|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
22-1160 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1574.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 22 GQANTLVTGLSPSAKVTMIAEKYAQSNQQLLLITNNLYQADKLETDLLQFIDAEELYKYPVQDIMTEEFSTQSPQLMSER 101
Cdd:COG1197 1 GGGRLTLSGLPGSARALLLAALARALGRPLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSER 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 102 IRTLTALAQGKKGLFIVPLNGLKKWLTPVEMWQNHQMTLRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDI 181
Cdd:COG1197 81 LATLRRLASGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 182 FPLIGE-PIRIELFDTEIDSIRDFDVETQRSKDNIEEVDITTASDYIITEEVISHLKEELKTAYEnTRPKIDksvrndlk 260
Cdd:COG1197 161 FPPGSEhPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFG-LDPKLD-------- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 261 ETYEsfKLFESTYFDHqiLRRLVAFMYETPSTIIDYFQKDAIIAVDEFNRIKETEESLTVESDSFISN-IIESGNGFIGQ 339
Cdd:COG1197 232 ELYE--ALSEGIAFAG--IEYYLPLFYEELATLFDYLPEDALVVLDEPERIEEAAEEFWEEIEERYEArRHDRGRPLLPP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 340 S--FIKYDDFETLIEGYPVTYFSLFATTMPIKlnHIIKFSCKPVQQFYGQYDIMRSEFQRYVNQNYHIVVLVETETKVER 417
Cdd:COG1197 308 EelFLDPEELFAALKRRPRVTLSPFAALPEGA--GVVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRRER 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 418 MQAMLSEMHI-PSITKLHRSMSSGQAVIIEGSLSEGFELPDMGLVVITERELFKSKQKKQRKRTkAISNAEKIKSYQDLN 496
Cdd:COG1197 386 LLELLRDHGIpARLVESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKK-KRSADAFIRDLSELK 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 497 VGDYIVHVHHGVGRYLGVETLEVGQTHRDYIKLQYKGTDQLFVPVDQMDQVQKYVASEDKTPKLNKLGGSEWKKTKAKVQ 576
Cdd:COG1197 465 PGDYVVHVDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAK 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 577 QSVEDIAEELIDLYKEREMAEGYQYGEDTAEQTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVA 656
Cdd:COG1197 545 KAVRDIAAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVA 624
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 657 VRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDI 736
Cdd:COG1197 625 LRAAFKAVMDGKQVAVLVPTTLLAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDV 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 737 QYKDLGLLIVDEEQRFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVLEQNMSFI 816
Cdd:COG1197 705 KFKDLGLLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALI 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 817 KEALERELSRDGQVFYLYNKVQSIYEKREQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVP 896
Cdd:COG1197 785 REAILRELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIP 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 897 NANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANKVLTETAEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNL 976
Cdd:COG1197 865 NANTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNL 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 977 LGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNLDAYLPTEYIANEQAKIEIYKKLRKTETFDQIID 1056
Cdd:COG1197 945 LGEEQSGHIAEVGFDLYLQMLEEAVAALKGGK-EPEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDE 1023
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 1057 IKDELIDRFNDYPVEVARLLDIVEIKVHALHSGITLIKDKGKIIDIHLSVKATenIDGEVLFKATQPLGRTMKVGVQNN- 1135
Cdd:COG1197 1024 LQEELIDRFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNTP--LDPEKLIRLIQKQPGRYKLDGDDKl 1101
|
1130 1140
....*....|....*....|....*
gi 446076395 1136 AMTITLTKQNQWLDSLKFLVKCIEE 1160
Cdd:COG1197 1102 VITLDLEDPEERLEALEELLEALAK 1126
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
155-1094 |
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: 1077.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 155 LVNMGYKRESVVSHIGEFSLRGGIIDIFPLIGE-PIRIELFDTEIDSIRDFDVETQRSKDNIEEVDITTASDYIITEEVI 233
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSElPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKEFILLEEET 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 234 SHLKEelktayentrpkiDKSVRNDLKETYESfKLFESTYFDHQILRRLVAFMYETPSTIIDYFQKDAIIAVDEFNRIKE 313
Cdd:TIGR00580 81 IARLK-------------DNAARVEDAKHLET-IEALSEGTLPAGEEMFLPLFFEDLSSLFDYLPDNTPILLDDPERFHS 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 314 TEESLTVESDSFISNIIESGNgfIGQSFIKYDDFETLieGYPVTYFSLFATTMPiklNHIIKF------SCKPVQQFYGQ 387
Cdd:TIGR00580 147 AARFLQRELEEFYNALEEAKK--LINPPRLDLDPSEL--AFEASAISLSRVQLE---NEHLSLkaseaiEGAQKHSRLEF 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 388 YDI--MRSEFQRYVNQNYHIVVLVETETKVERMQAMLSEMHI-PSITKLHRSMSSGQAVIIEGSLSEGFELPDMGLVVIT 464
Cdd:TIGR00580 220 GEIlaFKEELFRWLKAGFKITVAAESESQAERLKSLLAEHDIaAQVIDESCIIIPAVRYVMIGALSSGFILPTAGLAVIT 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 465 ERELFKSKQKKQRKRTKAISNAekIKSYQDLNVGDYIVHVHHGVGRYLGVETLEVGQTHRDYIKLQYKGTDQLFVPVDQM 544
Cdd:TIGR00580 300 ESELFGSRVLRRPKKSRLKSKP--IESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQL 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 545 DQVQKYVASEDKTPKLNKLGGSEWKKTKAKVQQSVEDIAEELIDLYKEREMAEGYQYGEDTAEQTTFELDFPYELTPDQA 624
Cdd:TIGR00580 378 HLISRYVGGSGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQL 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 625 KSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMSRF 704
Cdd:TIGR00580 458 KAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRF 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 705 RTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLIVDEEQRFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMS 784
Cdd:TIGR00580 538 RSAKEQNEILKELASGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMS 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 785 MLGVRDLSVIETPPENRFPVQTYVLEQNMSFIKEALERELSRDGQVFYLYNKVQSIYEKREQLQMLMPDANIAVAHGQMT 864
Cdd:TIGR00580 618 MSGIRDLSIIATPPEDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMT 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 865 ERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANKVLTETA 944
Cdd:TIGR00580 698 ENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDA 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 945 EDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKePESEVPEVEVDLNLD 1024
Cdd:TIGR00580 778 QKRLEAIQEFSELGAGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGK-PPKLEEETDIELPYS 856
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 1025 AYLPTEYIANEQAKIEIYKKLRKTETFDQIIDIKDELIDRFNDYPVEVARLLDIVEIKVHALHSGITLIK 1094
Cdd:TIGR00580 857 AFIPDDYIADDSLRLEFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLKLLARKLGIRKLK 926
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
28-1101 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 733.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 28 VTGLSPSAKVTMIAEKYAQSnqqLLLITNNLYQADKLETDLLQFIDaeelykYPVQ---DIMTEEFSTQSP--QLMSERI 102
Cdd:PRK10689 22 LTGAACATEVAEIAERHAGP---VVLIAPDMQNALRLHDEIQQFTD------QMVMnlaDWETLPYDSFSPhqDIISSRL 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 103 RTLTALAQGKKGLFIVPLNGLKKWLTPVEMWQNHQMTLRVGEDIDVDQFLNKLVNMGYKR-ESVVSHiGEFSLRGGIIDI 181
Cdd:PRK10689 93 STLYQLPTMQRGVLILPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLEQAGYRHvDQVMEH-GEYATRGALLDL 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 182 FPLIGE-PIRIELFDTEIDSIRDFDVETQRSKDNIEEVDITTASDYIITEEVISHLKEELKTAYEntrpkidksVRNDLK 260
Cdd:PRK10689 172 FPMGSEePYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFE---------VKRDAE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 261 ETYE--SFKLFESTYFDHQILrrlvaFMYETPSTIIDYFQKDAIIaVDEFNRIKETEESLTVESDSFISNIIESGNGFIG 338
Cdd:PRK10689 243 HIYQqvSKGTLPAGIEYWQPL-----FFSEPLPPLFSYFPANTLL-VNTGDLETSAERFWADTLARFENRGVDPMRPLLP 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 339 --QSFIKYDDFETLIEGYPvtYFSLFATTMPIKLNHI-IKFSCKPVQQFYGQYDIMRSEFQRYVNQ-NYHIVVLVETETK 414
Cdd:PRK10689 317 peSLWLRVDELFSELKNWP--RVQLKTEHLPTKAANTnLGYQKLPDLAVQAQQKAPLDALRRFLESfDGPVVFSVESEGR 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 415 VERMQAMLSEMHI-PS-ITKLHRSMSSGQAVIIeGSLSEGFELPDMGLVVITERELFKSKQKKQRKRTKAISNAEK-IKS 491
Cdd:PRK10689 395 REALGELLARIKIaPKrIMRLDEASDRGRYLMI-GAAEHGFIDTVRNLALICESDLLGERVARRRQDSRRTINPDTlIRN 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 492 YQDLNVGDYIVHVHHGVGRYLGVETLEVGQTHRDYIKLQYKGTDQLFVPVDQMDQVQKYVASEDKTPKLNKLGGSEWKKT 571
Cdd:PRK10689 474 LAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRA 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 572 KAKVQQSVEDIAEELIDLYKEREMAEGYQYGEDTAEQTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYG 651
Cdd:PRK10689 554 RQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFG 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 652 KTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKL 731
Cdd:PRK10689 634 KTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKL 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 732 LSKDIQYKDLGLLIVDEEQRFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVLEQ 811
Cdd:PRK10689 714 LQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREY 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 812 NMSFIKEALERELSRDGQVFYLYNKVQSIYEKREQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIET 891
Cdd:PRK10689 794 DSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIET 873
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 892 GVDVPNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANKVLTETAEDRLQAIKEFTELGSGFKIAMRDLNIR 971
Cdd:PRK10689 874 GIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIR 953
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 972 GAGNLLGKQQHGFIDTVGFDLYSQMLEEAVN---EKRGIKEPESEVPEVEVDLNLDAYLPTEYIANEQAKIEIYKKLRKT 1048
Cdd:PRK10689 954 GAGELLGEEQSGQMETIGFSLYMELLENAVDalkAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASA 1033
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*
gi 446076395 1049 ETFDQIIDIKDELIDRFNDYPVEVARLLDIVEIKVHALHSGITLIK--DKGKIID 1101
Cdd:PRK10689 1034 KNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEgnEKGGFIE 1088
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
586-986 |
1.39e-126 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 404.05 E-value: 1.39e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 586 LIDLYKEREMAEGYQYGEDTAEQTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVM 665
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 666 EGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLI 745
Cdd:COG1200 307 AGYQAALMAPTEILAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 746 VDEEQRFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDLSVI-ETPPeNRFPVQTYVL-EQNMSFIKEALERE 823
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIdELPP-GRKPIKTRVVpEERRDEVYERIREE 465
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 824 LSRDGQVFYLY--------NKVQSIYEKREQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDV 895
Cdd:COG1200 466 IAKGRQAYVVCplieesekLDLQAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDV 545
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 896 PNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANkvLTETAEDRLQAIKEFTelgSGFKIAMRDLNIRGAGN 975
Cdd:COG1200 546 PNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVMRETN---DGFEIAEEDLELRGPGE 620
|
410
....*....|.
gi 446076395 976 LLGKQQHGFID 986
Cdd:COG1200 621 FLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
616-1000 |
1.02e-124 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 398.75 E-value: 1.02e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 616 PYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFP 695
Cdd:PRK10917 259 PFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHYENLKKLLEPLG 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 696 VEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLIVDEEQRFGVRHKERIKTLKHNVDVLTLTAT 775
Cdd:PRK10917 339 IRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKGENPHVLVMTAT 418
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 776 PIPRTLHMSMLGVRDLSVI-ETPPEnRFPVQTYVLeqNMSFIKEALER---ELSRDGQVFYLYNKV--------QSIYEK 843
Cdd:PRK10917 419 PIPRTLAMTAYGDLDVSVIdELPPG-RKPITTVVI--PDSRRDEVYERireEIAKGRQAYVVCPLIeesekldlQSAEET 495
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 844 REQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGR 923
Cdd:PRK10917 496 YEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQLHQLRGRVGR 575
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446076395 924 SSRIGYAYFLHPANkvLTETAEDRLQAIKEFTelgSGFKIAMRDLNIRGAGNLLGKQQHGFIDTVGFDLY--SQMLEEA 1000
Cdd:PRK10917 576 GAAQSYCVLLYKDP--LSETARERLKIMRETN---DGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVrdEELLEEA 649
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
604-796 |
5.38e-120 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 368.05 E-value: 5.38e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 604 DTAEQTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQH 683
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 684 YETLIERMQDFPVEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLIVDEEQRFGVRHKERIKTL 763
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 446076395 764 KHNVDVLTLTATPIPRTLHMSMLGVRDLSVIET 796
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
616-986 |
2.72e-109 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 355.88 E-value: 2.72e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 616 PYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFP 695
Cdd:TIGR00643 233 PFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLG 312
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 696 VEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLIVDEEQRFGV--RHKERIK-TLKHNVDVLTL 772
Cdd:TIGR00643 313 IEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQHRFGVeqRKKLREKgQGGFTPHVLVM 392
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 773 TATPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVLEQNMSFI-KEALERELSRDGQVFYLYNKV--------QSIYEK 843
Cdd:TIGR00643 393 SATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIvYEFIEEEIAKGRQAYVVYPLIeesekldlKAAEAL 472
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 844 REQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGR 923
Cdd:TIGR00643 473 YERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGR 552
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446076395 924 SSRIGYAYFLHPANKvlTETAEDRLQAIKEFTElgsGFKIAMRDLNIRGAGNLLGKQQHGFID 986
Cdd:TIGR00643 553 GDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLLGTKQSGYPE 610
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
803-953 |
5.85e-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: 238.78 E-value: 5.85e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 803 PVQTYVLEQNMSFIKEALERELSRDGQVFYLYNKVQSIYEKREQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDI 882
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446076395 883 LVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANKVLTETAEDRLQAIKE 953
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQE 151
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
586-798 |
6.04e-66 |
|
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: 222.02 E-value: 6.04e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 586 LIDLYKEREMAEGYQYGEDTAEQTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVM 665
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 666 EGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMSRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDLGLLI 745
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 446076395 746 VDEEQRFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDLSVIETPP 798
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 ... |
803-953 |
1.80e-65 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 218.29 E-value: 1.80e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 803 PVQTYVLEQNMS-FIKEALERELSRDGQVFYLYNKV--------QSIYEKREQLQMLMPDANIAVAHGQMTERDLEETML 873
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIeesekldlKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 874 SFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHPANKVLTETAEDRLQAIKE 953
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
614-794 |
2.25e-61 |
|
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: 207.27 E-value: 2.25e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 614 DFPYELTPDQAKSIDEIKDDMQKSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQD 693
Cdd:cd17918 11 SLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLPF 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 694 FPVEiqLMSRFRTpkeiKQTKEGlktgfVDIVVGTHKLLSKDIQYKDLGLLIVDEEQRFGVRHKERIKTLKhNVDVLTLT 773
Cdd:cd17918 91 INVE--LVTGGTK----AQILSG-----ISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLG-ATHFLEAT 158
|
170 180
....*....|....*....|.
gi 446076395 774 ATPIPRTLHMSMLGVRDLSVI 794
Cdd:cd17918 159 ATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
494-590 |
1.59e-39 |
|
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: 141.82 E-value: 1.59e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 494 DLNVGDYIVHVHHGVGRYLGVETLEVGQTHRDYIKLQYKGTDQLFVPVDQMDQVQKYVASEDK-TPKLNKLGGSEWKKTK 572
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEvEPVLDKLGGGSWSKRK 80
|
90
....*....|....*...
gi 446076395 573 AKVQQSVEDIAEELIDLY 590
Cdd:smart01058 81 RKAKSGIRDIAAELLRLY 98
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
803-953 |
9.98e-39 |
|
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: 141.71 E-value: 9.98e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 803 PVQTYVL-EQNMSFIKEALERELSRDGQVFYLYN--------KVQSIYEKREQL-QMLMPDANIAVAHGQMTERDLEETM 872
Cdd:cd18811 1 PITTYLIfHTRLDKVYEFVREEIAKGRQAYVIYPlieeseklDLKAAVAMYEYLkERFRPELNVGLLHGRLKSDEKDAVM 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 873 LSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYQLRGRVGRSSRIGYAYFLHpaNKVLTETAEDRLQAIK 952
Cdd:cd18811 81 AEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVY--KDPLTETAKQRLRVMT 158
|
.
gi 446076395 953 E 953
Cdd:cd18811 159 E 159
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
138-226 |
2.31e-33 |
|
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: 123.66 E-value: 2.31e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 138 MTLRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDIFPLIGE--PIRIELFDTEIDSIRDFDVETQRSKDNI 215
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFPAYSEdeAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|.
gi 446076395 216 EEVDITTASDY 226
Cdd:pfam17757 81 DEVTIYPASHY 91
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
495-590 |
5.64e-31 |
|
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: 116.78 E-value: 5.64e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 495 LNVGDYIVHVHHGVGRYLGVETLEvgqtHRDYIKLQYKGTDQLFVPVDQMDQVQKYVASEdktpKLNKLG-GSEWKKTKA 573
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGdGRRWRKYKE 72
|
90
....*....|....*..
gi 446076395 574 KVQQSVEDIAEELIDLY 590
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1020-1119 |
1.17e-30 |
|
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.
Pssm-ID: 198050 [Multi-domain] Cd Length: 100 Bit Score: 116.41 E-value: 1.17e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 1020 DLNLDAYLPTEYIANEQAKIEIYKKLRKTETFDQIIDIKDELIDRFNDYPVEVARLLDIVEIKVHALHSGITLIKDKGKI 1099
Cdd:smart00982 1 DLPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKG 80
|
90 100
....*....|....*....|
gi 446076395 1100 IDIHLSVKATENIDGEVLFK 1119
Cdd:smart00982 81 IVIEFSPDTPIDPEKLILLI 100
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1021-1114 |
1.13e-27 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 107.51 E-value: 1.13e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 1021 LNLDAYLPTEYIANEQAKIEIYKKLRKTETFDQIIDIKDELIDRFNDYPVEVARLLDIVEIKVHALHSGITLIKDKGKII 1100
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
90
....*....|....
gi 446076395 1101 DIHLSVKATENIDG 1114
Cdd:pfam03461 81 RITFSEDAKIDPEK 94
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
620-783 |
6.35e-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: 6.35e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 620 TPDQAKSIDEIKDDMqksrpmDRLLCGDVGYGKTEVAVRAAFKAV---MEGKQVAFLVPTTILAQQHYETLIERMQdfPV 696
Cdd:pfam00270 1 TPIQAEAIPAILEGR------DVLVQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGK--GL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 697 EIQLMSRFrTPKEIKQTKEGLKTgfVDIVVGTHKLLSKDIQ----YKDLGLLIVDEEQR-----FGVRHKERIKTLKHNV 767
Cdd:pfam00270 73 GLKVASLL-GGDSRKEQLEKLKG--PDILVGTPGRLLDLLQerklLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|....*.
gi 446076395 768 DVLTLTATPiPRTLHM 783
Cdd:pfam00270 150 QILLLSATL-PRNLED 164
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
128-307 |
1.87e-24 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 110.14 E-value: 1.87e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 128 TPVEmWQNHQMTLRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDIFPLIGE--PIRIELFDTEIDSIRDFD 205
Cdd:PRK05298 150 SPEE-YLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFPAYYEerAIRIEFFGDEIERISEFD 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 206 VETQRSKDNIEEVDITTASDYIITEEVishlkeeLKTAYEntrpkidkSVRNDLKETYESFK----------LFESTYFD 275
Cdd:PRK05298 229 PLTGEVLGELDRVTIYPASHYVTPRER-------LERAIE--------SIKEELEERLKELEkegklleaqrLEQRTRYD 293
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 446076395 276 HQILRrlvAFMY-----------------ETPSTIIDYFQKDAIIAVDE 307
Cdd:PRK05298 294 LEMLR---ELGYcsgienysrhldgrkpgEPPYTLLDYFPDDFLLFIDE 339
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
611-801 |
2.22e-24 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 102.18 E-value: 2.22e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 611 FELDFPYELTPDQAKSIDEIKddmqkSRPMDRLLCGDVGYGKTEVAVRAAFKAVMEG--KQVAFLVPTTILAQQHYETLI 688
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALL-----SGLRDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 689 ERMQDFPVEIqlmSRFRTPKEIKQTKEGLKTGFVDIVVGT-----HKLLSKDIQYKDLGLLIVDEEQR-----FGVRHKE 758
Cdd:smart00487 76 KLGPSLGLKV---VGLYGGDSKREQLRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 446076395 759 RIKTLKHNVDVLTLTATP---IPRTLHMSMLGVRDLSVIETPPENR 801
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
130-307 |
2.45e-22 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 103.17 E-value: 2.45e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 130 VEMWQNHQMTLRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDIFP--LIGEPIRIELFDTEIDSIRDFDVE 207
Cdd:COG0556 148 PEEYLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFPaySEERAIRIEFFGDEIERISEFDPL 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 208 TQRSKDNIEEVDITTASDYIITEEVishlkeeLKTAyentrpkIdKSVRNDLKETYESFK----------LFESTYFDHQ 277
Cdd:COG0556 228 TGEVLGELDRVTIYPASHYVTPRER-------LERA-------I-ESIKEELEERLAEFEsegklleaqrLEQRTRYDLE 292
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 446076395 278 ILRrlvAFMY-----------------ETPSTIIDYFQKDAIIAVDE 307
Cdd:COG0556 293 MLR---ELGYcsgienysrhldgrkpgEPPPTLLDYFPDDFLLFIDE 336
|
|
| uvrb |
TIGR00631 |
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
131-307 |
1.31e-20 |
|
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain] Cd Length: 655 Bit Score: 97.75 E-value: 1.31e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 131 EMWQNHQMTLRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDIFPLIGE--PIRIELFDTEIDSIRDFDVET 208
Cdd:TIGR00631 149 EEYLKMVLHLEVGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAYEDefAVRIEFFGDEIERISRVDPLT 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 209 QRSKDNIEEVDITTASDYIITEEVISH--------LKEELKTAYENTRPkidksvrndlketYESFKLFESTYFDHQILR 280
Cdd:TIGR00631 229 GEVLRELDSFTIFPASHYVTPEERLERaikniekeLEERLKYFEEQGKL-------------LEAQRLKQRTEYDLEMLR 295
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 446076395 281 RLvAF--------MY-------ETPSTIIDYFQKDAIIAVDE 307
Cdd:TIGR00631 296 EM-GYcsgienysRHlsgrapgEPPYTLLDYFPDDFLLVIDE 336
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
613-934 |
5.47e-18 |
|
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: 88.39 E-value: 5.47e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 613 LDFPYELTPDQAKSIDEIKDDMQKSRPMdrLL---CGDvgyGKTEVAVRAAFKAVMEGKQVAFLVPTT--ILaqqhyEtL 687
Cdd:COG4098 105 LTWEGTLTPAQQKASDELLEAIKKKEEH--LVwavCGA---GKTEMLFPAIAEALKQGGRVCIATPRVdvVL-----E-L 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 688 IERMQ-DFP-VEIQLMSrfrtpkeikqTKEGLKTGFVDIVVGT-HKLLsKDIQYKDLglLIVDE---------EQ-RFGV 754
Cdd:COG4098 174 APRLQqAFPgVDIAALY----------GGSEEKYRYAQLVIATtHQLL-RFYQAFDL--LIIDEvdafpysgdPMlQYAV 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 755 RhkeriKTLKHNVDVLTLTATPiPRTLhMSMLGVRDLSVIETPpeNRF-----PVQTYVLEQNmsfIKEALERE------ 823
Cdd:COG4098 241 K-----RARKPDGKLIYLTATP-SKAL-QRQVKRGKLKVVKLP--ARYhghplPVPKFKWLGN---WKKRLRRGklprkl 308
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 824 -------LSRDGQVF------YLYNKVQsiyekrEQLQMLMPDANIAVAHGQMTERdlEETMLSFINNEYDILVTTTIIE 890
Cdd:COG4098 309 lkwlkkrLKEGRQLLifvptiELLEQLV------ALLQKLFPEERIAGVHAEDPER--KEKVQAFRDGEIPILVTTTILE 380
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 446076395 891 TGVDVPNANTLIIeDADR--FGLSQLYQLRGRVGRSSR--IGYAYFLH 934
Cdd:COG4098 381 RGVTFPNVDVAVL-GADHpvFTEAALVQIAGRVGRSADypTGEVIFFH 427
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
640-775 |
7.02e-18 |
|
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: 81.68 E-value: 7.02e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 640 MDRLLCGDVGYGKTEVAVRAAFKAVME-GKQVAFLVPTTILAQQHYETLIERMqDFPVEIQLMSRFRTPKEIKQTKEGLK 718
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEEREKNKLGDA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 719 tgfvDIVVGTHKLLSKDIQ------YKDLGLLIVDEEQRFGVRHKER-------IKTLKHNVDVLTLTAT 775
Cdd:cd00046 81 ----DIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGAlildlavRKAGLKNAQVILLSAT 146
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
818-923 |
8.54e-18 |
|
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: 79.95 E-value: 8.54e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 818 EALEREL--SRDGQVFYLYNKVQSIyekreQLQMLMPDANIAVA--HGQMTERDLEETMLSFINNEYDILVTTTIIETGV 893
Cdd:pfam00271 4 EALLELLkkERGGKVLIFSQTKKTL-----EAELLLEKEGIKVArlHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78
|
90 100 110
....*....|....*....|....*....|
gi 446076395 894 DVPNANTLIIEDADrFGLSQLYQLRGRVGR 923
Cdd:pfam00271 79 DLPDVDLVINYDLP-WNPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
845-923 |
3.69e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.56 E-value: 3.69e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 845 EQLQMLMPDANIAVA--HGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADrFGLSQLYQLRGRVG 922
Cdd:smart00490 1 EELAELLKELGIKVArlHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAG 79
|
.
gi 446076395 923 R 923
Cdd:smart00490 80 R 80
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
614-1087 |
4.70e-16 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 82.77 E-value: 4.70e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 614 DFPYELTPDQAKSIDEIKDDMQKSRpmDR-LLCGDVGYGKTEVAVRAAfKAVMEGKQVAFLVPTTILAQQHYETLIERMQ 692
Cdd:COG1061 76 GTSFELRPYQQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLG 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 693 DFPVeiqlmsrfrtpkeikqtKEGLKTGFVDIVVGTHKLLSKDIQYKDL----GLLIVDEEQRFGVRHKERIKTLKHNVD 768
Cdd:COG1061 153 DPLA-----------------GGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAY 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 769 VLTLTATPI---PRTLHMSMLG----------------VRDLSVIE-----TPPENRFPVQTYVLEQNMSFIKEALEREL 824
Cdd:COG1061 216 RLGLTATPFrsdGREILLFLFDgivyeyslkeaiedgyLAPPEYYGirvdlTDERAEYDALSERLREALAADAERKDKIL 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 825 SRDGQVFYLYNKV----QSIYEKREQLQML-MPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNAN 899
Cdd:COG1061 296 RELLREHPDDRKTlvfcSSVDHAEALAELLnEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLD 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 900 TLIIedADRFG-LSQLYQLRGRVGRSSRIG-YAYFLHPANKvltetAEDRLQAIKEFTELGSGFKIAMRDLNIRGAGNLL 977
Cdd:COG1061 376 VAIL--LRPTGsPREFIQRLGRGLRPAPGKeDALVYDFVGN-----DVPVLEELAKDLRDLAGYRVEFLDEEESEELALL 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 978 GKQQHGFIDTVGFDLYSQMLEEAVNEKRGIKEPESEVPEVEVDLNLDAYLPTEYIANEQAKIEIYKKLRKTETFDQIIDI 1057
Cdd:COG1061 449 IAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLL 528
|
490 500 510
....*....|....*....|....*....|
gi 446076395 1058 KDELIDRFNDYPVEVARLLDIVEIKVHALH 1087
Cdd:COG1061 529 LLLLLLLLELLELLAALLRLEELAALLLKE 558
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
643-928 |
2.44e-15 |
|
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: 80.50 E-value: 2.44e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 643 LLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQhyetLIERMQD-FPVEIQLMSRFRTPKEIKQTKEGLKTGF 721
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQ----MIQRFKYrFGSQVAVLHSGLSDSEKLQAWRKVKNGE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 722 VDIVVGTHKLLSkdIQYKDLGLLIVDEEQ----------RFGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDL 791
Cdd:TIGR00595 77 ILVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 792 SVIETPPENRFPVQTYVL----EQNMSFIK----EALERELSRDGQVFYLYNK----------------------VQSIY 841
Cdd:TIGR00595 155 LVLTRRVSGRKPPEVKLIdmrkEPRQSFLSpeliTAIEQTLAAGEQSILFLNRrgysknllcrscgyilccpncdVSLTY 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 842 EKREQ--------------------------------------LQMLMPDANIAVAHGQMTER--DLEETMLSFINNEYD 881
Cdd:TIGR00595 235 HKKEGklrchycgyqepipktcpqcgsedlvykgygteqveeeLAKLFPGARIARIDSDTTSRkgAHEALLNQFANGKAD 314
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 446076395 882 ILVTTTIIETGVDVPNANTLIIEDAD-----------RFGLSQLYQLRGRVGRSSRIG 928
Cdd:TIGR00595 315 ILIGTQMIAKGHHFPNVTLVGVLDADsglhspdfraaERGFQLLTQVAGRAGRAEDPG 372
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
623-776 |
5.39e-15 |
|
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: 74.17 E-value: 5.39e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 623 QAKSIDEIKDDMQKSRPMdrLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQhyetLIERMQD-FPVEIQLM 701
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQ----LIKRFKKrFGDKVAVL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 702 SRFRTPKEIKQTKEGLKTGFVDIVVGTHKLLSkdIQYKDLGLLIVDEE------QRFGVRHKER----IKTLKHNVDVLT 771
Cdd:cd17929 75 HSKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEEhdssykQDSGPRYHARdvaiYRAKLENAPVVL 152
|
....*
gi 446076395 772 LTATP 776
Cdd:cd17929 153 GSATP 157
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
608-749 |
1.66e-11 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 68.61 E-value: 1.66e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 608 QTTFELDFPYELTPDQAKSIDEIKDDMQKSRPMdrLLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPttilaqqhyetl 687
Cdd:COG1198 185 APDVPAEPPPTLNEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQALVLVP------------ 250
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 688 iermqdfpvEI----QLMSRFR--------------TPKEIKQTKEGLKTGFVDIVVGTHK-LLSkdiQYKDLGLLIVDE 748
Cdd:COG1198 251 ---------EIaltpQTVERFRarfgarvavlhsglSDGERLDEWRRARRGEARIVIGTRSaLFA---PFPNLGLIIVDE 318
|
.
gi 446076395 749 E 749
Cdd:COG1198 319 E 319
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
618-749 |
2.45e-11 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 67.87 E-value: 2.45e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 618 ELTPDQAKSIDEIKDDMQKSRPmdrLLCGDVGYGKTEV---AVRAAFKAvmeGKQVAFLVPttilaqqhyetliermqdf 694
Cdd:PRK05580 144 TLNPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVylqAIAEVLAQ---GKQALVLVP------------------- 198
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446076395 695 pvEI----QLMSRFR--------------TPKEIKQTKEGLKTGFVDIVVGTHK-LLSkdiQYKDLGLLIVDEE 749
Cdd:PRK05580 199 --EIaltpQMLARFRarfgapvavlhsglSDGERLDEWRKAKRGEAKVVIGARSaLFL---PFKNLGLIIVDEE 267
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
864-933 |
8.32e-09 |
|
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: 53.48 E-value: 8.32e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 864 TERDLEETMLSFInneydILVTTTIIETGVDVPNANTLIIEDADRFgLSQLYQLRGRVGRSSRIGYAYFL 933
Cdd:cd18785 12 SIEHAEEIASSLE-----ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDEGEVIL 75
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
649-926 |
2.04e-08 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 57.44 E-value: 2.04e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVRAAFKAVMEGK--QVAFLVPTTILAQQHYETLIERMQDfPVEIQLMSRFRTPKEIKQTKE----------- 715
Cdd:cd09639 9 GYGKTEAALLWALHSLKSQKadRVIIALPTRATINAMYRRAKEAFGE-TGLYHSSILSSRIKEMGDSEEfehlfplyihs 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 716 -------GLKTGFVDIV-------VGTHKLLSKDIQYkdlGLLIVDEEQRFGVRHKERI-KTLKH----NVDVLTLTATp 776
Cdd:cd09639 88 ndtlfldPITVCTIDQVlksvfgeFGHYEFTLASIAN---SLLIFDEVHFYDEYTLALIlAVLEVlkdnDVPILLMSAT- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 777 IP---RTLHMSMLGVRDLSVIETPPENRFPVQTYVLEQNMSF-IKEALERELSRDGQVFYLYNKVQSIYEKREQLQMLMP 852
Cdd:cd09639 164 LPkflKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEIsSLERLLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGP 243
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446076395 853 DANIAVAHGQMTERD----LEETMLSFINNEYDILVTTTIIETGVDVpNANTLIIEDADrfgLSQLYQLRGRVGRSSR 926
Cdd:cd09639 244 EEEIMLIHSRFTEKDrakkEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAP---IDSLIQRLGRLHRYGE 317
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
651-933 |
4.15e-08 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 57.21 E-value: 4.15e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 651 GKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLMS--RFRTPKEIKQtkeglktgfVDIVVGT 728
Cdd:COG1204 50 GKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEELGIKVGVSTgdYDSDDEWLGR---------YDILVAT 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 729 H-KLLS-----KDIqYKDLGLLIVDEEQRFGVRHK--------ERIKTLKHNVDVLTLTAT------------------- 775
Cdd:COG1204 121 PeKLDSllrngPSW-LRDVDLVVVDEAHLIDDESRgptlevllARLRRLNPEAQIVALSATignaeeiaewldaelvksd 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 776 --PIPRtlhmsMLGVRDLSVIETPPENRFPVQTyvleqnmsfIKEALERELSRDGQ--VF------------YLYNKVQ- 838
Cdd:COG1204 200 wrPVPL-----NEGVLYDGVLRFDDGSRRSKDP---------TLALALDLLEEGGQvlVFvssrrdaeslakKLADELKr 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 839 -SIYEKREQLQMLMPD--------------AN-----IAVAHGQMT--ERDLEETmlSFINNEYDILV-TTTIIEtGVDV 895
Cdd:COG1204 266 rLTPEEREELEELAEEllevseethtneklADclekgVAFHHAGLPseLRRLVED--AFREGLIKVLVaTPTLAA-GVNL 342
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 446076395 896 PnANTLIIEDADRFGLSQL-----YQLRGRVGRSSR--IGYAYFL 933
Cdd:COG1204 343 P-ARRVIIRDTKRGGMVPIpvlefKQMAGRAGRPGYdpYGEAILV 386
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
649-776 |
5.09e-08 |
|
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: 53.08 E-value: 5.09e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVRAAFKAvMEGKqVAFLVPTTILAQQHYETLIErmqdfpveiqlmsrFRTPKEIKQTKEGLKTGFVD--IVV 726
Cdd:cd17926 28 GSGKTLTALALIAYL-KELR-TLIVVPTDALLDQWKERFED--------------FLGDSSIGLIGGGKKKDFDDanVVV 91
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 446076395 727 GTHKLLSKDIQ-----YKDLGLLIVDEEQRFGVRHKERIKT-LKHNVdVLTLTATP 776
Cdd:cd17926 92 ATYQSLSNLAEeekdlFDQFGLLIVDEAHHLPAKTFSEILKeLNAKY-RLGLTATP 146
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
649-926 |
1.56e-07 |
|
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: 55.47 E-value: 1.56e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVRAAFKAVMEGKQ--VAFLVPTTILAQQHYETLIER----------MQDFPVEIQLMSRFRTPKEIKQTKEG 716
Cdd:COG1203 157 GGGKTEAALLFALRLAAKHGGrrIIYALPFTSIINQTYDRLRDLfgedvllhhsLADLDLLEEEEEYESEARWLKLLKEL 236
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 717 LKTgfvDIVVGTH----------------KLLSkdIQYKDLgllIVDEEQRFGVR-HKERIKTLKH----NVDVLTLTAT 775
Cdd:COG1203 237 WDA---PVVVTTIdqlfeslfsnrkgqerRLHN--LANSVI---ILDEVQAYPPYmLALLLRLLEWlknlGGSVILMTAT 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 776 pIPRTLHMSMLGVRDLSVIETPPENRFPVQ-----TYVLEQNMSF--IKEALERELSRDGQVFYLYNKV---QSIYEkre 845
Cdd:COG1203 309 -LPPLLREELLEAYELIPDEPEELPEYFRAfvrkrVELKEGPLSDeeLAELILEALHKGKSVLVIVNTVkdaQELYE--- 384
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 846 QLQMLMPDANIAVAHGQMTERD----LEETMLSFINNEYDILVTTTIIETGVDVpNANTLIIEDAdrfGLSQLYQLRGRV 921
Cdd:COG1203 385 ALKEKLPDEEVYLLHSRFCPADrseiEKEIKERLERGKPCILVSTQVVEAGVDI-DFDVVIRDLA---PLDSLIQRAGRC 460
|
....*
gi 446076395 922 GRSSR 926
Cdd:COG1203 461 NRHGR 465
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
496-608 |
6.67e-07 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 50.13 E-value: 6.67e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 496 NVGDYIVHVHHGVGRYLGVETLEVGQTHRDYIKLQYKGTD-QLFVPVDQMDQVQ-KYVASEDKTPK-LNKLGGSE----- 567
Cdd:COG1329 2 KVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYYVLRFPYDDmTIMVPVDKAESVGlRPVISKEEVEKvLDVLKGREtvkpt 81
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 446076395 568 -WKK----TKAKVQQ-SVEDIAEELIDLYKeREMAEGYQYGE----DTAEQ 608
Cdd:COG1329 82 nWSRryreYEEKIKSgDIFEIAEVVRDLYR-RDKEKKLSAGErkmlENARQ 131
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
845-954 |
2.99e-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: 49.94 E-value: 2.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 845 EQLQMLMPDANIAVAHGQMTER--DLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADrFGL----------- 911
Cdd:cd18804 108 EELKTLFPEARIARIDRDTTRKkgALEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNAD-SGLnspdfrasera 186
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 446076395 912 -SQLYQLRGRVGRSSRIGyayflhpanKVLTETAE---DRLQAIKEF 954
Cdd:cd18804 187 fQLLTQVSGRAGRGDKPG---------KVIIQTYNpehPLIQAAKEE 224
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
643-775 |
1.78e-05 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 46.49 E-value: 1.78e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 643 LLCGDVGYGKTEVAVRAAFKAVMEGKQVA-FLVPTTILAQQHYETLIERMQDFPVEIQLMSRFRT--PKEIKQTkeglkt 719
Cdd:cd17921 21 LVSAPTSSGKTLIAELAILRALATSGGKAvYIAPTRALVNQKEADLRERFGPLGKNVGLLTGDPSvnKLLLAEA------ 94
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446076395 720 gfvDIVVGT----HKLLSKDIQY--KDLGLLIVDE------EQRfGVRHKE---RIKTLKHNVDVLTLTAT 775
Cdd:cd17921 95 ---DILVATpeklDLLLRNGGERliQDVRLVVVDEahligdGER-GVVLELllsRLLRINKNARFVGLSAT 161
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
643-748 |
6.11e-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: 45.34 E-value: 6.11e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 643 LLCGDVGYGKTEVAVRAAfKAVME--------GKQVAFLVPTTILAQQHYETlIERMQDFPVeIQLMSRFRTPKEIKQTK 714
Cdd:cd18034 20 IVVLPTGSGKTLIAVMLI-KEMGElnrkeknpKKRAVFLVPTVPLVAQQAEA-IRSHTDLKV-GEYSGEMGVDKWTKERW 96
|
90 100 110
....*....|....*....|....*....|....*....
gi 446076395 715 EGLKTGFvDIVVGTHKLL-----SKDIQYKDLGLLIVDE 748
Cdd:cd18034 97 KEELEKY-DVLVMTAQILldalrHGFLSLSDINLLIFDE 134
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
649-747 |
1.59e-04 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 43.86 E-value: 1.59e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETLIERMQDFPVEIQLM---SRFRTpKEIKQTKEGLKTGFVDIV 725
Cdd:cd17924 42 GVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAGVEVKILvyhSRLKK-KEKEELLEKIEKGDFDIL 120
|
90 100
....*....|....*....|....*
gi 446076395 726 VGTHKLLSKD---IQYKDLGLLIVD 747
Cdd:cd17924 121 VTTNQFLSKNfdlLSNKKFDFVFVD 145
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
845-903 |
2.17e-04 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 43.01 E-value: 2.17e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 446076395 845 EQLQMLMPDANIAVAHGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLII 903
Cdd:cd18789 60 EALYRYAKRLLKPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
634-777 |
3.31e-04 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 43.43 E-value: 3.31e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 634 MQKSRPmdRLLCGD-VGYGKT-EVAvrAAFKAVM---EGKQVAFLVPTTILAQQHYEtLIERmqdFPVEIQLMSRFRtpK 708
Cdd:cd18011 13 LRKPPV--RLLLADeVGLGKTiEAG--LIIKELLlrgDAKRVLILCPASLVEQWQDE-LQDK---FGLPFLILDRET--A 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 709 EIKQTKEGLKTGFVDIVVGTHKLLSKDIQYKDL------GLLIVDEEQRFGVRHK-------ERIKTLKHNVD-VLTLTA 774
Cdd:cd18011 83 AQLRRLIGNPFEEFPIVIVSLDLLKRSEERRGLllseewDLVVVDEAHKLRNSGGgketkryKLGRLLAKRARhVLLLTA 162
|
...
gi 446076395 775 TPI 777
Cdd:cd18011 163 TPH 165
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
643-775 |
3.55e-04 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 42.71 E-value: 3.55e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 643 LLCGDVGYGKTEVAVRAAFKAVMEGKQVAFLVPTTILAQQHYETliermqdfpveiqlmsrFRTPKEIkQTKEGLKTG-- 720
Cdd:cd18028 21 LISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEE-----------------FKKLEEI-GLKVGISTGdy 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446076395 721 --------FVDIVVGTHK----LLSKDIQY-KDLGLLIVDEEQRFGVRHK--------ERIKTLKHNVDVLTLTAT 775
Cdd:cd18028 83 deddewlgDYDIIVATYEkfdsLLRHSPSWlRDVGVVVVDEIHLISDEERgptlesivARLRRLNPNTQIIGLSAT 158
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
845-931 |
1.11e-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: 40.18 E-value: 1.11e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 845 EQLQMLMPDANIAVA--HGQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLI-------IEDadrfglsqlY 915
Cdd:cd18787 41 DRLAELLEELGIKVAalHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVInydlprdAED---------Y 111
|
90
....*....|....*..
gi 446076395 916 QLR-GRVGRSSRIGYAY 931
Cdd:cd18787 112 VHRiGRTGRAGRKGTAI 128
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
649-776 |
1.39e-03 |
|
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: 40.96 E-value: 1.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVR-AAFKAVMEGKQVAFLVPTTILAQQHYETLiERMQDFPVEIQLMSRFRTPKEIKQTKEGLKtgfvdIVVG 727
Cdd:cd18035 26 GLGKTIIAILvAADRLTKKGGKVLILAPSRPLVEQHAENL-KRVLNIPDKITSLTGEVKPEERAERWDASK-----IIVA 99
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 446076395 728 T-----HKLLSKDIQYKDLGLLIVDEEQRFGVRHK-----ERIKTLKHNVDVLTLTATP 776
Cdd:cd18035 100 TpqvieNDLLAGRITLDDVSLLIFDEAHHAVGNYAyvyiaHRYKREANNPLILGLTASP 158
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
649-928 |
1.72e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 42.12 E-value: 1.72e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 649 GYGKTEVAVRAAFKAV---MEGKQVAFLVPTTILAQQhYETLIERMQDFpVEIQLMSRFrTPKEIKQTKEGLKTGfVDIV 725
Cdd:PTZ00424 75 GTGKTATFVIAALQLIdydLNACQALILAPTRELAQQ-IQKVVLALGDY-LKVRCHACV-GGTVVRDDINKLKAG-VHMV 150
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 726 VGT----HKLLSKD-IQYKDLGLLIVDEEQR-----FGVRHKERIKTLKHNVDVLTLTATPIPRTLHMSMLGVRDlsvie 795
Cdd:PTZ00424 151 VGTpgrvYDMIDKRhLRVDDLKLFILDEADEmlsrgFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRD----- 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446076395 796 tppenrfPVQTYVLEQNMSF--IKE---ALERELSRDGQVFYLYNKV---QSIY-----EKREQLQMLMPDANIAVA--H 860
Cdd:PTZ00424 226 -------PKRILVKKDELTLegIRQfyvAVEKEEWKFDTLCDLYETLtitQAIIycntrRKVDYLTKKMHERDFTVScmH 298
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446076395 861 GQMTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLSQLYqlrgRVGRSSRIG 928
Cdd:PTZ00424 299 GDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIH----RIGRSGRFG 362
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
140-205 |
2.94e-03 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 37.92 E-value: 2.94e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446076395 140 LRVGEDIDVDQFLNKLVNMGYKRESVVSHIGEFSLRGGIIDI------FPLIGEP---IRIELFDTEIDSIRDFD 205
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELyrrgfdFPDGAEParrVRLRFAGGRVARLQDLD 75
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| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
863-933 |
3.63e-03 |
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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: 3.63e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446076395 863 MTERDLEETMLSFINNEYDILVTTTIIETGVDVPNANTLIIEDADRFGLsQLYQLRGRVGRsSRIGYAYFL 933
Cdd:cd18801 74 MSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPI-RMIQRMGRTGR-KRQGRVVVL 142
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| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
960-992 |
9.10e-03 |
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ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 36.68 E-value: 9.10e-03
10 20 30
....*....|....*....|....*....|...
gi 446076395 960 GFKIAMRDLNIRGAGNLLGKQQHGfidtVGFDL 992
Cdd:pfam19833 4 GFEIAEADLKLRGPGDLEGTQQSG----IAFDL 32
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