSM-LGVRDLSVIetppANRY-----PIQTYVMEKN----------PGAIREAIHREMGR 829
Cdd:COG4098 244 RKPDGKLIYLTATP-SKALQRQVkRGKLKVVKL----PARYhghplPVPKFKWLGNwkkrlrrgklPRKLLKWLKKRLKE 318
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 830 GGQVFYLYNRVETIEQKVEEIQELVPEARIGYAHGQmTEAQLENTLfEFIEGQYDVLVTTTIIETGVDIPNAN------- 902
Cdd:COG4098 319 GRQLLIFVPTIELLEQLVALLQKLFPEERIAGVHAE-DPERKEKVQ-AFRDGEIPILVTTTILERGVTFPNVDvavlgad 396
|
330 340
....*....|....*....|....*.
gi 1080572589 903 -TLFVEnadymglSTLYQLRGRVGRS 927
Cdd:COG4098 397 hPVFTE-------AALVQIAGRVGRS 415
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
623-752 |
7.92e-14 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 75.96 E-value: 7.92e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 623 TDDQlRSAAEIKRDMEKEKPMdrLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQhyetMLERFEG-FPVNI 701
Cdd:PRK05580 146 NPEQ-AAAVEAIRAAAGFSPF--LLDGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQ----MLARFRArFGAPV 218
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1080572589 702 GLL-SRFrTRKQQKETIEQLRTGQVDIVVGThR---ILSkdieFSDLGLLIIDEE 752
Cdd:PRK05580 219 AVLhSGL-SDGERLDEWRKAKRGEAKVVIGA-RsalFLP----FKNLGLIIVDEE 267
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
608-752 |
1.93e-13 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 74.77 E-value: 1.93e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 608 DAYQKEFENAFPYSETDDQLRSAAEIKRDMEKEKPMdrLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQhy 687
Cdd:COG1198 182 DPFAPDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVPEIALTPQ-- 257
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1080572589 688 etMLERFEG-FPVNIGLL-SRFrTRKQQKETIEQLRTGQVDIVVGThR--ILSkdiEFSDLGLLIIDEE 752
Cdd:COG1198 258 --TVERFRArFGARVAVLhSGL-SDGERLDEWRRARRGEARIVIGT-RsaLFA---PFPNLGLIIVDEE 319
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
848-926 |
9.30e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 64.93 E-value: 9.30e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 848 EEIQELVPEARIGYA--HGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYmGLSTLYQLRGRVG 925
Cdd:smart00490 1 EELAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPW-SPASYIQRIGRAG 79
|
.
gi 1080572589 926 R 926
Cdd:smart00490 80 R 80
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
652-929 |
8.75e-12 |
|
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: 68.23 E-value: 8.75e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESK--QVAFLVPTTILAQQHYETMLERFeGFPVNIGLLSRFR--TRKQQKETIEQLRT----- 722
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAF-GETGLYHSSILSSriKEMGDSEEFEHLFPlyihs 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 723 ------GQVDIVVGTHRILSKDIEFSD---------LGLLIIDEEQRFGVKHKER-LKQLRAQVD----VLTLTATpIP- 781
Cdd:cd09639 88 ndtlflDPITVCTIDQVLKSVFGEFGHyeftlasiaNSLLIFDEVHFYDEYTLALiLAVLEVLKDndvpILLMSAT-LPk 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 782 --RTLHMSMLGVRDLSVIETPPANRYPIQTYVMEKNPG-AIREAIHREMGRGGQVFYLYNRVETIEQKVEEIQELVPEAR 858
Cdd:cd09639 167 flKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEiSSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEE 246
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080572589 859 IGYAHGQMTE---AQLENTLF-EFIEGQYDVLVTTTIIETGVDIpNANTLFVENADymgLSTLYQLRGRVGRSSR 929
Cdd:cd09639 247 IMLIHSRFTEkdrAKKEAELLlEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYGE 317
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
654-926 |
1.88e-10 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 64.92 E-value: 1.88e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 654 GKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRtrkqqkeTIEQLRTGQVDIVVGT-- 731
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTGDY-------DSDDEWLGRYDILVATpe 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 732 --HRILSKDIEF-SDLGLLIIDEEQRFGVKHK--------ERLKQLRAQVDVLTLTAT---------------------P 779
Cdd:COG1204 123 klDSLLRNGPSWlRDVDLVVVDEAHLIDDESRgptlevllARLRRLNPEAQIVALSATignaeeiaewldaelvksdwrP 202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 780 IPRtlhmsMLGV---RDLSVIETPPANRYPIQTYVM---EKNPGAI------REA------IHREMGRgGQVFYLYNRVE 841
Cdd:COG1204 203 VPL-----NEGVlydGVLRFDDGSRRSKDPTLALALdllEEGGQVLvfvssrRDAeslakkLADELKR-RLTPEEREELE 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 842 TIEQKVEEIQELVPEA---------RIGYAHGQMTEAQLENTLFEFIEGQYDVLV-TTTIIEtGVDIPnANTLFVENADY 911
Cdd:COG1204 277 ELAEELLEVSEETHTNekladclekGVAFHHAGLPSELRRLVEDAFREGLIKVLVaTPTLAA-GVNLP-ARRVIIRDTKR 354
|
330 340
....*....|....*....|
gi 1080572589 912 MG---LSTL--YQLRGRVGR 926
Cdd:COG1204 355 GGmvpIPVLefKQMAGRAGR 374
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
652-929 |
5.14e-10 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 62.86 E-value: 5.14e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESK--QVAFLVPTTILAQQHYETMLERFEGfpVNIGLLSRFRTRK----QQKETIEQLRT--- 722
Cdd:TIGR01587 9 GYGKTEAALLWALHSIKSQKadRVIIALPTRATINAMYRRAKELFGS--ELVGLHHSSSFSRikemGDSEEFEHLFPlyi 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 723 --------GQVDIVVGTHRILSKDIEFSD---------LGLLIIDEEQRFGVKHKER-LKQLRAQVD----VLTLTATpI 780
Cdd:TIGR01587 87 hsndklflDPITVCTIDQVLKSVFGEFGHyeftlasiaNSLLIFDEVHFYDEYTLALiLAVLEVLKDndvpILLMSAT-L 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 781 P---RTLHMSMLGVRDLSVIETPPANR---YPIQTYVMEKNPG-AIREAIHREMGRGGQVFYLYNRVETIEQKVEEIQEL 853
Cdd:TIGR01587 166 PkflKEYAEKIGYVEFNEPLDLKEERRfenHRFILIESDKVGEiSSLERLLEFIKKGGSIAIIVNTVDRAQEFYQQLKEK 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 854 VPEARIGYAHGQMT-------EAQLENTLFEFIEGQydVLVTTTIIETGVDIpNANTLFVENADymgLSTLYQLRGRVGR 926
Cdd:TIGR01587 246 APEEEIILYHSRFTekdrakkEAELLREMKKSNEKF--VIVATQVIEASLDI-SADVMITELAP---IDSLIQRLGRLHR 319
|
...
gi 1080572589 927 SSR 929
Cdd:TIGR01587 320 YGR 322
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
652-929 |
7.97e-10 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 62.79 E-value: 7.97e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESKQ--VAFLVPTTILAQQHYETMLERFEGfpvNIGLL-SRFRTRKQQKETIEQLRTGQV--- 725
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGrrIIYALPFTSIINQTYDRLRDLFGE---DVLLHhSLADLDLLEEEEEYESEARWLkll 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 726 ------DIVVGT-------------------HRILSKDIefsdlgllIIDEEQRFGVK-----HK--ERLKQLRAQVdVL 773
Cdd:COG1203 234 kelwdaPVVVTTidqlfeslfsnrkgqerrlHNLANSVI--------ILDEVQAYPPYmlallLRllEWLKNLGGSV-IL 304
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 774 tLTATpIPRTLHMSMLGVRDLSVIETPPANRYP-------IQTYVMEKNPGAIREAIHREMGRGGQVFYlynRVETIE-- 844
Cdd:COG1203 305 -MTAT-LPPLLREELLEAYELIPDEPEELPEYFrafvrkrVELKEGPLSDEELAELILEALHKGKSVLV---IVNTVKda 379
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 845 QKV-EEIQELVPEARIGYAHGQMTEA---QLENTLFEFIE-GQYDVLVTTTIIETGVDIpNANTLFVENAdymGLSTLYQ 919
Cdd:COG1203 380 QELyEALKEKLPDEEVYLLHSRFCPAdrsEIEKEIKERLErGKPCILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQ 455
|
330
....*....|
gi 1080572589 920 LRGRVGRSSR 929
Cdd:COG1203 456 RAGRCNRHGR 465
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
654-778 |
6.49e-09 |
|
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: 56.50 E-value: 6.49e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 654 GKTEVALRAAFKAIKESKQVA-FLVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKEtieqlrtGQVDIVVGTH 732
Cdd:cd17921 29 GKTLIAELAILRALATSGGKAvYIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSVNKLLL-------AEADILVATP 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 733 RIL------SKDIEFSDLGLLIIDEEQRFGVKHK--------ERLKQLRAQVDVLTLTAT 778
Cdd:cd17921 102 EKLdlllrnGGERLIQDVRLVVVDEAHLIGDGERgvvlelllSRLLRINKNARFVGLSAT 161
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
646-780 |
2.03e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 54.60 E-value: 2.03e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKTEVALRAAFKAIKES--KQVAFLVPTTILAQQHYETmLERFEGFPVNIGLLSRFRTRKQQKETIeqlrtg 723
Cdd:pfam04851 27 LIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEE-FKKFLPNYVEIGEIISGDKKDESVDDN------ 99
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080572589 724 qvDIVVGTHRILSKDIEFSDL-------GLLIIDEEQRFGVK-HKERLKQLRAQVdVLTLTATPI 780
Cdd:pfam04851 100 --KIVVTTIQSLYKALELASLellpdffDVIIIDEAHRSGASsYRNILEYFKPAF-LLGLTATPE 161
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
652-779 |
1.68e-07 |
|
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: 51.54 E-value: 1.68e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESkqVAFLVPTTILAQQhyetMLERFEGFpvnigllSRFRTRKQQKETIEQLRTGQvDIVVGT 731
Cdd:cd17926 28 GSGKTLTALALIAYLKELR--TLIVVPTDALLDQ----WKERFEDF-------LGDSSIGLIGGGKKKDFDDA-NVVVAT 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1080572589 732 HRILSKDIE-----FSDLGLLIIDEEQRFGVKHKER-LKQLRAQVdVLTLTATP 779
Cdd:cd17926 94 YQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTFSEiLKELNAKY-RLGLTATP 146
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
843-928 |
3.96e-06 |
|
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: 49.55 E-value: 3.96e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 843 IEQKVEEIQELVPEARIGyahgQM------TEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYM---- 912
Cdd:cd18804 103 TERVEEELKTLFPEARIA----RIdrdttrKKGALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGlnsp 178
|
90 100
....*....|....*....|...
gi 1080572589 913 -------GLSTLYQLRGRVGRSS 928
Cdd:cd18804 179 dfraserAFQLLTQVSGRAGRGD 201
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
645-780 |
5.12e-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: 48.82 E-value: 5.12e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 645 RLLVGD-VGYGKTEVALRAA--FKAIKESKQVAFLVPTTILAQQHYEtMLERFEgfpVNIGLLSRFRTRKQQKETIEQLR 721
Cdd:cd18011 19 RLLLADeVGLGKTIEAGLIIkeLLLRGDAKRVLILCPASLVEQWQDE-LQDKFG---LPFLILDRETAAQLRRLIGNPFE 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080572589 722 TGQVDIV----VGTHRILSKDIEFSDLGLLIIDEEQRF----GVKHKER---LKQLRAQVD-VLTLTATPI 780
Cdd:cd18011 95 EFPIVIVsldlLKRSEERRGLLLSEEWDLVVVDEAHKLrnsgGGKETKRyklGRLLAKRARhVLLLTATPH 165
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
499-600 |
5.27e-06 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 47.43 E-value: 5.27e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 499 KAGDYVVHANHGIGKYIGMETLEVDGVHQDYMTI-LYQNDDKLFIPVtqlnliqkyvaSEAKAPRInklggsewtktkRK 577
Cdd:COG1329 2 KVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLrFPYDDMTIMVPV-----------DKAESVGL------------RP 58
|
90 100
....*....|....*....|...
gi 1080572589 578 VSSKieDIADDLIKLYAARESEK 600
Cdd:COG1329 59 VISK--EEVEKVLDVLKGRETVK 79
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
652-779 |
5.89e-06 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 48.63 E-value: 5.89e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESKQ------VAFLVPTTILAQQHYETMLERFE-GFPVNigllsRFRTRKQQKETIEQLRTGQ 724
Cdd:cd18036 27 GSGKTRVAVYICRHHLEKRRSagekgrVVVLVNKVPLVEQQLEKFFKYFRkGYKVT-----GLSGDSSHKVSFGQIVKAS 101
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1080572589 725 vDIVVGTHRIL---------SKDIEFSDLGLLIIDE---EQRFGVKH-------KERLKQLRAQVDVLTLTATP 779
Cdd:cd18036 102 -DVIICTPQILinnllsgreEERVYLSDFSLLIFDEchhTQKEHPYNkimrmylDKKLSSQGPLPQILGLTASP 174
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
652-740 |
8.19e-06 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 47.71 E-value: 8.19e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLL---SRFRTrKQQKETIEQLRTGQVDIV 728
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILvyhSRLKK-KEKEELLEKIEKGDFDIL 120
|
90
....*....|..
gi 1080572589 729 VGTHRILSKDIE 740
Cdd:cd17924 121 VTTNQFLSKNFD 132
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
652-779 |
1.20e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 47.43 E-value: 1.20e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVAL-----RAAFKAIKESKQVAFLVPTTILAQQHYETMLERFEGFPVNIGLLSrfrtrkqqKETIEQLRTGQV- 725
Cdd:cd17927 27 GSGKTFVAVlicehHLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLS--------GDTSENVSVEQIv 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 726 ---DIVVGTHRILSKDI------EFSDLGLLIIDEEQRFGVKH----------KERLKQLRAQVDVLTLTATP 779
Cdd:cd17927 99 essDVIIVTPQILVNDLksgtivSLSDFSLLVFDECHNTTKNHpyneimfrylDQKLGSSGPLPQILGLTASP 171
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
646-780 |
1.43e-05 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 47.26 E-value: 1.43e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKTEVALRAafkaIKE-----------SKQVAFLVPTTILAQQHYETmLERFEGFPVNI---GLLSRFRTRK 711
Cdd:cd18034 20 IVVLPTGSGKTLIAVML----IKEmgelnrkeknpKKRAVFLVPTVPLVAQQAEA-IRSHTDLKVGEysgEMGVDKWTKE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 712 QQKETIEqlrtgQVDIVVGTHRIL-----SKDIEFSDLGLLIIDEEQRFGVKHK--------ERLKQLRAQVDVLTLTAT 778
Cdd:cd18034 95 RWKEELE-----KYDVLVMTAQILldalrHGFLSLSDINLLIFDECHHATGDHPyarimkefYHLEGRTSRPRILGLTAS 169
|
..
gi 1080572589 779 PI 780
Cdd:cd18034 170 PV 171
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
885-937 |
1.66e-05 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 43.85 E-value: 1.66e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1080572589 885 VLVTTTIIETGVDIPNANTL-FVENADYMGlsTLYQLRGRVGRSSRVAYAYFMY 937
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTViFFDPPSSAA--SYIQRVGRAGRGGKDEGEVILF 76
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
646-779 |
2.30e-04 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 43.27 E-value: 2.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKTEVA-LRAAFKAIKESKQVAFLVPTTILAQQHYETmLERFEGFPVNIGLLSrfrTRKQQKETIEQLRTGQ 724
Cdd:cd18035 20 LIVLPTGLGKTIIAiLVAADRLTKKGGKVLILAPSRPLVEQHAEN-LKRVLNIPDKITSLT---GEVKPEERAERWDASK 95
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1080572589 725 vdIVVGTHRILSKD-----IEFSDLGLLIIDEEQRFGVKHK-----ERLKQLRAQVDVLTLTATP 779
Cdd:cd18035 96 --IIVATPQVIENDllagrITLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| SNF2-rel_dom |
pfam00176 |
SNF2-related domain; This domain is found in proteins involved in a variety of processes ... |
646-785 |
1.03e-03 |
|
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 42.67 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 646 LLVGDVGYGKT--EVALRAAFKAIKESKQVAFLV--PTTILaqQHYETMLERFEGFPVnIGLLSRF-RTRKQQKETIEQL 720
Cdd:pfam00176 21 ILADEMGLGKTlqTISLLLYLKHVDKNWGGPTLIvvPLSLL--HNWMNEFERWVSPPA-LRVVVLHgNKRPQERWKNDPN 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1080572589 721 RTGQVDIVVGTHRILSKDIEFS---DLGLLIIDEEQRFG---VKHKERLKQLRAQVDVLtLTATPIPRTLH 785
Cdd:pfam00176 98 FLADFDVVITTYETLRKHKELLkkvHWHRIVLDEGHRLKnskSKLSKALKSLKTRNRWI-LTGTPLQNNLE 167
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
840-900 |
1.78e-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: 1.78e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 840 VETIEQkVEEIQELVPEARIGYA--HGQMTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPN 900
Cdd:cd18787 34 VNTKKR-VDRLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPG 95
|
|
| DEADc_DDX51 |
cd17956 |
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ... |
676-755 |
2.12e-03 |
|
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It 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: 350714 [Multi-domain] Cd Length: 231 Bit Score: 41.08 E-value: 2.12e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 676 LVPTTILAQQHYETMLERFEGFPVNIGLLSRFRTRKQQKETIEQLRTGQ----VDIVVGT------HRILSKDIEFSDLG 745
Cdd:cd17956 74 VVPTKELVQQVYKVFESLCKGTGLKVVSLSGQKSFKKEQKLLLVDTSGRylsrVDILVATpgrlvdHLNSTPGFTLKHLR 153
|
90
....*....|
gi 1080572589 746 LLIIDEEQRF 755
Cdd:cd17956 154 FLVIDEADRL 163
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
652-779 |
2.68e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350833 [Multi-domain] Cd Length: 200 Bit Score: 40.61 E-value: 2.68e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAI--KESKQVAFLVPTTILAQQHYEtmlerfEGFPVnigLLSRFRTRKQQKETIEQLRTGQV---- 725
Cdd:cd18075 27 GAGKTRAAVYVARRHLetKRGAKVAVLVNKVHLVDQHLE------KEFHV---LLDKYTVTAISGDSSHKCFFGQLargs 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 726 DIVVGTHRILS---------KDIEFSDLGLLIIDE---EQRFGVKHKERLKQLRAQV-------DVLTLTATP 779
Cdd:cd18075 98 DVVICTAQILQnallsgeeeAHVELTDFSLLVIDEchhTHKEAVYNKIMLSYLEKKLsrqgdlpQILGLTASP 170
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
829-890 |
4.28e-03 |
|
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: 39.62 E-value: 4.28e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1080572589 829 RGGQVFYLYNRVETIEQKVEEIQELVPEA----RIGYAHGQMTEAQLENTLFEFIEGQYDVLVTTT 890
Cdd:cd17924 59 KGKRSYLIFPTKSLVKQAYERLSKYAEKAgvevKILVYHSRLKKKEKEELLEKIEKGDFDILVTTN 124
|
|
| DEXHc_cas3 |
cd17930 |
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ... |
652-778 |
4.37e-03 |
|
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain] Cd Length: 186 Bit Score: 39.58 E-value: 4.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 652 GYGKTEVALRAAFKAIKESKQ--VAFLVPTTILAQQHYETMLERFEGF--PVNIGLL---SRFRTRKQQKETIEQLRTGQ 724
Cdd:cd17930 11 GSGKTEAALLWALKLAARGGKrrIIYALPTRATINQMYERIREILGRLddEDKVLLLhskAALELLESDEEPDDDPVEAV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 725 VD-----------IVVGT--------HRILSKDIEFSDLG--LLIIDEEQRFGVK----HKERLKQLRAQVD--VLTLTA 777
Cdd:cd17930 91 DWalllkrswlapIVVTTidqlleslLKYKHFERRLHGLAnsVVVLDEVQAYDPEymalLLKALLELLGELGgpVVLMTA 170
|
.
gi 1080572589 778 T 778
Cdd:cd17930 171 T 171
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
841-926 |
6.03e-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: 38.49 E-value: 6.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 841 ETIEQKVEEIQELVPEAR----IGYAHGQ----MTEAQLENTLFEFIEGQYDVLVTTTIIETGVDIPNANTLFVENADYM 912
Cdd:cd18801 41 DSAEEIVNFLSKIRPGIRatrfIGQASGKsskgMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPS 120
|
90
....*....|....
gi 1080572589 913 GLSTLyQLRGRVGR 926
Cdd:cd18801 121 PIRMI-QRMGRTGR 133
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
650-781 |
7.16e-03 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 40.59 E-value: 7.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 650 DVGYGKTEVALrAAFKAIKESKQVA---FLVPTTILAQQHYEtmLERFeGFPVNIGLLSRFRTRKQQKETIEQlrtgqVD 726
Cdd:COG0553 268 DMGLGKTIQAL-ALLLELKERGLARpvlIVAPTSLVGNWQRE--LAKF-APGLRVLVLDGTRERAKGANPFED-----AD 338
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1080572589 727 IVVGTHRILSKDIEF---SDLGLLIIDEEQRfgVKHKER-----LKQLRAQVdVLTLTATPIP 781
Cdd:COG0553 339 LVITSYGLLRRDIELlaaVDWDLVILDEAQH--IKNPATkrakaVRALKARH-RLALTGTPVE 398
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
835-904 |
8.07e-03 |
|
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: 37.54 E-value: 8.07e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 835 YLYNRVETI-----EQKVEEIQELVPEARI--GYAHGQMTEAQLEN---TLFEFIEGQYDVLVTTTIIETGVDIPNANTL 904
Cdd:cd18799 2 YKYVEIKTLifcvsIEHAEFMAEAFNEAGIdaVALNSDYSDRERGDealILLFFGELKPPILVTVDLLTTGVDIPEVDNV 81
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
630-778 |
8.44e-03 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 38.47 E-value: 8.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 630 AAEIKRDMEKEKPMdrLLVGDVGYGKTEVALRAAFKAIKESKQVAFLVPTTILAQQHYETmLERFEGFPVNIGLlsrfrT 709
Cdd:cd18028 7 AEAVRAGLLKGENL--LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEE-FKKLEEIGLKVGI-----S 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1080572589 710 RKQQKETIEQLrtGQVDIVVGTHRILSKDIEFS-----DLGLLIIDE------EQRFGVKHK--ERLKQLRAQVDVLTLT 776
Cdd:cd18028 79 TGDYDEDDEWL--GDYDIIVATYEKFDSLLRHSpswlrDVGVVVVDEihlisdEERGPTLESivARLRRLNPNTQIIGLS 156
|
..
gi 1080572589 777 AT 778
Cdd:cd18028 157 AT 158
|
|
| |
