|
Name |
Accession |
Description |
Interval |
E-value |
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
1-1522 |
0e+00 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 2007.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1 MTFDELIQLAREQSnEIQRDKGTLFEKIAQIYFKNEPTYKNLFSDVWLLNEVPEEYAIPKKDTGVDLVARNEATGELTAI 80
Cdd:COG4889 3 TTLDDLLDQLRNAA-RSEREKGTYFERLMRAYLRNDPTYADLYSDVWLWSDWPELYGRSKKDTGIDLVARDRDTGELWAI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 81 QAKFYDN--KIYKRHIDSFLAELGKSYYSDGIIVYSLDSLSSNADEAINQLSKPVAQIGLSDLRNSQVAWESFIPSRPNE 158
Cdd:COG4889 82 QCKFYDPdyTIQKADIDSFFTASGKKYFSRRLIVSTTDWWSNNAEAALAQQQIPVNRIGLSDLEESPIDWSQFQWEPPEE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 159 VKVKNVKKTRPYQNEAINLTIDYFKENDRGQLIMAPGTGKTFTSLKLVEKMAKQTnketFNVLYLVPSIQLLSQTLIGWN 238
Cdd:COG4889 162 VVLKAKKTLRPHQQEAIEAVLAGFKTHDRGKLIMACGTGKTFTSLRIAEELAGKG----GRVLFLVPSISLLSQTLREWT 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 239 NDTELSMHSFAVTSDRNASKKKNDD--ELSAKDIGFPATTDSEKLLSNYKKIENNQRdLTVVYSTYQSIEVLHEAQEKGF 316
Cdd:COG4889 238 AESEVPLRSFAVCSDSKVGKRRKKDdeDTSAHDLAYPATTDAEKLAAAAQKRHDADR-MTVVFSTYQSIDVVADAQKLGL 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 317 PEFDIIICDEAHRTTGAKALGEEASVFTRVHNNNYIKASKRLYQTATPKIYGTDAKQKAEDSSIVLSSMDNKDIYGEEIF 396
Cdd:COG4889 317 PEFDLIICDEAHRTTGATLAGEDESAFVRVHDNDYIKAKKRLYMTATPRIYGDDAKKKAKEASAVLASMDDEALFGPEFH 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 397 RLGFGQAVSNDILTDYKVIVLAVDEKVIQKDMQKVLSDSENGLDVDDVSKLIGVWNGLMKRSsVDKDAVFEGKPMQRAIS 476
Cdd:COG4889 397 RLGFGEAVERGLLTDYKVIVLAVDESHVSRRLQQLLADNGNELKLDDAAKIVGCWNGLAKRG-GEEDGTDDPAPMKRAVA 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 477 FINTINNSKKISSQFNEVVNEYL------DGNEIIQQSINVRHVDGMMNTLEKKEALDWLSEDFAEDETRVLSNVKFLTE 550
Cdd:COG4889 476 FCQTIKESKRIAEHFVSVVNIYLmfqddeAEEDAPSLRCEAEHVDGTMNALERNEKLDWLKAETPENTCRILSNARCLSE 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 551 GIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRKFKDKEYGYIILPIVIPEGTTPESILDNNKKYEAVWQILNALRSVDERF 630
Cdd:COG4889 556 GVDVPALDAVLFLTPRKSQVDVVQSVGRVMRKAPGKKYGYIILPVVIPAGVEPEEALDDNETYKVVWQVLNALRSHDDRF 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 631 SAMINKLELNRKKPENMDVIGIGEaPSVEDMENTSTIGEKDDAIyQTSLDLDWGEIENAIYAKVVKKVGDRRYLEDWSED 710
Cdd:COG4889 636 DAMINKIELNGPDPDKIEVIGITD-DIERDPSKTTGEQKKADPE-QQELEFELGEIERAIYAKIVKKVGNRRYWEDWAKD 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 711 VAKIAQRHIEQITIMIKDKNSKTAIEFEKFLKSLQHNINESIDEKQAIEMLAQHLITAPIFEALFGEYSFVNNNPVSEAM 790
Cdd:COG4889 714 VAKIAQRHITRIKAILENPDQPAREAFDRFLKGLRDNLNDSITEDEAIEMLAQHLITKPVFDALFAGYSFAAHNPVSQAM 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 791 DKIVEELSKFGgFNKEQDELKEFYDSVKLRAEGIDNAEAKQRIIITLYDKFFSKGFKETTQRLGIVFTPVEVVDFIVKSV 870
Cdd:COG4889 794 QRMLDVLDEHG-LEKETETLEKFYESVRMRAEGIDNAEGRQKIIVELYDKFFKTAFPKTTERLGIVYTPVEVVDFILHSV 872
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 871 DDVLKKHFGKAIEDEGVHILDPFTGTGTFIVRTLHylkdklsNGEITLADVTRKYTQELHANEIVLLSYYIAAINIESTF 950
Cdd:COG4889 873 DDVLRKEFGQSLADEGVHILDPFTGTGTFIVRLLQ-------SGLIPPEDLPRKYANELHANEIVLLAYYIAAINIEATY 945
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 951 AEINHEEYKPFEGIVLTDTFESTEQEDTLDDSFFGTNDERLKRQQEVPITAIIGNPPYSIGQSNANDNNKNIKYINLNKR 1030
Cdd:COG4889 946 HELMGGDYVPFEGIVLTDTFQMYEDEDDLDDEVFPDNSERRKRQKKLPIRVIVGNPPYSVGQKSANDNNANLKYPTLDAR 1025
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1031 IEETYSKYSNANLNKGLYDSYIQAIRWASDRLGDSGVIGFITPNSIIDKGSFDGFRKTLYEEFNHIYSINLRGAIKGKvG 1110
Cdd:COG4889 1026 IRSTYAARSTATNKNSLYDSYIRAIRWASDRIGDRGVIAFVTNAGWIDGNAADGMRKCLAEEFSSIYVFNLRGNQRTS-G 1104
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1111 VDATKEGQSVF--NILIGTAITILVKDD--SESHSINYFDIGDFLNRNKKLKKISELKSIKNISWNTVYPDENNDWINQR 1186
Cdd:COG4889 1105 ELSRKEGGKIFgsGSRAPIAITILVKNPdhSGPGRIHYHDIGDYLSREEKLAKIAEFGSIAGITWQRIIPNEHGDWLNQR 1184
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1187 DEKYANYPKMAGE-------IFEDWAVGISTNRDAWVISFGKENLVDNVQRMIKQYETERNNLKLNNSTTD----IDRDS 1255
Cdd:COG4889 1185 DDDFDSFIPLGDKkkksppsLFENYSRGVKTNRDAWVYNFSKEKLAENMQRMIEFYNSELDRYQAAVKQIDvddfIDNDP 1264
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1256 SKIKWSSGLIDKLNKQVEINFNNNRIQLIQYRPFTKKFIYYENNLVERPGKYRNW----QKGNPIIFITGKGSRREFSTA 1331
Cdd:COG4889 1265 TKISWSRSLKQDLERGKKLEFDPDAIVTSLYRPFTKQWLYFDRRLNDMVYQMPKIfptpTHENLVICVTGPGSGKGFSAL 1344
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1332 MINLIPSLD-LIEKGQGFYQWH----------LNEGNLLSEKSDNINGKK----------FGLSTEETFYYIYGLLHSKA 1390
Cdd:COG4889 1345 ITDVLPDLHlLIGGGQCFPLYLyekvesdgglLSAEDGSADRDDAITDEVldafaaaygdYFISKGDIFYYTYYYLDLLL 1424
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1391 YRENYASDLKKELPRIPLVKDKEKYVEIGKKLADLH---------LNYEDVPVYDGVNIVFKSDNPSF----KVKKMKHP 1457
Cdd:COG4889 1425 YSEEYRYYAAKELPKKPLRRFAPAFDAAARAPAELAilrfaaetlALEELIDLDLAEVPGEIGDNEEEvrvkKMKKGKET 1504
|
1530 1540 1550 1560 1570 1580
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1106661688 1458 KRGQLDTIIFNEDIVITDIPERAYEYVVNGKPAIEWIIDQYQVKKDKKSGIVDDPNEFSDNPKYI 1522
Cdd:COG4889 1505 KKKDKKDIIYNTIITITKIPLDAYGYVVNAKEALDWPYERYEVKVDGISGIANDAIDDVNDPNDD 1569
|
|
| Type_ISP_C |
pfam18135 |
Type ISP C-terminal specificity domain; This is the C-terminal domain of Type ISP ... |
1199-1525 |
7.97e-116 |
|
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: 368.50 E-value: 7.97e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1199 EIFEDWAVGISTNRDAWVISFGKENLVDNVQRMIKQYETERNNLKlnnsttDIDRDSSKIKWSSGLIDKLNKQVEINFNN 1278
Cdd:pfam18135 1 DLFPWYSPGVKTNRDAWVYNFSKEELEKRWKRLIDEYNEERRRLL------FLTRDSTKIKWSRALKGDLERGKKLSFDE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1279 NRIQLIQYRPFTKKFIYYENNLVERPGK--YRNWQKGNPIIFITGKGSRREFSTAMINLIPSLDLI--EKGQGFYQWHLN 1354
Cdd:pfam18135 75 PKIVRILYRPFDKQWLYYDPRLIDRPRPelFPHLDDDNLVIVVSGQGSGKGFSALVTDLIPDLHLFsgGGGQVFPLYRYP 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1355 EGN---LLSEKSDNIN----------GKKFGLSTEETFYYIYGLLHSKAYRENYASDLKKELPRIPLVKDKEKY---VEI 1418
Cdd:pfam18135 155 ETTpnlAPGERRDNITdellakfreaYGGATVTKEDIFYYIYAVLHSPEYRERYAEDLKKDFPRIPLTADFELFwelVEL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 1419 GKKLADLHLNYEDVPVYdGVNIVFKSDNPSFKVKKMKHPKRGQLDTIIFNEDIVITDIPERAYEYVVNGKPAIEWIIDQY 1498
Cdd:pfam18135 235 GRELADLHLNYERVAPL-PPGITTYPPDGDYRVEKMKYDKKKDKGTIIINGEGTFTGVPPEAWEYVVGGKSALEWLKDRY 313
|
330 340
....*....|....*....|....*....
gi 1106661688 1499 QVKKDKKSGIVDDPNEFS--DNPKYIFNL 1525
Cdd:pfam18135 314 GVKLDKDSGILNDPNDWAklDETEEILDL 342
|
|
| LlaBIII_nuclease-like |
cd22333 |
nuclease domain of type ISB restriction-modification enzyme LlaBIII and similar nuclease ... |
3-153 |
2.82e-59 |
|
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: 200.46 E-value: 2.82e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 3 FDELIQLAREQSNEiQRDKGTLFEKIAQIYFKNEPTYKNLFSDVWLLNEVPEEYaiPKKDTGVDLVARnEATGELTAIQA 82
Cdd:cd22333 1 FDDLLDQLRKLSKS-ERDKGTRFERLMKAYLLTDPTYADQFSEVWLWNEWPGRA--GGKDTGIDLVAK-TRDGELWAIQC 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1106661688 83 KFYDN--KIYKRHIDSFLAELGKSYYSDGIIVYSLDSLSSNADEAINQLSKPVAQIGLSDLRNSQVAWESFIP 153
Cdd:cd22333 77 KFYDPdhTISKADIDSFLSASGKKPFTHRLIVSTTDKWSSNAEEALENQSKPVTRIGLSDLENSPIDWSKFDK 149
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
168-753 |
1.79e-43 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 168.28 E-value: 1.79e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYF-KENDRGQLIMAPGTGKTFTSLKLVEKMAKQTNketfnVLYLVPSIQLLSQTLigwnndtelsmh 246
Cdd:COG1061 82 RPYQQEALEALLAALeRGGGRGLVVAPTGTGKTVLALALAAELLRGKR-----VLVLVPRRELLEQWA------------ 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 247 sfavtsdrnaskkkndDELSAKDIGFPATTDSekllsnykkienNQRDLTVVYSTYQSIeVLHEAQEKGFPEFDIIICDE 326
Cdd:COG1061 145 ----------------EELRRFLGDPLAGGGK------------KDSDAPITVATYQSL-ARRAHLDELGDRFGLVIIDE 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 327 AHRTTgakalgeeASVFTRVHNnnYIKASKRLYQTATPKiygtdakqkaedssivlsSMDNKDI----YGEEIFRLGFGQ 402
Cdd:COG1061 196 AHHAG--------APSYRRILE--AFPAAYRLGLTATPF------------------RSDGREIllflFDGIVYEYSLKE 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 403 AVSNDILTDYKVIVLAVDEKVIQKDMQKVLSDSENGLDVDDVskligvwnglMKRSSVDKDAVFEGKPMqRAISFINTIN 482
Cdd:COG1061 248 AIEDGYLAPPEYYGIRVDLTDERAEYDALSERLREALAADAE----------RKDKILRELLREHPDDR-KTLVFCSSVD 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 483 NSKKISSQFNEvvneyldgneiiqQSINVRHVDGMMNTLEKKEALDWlsedFAEDETRVLSNVKFLTEGIDVPNLDAVIF 562
Cdd:COG1061 317 HAEALAELLNE-------------AGIRAAVVTGDTPKKEREEILEA----FRDGELRILVTVDVLNEGVDVPRLDVAIL 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 563 LAPKKSQVDIVQAVGRIMRKFKDKEYGYIILpiVIPEGTTPESILDNNKKYEAVWQILNALRSVDERFSAMINKLELNRK 642
Cdd:COG1061 380 LRPTGSPREFIQRLGRGLRPAPGKEDALVYD--FVGNDVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEV 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 643 KPEnmDVIGIGEAPSVEDMENTSTIGEKDDAIYQTSLDLDWGEIENAIYAKVVKKVGDRRYLEDWSEDVAKIAQRHIEQI 722
Cdd:COG1061 458 KGE--LEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLL 535
|
570 580 590
....*....|....*....|....*....|.
gi 1106661688 723 TIMIKDKNSKTAIEFEKFLKSLQHNINESID 753
Cdd:COG1061 536 LELLELLAALLRLEELAALLLKELLRAALAA 566
|
|
| Mrr_cat_2 |
pfam13156 |
Restriction endonuclease; Prokaryotic family found in type II restriction enzymes containing ... |
34-158 |
3.44e-42 |
|
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: 150.89 E-value: 3.44e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 34 KNEPTYKNLFSDVWLLNEVPEEYAIPKKDTGVDLVARNEATGELTAIQAKFY--DNKIYKRHIDSFLAELGKSYYSDGII 111
Cdd:pfam13156 1 KTDPLYADEFDDVWLWKEWPTRKGLGGHDTGIDLVARTRDTGEYWAIQCKFYdpDHKIQKPDIDSFFSASGKSPFTDRLI 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1106661688 112 VYSLDSLSSNADEAINQLSKPVAQIGLSDLRNSQVAWESFIPSRPNE 158
Cdd:pfam13156 81 ISTTDKWSKNAEEALANQTIPVSRIGLADLAESPIDWSKLSPGAEGE 127
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
168-364 |
2.21e-25 |
|
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: 103.54 E-value: 2.21e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLtIDYFKENDRGQLIMAPGTGKTFTSLKLVEKMAKqtnketFNVLYLVPSIQLLSQTLIGWNNDTELSMhS 247
Cdd:cd17926 2 RPYQEEALEA-WLAHKNNRRGILVLPTGSGKTLTALALIAYLKE------LRTLIVVPTDALLDQWKERFEDFLGDSS-I 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 248 FAVTSDRNASKKKNDdelsakdigfpattdsekllsnykkiennqrdltVVYSTYQSIEVLHEAQEKGFPEFDIIICDEA 327
Cdd:cd17926 74 GLIGGGKKKDFDDAN----------------------------------VVVATYQSLSNLAEEEKDLFDQFGLLIVDEA 119
|
170 180 190
....*....|....*....|....*....|....*..
gi 1106661688 328 HRTTgakalgeeASVFTRVHnnNYIKASKRLYQTATP 364
Cdd:cd17926 120 HHLP--------AKTFSEIL--KELNAKYRLGLTATP 146
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
165-366 |
1.46e-22 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 95.82 E-value: 1.46e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 165 KKTRPYQNEAINLTIDYFKEND-RGQLIMAPGTGKTFTSLKLVEKMAKQTNKEtfNVLYLVPSIQLLSQTLigwNNDTEL 243
Cdd:pfam04851 2 LELRPYQIEAIENLLESIKNGQkRGLIVMATGSGKTLTAAKLIARLFKKGPIK--KVLFLVPRKDLLEQAL---EEFKKF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 244 SMhsfavtSDRNASKKKNDDElsakdigfpattdsekllsnyKKIENNQRDLTVvySTYQSI--EVLHEAQEKGFPEFDI 321
Cdd:pfam04851 77 LP------NYVEIGEIISGDK---------------------KDESVDDNKIVV--TTIQSLykALELASLELLPDFFDV 127
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 1106661688 322 IICDEAHRTTgakalgeeASVFTRVhnNNYIKASKRLYQTATPKI 366
Cdd:pfam04851 128 IIIDEAHRSG--------ASSYRNI--LEYFKPAFLLGLTATPER 162
|
|
| HsdM |
COG0286 |
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]; |
837-1094 |
4.53e-17 |
|
Type I restriction-modification system, DNA methylase subunit [Defense mechanisms];
Pssm-ID: 440055 [Multi-domain] Cd Length: 243 Bit Score: 82.54 E-value: 4.53e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 837 LYDKFFSKGFKETTQRLGIVFTPVEVVDFIVKSVDDvlkkhfgkaieDEGVHILDPFTGTGTFIVRTLHYLKDKLSNGEI 916
Cdd:COG0286 6 AYEYLLRKFAEESGKKAGEFYTPREVVRLMVELLDP-----------KPGETVYDPACGSGGFLVEAAEYLKEHGGDERK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 917 TLAdvtrkytqeLHANEIVLLSYYIAAINIestfaeINHEEYKPfeGIVLTDTFESteqEDTLDDSFfgtnderlkrqqe 996
Cdd:COG0286 75 KLS---------LYGQEINPTTYRLAKMNL------LLHGIGDP--NIELGDTLSN---DGDELEKF------------- 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 997 vpiTAIIGNPPYsiGQSNANDNNKNikyiNLNKRIEETYSKYSNANLNkglydsYIQ-AIRWasdrLGDSGVIGFITPNS 1075
Cdd:COG0286 122 ---DVVLANPPF--GGKWKKEELKD----DLLGRFGYGLPPKSNADLL------FLQhILSL----LKPGGRAAVVLPDG 182
|
250
....*....|....*....
gi 1106661688 1076 IIDKGSFDGFRKTLYEEFN 1094
Cdd:COG0286 183 VLFRGAEKEIRKKLLENDL 201
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
168-777 |
1.23e-15 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 82.58 E-value: 1.23e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYFKENDRGQLI-MAPGTGKTFTSLKLVEKMAKQTNKEtfNVLYLVpsiqllsqtligwnndtelsmh 246
Cdd:COG4096 160 RYYQIEAIRRVEEAIAKGQRRALLvMATGTGKTRTAIALIYRLLKAGRAK--RILFLA---------------------- 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 247 sfavtsDRNASKKKNDDELSAKDIGFPATTdseKLLSNYKKIENNQRdltVVYSTYQSI--EVLHEAQEKGFPE-----F 319
Cdd:COG4096 216 ------DRNALVDQAKNAFKPFLPDLDAFT---KLYNKSKDIDKSAR---VYFSTYQTMmnRIDGEEEEPGYRQfppdfF 283
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 320 DIIICDEAHRtTGAKALGEeasVFtrvhnnNYIKAskrlYQ---TATPKiygtdakqKAEDSsivlssmDNKDIY-GEEI 395
Cdd:COG4096 284 DLIIIDECHR-GIYSKWRA---IL------DYFDA----LQiglTATPK--------DTIDR-------NTYEYFnGNPV 334
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 396 FRLGFGQAVSNDILTDYKV--IVLAVDEKVIQKDMQKVLSDSENGL------------DVDDVSKLI-------GVWNGL 454
Cdd:COG4096 335 YTYSLEQAVADGFLVPYKVirIDTKFDREGIRYDAGEDLSDEEGEEieleeleedreyEAKDFNRKVvnedttrKVLEEL 414
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 455 MKRssVDKDavfEGKPMQRAISFINTINNSKKISSQFNEVVNEYldGNEIIQQsinvrhVDGmmntlEKKEALDWLsEDF 534
Cdd:COG4096 415 MEY--LDKP---GGDRLGKTIIFAKNDDHADRIVQALRELYPEL--GGDFVKK------ITG-----DDDYGKSLI-DNF 475
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 535 --AEDETRVLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRK----FKDKEYGYII-------------LPI 595
Cdd:COG4096 476 knPEKYPRIAVTVDMLDTGIDVPEVVNLVFMRPVKSRIKFEQMIGRGTRLcpdlFPGKTHFTIFdfvgntelfadpsFPL 555
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 596 VIPEGTTPEsildnnkkyEAVWQILNalrsvDERFSAMINKLeLNRKKPENMDVIGIGEApsvedmenTSTIGEKDDAIY 675
Cdd:COG4096 556 RIFEPRRER---------EKFWDLLG-----GEDPAKLAVHL-ADALDPDKVTIPVVAEA--------VQLLDDVPDLRD 612
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 676 QtsLDLDWGEIENAIYAKVVKKVGDRRyledWSEDVAKIAQRHIEqitimikdknsktaiEFEKFLKSLQHNINESI--- 752
Cdd:COG4096 613 L--LKFIDKDKRQIIYTDFEDELLEAE----EGYGKKLKAEDYRD---------------KFEAFLREHKEIPALQKlrn 671
|
650 660 670
....*....|....*....|....*....|
gi 1106661688 753 ----DEKQAIE-MLAQHLITAPIFEALFGE 777
Cdd:COG4096 672 rltrEDLKELEeELEEQGLGEEDLAEAYGE 701
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
168-392 |
3.52e-14 |
|
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: 71.82 E-value: 3.52e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYFKEN-DRGQLIMAPGTGKTFTSLKLVEKMAKQTNKEtfNVLYLVPSIQLLSQTligwnndtelsMH 246
Cdd:cd18032 2 RYYQQEAIEALEEAREKGqRRALLVMATGTGKTYTAAFLIKRLLEANRKK--RILFLAHREELLEQA-----------ER 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 247 SFavtsdrnaskKKNddeLSAKDIGfpattdsekllsnykKIENNQRDLT---VVYSTYQSI--EVLHEAQEKGFpeFDI 321
Cdd:cd18032 69 SF----------KEV---LPDGSFG---------------NLKGGKKKPDdarVVFATVQTLnkRKRLEKFPPDY--FDL 118
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1106661688 322 IICDEAHRTTgakalgeeASVFTRVHnnNYIKASKRLYQTATPKiygtdakqkaedssivlsSMDNKDIYG 392
Cdd:cd18032 119 IIIDEAHHAI--------ASSYRKIL--EYFEPAFLLGLTATPE------------------RTDGLDTYE 161
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
471-592 |
6.50e-12 |
|
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: 63.73 E-value: 6.50e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 471 MQRAISFINTINNSKKISSQFNEvvneyldgneiiqQSINVRHVDG---MMNTLEKKEALDWlsedFAEDETRVLSNVKF 547
Cdd:cd18799 6 EIKTLIFCVSIEHAEFMAEAFNE-------------AGIDAVALNSdysDRERGDEALILLF----FGELKPPILVTVDL 68
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 1106661688 548 LTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRKFKDKEYGYII 592
Cdd:cd18799 69 LTTGVDIPEVDNVVFLRPTESRTLFLQMLGRGLRLHEGKDFFTIL 113
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
541-595 |
3.32e-11 |
|
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: 60.41 E-value: 3.32e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1106661688 541 VLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRKFKDkeYGYIILPI 595
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKD--EGEVILFV 77
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
159-364 |
4.97e-11 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 63.67 E-value: 4.97e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 159 VKVKNVKKTRPYQNEAINLTIdyfkENDRGQLIMAP-GTGKTFTSLKLVEKMAKQTNKETfnVLYLVPSIQLLSQTLigw 237
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALL----SGLRDVILAAPtGSGKTLAALLPALEALKRGKGGR--VLVLVPTRELAEQWA--- 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 238 nndTELSmhsfavtsdrnaskkkndDELSAKDIGFPATTDSEKLLSNYKKIENNQRDltVVYSTYQSIEVLHEAQEKGFP 317
Cdd:smart00487 72 ---EELK------------------KLGPSLGLKVVGLYGGDSKREQLRKLESGKTD--ILVTTPGRLLDLLENDKLSLS 128
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1106661688 318 EFDIIICDEAHRTTGAKALGEEASVFTRVHNNNyikasKRLYQTATP 364
Cdd:smart00487 129 NVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNV-----QLLLLSATP 170
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
506-581 |
2.83e-09 |
|
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: 56.06 E-value: 2.83e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1106661688 506 QQSINVRHVDGMMNTLEKKEALdwlsEDFAEDETRVLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMR 581
Cdd:pfam00271 36 KEGIKVARLHGDLSQEEREEIL----EDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
509-582 |
1.95e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 52.98 E-value: 1.95e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1106661688 509 INVRHVDGMMNTLEKKEALDwlseDFAEDETRVLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRK 582
Cdd:smart00490 12 IKVARLHGGLSQEEREEILD----KFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81
|
|
| N6_Mtase |
pfam02384 |
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against ... |
838-1099 |
4.72e-06 |
|
N-6 DNA Methylase; Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.
Pssm-ID: 426749 [Multi-domain] Cd Length: 310 Bit Score: 50.40 E-value: 4.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 838 YDKFFSKGFKETTQRLGIVFTPVEVVDFIVKSVDDVLKKhfgkaiedegvHILDPFTGTGTFIVRTLHYLKDKL-SNGEI 916
Cdd:pfam02384 9 YEYLLRKFAPNAGKSGGEFFTPREVSKLIVELLDPKPGE-----------SIYDPACGSGGFLIQAEKFVKEHDgDTNDL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 917 TladvtrkytqeLHANEIVLLSYYIAAINIestfaeINHE-EYKPFeGIVLTDTFESTEQEDtlddsffgtnderlkrqq 995
Cdd:pfam02384 78 S-----------IYGQEKNPTTYRLARMNM------ILHGiEYDDF-HIRHGDTLTSPKFED------------------ 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 996 EVPITAIIGNPPYSIGQSNANDNNKNIKYinlnkRIEETYSKYSNANLnkglydSYIQAIRWAsdrLGDSGVIGFITPNS 1075
Cdd:pfam02384 122 DKKFDVVVANPPFSDKWDANDTLENDPRF-----RPAYGVAPKSNADL------AFLQHIIYY---LAPGGRAAVVLPNG 187
|
250 260
....*....|....*....|....*
gi 1106661688 1076 IIDKGSFDG-FRKTLYEEfNHIYSI 1099
Cdd:pfam02384 188 VLFRGGAEGkIRKALVDK-DLVETV 211
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
168-412 |
3.05e-05 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 48.79 E-value: 3.05e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYFKENDRGQLI-MAPGTGKTFTSLKLVEKMAKQtnkETFN-VLYLVPSIQLLSQTLiGWNNDTEL-S 244
Cdd:PRK11448 415 RYYQEDAIQAVEKAIVEGQREILLaMATGTGKTRTAIALMYRLLKA---KRFRrILFLVDRSALGEQAE-DAFKDTKIeG 490
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 245 MHSFAVTSD-RNASKKKNDDElsakdigfpattdsekllsnykkiennqrdlTVVY-STYQSI--EVLHEAQEKGFP--- 317
Cdd:PRK11448 491 DQTFASIYDiKGLEDKFPEDE-------------------------------TKVHvATVQGMvkRILYSDDPMDKPpvd 539
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 318 EFDIIICDEAHRttgAKALGEEAS---VFTRVHnNNYIKASKRLYQ---------TATPkiygtdAKQKAEdssivlssm 385
Cdd:PRK11448 540 QYDCIIVDEAHR---GYTLDKEMSegeLQFRDQ-LDYVSKYRRVLDyfdavkiglTATP------ALHTTE--------- 600
|
250 260
....*....|....*....|....*..
gi 1106661688 386 dnkdIYGEEIFRLGFGQAVSNDILTDY 412
Cdd:PRK11448 601 ----IFGEPVYTYSYREAVIDGYLIDH 623
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
165-377 |
3.81e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 46.27 E-value: 3.81e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 165 KKTRPYQNEAINLTIdyfkeNDRGQLIMAP-GTGKTFTSLKLVEK-MAKQTNKETFNVLYLVPSIQLLSQTLIGWNNDTE 242
Cdd:cd17927 1 FKPRNYQLELAQPAL-----KGKNTIICLPtGSGKTFVAVLICEHhLKKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 243 LSMHSFAVTSDRNASKkknddelsakdigfpattdseklLSNYKKIENNQrdltVVYSTYQSIE-VLHEAQEKGFPEFDI 321
Cdd:cd17927 76 RPGYKVTGLSGDTSEN-----------------------VSVEQIVESSD----VIIVTPQILVnDLKSGTIVSLSDFSL 128
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1106661688 322 IICDEAHRTTGAKALGEEASVFTRVHNNNYIKASKRLYQTATPKIYGTDAKQKAED 377
Cdd:cd17927 129 LVFDECHNTTKNHPYNEIMFRYLDQKLGSSGPLPQILGLTASPGVGGAKNTEEALE 184
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
472-593 |
1.81e-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: 1.81e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 472 QRAISFINTINNSKKIssqfnevVNEYLDGNEIIQQSINVRHVDGM----MNTLEKKEALdwlsEDFAEDETRVLSNVKF 547
Cdd:cd18801 31 TRVIIFSEFRDSAEEI-------VNFLSKIRPGIRATRFIGQASGKsskgMSQKEQKEVI----EQFRKGGYNVLVATSI 99
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 1106661688 548 LTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRkfkdKEYGYIIL 593
Cdd:cd18801 100 GEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR----KRQGRVVV 141
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
165-332 |
3.53e-04 |
|
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: 43.41 E-value: 3.53e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 165 KKTRPYQNEAINLTIdyfKENdrGQLIMAPGTGKTFTSLKLVEKMAKQTNKETFN---VLYLVPSIQLLSQ--TLIGWNN 239
Cdd:cd18034 1 FTPRSYQLELFEAAL---KRN--TIVVLPTGSGKTLIAVMLIKEMGELNRKEKNPkkrAVFLVPTVPLVAQqaEAIRSHT 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 240 DTELSMHSFAVTSDRNASKKKNDDelsakdigfpattdsekllsnykkIENNQrdltVVYSTYQsieVLHEAQEKGF--- 316
Cdd:cd18034 76 DLKVGEYSGEMGVDKWTKERWKEE------------------------LEKYD----VLVMTAQ---ILLDALRHGFlsl 124
|
170
....*....|....*.
gi 1106661688 317 PEFDIIICDEAHRTTG 332
Cdd:cd18034 125 SDINLLIFDECHHATG 140
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
168-334 |
2.39e-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: 41.06 E-value: 2.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYFKENDRGQLIM-------APGTGKTFTSLKLVEKMAKQTNKETfnVLYLVPSIQLLSQTligwnND 240
Cdd:cd18030 23 RYYQYYAVEAALERIKTATNKDGDKkggyiwhTQGSGKSLTMFKAAKLLIEDPKNPK--VVFVVDRKDLDYQT-----SS 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 241 TelsMHSFAVTSDRNASKKKNDDELSAKDIGFPATTDSEKLLSNYKKIENNqrdltvVYSTYQSIevlheaqekgfpefd 320
Cdd:cd18030 96 T---FSRFAAEDVVRANSTKELKELLKNLSGGIIVTTIQKFNNAVKEESKP------VLIYRKNI--------------- 151
|
170
....*....|....
gi 1106661688 321 IIICDEAHRTTGAK 334
Cdd:cd18030 152 VVIVDEAHRSQFGE 165
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
510-587 |
2.95e-03 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 41.92 E-value: 2.95e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1106661688 510 NVRHVDGMMNTlEKKEALDWLSEDfaEDETRVLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRKFKDKE 587
Cdd:PHA02558 370 KVYYVSGEVDT-EDRNEMKKIAEG--GKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKS 444
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
190-232 |
4.52e-03 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain] Cd Length: 121 Bit Score: 38.62 E-value: 4.52e-03
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 1106661688 190 LIMA-PGTGKTFTSLKLVEKMAKQTNKETFNVLYLVPSIQLLSQ 232
Cdd:cd17914 3 LIQGpPGTGKTRVLVKIVAALMQNKNGEPGRILLVTPTNKAAAQ 46
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
515-673 |
4.59e-03 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 41.78 E-value: 4.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 515 DGMMNTlEKKEALDwlseDFAEDETRVLSNVKFLTEGIDVPNLDAVIFLAPKKSQVDIVQAVGRIMRkfkdKEYGYIIlp 594
Cdd:PRK13766 405 KGMSQK-EQIEILD----KFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGR----QEEGRVV-- 473
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1106661688 595 IVIPEGTTPESILDNNKKYEAvwQILNALRSVderfSAMINKLELNRKKPENMDVIGIGEAPSVEDMENTSTIGEKDDA 673
Cdd:PRK13766 474 VLIAKGTRDEAYYWSSRRKEK--KMKEELKNL----KGILNKKLQELDEEQKGEEEEKDEQLSLDDFVKSKGKEEEEEE 546
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
168-364 |
8.91e-03 |
|
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: 39.09 E-value: 8.91e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 168 RPYQNEAINLTIDYFKENDRGQLIMAPGTGKTFTSLKLVEKMAKQtNKETFNVLYLVPsiqlLSqTLIGWNNDTE---LS 244
Cdd:cd17919 2 RPYQLEGLNFLLELYENGPGGILADEMGLGKTLQAIAFLAYLLKE-GKERGPVLVVCP----LS-VLENWEREFEkwtPD 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1106661688 245 MHSFAVTSDRNASKKKNDDELSAKdigfpattdsekllsnykkiennqRDLTVVysTYQSIEVLHEAQEKgfPEFDIIIC 324
Cdd:cd17919 76 LRVVVYHGSQRERAQIRAKEKLDK------------------------FDVVLT--TYETLRRDKASLRK--FRWDLVVV 127
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1106661688 325 DEAHRttgakaLGEEASVFTRVHNNnyIKASKRLYQTATP 364
Cdd:cd17919 128 DEAHR------LKNPKSQLSKALKA--LRAKRRLLLTGTP 159
|
|
| |
