|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
1-1036 |
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: 1099.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 1 MITEQKLEDGSITWFQELGWQHVQGSSISPDgespartDYHQAVLRDRLLAALSRINPHVPATVLEQAIHELLTVSEPLL 80
Cdd:COG0610 3 KFSEAALEQAIIELLQELGYEYLSGPDIAPE-------DESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNGL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 81 IARNRRVHRLLLSGIPVEFsvGDEKRSDLVNLIDFAEPRNNDFLLVSQFTVSGTKQPRRPDLVAFVNGLPLAVIELKNPA 160
Cdd:COG0610 76 LEANKGFYDLLRNGVKVEY--DGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNPL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 161 NeQTDIWDAFNQIQTYKEEISDLFNANVAVVASDGFTARLGSLTANQERMQPWRAIANEDDRPLLAFELETLVRGFFEPA 240
Cdd:COG0610 154 T-QVTIKEAFNQIQRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWKDGDGNDLNPDGITDLDYLIEGLLSKE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 241 LFLDYVRHFVLFEQDADQIIKKIAGYHQFHAVREAVKATVIAAadntkvaeqratygrnvqpGSRKAGVVWHTQGSGKSI 320
Cdd:COG0610 233 RLLDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKEAE-------------------GDGKGGVIWHTQGSGKSL 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 321 TMACYAGKLLQQPQMKNPTLVVVTDRNDLDGQLYGTFCAAEdllRQTPVQAGSREELREMLaSREAGGIIFTTVQKFALL 400
Cdd:COG0610 294 TMVFLAQKLARLPDLDNPTVVVVTDRKDLDDQLFDTFKAFG---RESVVQAESRADLRELL-ESDSGGIIVTTIQKFPEA 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 401 DDEEQHPPLSDRSNIVVISDEAHRSQYGmkgrldtktgkyvfGYAKHLRDALTNATFIGFTGTPIAQEDKDTRAVFGDYV 480
Cdd:COG0610 370 LDEIKYPELSDRKNIIVIVDEAHRSQYG--------------GLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVFGDYI 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 481 SIYDIQDAVDDGATVPIYYESRLAKLDVNQAEIDAlnaQVDEVIEDEEDlTAREKAKSDWAALTKLVGAKPRLEQVAADL 560
Cdd:COG0610 436 HTYTITQAIEDGATLPLLYEYRLAKLKLDKEKIDE---EFDELTEGLDD-EEKEKLKAKWALLEEVLGAPERIEQIAEDI 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 561 VQHFETRTATLEGKAMIVCMSRDICAELYNAIIALRPDWHDADPErgaIKVVMTGSAADKP-LLQPHLNSQQvKKRLEKR 639
Cdd:COG0610 512 VEHFEERTRPGKGKAMVVTSSREAAVRYYEAFDKLRPEWGYKPLK---IAVVFSGSANDDPeELKEHGNKEY-EKDLAKR 587
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 640 FKDPADPLKLVIVRDMWLTGFDAPCCHTMYADKPMKGHNLMQAIARVNRVFRNKPGGLVVDYIGIANELKAALKTYTESK 719
Cdd:COG0610 588 FKDPDDPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFPGKPYGLIVDYRGIFENLKKALALYSEED 667
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 720 GKGNPAHNAAEALAVLLEKLDIVRGLM-HGFDYSGFE-TDAMQLLVPVANHILGLKDGKQRFLDAMLAVSKAFSLCNTLD 797
Cdd:COG0610 668 GKEDVLTDPEEALEELKEALDELRALFpEGVDFSAFDpTEKLEALDEAVERFLGDEEARKEFKKLFKELSRLYNLLSPDD 747
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 798 EAAALRTEIAFFAAIKAAIV--KFTTVDRKRSDADKNSALKQILDNAIVADgvadifalagldkpnigllsdefledvrq 875
Cdd:COG0610 748 EFGDLELEKYRDDVSFYLALraKLRKLGEKLDLKEYEEKIRQLLDEAIDLE----------------------------- 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 876 mksrnlavellekllRDEIKARARNNVVQEKKYGDRLLETLRKYHNRAVETAQVIEELIQMAKDFQEVLEREAALGLNQD 955
Cdd:COG0610 799 ---------------RKEIKPRIKQNPVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEE 863
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 956 EIAFYDALANNesaareLGDDILKKIAIEITEKLRNSTTVDWQVRESVRAKLRILVRRTLQKWKYPpdKQPEAVELVLKQ 1035
Cdd:COG0610 864 ELAFYDALAEN------LGDEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYP--KQDEAVEEVYEQ 935
|
.
gi 1248764712 1036 A 1036
Cdd:COG0610 936 A 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
4-721 |
0e+00 |
|
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: 545.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 4 EQKLEDGSITWFQELGWQHVQGSSISPDGEspartdyhqavLRDRLLAALSRINPHVPATVLEQAIHELltVSEPLLIAR 83
Cdd:TIGR00348 1 EEEVEDLFIQRLKSLGWEYLKGSELNVEEN-----------EKQELIEALKIINDHIEPERWDEVYKKI--TNKGDLYET 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 84 NRRVHRLLLSGIPVEFSVGDEKRsDLVNLIDFAEPRNNDFLLVSQFTVSGtkQPRRPDLVAFVNGLPLAVIELKNpanEQ 163
Cdd:TIGR00348 68 NKIFYDYIKNGVKIKESQKGEKK-RIVKLIDFRNISQNIFQFANQVSFKG--HNIRPDVTLFVNGIPLVIIELKK---RS 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 164 TDIWDAFNQIQTYKEEISDLFNANVAVVASDGFTAR--LGSLTANQERMQPWRAIANEDDRPLLAFELEtlvrgFFEPAL 241
Cdd:TIGR00348 142 VTIREAFNQIKRYEKEIPELFKYVQIFVISNGTDTRyyTGSDEDDFDFTFNWKESDNKLIEDLKEFDIL-----LLKKER 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 242 FLDYVRHFVLFEQDADQIIKKIAGYHQFHAVREAVKATviaaadntkvaeQRATYGRNvqpgsRKAGVVWHTQGSGKSIT 321
Cdd:TIGR00348 217 LLDFIRNFIIFDKDTGLVTKPYQRYMQYRAVKKIVESI------------TRKTWGKD-----ERGGLIWHTQGSGKTLT 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 322 MACYAGKLLqqPQMKNPTLVVVTDRNDLDGQLYGTFCAaedLLRQTPVQAGSREELREMLASREaGGIIFTTVQKFA--L 399
Cdd:TIGR00348 280 MLFAARKAL--ELLKNPKVFFVVDRRELDYQLMKEFQS---LQKDCAERIESIAELKELLEKDD-GGIIITTIQKFDdkL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 400 LDDEEQHPplSDRSNIVVISDEAHRSQYGMkgrldtktgkyvfgYAKHLRDALTNATFIGFTGTPIAQEDKDT----RAV 475
Cdd:TIGR00348 354 KEEEEKFP--VDRKEVVVIFDEAHRSQYGE--------------LAKNLKKALKNASFFGFTGTPIFKKDRDTsltfAYV 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 476 FGDYVSIYDIQDAVDDGATVPIYYESRLAKLDVNQAEIDALNAQVDEVIEDEEDLTAREKAKSDWAALTKLVGAKPRLEQ 555
Cdd:TIGR00348 418 FGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDKKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNEDRLES 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 556 VAADLVQHFETRTATLEGKAMIVCMSRDICAELYNAIIALRPDWHDAdpergaIKVVMTGSAADKPLL---QPHL----- 627
Cdd:TIGR00348 498 IAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEA------SAIVMTGKESDDAEIrdyNKHIrtkfd 571
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 628 --NSQQVKKRLEKRFKDPaDPLKLVIVRDMWLTGFDAPCCHTMYADKPMKGHNLMQAIARVNRV-FRNKPGGLVVDYIGI 704
Cdd:TIGR00348 572 ksDGFEIYYKDLERFKKN-ENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIdGKDKTFGLIVDYRGL 650
|
730
....*....|....*..
gi 1248764712 705 ANELKAALKTYTESKGK 721
Cdd:TIGR00348 651 EKSLIDALSLYGNEAIK 667
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
719-1041 |
6.22e-147 |
|
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313.
Pssm-ID: 432144 Cd Length: 331 Bit Score: 441.20 E-value: 6.22e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 719 KGKGNPAHNAAEALAVLLEKLDIVRGLMHGFDYSGFETD----AMQLLVPVANHILGLK-DGKQRFLDAMLAVSKAFSLC 793
Cdd:pfam11867 1 GGKGKPGEDIEEAVAVLLEKLEIVRGLFHGFDYSAFFTGdpkeRLQLLLAAAEHILSLEdDGKKRFLDLVKALSKAYALC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 794 NTLDEAAALRTEIAFFAAIKAAIVKFTTVDRKRS--DADKNSALKQILDNAIVADGVADIFALAGLDKPNIGLLSDEFLE 871
Cdd:pfam11867 81 APHDEADAIRDEIAFFQAVRAILVKLTATDRGGSpdTAEVNAAIRQLIDKAIVSEGVVDIFAAAGLEKPDISILSEEFLA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 872 DVRQMKSRNLAVELLEKLLRDEIKARARNNVVQEKKYGDRLLETLRKYHNRAVETAQVIEELIQMAKDFQEVLEREAALG 951
Cdd:pfam11867 161 EVKKMKQKNLAIELLRKLLNDEIKARSRTNLVQSKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 952 LNQDEIAFYDALANNESAARELGDDILKKIAIEITEKLRNSTTVDWQVRESVRAKLRILVRRTLQKWKYPPDKQPEAVEL 1031
Cdd:pfam11867 241 LSEEELAFYDALAENESAVEVMGDDKLKEIARELVETVRKNATVDWTKREDVRAKLRVAVKRLLRKYGYPPDKQEEAVEL 320
|
330
....*....|
gi 1248764712 1032 VLKQAESLSN 1041
Cdd:pfam11867 321 VLEQAELLAK 330
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
242-485 |
1.30e-79 |
|
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: 258.31 E-value: 1.30e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 242 FLDYVRHFVLFEQDaDQIIKKIAGYHQFHAVREAVKAtvIAAADNTKvaeqratygrnvqpGSRKAGVVWHTQGSGKSIT 321
Cdd:cd18030 1 LLDVLRNFIVFDED-DDKTKKVARYYQYYAVEAALER--IKTATNKD--------------GDKKGGYIWHTQGSGKSLT 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 322 MACYAGKLLQQPqmKNPTLVVVTDRNDLDGQLYGTFcaaEDLLRQTPVQAGSREELREmLASREAGGIIFTTVQKFALLD 401
Cdd:cd18030 64 MFKAAKLLIEDP--KNPKVVFVVDRKDLDYQTSSTF---SRFAAEDVVRANSTKELKE-LLKNLSGGIIVTTIQKFNNAV 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 402 DEEQHPPLSDRSNIVVISDEAHRSQYGmkgrldtktgkyvfGYAKHLRDALTNATFIGFTGTPI-AQEDKDTRAVFGDYV 480
Cdd:cd18030 138 KEESKPVLIYRKNIVVIVDEAHRSQFG--------------ELAKALKKALPNATFIGFTGTPIfKEGDKTTEKVFGDYL 203
|
....*
gi 1248764712 481 SIYDI 485
Cdd:cd18030 204 HKYTI 208
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
401-663 |
3.64e-06 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 51.11 E-value: 3.64e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 401 DDEEQHPPLSDRSNIVVisDEAHR----------SQYGMKGRLDtktgkYVFGYAKHLrDALtNATFIGFTGTPIaqedK 470
Cdd:PRK11448 530 DDPMDKPPVDQYDCIIV--DEAHRgytldkemseGELQFRDQLD-----YVSKYRRVL-DYF-DAVKIGLTATPA----L 596
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 471 DTRAVFGDYVSIYDIQDAVDDGATV----PIYYESRLAKLDVN---QAEIDALNAQVDEVI----EDEEDLtarekaksD 539
Cdd:PRK11448 597 HTTEIFGEPVYTYSYREAVIDGYLIdhepPIRIETRLSQEGIHfekGEEVEVINTQTGEIDlatlEDEVDF--------E 668
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 540 WAALTKLVGAKPRLEQVAADLVQHFEtrtATLEGKAMIVCMSRD----ICAELYNAIIALRPDWHDAdpergAIKVVmTG 615
Cdd:PRK11448 669 VEDFNRRVITESFNRVVCEELAKYLD---PTGEGKTLIFAATDAhadmVVRLLKEAFKKKYGQVEDD-----AVIKI-TG 739
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1248764712 616 SaADKPLlqphlnsqqvkkRLEKRFKDPADPlKLVIVRDMWLTGFDAP 663
Cdd:PRK11448 740 S-IDKPD------------QLIRRFKNERLP-NIVVTVDLLTTGIDVP 773
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
1-1036 |
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: 1099.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 1 MITEQKLEDGSITWFQELGWQHVQGSSISPDgespartDYHQAVLRDRLLAALSRINPHVPATVLEQAIHELLTVSEPLL 80
Cdd:COG0610 3 KFSEAALEQAIIELLQELGYEYLSGPDIAPE-------DESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNGL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 81 IARNRRVHRLLLSGIPVEFsvGDEKRSDLVNLIDFAEPRNNDFLLVSQFTVSGTKQPRRPDLVAFVNGLPLAVIELKNPA 160
Cdd:COG0610 76 LEANKGFYDLLRNGVKVEY--DGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNPL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 161 NeQTDIWDAFNQIQTYKEEISDLFNANVAVVASDGFTARLGSLTANQERMQPWRAIANEDDRPLLAFELETLVRGFFEPA 240
Cdd:COG0610 154 T-QVTIKEAFNQIQRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWKDGDGNDLNPDGITDLDYLIEGLLSKE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 241 LFLDYVRHFVLFEQDADQIIKKIAGYHQFHAVREAVKATVIAAadntkvaeqratygrnvqpGSRKAGVVWHTQGSGKSI 320
Cdd:COG0610 233 RLLDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKEAE-------------------GDGKGGVIWHTQGSGKSL 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 321 TMACYAGKLLQQPQMKNPTLVVVTDRNDLDGQLYGTFCAAEdllRQTPVQAGSREELREMLaSREAGGIIFTTVQKFALL 400
Cdd:COG0610 294 TMVFLAQKLARLPDLDNPTVVVVTDRKDLDDQLFDTFKAFG---RESVVQAESRADLRELL-ESDSGGIIVTTIQKFPEA 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 401 DDEEQHPPLSDRSNIVVISDEAHRSQYGmkgrldtktgkyvfGYAKHLRDALTNATFIGFTGTPIAQEDKDTRAVFGDYV 480
Cdd:COG0610 370 LDEIKYPELSDRKNIIVIVDEAHRSQYG--------------GLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVFGDYI 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 481 SIYDIQDAVDDGATVPIYYESRLAKLDVNQAEIDAlnaQVDEVIEDEEDlTAREKAKSDWAALTKLVGAKPRLEQVAADL 560
Cdd:COG0610 436 HTYTITQAIEDGATLPLLYEYRLAKLKLDKEKIDE---EFDELTEGLDD-EEKEKLKAKWALLEEVLGAPERIEQIAEDI 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 561 VQHFETRTATLEGKAMIVCMSRDICAELYNAIIALRPDWHDADPErgaIKVVMTGSAADKP-LLQPHLNSQQvKKRLEKR 639
Cdd:COG0610 512 VEHFEERTRPGKGKAMVVTSSREAAVRYYEAFDKLRPEWGYKPLK---IAVVFSGSANDDPeELKEHGNKEY-EKDLAKR 587
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 640 FKDPADPLKLVIVRDMWLTGFDAPCCHTMYADKPMKGHNLMQAIARVNRVFRNKPGGLVVDYIGIANELKAALKTYTESK 719
Cdd:COG0610 588 FKDPDDPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFPGKPYGLIVDYRGIFENLKKALALYSEED 667
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 720 GKGNPAHNAAEALAVLLEKLDIVRGLM-HGFDYSGFE-TDAMQLLVPVANHILGLKDGKQRFLDAMLAVSKAFSLCNTLD 797
Cdd:COG0610 668 GKEDVLTDPEEALEELKEALDELRALFpEGVDFSAFDpTEKLEALDEAVERFLGDEEARKEFKKLFKELSRLYNLLSPDD 747
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 798 EAAALRTEIAFFAAIKAAIV--KFTTVDRKRSDADKNSALKQILDNAIVADgvadifalagldkpnigllsdefledvrq 875
Cdd:COG0610 748 EFGDLELEKYRDDVSFYLALraKLRKLGEKLDLKEYEEKIRQLLDEAIDLE----------------------------- 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 876 mksrnlavellekllRDEIKARARNNVVQEKKYGDRLLETLRKYHNRAVETAQVIEELIQMAKDFQEVLEREAALGLNQD 955
Cdd:COG0610 799 ---------------RKEIKPRIKQNPVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEE 863
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 956 EIAFYDALANNesaareLGDDILKKIAIEITEKLRNSTTVDWQVRESVRAKLRILVRRTLQKWKYPpdKQPEAVELVLKQ 1035
Cdd:COG0610 864 ELAFYDALAEN------LGDEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYP--KQDEAVEEVYEQ 935
|
.
gi 1248764712 1036 A 1036
Cdd:COG0610 936 A 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
4-721 |
0e+00 |
|
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: 545.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 4 EQKLEDGSITWFQELGWQHVQGSSISPDGEspartdyhqavLRDRLLAALSRINPHVPATVLEQAIHELltVSEPLLIAR 83
Cdd:TIGR00348 1 EEEVEDLFIQRLKSLGWEYLKGSELNVEEN-----------EKQELIEALKIINDHIEPERWDEVYKKI--TNKGDLYET 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 84 NRRVHRLLLSGIPVEFSVGDEKRsDLVNLIDFAEPRNNDFLLVSQFTVSGtkQPRRPDLVAFVNGLPLAVIELKNpanEQ 163
Cdd:TIGR00348 68 NKIFYDYIKNGVKIKESQKGEKK-RIVKLIDFRNISQNIFQFANQVSFKG--HNIRPDVTLFVNGIPLVIIELKK---RS 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 164 TDIWDAFNQIQTYKEEISDLFNANVAVVASDGFTAR--LGSLTANQERMQPWRAIANEDDRPLLAFELEtlvrgFFEPAL 241
Cdd:TIGR00348 142 VTIREAFNQIKRYEKEIPELFKYVQIFVISNGTDTRyyTGSDEDDFDFTFNWKESDNKLIEDLKEFDIL-----LLKKER 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 242 FLDYVRHFVLFEQDADQIIKKIAGYHQFHAVREAVKATviaaadntkvaeQRATYGRNvqpgsRKAGVVWHTQGSGKSIT 321
Cdd:TIGR00348 217 LLDFIRNFIIFDKDTGLVTKPYQRYMQYRAVKKIVESI------------TRKTWGKD-----ERGGLIWHTQGSGKTLT 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 322 MACYAGKLLqqPQMKNPTLVVVTDRNDLDGQLYGTFCAaedLLRQTPVQAGSREELREMLASREaGGIIFTTVQKFA--L 399
Cdd:TIGR00348 280 MLFAARKAL--ELLKNPKVFFVVDRRELDYQLMKEFQS---LQKDCAERIESIAELKELLEKDD-GGIIITTIQKFDdkL 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 400 LDDEEQHPplSDRSNIVVISDEAHRSQYGMkgrldtktgkyvfgYAKHLRDALTNATFIGFTGTPIAQEDKDT----RAV 475
Cdd:TIGR00348 354 KEEEEKFP--VDRKEVVVIFDEAHRSQYGE--------------LAKNLKKALKNASFFGFTGTPIFKKDRDTsltfAYV 417
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 476 FGDYVSIYDIQDAVDDGATVPIYYESRLAKLDVNQAEIDALNAQVDEVIEDEEDLTAREKAKSDWAALTKLVGAKPRLEQ 555
Cdd:TIGR00348 418 FGRYLHRYFITDAIRDGLTVKIDYEDRLPEDHLDKKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNEDRLES 497
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 556 VAADLVQHFETRTATLEGKAMIVCMSRDICAELYNAIIALRPDWHDAdpergaIKVVMTGSAADKPLL---QPHL----- 627
Cdd:TIGR00348 498 IAKDIAEHYAKFKELFKFKAMVVAISRYACVEEKNALDEELNEKFEA------SAIVMTGKESDDAEIrdyNKHIrtkfd 571
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 628 --NSQQVKKRLEKRFKDPaDPLKLVIVRDMWLTGFDAPCCHTMYADKPMKGHNLMQAIARVNRV-FRNKPGGLVVDYIGI 704
Cdd:TIGR00348 572 ksDGFEIYYKDLERFKKN-ENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIdGKDKTFGLIVDYRGL 650
|
730
....*....|....*..
gi 1248764712 705 ANELKAALKTYTESKGK 721
Cdd:TIGR00348 651 EKSLIDALSLYGNEAIK 667
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
719-1041 |
6.22e-147 |
|
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313.
Pssm-ID: 432144 Cd Length: 331 Bit Score: 441.20 E-value: 6.22e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 719 KGKGNPAHNAAEALAVLLEKLDIVRGLMHGFDYSGFETD----AMQLLVPVANHILGLK-DGKQRFLDAMLAVSKAFSLC 793
Cdd:pfam11867 1 GGKGKPGEDIEEAVAVLLEKLEIVRGLFHGFDYSAFFTGdpkeRLQLLLAAAEHILSLEdDGKKRFLDLVKALSKAYALC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 794 NTLDEAAALRTEIAFFAAIKAAIVKFTTVDRKRS--DADKNSALKQILDNAIVADGVADIFALAGLDKPNIGLLSDEFLE 871
Cdd:pfam11867 81 APHDEADAIRDEIAFFQAVRAILVKLTATDRGGSpdTAEVNAAIRQLIDKAIVSEGVVDIFAAAGLEKPDISILSEEFLA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 872 DVRQMKSRNLAVELLEKLLRDEIKARARNNVVQEKKYGDRLLETLRKYHNRAVETAQVIEELIQMAKDFQEVLEREAALG 951
Cdd:pfam11867 161 EVKKMKQKNLAIELLRKLLNDEIKARSRTNLVQSKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 952 LNQDEIAFYDALANNESAARELGDDILKKIAIEITEKLRNSTTVDWQVRESVRAKLRILVRRTLQKWKYPPDKQPEAVEL 1031
Cdd:pfam11867 241 LSEEELAFYDALAENESAVEVMGDDKLKEIARELVETVRKNATVDWTKREDVRAKLRVAVKRLLRKYGYPPDKQEEAVEL 320
|
330
....*....|
gi 1248764712 1032 VLKQAESLSN 1041
Cdd:pfam11867 321 VLEQAELLAK 330
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
267-528 |
2.18e-114 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 352.12 E-value: 2.18e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 267 HQFHAVREAVKATViaaadntkvaeqratygrnvQPGSRKAGVVWHTQGSGKSITMACYAGKLLQQpqMKNPTLVVVTDR 346
Cdd:pfam18766 1 QQYFAVNKAVERVL--------------------EDGDRRGGVIWHTQGSGKSLTMVFLARKLRRE--LKNPTVVVVTDR 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 347 NDLDGQLYGTFCAAedlLRQTPVQAGSREELREMLasREAGGIIFTTVQKFALLDDEEqHPPLSDRSNIVVISDEAHRSQ 426
Cdd:pfam18766 59 NDLDDQLTKTFAAC---GREVPVQAESRKDLRELL--RGSGGIIFTTIQKFGETPDEG-FPVLSDRRNIIVLVDEAHRSQ 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 427 YGmkgrldtktgkyvfGYAKHLRDALTNATFIGFTGTPIAQEDKDTRAVFGDYVSIYDIQDAVDDGATVPIYYESRLAKL 506
Cdd:pfam18766 133 YG--------------GLAANMRDALPNAAFIGFTGTPILKKDKNTRAVFGDYIDTYTIQDAVEDGATVPILYEGRLAEL 198
|
250 260
....*....|....*....|..
gi 1248764712 507 DVNQAEIDALNAQVDEVIEDEE 528
Cdd:pfam18766 199 ELDDEALDEEFEEITEDLEDEE 220
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
242-485 |
1.30e-79 |
|
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: 258.31 E-value: 1.30e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 242 FLDYVRHFVLFEQDaDQIIKKIAGYHQFHAVREAVKAtvIAAADNTKvaeqratygrnvqpGSRKAGVVWHTQGSGKSIT 321
Cdd:cd18030 1 LLDVLRNFIVFDED-DDKTKKVARYYQYYAVEAALER--IKTATNKD--------------GDKKGGYIWHTQGSGKSLT 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 322 MACYAGKLLQQPqmKNPTLVVVTDRNDLDGQLYGTFcaaEDLLRQTPVQAGSREELREmLASREAGGIIFTTVQKFALLD 401
Cdd:cd18030 64 MFKAAKLLIEDP--KNPKVVFVVDRKDLDYQTSSTF---SRFAAEDVVRANSTKELKE-LLKNLSGGIIVTTIQKFNNAV 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 402 DEEQHPPLSDRSNIVVISDEAHRSQYGmkgrldtktgkyvfGYAKHLRDALTNATFIGFTGTPI-AQEDKDTRAVFGDYV 480
Cdd:cd18030 138 KEESKPVLIYRKNIVVIVDEAHRSQFG--------------ELAKALKKALPNATFIGFTGTPIfKEGDKTTEKVFGDYL 203
|
....*
gi 1248764712 481 SIYDI 485
Cdd:cd18030 204 HKYTI 208
|
|
| HsdR_N |
cd22332 |
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and ... |
3-248 |
6.30e-59 |
|
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: 201.73 E-value: 6.30e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 3 TEQKLEDGSITWFQELGWQHVQGSSISpdgesparTDYHQAVLRDRLLAALSRINPHVPATVLeqaihelLTVSEpllia 82
Cdd:cd22332 1 TESQLEEALIELLQELGYEYLPGPELE--------RDKTEVLLEDNLREALERLNPDIPSGVP-------LTDNE----- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 83 RNRRVHRLLLSGIPVEF-SVGDEKRSDLVNLIDFAEPRNNDFLLVSQFTVSGTKQPRRPDLVAFVNGLPLAVIELKNPan 161
Cdd:cd22332 61 FNQLLLELGRDVTPLLTlDDDGGKEKTRVILIDFENPENNDFQVVNQFTVEGGKHNRRPDVVLFVNGLPLVVIELKNP-- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 162 eQTDIWDAFNQIQTYKEE--ISDLFNANVAVVASDGFTARLGSLTANQERMQPWRAIANEDDRPLLAFELETLVRGFFEP 239
Cdd:cd22332 139 -GVTIREAYNQIKRYYKEifIPGLFKYNQLFVISNGTETRYGANTAPYERFNEWFTFDWADEDNEPITDLETFIKGLLSK 217
|
....*....
gi 1248764712 240 ALFLDYVRH 248
Cdd:cd22332 218 ERLLDLIRN 226
|
|
| SF2_C_EcoR124I-like |
cd18800 |
C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases; This ... |
574-701 |
1.38e-31 |
|
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: 118.05 E-value: 1.38e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 574 KAMIVCMSRDICAELYNAIIalrpdwhdadpergaikvvmtgsaadkpllqphlnsqqvkkrlekrfkdpadplkLVIVR 653
Cdd:cd18800 8 KAMVVTSSRRAAVRYYKALD-------------------------------------------------------LLIVV 32
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1248764712 654 DMWLTGFDAPCCHTMYADKPMKGHNLMQAIARVNRVFRN-KPGGLVVDY 701
Cdd:cd18800 33 DMLLTGFDAPSLNTLYVDKPLKYHGLIQAIARVNRVYKDeKEFGLIVDY 81
|
|
| HSDR_N |
pfam04313 |
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
81-209 |
2.50e-22 |
|
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: 94.29 E-value: 2.50e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 81 IARNRRVHRLLLSGIPVEFSVGDekrsdlvnlidfaeprNNDFLLVSQFTVSGTkQPRRPDLVAFVNGLPLAVIELKNPA 160
Cdd:pfam04313 39 LDGNEAFYRLLKYGVTDGITKTE----------------NNSFQVANQVEVKGV-QKRRPDYVLFVNGLPLAVIELKRPG 101
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 1248764712 161 NeqtdiWDAFNQIQTYKEE----ISDLFNANVA--VVASDGFTARLGSLTANQER 209
Cdd:pfam04313 102 T-----EEAINQIRRYEKDsfnaIPQLFRYANVqfGILSNGRETRFYTKTAKENR 151
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
305-465 |
4.83e-18 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 82.33 E-value: 4.83e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 305 RKAGVVWHTQGSGKSITMACYAGKLLQQPQMKNpTLVVVtDRNDLDGQLYGTFcaaedlLRQTPVQAGSREEL--REMLA 382
Cdd:pfam04851 23 QKRGLIVMATGSGKTLTAAKLIARLFKKGPIKK-VLFLV-PRKDLLEQALEEF------KKFLPNYVEIGEIIsgDKKDE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 383 SREAGGIIFTTVQKFALLDDEEQHPPLSDRsNIVVISDEAHRSQYGMkgrldtktgkyvfgyAKHLRDALTNATFIGFTG 462
Cdd:pfam04851 95 SVDDNKIVVTTIQSLYKALELASLELLPDF-FDVIIIDEAHRSGASS---------------YRNILEYFKPAFLLGLTA 158
|
...
gi 1248764712 463 TPI 465
Cdd:pfam04851 159 TPE 161
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
315-712 |
1.06e-15 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 81.61 E-value: 1.06e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 315 GSGKSITMAcyagKLLQQPQMKNPTLVVVTDRndldgqlygtfcaaeDLLRQTpvqagsREELREMLASREAGG------ 388
Cdd:COG1061 110 GTGKTVLAL----ALAAELLRGKRVLVLVPRR---------------ELLEQW------AEELRRFLGDPLAGGgkkdsd 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 389 --IIFTTVQKFALLDDEEQhppLSDRSNIVVIsDEAHRSQygmkgrldtkTGKYvfgyaKHLRDALTNATFIGFTGTPIA 466
Cdd:COG1061 165 apITVATYQSLARRAHLDE---LGDRFGLVII-DEAHHAG----------APSY-----RRILEAFPAAYRLGLTATPFR 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 467 QEDKDTRAV-FGDYVSIYDIQDAVDDGATVPIYYESRLAKLDVNQAEIDALNAQVDEViedeedLTAREKAKsdwaaltk 545
Cdd:COG1061 226 SDGREILLFlFDGIVYEYSLKEAIEDGYLAPPEYYGIRVDLTDERAEYDALSERLREA------LAADAERK-------- 291
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 546 lvgakprLEQVAADLVQHFETRtatlegKAMIVCMSRDICAELYNAIialrpdwhdadPERGAIKVVMTGSaadkpllqp 625
Cdd:COG1061 292 -------DKILRELLREHPDDR------KTLVFCSSVDHAEALAELL-----------NEAGIRAAVVTGD--------- 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 626 hlNSQQVKKRLEKRFKDpaDPLKLVIVRDMWLTGFDAPCCHTMYADKPMKGHNLM-QAIARVNRVFRNKPGGLVVDYIGI 704
Cdd:COG1061 339 --TPKKEREEILEAFRD--GELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFiQRLGRGLRPAPGKEDALVYDFVGN 414
|
....*...
gi 1248764712 705 ANELKAAL 712
Cdd:COG1061 415 DVPVLEEL 422
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
389-919 |
4.10e-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: 4.10e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 389 IIFTTVQKFA-LLDDEEQHPPLSDRSN-----IVVisDEAHRSQYgmkgrldtktGKY--VFGYakhlrdalTNATFIGF 460
Cdd:COG4096 254 VYFSTYQTMMnRIDGEEEEPGYRQFPPdffdlIII--DECHRGIY----------SKWraILDY--------FDALQIGL 313
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 461 TGTPIAQEDKDTRAVF-GDYVSIYDIQDAVDDGATVP--------------IYYESRLAKLDVNQAEIDalnaqvDEVIE 525
Cdd:COG4096 314 TATPKDTIDRNTYEYFnGNPVYTYSLEQAVADGFLVPykviridtkfdregIRYDAGEDLSDEEGEEIE------LEELE 387
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 526 DEEDLTArekaksdwAALTKLVGAKPRLEQVAADLVQHFETRTATLEGKAMIVCMS-------RDICAELYnaiialrPD 598
Cdd:COG4096 388 EDREYEA--------KDFNRKVVNEDTTRKVLEELMEYLDKPGGDRLGKTIIFAKNddhadriVQALRELY-------PE 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 599 WHDAdpergAIKVVmTGSAADkpllqphlnsqqvKKRLEKRFKDPADPLKLVIVRDMWLTGFDAP-CCHTMYaDKPMKGH 677
Cdd:COG4096 453 LGGD-----FVKKI-TGDDDY-------------GKSLIDNFKNPEKYPRIAVTVDMLDTGIDVPeVVNLVF-MRPVKSR 512
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 678 NL-MQAIARVNRVFRNKPGG----LVVDYIGIanelKAALKTYTES--KGKGNPAHNAAEALAVLLEKLDIVRGLMHGFD 750
Cdd:COG4096 513 IKfEQMIGRGTRLCPDLFPGkthfTIFDFVGN----TELFADPSFPlrIFEPRREREKFWDLLGGEDPAKLAVHLADALD 588
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 751 YSGFE----TDAMQLLVPVANHILGLKDGKQRFLDAMLAVSKAFSLCNTLDEAAALRTEIAFFAAIK--AAIVKFTTVD- 823
Cdd:COG4096 589 PDKVTipvvAEAVQLLDDVPDLRDLLKFIDKDKRQIIYTDFEDELLEAEEGYGKKLKAEDYRDKFEAflREHKEIPALQk 668
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 824 -RKRSDADKNSALKQILD-NAIVADGVADIFALAGLDKPNIGLLsdefledVRQmksrnlAVELLEKLL-RDEIKARARN 900
Cdd:COG4096 669 lRNRLTREDLKELEEELEeQGLGEEDLAEAYGEVGNELADLIDL-------IRH------IAGLDQPLLtRRERVERAFK 735
|
570 580
....*....|....*....|..
gi 1248764712 901 NVVQEKKYGD---RLLETLRKY 919
Cdd:COG4096 736 RFLAGHKYTEeqrEFLERILDH 757
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
308-464 |
1.81e-08 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 54.23 E-value: 1.81e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 308 GVVWHTQGSGKSITMACYAGKLlqqpqMKNPTLVVVtDRNDLDGQLYGTFcaaEDLLRQTPV---QAGSREELREMLasr 384
Cdd:cd17926 21 GILVLPTGSGKTLTALALIAYL-----KELRTLIVV-PTDALLDQWKERF---EDFLGDSSIgliGGGKKKDFDDAN--- 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 385 eaggIIFTTVQKfaLLDDEEQHPPLSDRsNIVVISDEAHrsqygmkgRLDTKTGKYVFGYAKHLRdaltnatFIGFTGTP 464
Cdd:cd17926 89 ----VVVATYQS--LSNLAEEEKDLFDQ-FGLLIVDEAH--------HLPAKTFSEILKELNAKY-------RLGLTATP 146
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
300-476 |
2.68e-08 |
|
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: 54.10 E-value: 2.68e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 300 VQPGSRKAGVVWHTqGSGKSITmACYAGKLLQQPQMKNPTLVVVtDRNDLDGQLYGTFcaaedllrQTPVQAGSREELRE 379
Cdd:cd18032 16 REKGQRRALLVMAT-GTGKTYT-AAFLIKRLLEANRKKRILFLA-HREELLEQAERSF--------KEVLPDGSFGNLKG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 380 MLASREAGGIIFTTVQKFALLDDEEQHPPlsDRSNIVVIsDEAHRSQYGMKGRLdtktgkyvfgyAKHLRDAltnaTFIG 459
Cdd:cd18032 85 GKKKPDDARVVFATVQTLNKRKRLEKFPP--DYFDLIII-DEAHHAIASSYRKI-----------LEYFEPA----FLLG 146
|
170
....*....|....*..
gi 1248764712 460 FTGTPIAQEDKDTRAVF 476
Cdd:cd18032 147 LTATPERTDGLDTYELF 163
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
306-463 |
2.49e-06 |
|
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: 48.17 E-value: 2.49e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 306 KAGVVWHTQGSGKSItmaCYAGKLLQQPQMKNPTLVVVTDRNDLDGQLYGTFCAAEDL-LRQTPVQAGSREELREMLASR 384
Cdd:cd00046 2 ENVLITAPTGSGKTL---AALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGPgIRVAVLVGGSSAEEREKNKLG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1248764712 385 EAGgIIFTTVQKfaLLDDEEQHPPLSDRSNIVVISDEAHRSQYGMKGRLDtktgkyvfGYAKHLRDALTNATFIGFTGT 463
Cdd:cd00046 79 DAD-IIIATPDM--LLNLLLREDRLFLKDLKLIIVDEAHALLIDSRGALI--------LDLAVRKAGLKNAQVILLSAT 146
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
401-663 |
3.64e-06 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 51.11 E-value: 3.64e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 401 DDEEQHPPLSDRSNIVVisDEAHR----------SQYGMKGRLDtktgkYVFGYAKHLrDALtNATFIGFTGTPIaqedK 470
Cdd:PRK11448 530 DDPMDKPPVDQYDCIIV--DEAHRgytldkemseGELQFRDQLD-----YVSKYRRVL-DYF-DAVKIGLTATPA----L 596
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 471 DTRAVFGDYVSIYDIQDAVDDGATV----PIYYESRLAKLDVN---QAEIDALNAQVDEVI----EDEEDLtarekaksD 539
Cdd:PRK11448 597 HTTEIFGEPVYTYSYREAVIDGYLIdhepPIRIETRLSQEGIHfekGEEVEVINTQTGEIDlatlEDEVDF--------E 668
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1248764712 540 WAALTKLVGAKPRLEQVAADLVQHFEtrtATLEGKAMIVCMSRD----ICAELYNAIIALRPDWHDAdpergAIKVVmTG 615
Cdd:PRK11448 669 VEDFNRRVITESFNRVVCEELAKYLD---PTGEGKTLIFAATDAhadmVVRLLKEAFKKKYGQVEDD-----AVIKI-TG 739
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1248764712 616 SaADKPLlqphlnsqqvkkRLEKRFKDPADPlKLVIVRDMWLTGFDAP 663
Cdd:PRK11448 740 S-IDKPD------------QLIRRFKNERLP-NIVVTVDLLTTGIDVP 773
|
|
| |
