|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
1-1016 |
0e+00 |
|
Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms];
Pssm-ID: 440375 [Multi-domain] Cd Length: 936 Bit Score: 734.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 1 MFNEQTVtENGIIDRLKGLsgvKWTYCHGENLPKQAQDIFVDE-WLKDALCSLNPDIgrQPDYADEVIYKLRGVVLearh 79
Cdd:COG0610 3 KFSEAAL-EQAIIELLQEL---GYEYLSGPDIAPEDESEVLLEdNLRAALERLNPGL--SDDEIERALRELTKPES---- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 80 TGLVKANENFQEWLMADKTLPFGKNGDHITINLIDFDNIENNHFVVAQQVHYIAAT-EVYFDIVLYVNGIPLVVGEVKTA 158
Cdd:COG0610 73 NGLLEANKGFYDLLRNGVKVEYDGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNyKRRPDVVLFVNGLPLVVIELKNP 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 159 TRpSVTWQDGAADFmggkKYYWKNVESFFVPNLLCFASEGKTFAYGAINARVKDWGPW---HNTELRDDILPGLASVLns 235
Cdd:COG0610 153 LT-QVTIKEAFNQI----QRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWkdgDGNDLNPDGITDLDYLI-- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 236 cESLLNPQTLLQLLESFALFSTVKTGkntppkRVKILPRYPQFEAAKQIVERVRR--GYPKKGLIWHFQGSGKSLLMLYA 313
Cdd:COG0610 226 -EGLLSKERLLDIIRNFIVFDEDEGG------LIKIVARYHQYFAVRKAVERVKEaeGDGKGGVIWHTQGSGKSLTMVFL 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 314 AKMLRADNALKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFKDIEIYDSNPNg 393
Cdd:COG0610 299 AQKLARLPDLDNPTVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELLESDSGGIIVTTIQKFPEALDEIKYPE- 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 394 LNNRDNIIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGIDRNTFKLFgaeedpGRYMSRYSYKQSIRDGATNP 473
Cdd:COG0610 378 LSDRKNIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVF------GDYIHTYTITQAIEDGATLP 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 474 VKFEPRLAELRVDRDAINEEFEQLATEnnLDEEEKAALSRRAGKLAIMLKSPRRMAAVSNDIAEHFTNHVMPKKMKGMVV 553
Cdd:COG0610 452 LLYEYRLAKLKLDKEKIDEEFDELTEG--LDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRPGKGKAMVV 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 554 VYDREACVQMY-----YLLGEKLGFDAVEVVM--NVDQAPVKVEEGGKKdklnkdwlkwhdelelpvkqvdferwqhida 626
Cdd:COG0610 530 TSSREAAVRYYeafdkLRPEWGYKPLKIAVVFsgSANDDPEELKEHGNK------------------------------- 578
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 627 eeQVQKDLIECFKDPEHPLQLIIVTAKLLTGFDAPICYCMYLDKPLRDHTLLQAMCRTNRLYEtdtvRKDMGLIIDYLGV 706
Cdd:COG0610 579 --EYEKDLAKRFKDPDDPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFP----GKPYGLIVDYRGI 652
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 707 FENLRTALA--YNPEEIEGVVEGIEAFKELLPLQLNKCLSFFP-GVDRSI----AGFEGIMAAQEC-LPTNEKRDEFAAS 778
Cdd:COG0610 653 FENLKKALAlySEEDGKEDVLTDPEEALEELKEALDELRALFPeGVDFSAfdptEKLEALDEAVERfLGDEEARKEFKKL 732
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 779 FGVLSKLWSAINPDPF-----LTPYRQDYKWLAQIYESVRPVGQTgaLVWAALGPETIKMIHEHTDINriRDDIDELVMD 853
Cdd:COG0610 733 FKELSRLYNLLSPDDEfgdleLEKYRDDVSFYLALRAKLRKLGEK--LDLKEYEEKIRQLLDEAIDLE--RKEIKPRIKQ 808
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 854 EhaiftltakeqeqrakrleidlmgrlrgshDPKFVALGERLEKLRQDYEAGVIKAIDWLKGLLDAAKDTVQAERETGER 933
Cdd:COG0610 809 N------------------------------PVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEE 858
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 934 PVTEAdnKQALTKLFLETRPEttpKLIGDVVEQIDKIVKATRFDGWQNSNSGPREIQKALLLTLAQFGLGKDKELFQKAY 1013
Cdd:COG0610 859 GLNEE--ELAFYDALAENLGD---EKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYPKQDEAVEEVY 933
|
...
gi 446403616 1014 GYI 1016
Cdd:COG0610 934 EQA 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
9-722 |
1.81e-132 |
|
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification]
Pssm-ID: 273028 [Multi-domain] Cd Length: 667 Bit Score: 415.26 E-value: 1.81e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 9 ENGIIDRLKGLSgvkWTYCHGenLPKQAQDIFVDEwLKDALCSLNPDIGrqPDYADEVIYKLRGvvlearHTGLVKANEN 88
Cdd:TIGR00348 5 EDLFIQRLKSLG---WEYLKG--SELNVEENEKQE-LIEALKIINDHIE--PERWDEVYKKITN------KGDLYETNKI 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 89 FQEWLMADKTLPFGKNGD-HITINLIDFDNIENNHFVVAQQVHYIAATEVYfDIVLYVNGIPLVVGEVKtatRPSVTWQD 167
Cdd:TIGR00348 71 FYDYIKNGVKIKESQKGEkKRIVKLIDFRNISQNIFQFANQVSFKGHNIRP-DVTLFVNGIPLVIIELK---KRSVTIRE 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 168 GAADFmggkKYYWKNVESFFVPNLLCFASEGKT--FAYGAINARVKDWGPWHNTELRDDI-LPGLAsvlnscESLLNPQT 244
Cdd:TIGR00348 147 AFNQI----KRYEKEIPELFKYVQIFVISNGTDtrYYTGSDEDDFDFTFNWKESDNKLIEdLKEFD------ILLLKKER 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 245 LLQLLESFALFSTvKTGKNTppkrvKILPRYPQFEAAKQIVERVRRG-YPK---KGLIWHFQGSGKSLLMLYAAKMLRAD 320
Cdd:TIGR00348 217 LLDFIRNFIIFDK-DTGLVT-----KPYQRYMQYRAVKKIVESITRKtWGKderGGLIWHTQGSGKTLTMLFAARKALEL 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 321 naLKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFkDIEIYDSNPNGLNNRDNI 400
Cdd:TIGR00348 291 --LKNPKVFFVVDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDDGGIIITTIQKF-DDKLKEEEEKFPVDRKEV 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 401 IVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGIDRNTFKLFGAEEdpGRYMSRYSYKQSIRDGATNPVKFEPRL 480
Cdd:TIGR00348 368 VVIFDEAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFAYVF--GRYLHRYFITDAIRDGLTVKIDYEDRL 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 481 AELRVDRDAINEEFEQLAT--ENNLDEEEKAALSRRAGKLAIMLKSPRRMAAVSNDIAEHFTNHVMPKKMKGMVVVYDRE 558
Cdd:TIGR00348 446 PEDHLDKKKLDAFFDEIFEllPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRY 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 559 ACVQMYYLLGEKL--GFDAVEVVMNVDQApvkveeggkkdklnkdwlkwhDELELPVKQVDFERWQHIDAEEQVQKDLIE 636
Cdd:TIGR00348 526 ACVEEKNALDEELneKFEASAIVMTGKES---------------------DDAEIRDYNKHIRTKFDKSDGFEIYYKDLE 584
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 637 CFKDPEhPLQLIIVTAKLLTGFDAPICYCMYLDKPLRDHTLLQAMCRTNRLYETDtvrKDMGLIIDYLGVFENLRTALA- 715
Cdd:TIGR00348 585 RFKKNE-NPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKD---KTFGLIVDYRGLEKSLIDALSl 660
|
....*..
gi 446403616 716 YNPEEIE 722
Cdd:TIGR00348 661 YGNEAIK 667
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
277-509 |
5.57e-86 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 275.85 E-value: 5.57e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 277 QFEAAKQIVERVRR-GYPKKGLIWHFQGSGKSLLMLYAAKMLRADnaLKNPTVLIVVDRRDLDSQINETFGGADVKNLIK 355
Cdd:pfam18766 2 QYFAVNKAVERVLEdGDRRGGVIWHTQGSGKSLTMVFLARKLRRE--LKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQ 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 356 VQSCKKLGEYIeQDSRGILITTIFKFKDIEIYDSNPngLNNRDNIIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTP 435
Cdd:pfam18766 80 AESRKDLRELL-RGSGGIIFTTIQKFGETPDEGFPV--LSDRRNIIVLVDEAHRSQYGGLAANMRDALPNAAFIGFTGTP 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446403616 436 ISGIDRNTFKLFgaeedpGRYMSRYSYKQSIRDGATNPVKFEPRLAELRVDRDAINEEFEQLaTEnNLDEEEKA 509
Cdd:pfam18766 157 ILKKDKNTRAVF------GDYIDTYTIQDAVEDGATVPILYEGRLAELELDDEALDEEFEEI-TE-DLEDEERE 222
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
245-462 |
9.38e-80 |
|
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: 258.70 E-value: 9.38e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 245 LLQLLESFALFSTVKtgkntppKRVKILPRYPQFEAAKQIVERVRR-----GYPKKGLIWHFQGSGKSLLMLYAAKMLRA 319
Cdd:cd18030 1 LLDVLRNFIVFDEDD-------DKTKKVARYYQYYAVEAALERIKTatnkdGDKKGGYIWHTQGSGKSLTMFKAAKLLIE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 320 DNalKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFKDIEIYDSNPNgLNNRDN 399
Cdd:cd18030 74 DP--KNPKVVFVVDRKDLDYQTSSTFSRFAAEDVVRANSTKELKELLKNLSGGIIVTTIQKFNNAVKEESKPV-LIYRKN 150
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446403616 400 IIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGI-DRNTFKLFgaeedpGRYMSRYSY 462
Cdd:cd18030 151 IVVIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIFKEgDKTTEKVF------GDYLHKYTI 208
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
273-447 |
4.94e-16 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 77.92 E-value: 4.94e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 273 PRYPQFEAAKQIVERVRRGypkkgLIWHFQGSGKSLLMLYAakMLRADNALKNPTVLIVVDRRDLDSQI----NETFGGA 348
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDV-----ILAAPTGSGKTLAALLP--ALEALKRGKGGRVLVLVPTRELAEQWaeelKKLGPSL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 349 DVKNLIKV--QSCKKLGEYIEQDSRGILITTIFKFKDieiyDSNPNGLNNRDNIIVLVDEAHRTQEGGLGEKMRWAL--- 423
Cdd:smart00487 82 GLKVVGLYggDSKREQLRKLESGKTDILVTTPGRLLD----LLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLkll 157
|
170 180
....*....|....*....|....*
gi 446403616 424 -PNAHFYGLTGTPISGIDRNTFKLF 447
Cdd:smart00487 158 pKNVQLLLLSATPPEEIENLLELFL 182
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
1-1016 |
0e+00 |
|
Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms];
Pssm-ID: 440375 [Multi-domain] Cd Length: 936 Bit Score: 734.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 1 MFNEQTVtENGIIDRLKGLsgvKWTYCHGENLPKQAQDIFVDE-WLKDALCSLNPDIgrQPDYADEVIYKLRGVVLearh 79
Cdd:COG0610 3 KFSEAAL-EQAIIELLQEL---GYEYLSGPDIAPEDESEVLLEdNLRAALERLNPGL--SDDEIERALRELTKPES---- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 80 TGLVKANENFQEWLMADKTLPFGKNGDHITINLIDFDNIENNHFVVAQQVHYIAAT-EVYFDIVLYVNGIPLVVGEVKTA 158
Cdd:COG0610 73 NGLLEANKGFYDLLRNGVKVEYDGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNyKRRPDVVLFVNGLPLVVIELKNP 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 159 TRpSVTWQDGAADFmggkKYYWKNVESFFVPNLLCFASEGKTFAYGAINARVKDWGPW---HNTELRDDILPGLASVLns 235
Cdd:COG0610 153 LT-QVTIKEAFNQI----QRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWkdgDGNDLNPDGITDLDYLI-- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 236 cESLLNPQTLLQLLESFALFSTVKTGkntppkRVKILPRYPQFEAAKQIVERVRR--GYPKKGLIWHFQGSGKSLLMLYA 313
Cdd:COG0610 226 -EGLLSKERLLDIIRNFIVFDEDEGG------LIKIVARYHQYFAVRKAVERVKEaeGDGKGGVIWHTQGSGKSLTMVFL 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 314 AKMLRADNALKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFKDIEIYDSNPNg 393
Cdd:COG0610 299 AQKLARLPDLDNPTVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELLESDSGGIIVTTIQKFPEALDEIKYPE- 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 394 LNNRDNIIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGIDRNTFKLFgaeedpGRYMSRYSYKQSIRDGATNP 473
Cdd:COG0610 378 LSDRKNIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVF------GDYIHTYTITQAIEDGATLP 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 474 VKFEPRLAELRVDRDAINEEFEQLATEnnLDEEEKAALSRRAGKLAIMLKSPRRMAAVSNDIAEHFTNHVMPKKMKGMVV 553
Cdd:COG0610 452 LLYEYRLAKLKLDKEKIDEEFDELTEG--LDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRPGKGKAMVV 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 554 VYDREACVQMY-----YLLGEKLGFDAVEVVM--NVDQAPVKVEEGGKKdklnkdwlkwhdelelpvkqvdferwqhida 626
Cdd:COG0610 530 TSSREAAVRYYeafdkLRPEWGYKPLKIAVVFsgSANDDPEELKEHGNK------------------------------- 578
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 627 eeQVQKDLIECFKDPEHPLQLIIVTAKLLTGFDAPICYCMYLDKPLRDHTLLQAMCRTNRLYEtdtvRKDMGLIIDYLGV 706
Cdd:COG0610 579 --EYEKDLAKRFKDPDDPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFP----GKPYGLIVDYRGI 652
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 707 FENLRTALA--YNPEEIEGVVEGIEAFKELLPLQLNKCLSFFP-GVDRSI----AGFEGIMAAQEC-LPTNEKRDEFAAS 778
Cdd:COG0610 653 FENLKKALAlySEEDGKEDVLTDPEEALEELKEALDELRALFPeGVDFSAfdptEKLEALDEAVERfLGDEEARKEFKKL 732
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 779 FGVLSKLWSAINPDPF-----LTPYRQDYKWLAQIYESVRPVGQTgaLVWAALGPETIKMIHEHTDINriRDDIDELVMD 853
Cdd:COG0610 733 FKELSRLYNLLSPDDEfgdleLEKYRDDVSFYLALRAKLRKLGEK--LDLKEYEEKIRQLLDEAIDLE--RKEIKPRIKQ 808
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 854 EhaiftltakeqeqrakrleidlmgrlrgshDPKFVALGERLEKLRQDYEAGVIKAIDWLKGLLDAAKDTVQAERETGER 933
Cdd:COG0610 809 N------------------------------PVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEE 858
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 934 PVTEAdnKQALTKLFLETRPEttpKLIGDVVEQIDKIVKATRFDGWQNSNSGPREIQKALLLTLAQFGLGKDKELFQKAY 1013
Cdd:COG0610 859 GLNEE--ELAFYDALAENLGD---EKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYPKQDEAVEEVY 933
|
...
gi 446403616 1014 GYI 1016
Cdd:COG0610 934 EQA 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
9-722 |
1.81e-132 |
|
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification]
Pssm-ID: 273028 [Multi-domain] Cd Length: 667 Bit Score: 415.26 E-value: 1.81e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 9 ENGIIDRLKGLSgvkWTYCHGenLPKQAQDIFVDEwLKDALCSLNPDIGrqPDYADEVIYKLRGvvlearHTGLVKANEN 88
Cdd:TIGR00348 5 EDLFIQRLKSLG---WEYLKG--SELNVEENEKQE-LIEALKIINDHIE--PERWDEVYKKITN------KGDLYETNKI 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 89 FQEWLMADKTLPFGKNGD-HITINLIDFDNIENNHFVVAQQVHYIAATEVYfDIVLYVNGIPLVVGEVKtatRPSVTWQD 167
Cdd:TIGR00348 71 FYDYIKNGVKIKESQKGEkKRIVKLIDFRNISQNIFQFANQVSFKGHNIRP-DVTLFVNGIPLVIIELK---KRSVTIRE 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 168 GAADFmggkKYYWKNVESFFVPNLLCFASEGKT--FAYGAINARVKDWGPWHNTELRDDI-LPGLAsvlnscESLLNPQT 244
Cdd:TIGR00348 147 AFNQI----KRYEKEIPELFKYVQIFVISNGTDtrYYTGSDEDDFDFTFNWKESDNKLIEdLKEFD------ILLLKKER 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 245 LLQLLESFALFSTvKTGKNTppkrvKILPRYPQFEAAKQIVERVRRG-YPK---KGLIWHFQGSGKSLLMLYAAKMLRAD 320
Cdd:TIGR00348 217 LLDFIRNFIIFDK-DTGLVT-----KPYQRYMQYRAVKKIVESITRKtWGKderGGLIWHTQGSGKTLTMLFAARKALEL 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 321 naLKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFkDIEIYDSNPNGLNNRDNI 400
Cdd:TIGR00348 291 --LKNPKVFFVVDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDDGGIIITTIQKF-DDKLKEEEEKFPVDRKEV 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 401 IVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGIDRNTFKLFGAEEdpGRYMSRYSYKQSIRDGATNPVKFEPRL 480
Cdd:TIGR00348 368 VVIFDEAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFAYVF--GRYLHRYFITDAIRDGLTVKIDYEDRL 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 481 AELRVDRDAINEEFEQLAT--ENNLDEEEKAALSRRAGKLAIMLKSPRRMAAVSNDIAEHFTNHVMPKKMKGMVVVYDRE 558
Cdd:TIGR00348 446 PEDHLDKKKLDAFFDEIFEllPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFKFKAMVVAISRY 525
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 559 ACVQMYYLLGEKL--GFDAVEVVMNVDQApvkveeggkkdklnkdwlkwhDELELPVKQVDFERWQHIDAEEQVQKDLIE 636
Cdd:TIGR00348 526 ACVEEKNALDEELneKFEASAIVMTGKES---------------------DDAEIRDYNKHIRTKFDKSDGFEIYYKDLE 584
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 637 CFKDPEhPLQLIIVTAKLLTGFDAPICYCMYLDKPLRDHTLLQAMCRTNRLYETDtvrKDMGLIIDYLGVFENLRTALA- 715
Cdd:TIGR00348 585 RFKKNE-NPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKD---KTFGLIVDYRGLEKSLIDALSl 660
|
....*..
gi 446403616 716 YNPEEIE 722
Cdd:TIGR00348 661 YGNEAIK 667
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
277-509 |
5.57e-86 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 275.85 E-value: 5.57e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 277 QFEAAKQIVERVRR-GYPKKGLIWHFQGSGKSLLMLYAAKMLRADnaLKNPTVLIVVDRRDLDSQINETFGGADVKNLIK 355
Cdd:pfam18766 2 QYFAVNKAVERVLEdGDRRGGVIWHTQGSGKSLTMVFLARKLRRE--LKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQ 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 356 VQSCKKLGEYIeQDSRGILITTIFKFKDIEIYDSNPngLNNRDNIIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTP 435
Cdd:pfam18766 80 AESRKDLRELL-RGSGGIIFTTIQKFGETPDEGFPV--LSDRRNIIVLVDEAHRSQYGGLAANMRDALPNAAFIGFTGTP 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446403616 436 ISGIDRNTFKLFgaeedpGRYMSRYSYKQSIRDGATNPVKFEPRLAELRVDRDAINEEFEQLaTEnNLDEEEKA 509
Cdd:pfam18766 157 ILKKDKNTRAVF------GDYIDTYTIQDAVEDGATVPILYEGRLAELELDDEALDEEFEEI-TE-DLEDEERE 222
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
245-462 |
9.38e-80 |
|
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: 258.70 E-value: 9.38e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 245 LLQLLESFALFSTVKtgkntppKRVKILPRYPQFEAAKQIVERVRR-----GYPKKGLIWHFQGSGKSLLMLYAAKMLRA 319
Cdd:cd18030 1 LLDVLRNFIVFDEDD-------DKTKKVARYYQYYAVEAALERIKTatnkdGDKKGGYIWHTQGSGKSLTMFKAAKLLIE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 320 DNalKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSRGILITTIFKFKDIEIYDSNPNgLNNRDN 399
Cdd:cd18030 74 DP--KNPKVVFVVDRKDLDYQTSSTFSRFAAEDVVRANSTKELKELLKNLSGGIIVTTIQKFNNAVKEESKPV-LIYRKN 150
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446403616 400 IIVLVDEAHRTQEGGLGEKMRWALPNAHFYGLTGTPISGI-DRNTFKLFgaeedpGRYMSRYSY 462
Cdd:cd18030 151 IVVIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIFKEgDKTTEKVF------GDYLHKYTI 208
|
|
| HsdR_N |
cd22332 |
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and ... |
8-250 |
5.70e-34 |
|
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and similar systems; The N-terminal endonuclease-like domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I belongs to a wider 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: 411736 [Multi-domain] Cd Length: 226 Bit Score: 130.47 E-value: 5.70e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 8 TENGIIDRLKGLsgvKWTYCHGENLPKQAQDIFVDEWLKDALCSLNPDIGRQPDYADEVIYKLRGVVLEARhtglvkane 87
Cdd:cd22332 5 LEEALIELLQEL---GYEYLPGPELERDKTEVLLEDNLREALERLNPDIPSGVPLTDNEFNQLLLELGRDV--------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 88 nfqewlMADKTLPFGKNGDHITINLIDFDNIENNHFVVAQQVHYIAATEVY-FDIVLYVNGIPLVVGEVKtatRPSVTWQ 166
Cdd:cd22332 73 ------TPLLTLDDDGGKEKTRVILIDFENPENNDFQVVNQFTVEGGKHNRrPDVVLFVNGLPLVVIELK---NPGVTIR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 167 DGAADFmggKKYYWKNV-ESFFVPNLLCFASEGKTFAYGAINARVKDWGPWHNTELRDDILPGLASVLNSCESLLNPQTL 245
Cdd:cd22332 144 EAYNQI---KRYYKEIFiPGLFKYNQLFVISNGTETRYGANTAPYERFNEWFTFDWADEDNEPITDLETFIKGLLSKERL 220
|
....*
gi 446403616 246 LQLLE 250
Cdd:cd22332 221 LDLIR 225
|
|
| SF2_C_EcoR124I-like |
cd18800 |
C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases; This ... |
645-704 |
5.64e-23 |
|
C-terminal helicase domain of EcoR124I 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 EcoR124I R protein. EcoR124I recognizes the sequence, 5'-GAAN(6)RTCG-3', and cleaves at random sites. 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: 350187 [Multi-domain] Cd Length: 82 Bit Score: 93.78 E-value: 5.64e-23
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 645 LQLIIVTAKLLTGFDAPICYCMYLDKPLRDHTLLQAMCRTNRLYETdtvRKDMGLIIDYL 704
Cdd:cd18800 26 LDLLIVVDMLLTGFDAPSLNTLYVDKPLKYHGLIQAIARVNRVYKD---EKEFGLIVDYR 82
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
270-436 |
2.96e-20 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 88.88 E-value: 2.96e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 270 KILPRYPQFEAAKQIVERVRRGyPKKGLIWHFQGSGKSLLMLYAAKMLRADNALKNptVLIVVDRRDLDSQINETF---G 346
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKNG-QKRGLIVMATGSGKTLTAAKLIARLFKKGPIKK--VLFLVPRKDLLEQALEEFkkfL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 347 GADVKNLIKVQSCKKLgeyIEQDSRGILITTIFKFKDIEIYDSNPNGLNNRDNIIvlVDEAHRTQegglGEKMRWAL--- 423
Cdd:pfam04851 78 PNYVEIGEIISGDKKD---ESVDDNKIVVTTIQSLYKALELASLELLPDFFDVII--IDEAHRSG----ASSYRNILeyf 148
|
170
....*....|...
gi 446403616 424 PNAHFYGLTGTPI 436
Cdd:pfam04851 149 KPAFLLGLTATPE 161
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
273-844 |
1.20e-18 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 90.85 E-value: 1.20e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 273 PRYPQFEAAKQIVERVRRGyPKKGLIwhfQ---GSGKSLLMLYAAKMLradnaLKNPTVLIVVDRRDLDSQINETFggAD 349
Cdd:COG1061 81 LRPYQQEALEALLAALERG-GGRGLV---VaptGTGKTVLALALAAEL-----LRGKRVLVLVPRRELLEQWAEEL--RR 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 350 VKNLIKVQSCKKlgeyieQDSRGILITTIFKFkdieIYDSNPNGLNNRDNIIVlVDEAHRTQEGGLGEKMRwALPNAHFY 429
Cdd:COG1061 150 FLGDPLAGGGKK------DSDAPITVATYQSL----ARRAHLDELGDRFGLVI-IDEAHHAGAPSYRRILE-AFPAAYRL 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 430 GLTGTPisgidrntFKLFGAEEDPGRYM---SRYSYKQSIRDGATNPVKFEPRLAELRVDRDAINEEFEQLATennldee 506
Cdd:COG1061 218 GLTATP--------FRSDGREILLFLFDgivYEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERLRE------- 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 507 ekaalsrragklAIMLKSPRRMAAVSNDIAEHftnhvmPKKMKGMVVVYDREACVQMYYLLGEKlGFDAVEVVMNVDQAp 586
Cdd:COG1061 283 ------------ALAADAERKDKILRELLREH------PDDRKTLVFCSSVDHAEALAELLNEA-GIRAAVVTGDTPKK- 342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 587 vkveeggkkdklnkdwlkwhdelelpvkqvdfERWQHIDAeeqvqkdliecFKDPEHPlqlIIVTAKLLT-GFDAPICYC 665
Cdd:COG1061 343 --------------------------------EREEILEA-----------FRDGELR---ILVTVDVLNeGVDVPRLDV 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 666 MYLDKPLRDHTL-LQAMCRTNRLYEtdtvRKDMGLIIDYLG--------VFENLRTALAYNPEEIEGVVEGIEAFKELLP 736
Cdd:COG1061 377 AILLRPTGSPREfIQRLGRGLRPAP----GKEDALVYDFVGndvpvleeLAKDLRDLAGYRVEFLDEEESEELALLIAVK 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 737 LQLNKCLSFFPGVDRSIAGFEGIMAAQECLPTNEKRDEFAASFGVLSKLWSAINPDPFLTPYRQDYKWLAQIYESVRPVG 816
Cdd:COG1061 453 PALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLL 532
|
570 580
....*....|....*....|....*...
gi 446403616 817 QTGALVWAALGPETIKMIHEHTDINRIR 844
Cdd:COG1061 533 LLLLELLELLAALLRLEELAALLLKELL 560
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
273-447 |
4.94e-16 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 77.92 E-value: 4.94e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 273 PRYPQFEAAKQIVERVRRGypkkgLIWHFQGSGKSLLMLYAakMLRADNALKNPTVLIVVDRRDLDSQI----NETFGGA 348
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDV-----ILAAPTGSGKTLAALLP--ALEALKRGKGGRVLVLVPTRELAEQWaeelKKLGPSL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 349 DVKNLIKV--QSCKKLGEYIEQDSRGILITTIFKFKDieiyDSNPNGLNNRDNIIVLVDEAHRTQEGGLGEKMRWAL--- 423
Cdd:smart00487 82 GLKVVGLYggDSKREQLRKLESGKTDILVTTPGRLLD----LLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLkll 157
|
170 180
....*....|....*....|....*
gi 446403616 424 -PNAHFYGLTGTPISGIDRNTFKLF 447
Cdd:smart00487 158 pKNVQLLLLSATPPEEIENLLELFL 182
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
273-435 |
4.07e-13 |
|
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: 67.72 E-value: 4.07e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 273 PRYPQFEAAKQIVervRRGYPKKGLIWHFQGSGKSLLMLYAAKmlradnALKNPTVLIVVDRRDLDSQINE---TFGGAD 349
Cdd:cd17926 1 LRPYQEEALEAWL---AHKNNRRGILVLPTGSGKTLTALALIA------YLKELRTLIVVPTDALLDQWKErfeDFLGDS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 350 VKNLIKVqsckklGEYIEQDSRGILITTIFKfkdIEIYDSNPNGLNNRDNIIVlVDEAHRTQegglGEKMRWALPNAHFY 429
Cdd:cd17926 72 SIGLIGG------GKKKDFDDANVVVATYQS---LSNLAEEEKDLFDQFGLLI-VDEAHHLP----AKTFSEILKELNAK 137
|
....*....
gi 446403616 430 ---GLTGTP 435
Cdd:cd17926 138 yrlGLTATP 146
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
273-447 |
9.15e-13 |
|
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: 67.20 E-value: 9.15e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 273 PRYPQFEAAKQIVERVRRGYpKKGLIWHFQGSGKSLLMLYAAKMLRADNALKNptVLIVVDRRDLDSQINETFGgadvKN 352
Cdd:cd18032 1 PRYYQQEAIEALEEAREKGQ-RRALLVMATGTGKTYTAAFLIKRLLEANRKKR--ILFLAHREELLEQAERSFK----EV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 353 LIKVQSCKKLGEYIEQDSRGILITTI---FKFKDIEIYDSNPNGLnnrdniiVLVDEAHRtqegGLGEKMRWALpnAHFY 429
Cdd:cd18032 74 LPDGSFGNLKGGKKKPDDARVVFATVqtlNKRKRLEKFPPDYFDL-------IIIDEAHH----AIASSYRKIL--EYFE 140
|
170 180
....*....|....*....|...
gi 446403616 430 -----GLTGTPISGIDRNTFKLF 447
Cdd:cd18032 141 pafllGLTATPERTDGLDTYELF 163
|
|
| HSDR_N |
pfam04313 |
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
119-209 |
2.02e-09 |
|
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
Pssm-ID: 427858 [Multi-domain] Cd Length: 151 Bit Score: 57.31 E-value: 2.02e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 119 ENNHFVVAQQVHYIAATEVYFDIVLYVNGIPLVVGEVKTatrpSVTWqDGAADFMGGKKYYWKNVESFFVPNL--LCFAS 196
Cdd:pfam04313 61 ENNSFQVANQVEVKGVQKRRPDYVLFVNGLPLAVIELKR----PGTE-EAINQIRRYEKDSFNAIPQLFRYANvqFGILS 135
|
90
....*....|...
gi 446403616 197 EGKTFAYGAINAR 209
Cdd:pfam04313 136 NGRETRFYTKTAK 148
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
271-736 |
1.36e-08 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 59.08 E-value: 1.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 271 ILPRYPQFEAAKQIVERVRRGYPKkGLIwhfQ---GSGK---SLLMLYaaKMLRADNAlKNptVLIVVDRRDLDSQINET 344
Cdd:COG4096 157 IALRYYQIEAIRRVEEAIAKGQRR-ALL---VmatGTGKtrtAIALIY--RLLKAGRA-KR--ILFLADRNALVDQAKNA 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 345 FGgadvKNLIKVQSCKKLGE---YIEQDSRgILITTIFKFKDIEIYDSNPNGLNNR-----DNIIVlvDEAHRtqeGGLG 416
Cdd:COG4096 228 FK----PFLPDLDAFTKLYNkskDIDKSAR-VYFSTYQTMMNRIDGEEEEPGYRQFppdffDLIII--DECHR---GIYS 297
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 417 eKMRWALpnAHF----YGLTGTPISGIDRNTFKLFGaeEDPgryMSRYSYKQSIRDGATNPvkFEPRLAELRVDRDAI-- 490
Cdd:COG4096 298 -KWRAIL--DYFdalqIGLTATPKDTIDRNTYEYFN--GNP---VYTYSLEQAVADGFLVP--YKVIRIDTKFDREGIry 367
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 491 -------NEEFEQLATENNLDEEE--KAALSRRagklaIMLKSPRRMaavsndIAEHFTNHV-------MPKKM------ 548
Cdd:COG4096 368 dagedlsDEEGEEIELEELEEDREyeAKDFNRK-----VVNEDTTRK------VLEELMEYLdkpggdrLGKTIifaknd 436
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 549 ---KGMvvvydREACVQMYyllgEKLGFDAVEVVMNvdqapvKVEEGgkkdklnkdwlkwhdelelpvkqvdferwqhid 625
Cdd:COG4096 437 dhaDRI-----VQALRELY----PELGGDFVKKITG------DDDYG--------------------------------- 468
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 626 aeeqvqKDLIECFKDPEHPLQlIIVTAKLL-TGFDAPICYCMYLDKPLRDHTLL-QAMCRTNRLYETDTVRKDMGLIIDY 703
Cdd:COG4096 469 ------KSLIDNFKNPEKYPR-IAVTVDMLdTGIDVPEVVNLVFMRPVKSRIKFeQMIGRGTRLCPDLFPGKTHFTIFDF 541
|
490 500 510
....*....|....*....|....*....|...
gi 446403616 704 LGVFENLRTalAYNPEEIEGVVEGIEAFKELLP 736
Cdd:COG4096 542 VGNTELFAD--PSFPLRIFEPRREREKFWDLLG 572
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
294-434 |
4.75e-04 |
|
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: 41.62 E-value: 4.75e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 294 KKGLIWHFQGSGKSLLmlyAAKMLRADNALKNPTVLIVVDRRDLDSQINETF-----GGADVKNLIKVQSCKKLGEYIEQ 368
Cdd:cd00046 2 ENVLITAPTGSGKTLA---ALLAALLLLLKKGKKVLVLVPTKALALQTAERLrelfgPGIRVAVLVGGSSAEEREKNKLG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446403616 369 DSRgILITTIFKFKDieiyDSNPNGLNNRDNIIVL-VDEAHRTQEGGLGEKM-----RWA-LPNAHFYGLTGT 434
Cdd:cd00046 79 DAD-IIIATPDMLLN----LLLREDRLFLKDLKLIiVDEAHALLIDSRGALIldlavRKAgLKNAQVILLSAT 146
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
303-441 |
1.21e-03 |
|
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: 40.69 E-value: 1.21e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446403616 303 GSGKSLL-MLYAAKMLraDNALKNPTVLIVVDRRDLDSQINETFGGADVKNLIKVQSCKKLGEYIEQDSR----GILITT 377
Cdd:pfam00270 24 GSGKTLAfLLPALEAL--DKLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGDSRKEQLEKlkgpDILVGT 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446403616 378 IFKFKDIEIydsNPNGLNNRDNIIVlvDEAHRTQEGGLGEKMRWAL----PNAHFYGLTGTPISGIDR 441
Cdd:pfam00270 102 PGRLLDLLQ---ERKLLKNLKLLVL--DEAHRLLDMGFGPDLEEILrrlpKKRQILLLSATLPRNLED 164
|
|
| |
