|
Name |
Accession |
Description |
Interval |
E-value |
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
1-1576 |
0e+00 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 2187.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1 MTTTVDEVLERFRERAQSEREKGGLFERLVANYLMTDPQYADLFDQVWLWDEWPARIGA---DAGIDLVAREQATGDYWA 77
Cdd:COG4889 1 MMTTLDDLLDQLRNAARSEREKGTYFERLMRAYLRNDPTYADLYSDVWLWSDWPELYGRskkDTGIDLVARDRDTGELWA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 78 IQCKFFDPDATIQKSDIDSFFTASGKRfatnegerYFARRLIVTTAEHWSKKAEEALADQTIPVTRLFFKDLEESPIDWT 157
Cdd:COG4889 81 IQCKFYDPDYTIQKADIDSFFTASGKK--------YFSRRLIVSTTDWWSNNAEAALAQQQIPVNRIGLSDLEESPIDWS 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 158 VFQLDRPQDLRLQVKNEVRPHQKEALEDCLRGFGQHERGKLIMACGTGKTFTSLRLAEEMVPEGGRILFLAPSISLVGQT 237
Cdd:COG4889 153 QFQWEPPEEVVLKAKKTLRPHQQEAIEAVLAGFKTHDRGKLIMACGTGKTFTSLRIAEELAGKGGRVLFLVPSISLLSQT 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 238 LREWTAQAHAPLRALVACSDTKVSK----DAEDLPVHDLAYPATTDPRKLALHGSQ-ETTDRRTVVFATYQSIQVVADAQ 312
Cdd:COG4889 233 LREWTAESEVPLRSFAVCSDSKVGKrrkkDDEDTSAHDLAYPATTDAEKLAAAAQKrHDADRMTVVFSTYQSIDVVADAQ 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 313 SQGLGTFDLVICDEAHRTTGLTLPGEDPSDFVKVHDNDKLTAHRRLYMTATPRIFAEQSKSKAEEKDAEIFSMDDEAAYG 392
Cdd:COG4889 313 KLGLPEFDLIICDEAHRTTGATLAGEDESAFVRVHDNDYIKAKKRLYMTATPRIYGDDAKKKAKEASAVLASMDDEALFG 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 393 PEFHRLSFGKAVERDLLTDYKVLIVAVQEETMASLAnaynQTYKLDDKKAVDINFATRMIGAWKGLSKRGLvavdeqgaE 472
Cdd:COG4889 393 PEFHRLGFGEAVERGLLTDYKVIVLAVDESHVSRRL----QQLLADNGNELKLDDAAKIVGCWNGLAKRGG--------E 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 473 EAVTEDTNPMQRAVAFSRSIKASKQTTEAFSSMAELYSN-ALPEKHQQGL-VPCELRHVDGTMNAHQRQVELEWLKESSE 550
Cdd:COG4889 461 EDGTDDPAPMKRAVAFCQTIKESKRIAEHFVSVVNIYLMfQDDEAEEDAPsLRCEAEHVDGTMNALERNEKLDWLKAETP 540
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 551 DTSCRILSNARCLSEGVDVPALDAVVFFDTRESIVDIVQSVGRVMRKAPGKQYGHIILPVAIPAtqVQNYNAYLESDSRF 630
Cdd:COG4889 541 ENTCRILSNARCLSEGVDVPALDAVLFLTPRKSQVDVVQSVGRVMRKAPGKKYGYIILPVVIPA--GVEPEEALDDNETY 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 631 RGIWKVIKALRAHDESL---VDEAEFRR----KVNVV----GGEGEGEGDSSGSGEEQLSLEFPDLPVGQISEAVYAAIP 699
Cdd:COG4889 619 KVVWQVLNALRSHDDRFdamINKIELNGpdpdKIEVIgitdDIERDPSKTTGEQKKADPEQQELEFELGEIERAIYAKIV 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 700 KKLGDREYWSQWAKQVADIARRVTERIRQLTESGET--QEAFDEFLKEVRANTNPNVREDEAIEMLAQHVVTRPVFEALF 777
Cdd:COG4889 699 KKVGNRRYWEDWAKDVAKIAQRHITRIKAILENPDQpaREAFDRFLKGLRDNLNDSITEDEAIEMLAQHLITKPVFDALF 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 778 AESSFTKDNPISRGMEALLEALDEYAVSSETDELERFYEVIRERVQYAQSDKSRQEIIRNLYDTFFQTAFPALSDRLGIV 857
Cdd:COG4889 779 AGYSFAAHNPVSQAMQRMLDVLDEHGLEKETETLEKFYESVRMRAEGIDNAEGRQKIIVELYDKFFKTAFPKTTERLGIV 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 858 YTPVEVVDFINRSADTILRKHFNRGLADQGVQILEPFAGTGTFVTRLIQSGLLGgAETLSRKYTEELHANEIVLLAYYIA 937
Cdd:COG4889 859 YTPVEVVDFILHSVDDVLRKEFGQSLADEGVHILDPFTGTGTFIVRLLQSGLIP-PEDLPRKYANELHANEIVLLAYYIA 937
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 938 TLNIEATFHEWTGEQ-RPFEGMVLTDTFNMAEERNrDWEreQRWLAENSERARRQRESDIRVIVGNPPYSAWQESGHEGN 1016
Cdd:COG4889 938 AINIEATYHELMGGDyVPFEGIVLTDTFQMYEDED-DLD--DEVFPDNSERRKRQKKLPIRVIVGNPPYSVGQKSANDNN 1014
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1017 ANRPYPTLDERIRETYVAQSSATLNNSLYDSYIRAIRWASDRIGEQGIIAFVTNGSFIDGNATEGLRRCLAAEFSHLYIL 1096
Cdd:COG4889 1015 ANLKYPTLDARIRSTYAARSTATNKNSLYDSYIRAIRWASDRIGDRGVIAFVTNAGWIDGNAADGMRKCLAEEFSSIYVF 1094
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1097 HLRGNQRTSGEESRREGGKVFGQGSRAPVAITLLVKDPAHQGDCRILYHDIGDYLSRTEKLEALDHFQEITSTPLTTITP 1176
Cdd:COG4889 1095 NLRGNQRTSGELSRKEGGKIFGSGSRAPIAITILVKNPDHSGPGRIHYHDIGDYLSREEKLAKIAEFGSIAGITWQRIIP 1174
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1177 SPQGEWINQSDPAFDDFLAIGRKREREGTAIFGTYSSGVKTNRDAWVYNFSREALQENMAEMIDRYNEEVEAVRQAGGAN 1256
Cdd:COG4889 1175 NEHGDWLNQRDDDFDSFIPLGDKKKKSPPSLFENYSRGVKTNRDAWVYNFSKEKLAENMQRMIEFYNSELDRYQAAVKQI 1254
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1257 SVDEarrLVDTNPAHIGWDNDLFQRAIRGQQADFREAAVFNAIYRPFTKNAYYFDRHFNNRLYQMPHLFPTQEHGNYVIA 1336
Cdd:COG4889 1255 DVDD---FIDNDPTKISWSRSLKQDLERGKKLEFDPDAIVTSLYRPFTKQWLYFDRRLNDMVYQMPKIFPTPTHENLVIC 1331
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1337 VTGTGASKPFSALITDCVPNLHM-IDSSQCFPRYYYEYVGDrsaqppDLLDDSPQTPDAHgyiRRDTITAEALKIFQDHY 1415
Cdd:COG4889 1332 VTGPGSGKGFSALITDVLPDLHLlIGGGQCFPLYLYEKVES------DGGLLSAEDGSAD---RDDAITDEVLDAFAAAY 1402
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1416 ADASITKEDLFWYVYGVLHAEDYRERFRNNLRRGLPRIPLAGDFWAFS---RAGRELGEWHLNYEAVDPYPL-----DEE 1487
Cdd:COG4889 1403 GDYFISKGDIFYYTYYYLDLLLYSEEYRYYAAKELPKKPLRRFAPAFDaaaRAPAELAILRFAAETLALEELidldlAEV 1482
|
1530 1540 1550 1560 1570 1580 1590 1600
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1488 NKRLSLDDEDYQVHKMRFAGSGRQKDRSTIIYNEHLTLRGIPPEAYEYQVNGRSPIEWVMERYQVSKDKKTGIGNDPNDY 1567
Cdd:COG4889 1483 PGEIGDNEEEVRVKKMKKGKETKKKDKKDIIYNTIITITKIPLDAYGYVVNAKEALDWPYERYEVKVDGISGIANDAIDD 1562
|
....*....
gi 518420321 1568 SNDPRYILD 1576
Cdd:COG4889 1563 VNDPNDDPL 1571
|
|
| Type_ISP_C |
pfam18135 |
Type ISP C-terminal specificity domain; This is the C-terminal domain of Type ISP ... |
1206-1577 |
1.93e-123 |
|
Type ISP C-terminal specificity domain; This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DNA. This domain interacts extensively with DNA and is known as the target recognition domain (TRD). TRD works by recognising 6/7 base pairs of asymmetric sequence.
Pssm-ID: 465663 Cd Length: 342 Bit Score: 390.08 E-value: 1.93e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1206 AIFGTYSSGVKTNRDAWVYNFSREALQENMAEMIDRYNEEVEAvrqaggansvdeaRRLVDTNPAHIGWDNDLFQRAIRG 1285
Cdd:pfam18135 1 DLFPWYSPGVKTNRDAWVYNFSKEELEKRWKRLIDEYNEERRR-------------LLFLTRDSTKIKWSRALKGDLERG 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1286 QQADFREAAVFNAIYRPFTKNAYYFDRHFNNRLYqmPHLFPTQEHGNYVIAVTGTGASKPFSALITDCVPNLHMIDS--S 1363
Cdd:pfam18135 68 KKLSFDEPKIVRILYRPFDKQWLYYDPRLIDRPR--PELFPHLDDDNLVIVVSGQGSGKGFSALVTDLIPDLHLFSGggG 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1364 QCFPRYYYEyvgdrsaqppdllddsPQTPDAHGYIRRDTITAEALKIFQDHYADASITKEDLFWYVYGVLHAEDYRERFR 1443
Cdd:pfam18135 146 QVFPLYRYP----------------ETTPNLAPGERRDNITDELLAKFREAYGGATVTKEDIFYYIYAVLHSPEYRERYA 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1444 NNLRRGLPRIPLAGD---FWAFSRAGRELGEWHLNYEAVDPYPLDEENKRlslDDEDYQVHKMRFagsGRQKDRSTIIYN 1520
Cdd:pfam18135 210 EDLKKDFPRIPLTADfelFWELVELGRELADLHLNYERVAPLPPGITTYP---PDGDYRVEKMKY---DKKKDKGTIIIN 283
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*....
gi 518420321 1521 EHLTLRGIPPEAYEYQVNGRSPIEWVMERYQVSKDKKTGIGNDPNDYS--NDPRYILDL 1577
Cdd:pfam18135 284 GEGTFTGVPPEAWEYVVGGKSALEWLKDRYGVKLDKDSGILNDPNDWAklDETEEILDL 342
|
|
| LlaBIII_nuclease-like |
cd22333 |
nuclease domain of type ISB restriction-modification enzyme LlaBIII and similar nuclease ... |
5-161 |
6.59e-74 |
|
nuclease domain of type ISB restriction-modification enzyme LlaBIII and similar nuclease domains; This N-terminal nuclease domain belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411737 Cd Length: 149 Bit Score: 242.44 E-value: 6.59e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 5 VDEVLERFRERAQSEREKGGLFERLVANYLMTDPQYADLFDQVWLWDEWPAR-IGADAGIDLVAREqATGDYWAIQCKFF 83
Cdd:cd22333 1 FDDLLDQLRKLSKSERDKGTRFERLMKAYLLTDPTYADQFSEVWLWNEWPGRaGGKDTGIDLVAKT-RDGELWAIQCKFY 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 518420321 84 DPDATIQKSDIDSFFTASGKrfatnegeRYFARRLIVTTAEHWSKKAEEALADQTIPVTRLFFKDLEESPIDWTVFQL 161
Cdd:cd22333 80 DPDHTISKADIDSFLSASGK--------KPFTHRLIVSTTDKWSSNAEEALENQSKPVTRIGLSDLENSPIDWSKFDK 149
|
|
| Mrr_cat_2 |
pfam13156 |
Restriction endonuclease; Prokaryotic family found in type II restriction enzymes containing ... |
36-164 |
2.04e-58 |
|
Restriction endonuclease; Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA
Pssm-ID: 433001 Cd Length: 127 Bit Score: 197.12 E-value: 2.04e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 36 TDPQYADLFDQVWLWDEWPARI---GADAGIDLVAREQATGDYWAIQCKFFDPDATIQKSDIDSFFTASGKrfatnegeR 112
Cdd:pfam13156 2 TDPLYADEFDDVWLWKEWPTRKglgGHDTGIDLVARTRDTGEYWAIQCKFYDPDHKIQKPDIDSFFSASGK--------S 73
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 518420321 113 YFARRLIVTTAEHWSKKAEEALADQTIPVTRLFFKDLEESPIDWTVFQLDRP 164
Cdd:pfam13156 74 PFTDRLIISTTDKWSKNAEEALANQTIPVSRIGLADLAESPIDWSKLSPGAE 125
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
112-731 |
8.38e-37 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 148.25 E-value: 8.38e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 112 RYFARRLIVTTAEHWSKKAEEALADQTIPVTRLFFKDLEESPIDWTVF------QLDRPQDLRLQVKNEVRPHQKEALED 185
Cdd:COG1061 12 DKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTErelaeaEALEAGDEASGTSFELRPYQQEALEA 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 186 CLRGFGQ-HERGKLIMACGTGKTFTSLRLAEEMVpEGGRILFLAPSISLVGQTLREwtaqahapLRALvacsdtkvskda 264
Cdd:COG1061 92 LLAALERgGGRGLVVAPTGTGKTVLALALAAELL-RGKRVLVLVPRRELLEQWAEE--------LRRF------------ 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 265 edlpvhdlaypattdpRKLALHGSQETTDRRTVVFATYQSiqVVADAQSQGLG-TFDLVICDEAHRTTGLTlpgedpsdF 343
Cdd:COG1061 151 ----------------LGDPLAGGGKKDSDAPITVATYQS--LARRAHLDELGdRFGLVIIDEAHHAGAPS--------Y 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 344 VKVHDNdkLTAHRRLYMTATPrifaeqskskaeekdaeiFSMDDEAAYGPEF----HRLSFGKAVERDLLTDYKVLIVAV 419
Cdd:COG1061 205 RRILEA--FPAAYRLGLTATP------------------FRSDGREILLFLFdgivYEYSLKEAIEDGYLAPPEYYGIRV 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 420 qeeTMASLANAYNQTYKLDDKKavdinfatrmigawkglskrglVAVDEQGAEEAVTE---DTNPMQRAVAFSRSIKASK 496
Cdd:COG1061 265 ---DLTDERAEYDALSERLREA----------------------LAADAERKDKILREllrEHPDDRKTLVFCSSVDHAE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 497 QTTEAFssmaelysnalpekHQQGLvpcELRHVDGTMNAHQRQVELEWLKESSedtsCRILSNARCLSEGVDVPALDAVV 576
Cdd:COG1061 320 ALAELL--------------NEAGI---RAAVVTGDTPKKEREEILEAFRDGE----LRILVTVDVLNEGVDVPRLDVAI 378
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 577 FFDTRESIVDIVQSVGRVMRKAPGKQYGHIILPVAIPATQVQNynayLESDSRFRGIWKVIKALRAHDESLVDEAEFRRK 656
Cdd:COG1061 379 LLRPTGSPREFIQRLGRGLRPAPGKEDALVYDFVGNDVPVLEE----LAKDLRDLAGYRVEFLDEEESEELALLIAVKPA 454
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518420321 657 VNVVGGEGEGEGDSSGSGEEQLSLEFPDLPVGQISEAVYAAIPKKLGDREYWSQWAKQVADIARRVTERIRQLTE 731
Cdd:COG1061 455 LEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLL 529
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
174-366 |
1.33e-23 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 98.90 E-value: 1.33e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 174 EVRPHQKEALEDCLRGFG-QHERGKLIMACGTGKTFTSLRLAEEMVPEGG--RILFLAPSISLVGQTLREWTAQAHAPLR 250
Cdd:pfam04851 3 ELRPYQIEAIENLLESIKnGQKRGLIVMATGSGKTLTAAKLIARLFKKGPikKVLFLVPRKDLLEQALEEFKKFLPNYVE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 251 AlvacsDTKVSKDAEDLPVHDlaypattdprklalhgsqettdrRTVVFATYQSIQ--VVADAQSQGLGTFDLVICDEAH 328
Cdd:pfam04851 83 I-----GEIISGDKKDESVDD-----------------------NKIVVTTIQSLYkaLELASLELLPDFFDVIIIDEAH 134
|
170 180 190
....*....|....*....|....*....|....*...
gi 518420321 329 RTTGLTlpgedpsdFVKVhdNDKLTAHRRLYMTATPRI 366
Cdd:pfam04851 135 RSGASS--------YRNI--LEYFKPAFLLGLTATPER 162
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
176-364 |
1.15e-20 |
|
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: 90.06 E-value: 1.15e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGFGQHeRGKLIMACGTGKTFTSLRLAEEMVPEggRILFLAPSISLVGQTLREWTAqahaplralvac 255
Cdd:cd17926 2 RPYQEEALEAWLAHKNNR-RGILVLPTGSGKTLTALALIAYLKEL--RTLIVVPTDALLDQWKERFED------------ 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 256 sdtkvskdaedlpvhdlayPATTDPRKLALHGSQETTDRRTVVFATYQSIQVVADAQSQGLGTFDLVICDEAHRTTGLTl 335
Cdd:cd17926 67 -------------------FLGDSSIGLIGGGKKKDFDDANVVVATYQSLSNLAEEEKDLFDQFGLLIVDEAHHLPAKT- 126
|
170 180
....*....|....*....|....*....
gi 518420321 336 pgedpsdFVKVHDNDKltAHRRLYMTATP 364
Cdd:cd17926 127 -------FSEILKELN--AKYRLGLTATP 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
174-382 |
2.23e-16 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 79.46 E-value: 2.23e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 174 EVRPHQKEALEDCLRGfgqHERGKLIMACGTGKTFTSLRLAEEMVPEG--GRILFLAPSISLVGQTLREWTAQA-HAPLR 250
Cdd:smart00487 8 PLRPYQKEAIEALLSG---LRDVILAAPTGSGKTLAALLPALEALKRGkgGRVLVLVPTRELAEQWAEELKKLGpSLGLK 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 251 ALVACSDTKVSKDAEDLpvhdlaypattdprklalhgsqeTTDRRTVVFATYQSIQVVADAQSQGLGTFDLVICDEAHRt 330
Cdd:smart00487 85 VVGLYGGDSKREQLRKL-----------------------ESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR- 140
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 518420321 331 tgltLPGEDPSDFVKVHDNDKLTAHRRLYMTATPRIFAEQSKSKAEEKDAEI 382
Cdd:smart00487 141 ----LLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFI 188
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
176-329 |
9.95e-16 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350790 [Multi-domain] Cd Length: 163 Bit Score: 76.45 E-value: 9.95e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGFGQ-HERGKLIMACGTGKTFTSLRLAEEMVPEGG--RILFLAPSISLVGQTLRewtaqahaplral 252
Cdd:cd18032 2 RYYQQEAIEALEEAREKgQRRALLVMATGTGKTYTAAFLIKRLLEANRkkRILFLAHREELLEQAER------------- 68
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518420321 253 vACSDTKVSKDAEDLPVhdlaypattdprklalhGSQETTDRRtVVFATYQSIQVVADAQSQGLGTFDLVICDEAHR 329
Cdd:cd18032 69 -SFKEVLPDGSFGNLKG-----------------GKKKPDDAR-VVFATVQTLNKRKRLEKFPPDYFDLIIIDEAHH 126
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
546-610 |
5.70e-12 |
|
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: 62.72 E-value: 5.70e-12
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 518420321 546 KESSEDTSCR--ILSNARCLSEGVDVPALDAVVFFDTRESIVDIVQSVGRVMRkaPGKQYGHIILPV 610
Cdd:cd18785 13 IEHAEEIASSleILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGR--GGKDEGEVILFV 77
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
176-329 |
6.54e-11 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 67.17 E-value: 6.54e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGFGQHERGKLI-MACGTGKTFTSLRLAEEMVPEGG--RILFLAPSISLVGQTLREWtaQAHAP-LRA 251
Cdd:COG4096 160 RYYQIEAIRRVEEAIAKGQRRALLvMATGTGKTRTAIALIYRLLKAGRakRILFLADRNALVDQAKNAF--KPFLPdLDA 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 252 LvacsdTKVSKDAEDLPvhdlaypattdprklalhgsqetTDRRtVVFATYQS----IQVVADAQSQGL---GTFDLVIC 324
Cdd:COG4096 238 F-----TKLYNKSKDID-----------------------KSAR-VYFSTYQTmmnrIDGEEEEPGYRQfppDFFDLIII 288
|
....*
gi 518420321 325 DEAHR 329
Cdd:COG4096 289 DECHR 293
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
7-364 |
1.44e-10 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 66.02 E-value: 1.44e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 7 EVLERFRERAQSEREKGGLFERLVANYLMTDPQYADLFDQVWLWDEWPARIGADAGIDLVAREQATGDYWAIQCKFFDPD 86
Cdd:COG0553 67 LLLLALLLLALSALALLLLRLLLALLLLALLLLLAGLLALALLLLALLGLLLSLALLLLLLLLLLLLLLALLLVLLAALL 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 87 ATIQKSDIDSFFTASGKRFATNEGERYFARRLIVTTAEHWSKKAEEALADQTIPVTRLFFKDLEESPIDWTVFQLDRPQD 166
Cdd:COG0553 147 LLLLLLLLLALLLGRLLLLALLLLALEALLLLGLLLALALLALLELALLAAEAELLLLLELLLELELLAEAAVDAFRLRR 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 167 LRLQVKN-------EVRPHQKEALEDCLRGFGQHERGKLIMACGTGKTFTSLRLAEEMVPEG--GRILFLAPSiSLVGQT 237
Cdd:COG0553 227 LREALESlpaglkaTLRPYQLEGAAWLLFLRRLGLGGLLADDMGLGKTIQALALLLELKERGlaRPVLIVAPT-SLVGNW 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 238 LREwtAQAHAP-LRALVACSDTKVSKDAEDLPVHDlaypattdprklalhgsqettdrrtVVFATY----QSIQVVADAQ 312
Cdd:COG0553 306 QRE--LAKFAPgLRVLVLDGTRERAKGANPFEDAD-------------------------LVITSYgllrRDIELLAAVD 358
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 518420321 313 sqglgtFDLVICDEAHRttgltlpgedpsdfVKVHDND------KLTAHRRLYMTATP 364
Cdd:COG0553 359 ------WDLVILDEAQH--------------IKNPATKrakavrALKARHRLALTGTP 396
|
|
| DEXHc_RAD54 |
cd18004 |
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ... |
176-364 |
7.12e-10 |
|
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They 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: 350762 [Multi-domain] Cd Length: 240 Bit Score: 61.15 E-value: 7.12e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALE---DCLRGFGQHERGKLIMA--CGTGKTFTSLRLAEEMV-------PEGGRILFLAPSiSLVGQtlreWTA 243
Cdd:cd18004 2 RPHQREGVQflyDCLTGRRGYGGGGAILAdeMGLGKTLQAIALVWTLLkqgpygkPTAKKALIVCPS-SLVGN----WKA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 244 Q-----AHAPLRALVACSDTKVSKDAEDLPVHDLAYPattdprklalhgsqettdrrtVVFATYQSIQVVAdAQSQGLGT 318
Cdd:cd18004 77 EfdkwlGLRRIKVVTADGNAKDVKASLDFFSSASTYP---------------------VLIISYETLRRHA-EKLSKKIS 134
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 518420321 319 FDLVICDEAHR------TTGLTLpgedpsdfvkvhdnDKLTAHRRLYMTATP 364
Cdd:cd18004 135 IDLLICDEGHRlknsesKTTKAL--------------NSLPCRRRLLLTGTP 172
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
528-596 |
3.93e-08 |
|
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: 52.98 E-value: 3.93e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518420321 528 HVDGTMNAHQRQVELEWLKESSedtsCRILSNARCLSEGVDVPALDAVVFFDTRESIVDIVQSVGRVMR 596
Cdd:pfam00271 43 RLHGDLSQEEREEILEDFRKGK----IDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGR 107
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
176-367 |
2.91e-07 |
|
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: 52.65 E-value: 2.91e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRgfgqhERGKLIMACGTGKTFTSLRLAEEM-------VPEGGRILFLAPSISLVGQ---TLREWTaqa 245
Cdd:cd18034 4 RSYQLELFEAALK-----RNTIVVLPTGSGKTLIAVMLIKEMgelnrkeKNPKKRAVFLVPTVPLVAQqaeAIRSHT--- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 246 haPLRALVACSDTKVSKdaedlpvhdlaypattdPRKLALHGSQETTDrrtVVFATYqsiQVVADAQSQG---LGTFDLV 322
Cdd:cd18034 76 --DLKVGEYSGEMGVDK-----------------WTKERWKEELEKYD---VLVMTA---QILLDALRHGflsLSDINLL 130
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 518420321 323 ICDEAHRTTgltlpGEDP-SDFVKVHDNDKLTAHRrlymtatPRIF 367
Cdd:cd18034 131 IFDECHHAT-----GDHPyARIMKEFYHLEGRTSR-------PRIL 164
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
529-597 |
3.20e-07 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 49.52 E-value: 3.20e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 518420321 529 VDGTMNAHQRQVELEWLKESSedtsCRILSNARCLSEGVDVPALDAVVFFDTRESIVDIVQSVGRVMRK 597
Cdd:smart00490 17 LHGGLSQEEREEILDKFNNGK----IKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
176-378 |
4.09e-07 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 52.43 E-value: 4.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGfgqhergKLIMAC---GTGKTFTSLRLAEEMV-----PEGGRILFLAPSISLVGQTLRewtaqaha 247
Cdd:cd17927 4 RNYQLELAQPALKG-------KNTIIClptGSGKTFVAVLICEHHLkkfpaGRKGKVVFLANKVPLVEQQKE-------- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 248 plralvacsdtKVSKDAEDLPVHDLAYPATTDPRKlalhGSQETTDRRTVVFATYQSIQ-VVADAQSQGLGTFDLVICDE 326
Cdd:cd17927 69 -----------VFRKHFERPGYKVTGLSGDTSENV----SVEQIVESSDVIIVTPQILVnDLKSGTIVSLSDFSLLVFDE 133
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 518420321 327 AHRTTgltlpGEDPSDFV-------KVHDNDKLTahRRLYMTATPRIFAEQSKSKAEEK 378
Cdd:cd17927 134 CHNTT-----KNHPYNEImfryldqKLGSSGPLP--QILGLTASPGVGGAKNTEEALEH 185
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
193-363 |
9.44e-07 |
|
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: 50.09 E-value: 9.44e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 193 HERGKLIMACGTGKTFTSLR-LAEEMVPEGGRILFLAPSISLVGQTLREwtaqahapLRALVacsdtkvskdAEDLPVHd 271
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLaALLLLLKKGKKVLVLVPTKALALQTAER--------LRELF----------GPGIRVA- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 272 LAYPATTDPRKLALhgsqeTTDRRTVVFATYQSIQ--VVADAQSqGLGTFDLVICDEAHRttglTLPGEDPSDFVK-VHD 348
Cdd:cd00046 62 VLVGGSSAEEREKN-----KLGDADIIIATPDMLLnlLLREDRL-FLKDLKLIIVDEAHA----LLIDSRGALILDlAVR 131
|
170
....*....|....*
gi 518420321 349 NDKLTAHRRLYMTAT 363
Cdd:cd00046 132 KAGLKNAQVILLSAT 146
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
176-364 |
2.31e-06 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 49.49 E-value: 2.31e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGFGQHERGKLIMACGTGKT------FTSLRLAEemvPEGGRILFLAPSiSLVGQTLREwtAQAHAPl 249
Cdd:cd17919 2 RPYQLEGLNFLLELYENGPGGILADEMGLGKTlqaiafLAYLLKEG---KERGPVLVVCPL-SVLENWERE--FEKWTP- 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 250 ralvacsdtkvskdaedlPVHDLAYPATTDPRKlaLHGSQETTDRRTVVFATYQSIQvvADAQSQGLGTFDLVICDEAHR 329
Cdd:cd17919 75 ------------------DLRVVVYHGSQRERA--QIRAKEKLDKFDVVLTTYETLR--RDKASLRKFRWDLVVVDEAHR 132
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 518420321 330 ttgltlpgedpsdfVKVHDN------DKLTAHRRLYMTATP 364
Cdd:cd17919 133 --------------LKNPKSqlskalKALRAKRRLLLTGTP 159
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
176-364 |
2.36e-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: 49.98 E-value: 2.36e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRgfgqHERGKLIMA--CGTGKTFTSLRLAEEMVPEG--GRILFLAPSiSLVGQtlreWTA--QAHAPL 249
Cdd:cd18011 2 LPHQIDAVLRALR----KPPVRLLLAdeVGLGKTIEAGLIIKELLLRGdaKRVLILCPA-SLVEQ----WQDelQDKFGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 250 RALVACSDTKvskdaedlpvhdlaypattdPRKLALHGSQETTDRRTVVfaTYQSIQVVADAQSQGLGT-FDLVICDEAH 328
Cdd:cd18011 73 PFLILDRETA--------------------AQLRRLIGNPFEEFPIVIV--SLDLLKRSEERRGLLLSEeWDLVVVDEAH 130
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 518420321 329 RTTgltlpgedPSDFVKVHDNDKL------TAHRRLYMTATP 364
Cdd:cd18011 131 KLR--------NSGGGKETKRYKLgrllakRARHVLLLTATP 164
|
|
| HsdM |
COG0286 |
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]; |
855-1084 |
6.96e-06 |
|
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
Pssm-ID: 440055 [Multi-domain] Cd Length: 243 Bit Score: 49.42 E-value: 6.96e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 855 GIVYTPVEVVDFINRSADtilrkhfnrglADQGVQILEPFAGTGTFvtrLIQSGLLGGAETLSRKYTEELHANEIVLLAY 934
Cdd:COG0286 23 GEFYTPREVVRLMVELLD-----------PKPGETVYDPACGSGGF---LVEAAEYLKEHGGDERKKLSLYGQEINPTTY 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 935 YIATLN----------IEA--TFHEWTGEQRPFEgmvltdtfnmaeernrdwereqrwlaenserarrqresdirVIVGN 1002
Cdd:COG0286 89 RLAKMNlllhgigdpnIELgdTLSNDGDELEKFD-----------------------------------------VVLAN 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 1003 PPYSawQESGHEGNANRPYPtldeRIRETYVAQSSATLNnslydsYI-RAIRWASDRigeqGIIAFVTNGSFIDGNATEG 1081
Cdd:COG0286 128 PPFG--GKWKKEELKDDLLG----RFGYGLPPKSNADLL------FLqHILSLLKPG----GRAAVVLPDGVLFRGAEKE 191
|
...
gi 518420321 1082 LRR 1084
Cdd:COG0286 192 IRK 194
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
176-329 |
1.46e-05 |
|
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: 46.85 E-value: 1.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 176 RPHQKEALEDCLRGFGqhergklIMAC---GTGKTFTSLRLAEEMV---PEGGRILFLAPSISLVGQTLREWTAQA-HAP 248
Cdd:pfam00270 1 TPIQAEAIPAILEGRD-------VLVQaptGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKLGkGLG 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 249 LRALVACSDTKVSKDAEdlpvhdlaypattdprklALHGSQettdrrtVVFATYQSIQVVADaQSQGLGTFDLVICDEAH 328
Cdd:pfam00270 74 LKVASLLGGDSRKEQLE------------------KLKGPD-------ILVGTPGRLLDLLQ-ERKLLKNLKLLVLDEAH 127
|
.
gi 518420321 329 R 329
Cdd:pfam00270 128 R 128
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
549-607 |
1.78e-05 |
|
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: 45.63 E-value: 1.78e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 518420321 549 SEDTSCRILSNARCLSEGVDVPALDAVVFFDTRESIVDIVQSVGRVMRKAPGKQYGHII 607
Cdd:cd18799 55 FGELKPPILVTVDLLTTGVDIPEVDNVVFLRPTESRTLFLQMLGRGLRLHEGKDFFTIL 113
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
174-332 |
1.53e-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: 44.43 E-value: 1.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 174 EVRPHQKEALEDCLRGfgqheRGKLIMACGTGKTFTSLRLAEE-MVPEGGRILFLAPSISLVgqtlrewtAQAHAPLRAL 252
Cdd:cd18035 2 ERRLYQVLIAAVALNG-----NTLIVLPTGLGKTIIAILVAADrLTKKGGKVLILAPSRPLV--------EQHAENLKRV 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 253 VACSDTKVSKDAEdlpvhdlaypatTDPRKLAlhgsqETTDRRTVVFATYQSIQVVADAQSQGLGTFDLVICDEAHRTTG 332
Cdd:cd18035 69 LNIPDKITSLTGE------------VKPEERA-----ERWDASKIIVATPQVIENDLLAGRITLDDVSLLIFDEAHHAVG 131
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
177-328 |
1.60e-04 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 44.17 E-value: 1.60e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 177 PHQKEALedclRGFGQHERGKLIMA-CGTGKTFTS-LRLAEEMVPEGGRILFLAPSISLVGQTLREWTAQAhAPLRALVA 254
Cdd:cd17921 4 PIQREAL----RALYLSGDSVLVSApTSSGKTLIAeLAILRALATSGGKAVYIAPTRALVNQKEADLRERF-GPLGKNVG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 518420321 255 CSDTKVSKDAEDLPvhdlaypattdprklalhgsqettdRRTVVFATYQSIQVVADAQSQGLGT-FDLVICDEAH 328
Cdd:cd17921 79 LLTGDPSVNKLLLA-------------------------EADILVATPEKLDLLLRNGGERLIQdVRLVVVDEAH 128
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
565-603 |
2.16e-04 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 43.11 E-value: 2.16e-04
10 20 30
....*....|....*....|....*....|....*....
gi 518420321 565 EGVDVPALDAVVFFDTRESIVDIVQSVGRVMRKAPGKQY 603
Cdd:cd18801 102 EGLDIGEVDLIICYDASPSPIRMIQRMGRTGRKRQGRVV 140
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
179-240 |
7.31e-04 |
|
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: 42.20 E-value: 7.31e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 518420321 179 QKEALEDCLRGFGQHERGKLIMACGTGKTFTSLRLAEEMVPEGGRILFLAPSISLVGQTLRE 240
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKR 62
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
174-239 |
2.33e-03 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 41.31 E-value: 2.33e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 518420321 174 EVRPHQKEALEDCLRGfgqheRGKLIMA-CGTGKTFTSLRLAEEMV------PEGGRILFLAPSISLVGQTLR 239
Cdd:cd18036 2 ELRNYQLELVLPALRG-----KNTIICApTGSGKTRVAVYICRHHLekrrsaGEKGRVVVLVNKVPLVEQQLE 69
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
155-331 |
4.18e-03 |
|
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It 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: 350788 [Multi-domain] Cd Length: 208 Bit Score: 40.29 E-value: 4.18e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 155 DWTVFqlDRPQDLRLQVkneVRPHQ----KEALEDCLRGF---GQHERGKLIMACGTGKTFTSLRLAEEMV--PEGGRIL 225
Cdd:cd18030 7 NFIVF--DEDDDKTKKV---ARYYQyyavEAALERIKTATnkdGDKKGGYIWHTQGSGKSLTMFKAAKLLIedPKNPKVV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 518420321 226 FLAPSISLVGQTLREWTAqahaplralVACSDTKVSKDAEDLpvhdlaypattdpRKLALHgsqettDRRTVVFATYQSI 305
Cdd:cd18030 82 FVVDRKDLDYQTSSTFSR---------FAAEDVVRANSTKEL-------------KELLKN------LSGGIIVTTIQKF 133
|
170 180
....*....|....*....|....*....
gi 518420321 306 QVVADAQSQGLGTFD---LVICDEAHRTT 331
Cdd:cd18030 134 NNAVKEESKPVLIYRkniVVIVDEAHRSQ 162
|
|
| |
