|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
22-1029 |
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: 988.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 22 MDPLNEEWYENLIVEHLTEkLGYEHLYGPDVRRTDdsYRDVFLPDILPDALRRINRNLPEAAVEEAIRKIQNVEIGSLEQ 101
Cdd:COG0610 1 MSKFSEAALEQAIIELLQE-LGYEYLSGPDIAPED--ESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNGLLE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 102 RNEIFNDYLQSGVEVHFFDgkEERDDIVRLLDFDDPENNDFHVVNQWTFVE-YSEKRPDVIIFVNGMPLVLFELKSPSRE 180
Cdd:COG0610 78 ANKGFYDLLRNGVKVEYDG--EEKTKTVRLIDFKNPENNDFLVVNQFTVSGgNYKRRPDVVLFVNGLPLVVIELKNPLTQ 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 181 eTDASHAYLQLRQYMKQIPSMFVPNVFCVMSDMTQTRVGTITSDEDRYVAWKSADGDY-SGTKAAAWSTMIDGMLPKERL 259
Cdd:COG0610 156 -VTIKEAFNQIQRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWKDGDGNDlNPDGITDLDYLIEGLLSKERL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 260 LDIIQNFVCFNDSSEKVVKIIAAYHQYFAVRKAIVRAEEAvNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRY--LESPTI 337
Cdd:COG0610 235 LDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKEA-EGDGKGGVIWHTQGSGKSLTMVFLAQKLARLpdLDNPTV 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 338 VVITDRNDLDDQLFGQFSRcarFLRQKAVQAESRRNLQELLEgREANGIIFTTMQKFSDGDE-----PLCDRSNVVVMVD 412
Cdd:COG0610 314 VVVTDRKDLDDQLFDTFKA---FGRESVVQAESRADLRELLE-SDSGGIIVTTIQKFPEALDeikypELSDRKNIIVIVD 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 413 EAHRGQYGlterinadghvsvGAARVVRKALPNASYIGFTGTPISTDDRNTREIFGDYIDVYDMTQSVEDESTKPVYYES 492
Cdd:COG0610 390 EAHRSQYG-------------GLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVFGDYIHTYTITQAIEDGATLPLLYEY 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 493 RVVSLHLDENAlgrIDAVYKEFADQADEASVEKSKHDLGGLDAIFDTPETIDALCRDIVDHYENNRADvLAGKALIVAYS 572
Cdd:COG0610 457 RLAKLKLDKEK---IDEEFDELTEGLDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRP-GKGKAMVVTSS 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 573 RPIAMKIYYRIMELRPEWKD---KVGVVMTMSNQDPEEWFDVCGGTTHKKEMERRFKDDSDSLKIAIVVDMWLTGFDVPS 649
Cdd:COG0610 533 REAAVRYYEAFDKLRPEWGYkplKIAVVFSGSANDDPEELKEHGNKEYEKDLAKRFKDPDDPLKLLIVVDMLLTGFDAPS 612
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 650 LSTMYVFKPMKGHNLMQAIARVNRVCKGKEGGLVVDYIGIAGALKRAMKDYTSRDQHNYGDMNIAEtAYPKFLEKLDVCR 729
Cdd:COG0610 613 LHTLYVDKPLKGHNLMQAISRVNRVFPGKPYGLIVDYRGIFENLKKALALYSEEDGKEDVLTDPEE-ALEELKEALDELR 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 730 DLM-YGFDYRKLIFQNSREALADAIaegtDWLLDPErhEDMESFLKQCQLMNQALSLCKSMVSEEDA------HEAAYLS 802
Cdd:COG0610 692 ALFpEGVDFSAFDPTEKLEALDEAV----ERFLGDE--EARKEFKKLFKELSRLYNLLSPDDEFGDLelekyrDDVSFYL 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 803 VLRVQVLRLTGRGsgggggmTYTEFNKQVSEILQQSVHADgvlnlfekdsveislfdeaflqevagmkekniaieslkrl 882
Cdd:COG0610 766 ALRAKLRKLGEKL-------DLKEYEEKIRQLLDEAIDLE---------------------------------------- 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 883 iKEKVRAYGRTSVVKSQKFSEMLQNTLNAYLNGMLTNAQVIEELVNMAKEIMKDRDDAQKLGLSDEEMAFYDAITQPqav 962
Cdd:COG0610 799 -RKEIKPRIKQNPVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEEELAFYDALAEN--- 874
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386414507 963 kdfYDNDQLVSIARELTDAMRSNATIDWQKKESARAGMRRAIKRLLRKYKYPpeGVEDAMKTVMEQC 1029
Cdd:COG0610 875 ---LGDEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYP--KQDEAVEEVYEQA 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
27-704 |
6.76e-160 |
|
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: 487.68 E-value: 6.76e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 27 EEWYENLIVEHLtEKLGYEHLYGPDVRRTDDsyrdvfLPDILPDALRRINRNLPEAAVEEAIRKIQNveIGSLEQRNEIF 106
Cdd:TIGR00348 1 EEEVEDLFIQRL-KSLGWEYLKGSELNVEEN------EKQELIEALKIINDHIEPERWDEVYKKITN--KGDLYETNKIF 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 107 NDYLQSGVEVHFfDGKEERDDIVRLLDFDDPENNDFHVVNQWTFvEYSEKRPDVIIFVNGMPLVLFELKspsREETDASH 186
Cdd:TIGR00348 72 YDYIKNGVKIKE-SQKGEKKRIVKLIDFRNISQNIFQFANQVSF-KGHNIRPDVTLFVNGIPLVIIELK---KRSVTIRE 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 187 AYLQLRQYMKQIPSMFVPNVFCVMSDMTQTR--VGTITSDEDRYVAWKSADGDYSGTKAAAWSTMidgmLPKERLLDIIQ 264
Cdd:TIGR00348 147 AFNQIKRYEKEIPELFKYVQIFVISNGTDTRyyTGSDEDDFDFTFNWKESDNKLIEDLKEFDILL----LKKERLLDFIR 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 265 NFVCFNDSSEKVVKIIAAYHQYFAVRKAIVRAEEAVNG-DGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDR 343
Cdd:TIGR00348 223 NFIIFDKDTGLVTKPYQRYMQYRAVKKIVESITRKTWGkDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDR 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 344 NDLDDQLFGQFSRcarFLRQKAVQAESRRNLQELLEGREaNGIIFTTMQKFSDGD----EPL-CDRSNVVVMVDEAHRGQ 418
Cdd:TIGR00348 303 RELDYQLMKEFQS---LQKDCAERIESIAELKELLEKDD-GGIIITTIQKFDDKLkeeeEKFpVDRKEVVVIFDEAHRSQ 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 419 YGLterinadghvsvgAARVVRKALPNASYIGFTGTPISTDDRNTREIF----GDYIDVYDMTQSVEDESTKPVYYESRV 494
Cdd:TIGR00348 379 YGE-------------LAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFayvfGRYLHRYFITDAIRDGLTVKIDYEDRL 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 495 VSLHLDENALGRIDAVYKEF-ADQADEASVEKSKHDLGGLDAIFDTPETIDALCRDIVDHYeNNRADVLAGKALIVAYSR 573
Cdd:TIGR00348 446 PEDHLDKKKLDAFFDEIFELlPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHY-AKFKELFKFKAMVVAISR 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 574 PIAMKIYYRIMELRPEWKDKVGVVMTMSNQDPEEWFDVCG------GTTHKKEME----RRFKDDSDsLKIAIVVDMWLT 643
Cdd:TIGR00348 525 YACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKhirtkfDKSDGFEIYykdlERFKKNEN-PKLLIVVDMLLT 603
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386414507 644 GFDVPSLSTMYVFKPMKGHNLMQAIARVNRVC-KGKEGGLVVDYIGIAGALKRAMKDYTSRD 704
Cdd:TIGR00348 604 GFDAPILNTLYLDKPLKYHGLLQAIARTNRIDgKDKTFGLIVDYRGLEKSLIDALSLYGNEA 665
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
714-1034 |
1.20e-105 |
|
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: 332.96 E-value: 1.20e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 714 AETAYPKFLEKLDVCRDLMYGFDYRKLIFQNSREALaDAIAEGTDWLLDPErHEDMESFLKQCQLMNQALSLCKSM-VSE 792
Cdd:pfam11867 10 IEEAVAVLLEKLEIVRGLFHGFDYSAFFTGDPKERL-QLLLAAAEHILSLE-DDGKKRFLDLVKALSKAYALCAPHdEAD 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 793 EDAHEAAYLSVLRVQVLRLTGRGSGGGGGMTytEFNKQVSEILQQSVHADGVLNLFE---KDSVEISLFDEAFLQEVAGM 869
Cdd:pfam11867 88 AIRDEIAFFQAVRAILVKLTATDRGGSPDTA--EVNAAIRQLIDKAIVSEGVVDIFAaagLEKPDISILSEEFLAEVKKM 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 870 KEKNIAIESLKRLIKEKVRAYGRTSVVKSQKFSEMLQNTLNAYLNGMLTNAQVIEELVNMAKEIMKDRDDAQKLGLSDEE 949
Cdd:pfam11867 166 KQKNLAIELLRKLLNDEIKARSRTNLVQSKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELGLSEEE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 950 MAFYDAITQPQAVKDFYDNDQLVSIARELTDAMRSNATIDWQKKESARAGMRRAIKRLLRKYKYPPEGVEDAMKTVMEQC 1029
Cdd:pfam11867 246 LAFYDALAENESAVEVMGDDKLKEIARELVETVRKNATVDWTKREDVRAKLRVAVKRLLRKYGYPPDKQEEAVELVLEQA 325
|
....*
gi 386414507 1030 ELWAD 1034
Cdd:pfam11867 326 ELLAK 330
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
259-476 |
5.33e-81 |
|
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: 262.16 E-value: 5.33e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 259 LLDIIQNFVCFnDSSEKVVKIIAAYHQYFAVRKAIVRAEEAVNGDG--RIGVFWHTQGSGKSLSMVFFAHLLQRYLESPT 336
Cdd:cd18030 1 LLDVLRNFIVF-DEDDDKTKKVARYYQYYAVEAALERIKTATNKDGdkKGGYIWHTQGSGKSLTMFKAAKLLIEDPKNPK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 337 IVVITDRNDLDDQLFGQFSRCArflRQKAVQAESRRNLQELLEGrEANGIIFTTMQKF-----SDGDEPLCDRSNVVVMV 411
Cdd:cd18030 80 VVFVVDRKDLDYQTSSTFSRFA---AEDVVRANSTKELKELLKN-LSGGIIVTTIQKFnnavkEESKPVLIYRKNIVVIV 155
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386414507 412 DEAHRGQYGlterinadghvsvGAARVVRKALPNASYIGFTGTPI-STDDRNTREIFGDYIDVYDM 476
Cdd:cd18030 156 DEAHRSQFG-------------ELAKALKKALPNATFIGFTGTPIfKEGDKTTEKVFGDYLHKYTI 208
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
286-482 |
3.03e-13 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 69.83 E-value: 3.03e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 286 YFAVRKAIVRAEEAVNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDRNDLDDQLFGQFSRCARFLRQKA 365
Cdd:smart00487 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 366 VQAESRRNLQELLE--GREANGIIFTTMQKFSD-GDEPLCDRSNV-VVMVDEAHR-GQYGLTERInadghvsvgaARVVR 440
Cdd:smart00487 86 VGLYGGDSKREQLRklESGKTDILVTTPGRLLDlLENDKLSLSNVdLVILDEAHRlLDGGFGDQL----------EKLLK 155
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 386414507 441 KALPNASYIGFTGTPISTDDRNTREIFGDYIDVYDMTQSVED 482
Cdd:smart00487 156 LLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
22-1029 |
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: 988.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 22 MDPLNEEWYENLIVEHLTEkLGYEHLYGPDVRRTDdsYRDVFLPDILPDALRRINRNLPEAAVEEAIRKIQNVEIGSLEQ 101
Cdd:COG0610 1 MSKFSEAALEQAIIELLQE-LGYEYLSGPDIAPED--ESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNGLLE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 102 RNEIFNDYLQSGVEVHFFDgkEERDDIVRLLDFDDPENNDFHVVNQWTFVE-YSEKRPDVIIFVNGMPLVLFELKSPSRE 180
Cdd:COG0610 78 ANKGFYDLLRNGVKVEYDG--EEKTKTVRLIDFKNPENNDFLVVNQFTVSGgNYKRRPDVVLFVNGLPLVVIELKNPLTQ 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 181 eTDASHAYLQLRQYMKQIPSMFVPNVFCVMSDMTQTRVGTITSDEDRYVAWKSADGDY-SGTKAAAWSTMIDGMLPKERL 259
Cdd:COG0610 156 -VTIKEAFNQIQRYRREIPGLFAYNQLFVISDGVEARYGTNTAPFEFFLPWKDGDGNDlNPDGITDLDYLIEGLLSKERL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 260 LDIIQNFVCFNDSSEKVVKIIAAYHQYFAVRKAIVRAEEAvNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRY--LESPTI 337
Cdd:COG0610 235 LDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKEA-EGDGKGGVIWHTQGSGKSLTMVFLAQKLARLpdLDNPTV 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 338 VVITDRNDLDDQLFGQFSRcarFLRQKAVQAESRRNLQELLEgREANGIIFTTMQKFSDGDE-----PLCDRSNVVVMVD 412
Cdd:COG0610 314 VVVTDRKDLDDQLFDTFKA---FGRESVVQAESRADLRELLE-SDSGGIIVTTIQKFPEALDeikypELSDRKNIIVIVD 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 413 EAHRGQYGlterinadghvsvGAARVVRKALPNASYIGFTGTPISTDDRNTREIFGDYIDVYDMTQSVEDESTKPVYYES 492
Cdd:COG0610 390 EAHRSQYG-------------GLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVFGDYIHTYTITQAIEDGATLPLLYEY 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 493 RVVSLHLDENAlgrIDAVYKEFADQADEASVEKSKHDLGGLDAIFDTPETIDALCRDIVDHYENNRADvLAGKALIVAYS 572
Cdd:COG0610 457 RLAKLKLDKEK---IDEEFDELTEGLDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRP-GKGKAMVVTSS 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 573 RPIAMKIYYRIMELRPEWKD---KVGVVMTMSNQDPEEWFDVCGGTTHKKEMERRFKDDSDSLKIAIVVDMWLTGFDVPS 649
Cdd:COG0610 533 REAAVRYYEAFDKLRPEWGYkplKIAVVFSGSANDDPEELKEHGNKEYEKDLAKRFKDPDDPLKLLIVVDMLLTGFDAPS 612
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 650 LSTMYVFKPMKGHNLMQAIARVNRVCKGKEGGLVVDYIGIAGALKRAMKDYTSRDQHNYGDMNIAEtAYPKFLEKLDVCR 729
Cdd:COG0610 613 LHTLYVDKPLKGHNLMQAISRVNRVFPGKPYGLIVDYRGIFENLKKALALYSEEDGKEDVLTDPEE-ALEELKEALDELR 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 730 DLM-YGFDYRKLIFQNSREALADAIaegtDWLLDPErhEDMESFLKQCQLMNQALSLCKSMVSEEDA------HEAAYLS 802
Cdd:COG0610 692 ALFpEGVDFSAFDPTEKLEALDEAV----ERFLGDE--EARKEFKKLFKELSRLYNLLSPDDEFGDLelekyrDDVSFYL 765
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 803 VLRVQVLRLTGRGsgggggmTYTEFNKQVSEILQQSVHADgvlnlfekdsveislfdeaflqevagmkekniaieslkrl 882
Cdd:COG0610 766 ALRAKLRKLGEKL-------DLKEYEEKIRQLLDEAIDLE---------------------------------------- 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 883 iKEKVRAYGRTSVVKSQKFSEMLQNTLNAYLNGMLTNAQVIEELVNMAKEIMKDRDDAQKLGLSDEEMAFYDAITQPqav 962
Cdd:COG0610 799 -RKEIKPRIKQNPVQYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEEELAFYDALAEN--- 874
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 386414507 963 kdfYDNDQLVSIARELTDAMRSNATIDWQKKESARAGMRRAIKRLLRKYKYPpeGVEDAMKTVMEQC 1029
Cdd:COG0610 875 ---LGDEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYP--KQDEAVEEVYEQA 936
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
27-704 |
6.76e-160 |
|
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: 487.68 E-value: 6.76e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 27 EEWYENLIVEHLtEKLGYEHLYGPDVRRTDDsyrdvfLPDILPDALRRINRNLPEAAVEEAIRKIQNveIGSLEQRNEIF 106
Cdd:TIGR00348 1 EEEVEDLFIQRL-KSLGWEYLKGSELNVEEN------EKQELIEALKIINDHIEPERWDEVYKKITN--KGDLYETNKIF 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 107 NDYLQSGVEVHFfDGKEERDDIVRLLDFDDPENNDFHVVNQWTFvEYSEKRPDVIIFVNGMPLVLFELKspsREETDASH 186
Cdd:TIGR00348 72 YDYIKNGVKIKE-SQKGEKKRIVKLIDFRNISQNIFQFANQVSF-KGHNIRPDVTLFVNGIPLVIIELK---KRSVTIRE 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 187 AYLQLRQYMKQIPSMFVPNVFCVMSDMTQTR--VGTITSDEDRYVAWKSADGDYSGTKAAAWSTMidgmLPKERLLDIIQ 264
Cdd:TIGR00348 147 AFNQIKRYEKEIPELFKYVQIFVISNGTDTRyyTGSDEDDFDFTFNWKESDNKLIEDLKEFDILL----LKKERLLDFIR 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 265 NFVCFNDSSEKVVKIIAAYHQYFAVRKAIVRAEEAVNG-DGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDR 343
Cdd:TIGR00348 223 NFIIFDKDTGLVTKPYQRYMQYRAVKKIVESITRKTWGkDERGGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFVVDR 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 344 NDLDDQLFGQFSRcarFLRQKAVQAESRRNLQELLEGREaNGIIFTTMQKFSDGD----EPL-CDRSNVVVMVDEAHRGQ 418
Cdd:TIGR00348 303 RELDYQLMKEFQS---LQKDCAERIESIAELKELLEKDD-GGIIITTIQKFDDKLkeeeEKFpVDRKEVVVIFDEAHRSQ 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 419 YGLterinadghvsvgAARVVRKALPNASYIGFTGTPISTDDRNTREIF----GDYIDVYDMTQSVEDESTKPVYYESRV 494
Cdd:TIGR00348 379 YGE-------------LAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFayvfGRYLHRYFITDAIRDGLTVKIDYEDRL 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 495 VSLHLDENALGRIDAVYKEF-ADQADEASVEKSKHDLGGLDAIFDTPETIDALCRDIVDHYeNNRADVLAGKALIVAYSR 573
Cdd:TIGR00348 446 PEDHLDKKKLDAFFDEIFELlPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHY-AKFKELFKFKAMVVAISR 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 574 PIAMKIYYRIMELRPEWKDKVGVVMTMSNQDPEEWFDVCG------GTTHKKEME----RRFKDDSDsLKIAIVVDMWLT 643
Cdd:TIGR00348 525 YACVEEKNALDEELNEKFEASAIVMTGKESDDAEIRDYNKhirtkfDKSDGFEIYykdlERFKKNEN-PKLLIVVDMLLT 603
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 386414507 644 GFDVPSLSTMYVFKPMKGHNLMQAIARVNRVC-KGKEGGLVVDYIGIAGALKRAMKDYTSRD 704
Cdd:TIGR00348 604 GFDAPILNTLYLDKPLKYHGLLQAIARTNRIDgKDKTFGLIVDYRGLEKSLIDALSLYGNEA 665
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
714-1034 |
1.20e-105 |
|
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: 332.96 E-value: 1.20e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 714 AETAYPKFLEKLDVCRDLMYGFDYRKLIFQNSREALaDAIAEGTDWLLDPErHEDMESFLKQCQLMNQALSLCKSM-VSE 792
Cdd:pfam11867 10 IEEAVAVLLEKLEIVRGLFHGFDYSAFFTGDPKERL-QLLLAAAEHILSLE-DDGKKRFLDLVKALSKAYALCAPHdEAD 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 793 EDAHEAAYLSVLRVQVLRLTGRGSGGGGGMTytEFNKQVSEILQQSVHADGVLNLFE---KDSVEISLFDEAFLQEVAGM 869
Cdd:pfam11867 88 AIRDEIAFFQAVRAILVKLTATDRGGSPDTA--EVNAAIRQLIDKAIVSEGVVDIFAaagLEKPDISILSEEFLAEVKKM 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 870 KEKNIAIESLKRLIKEKVRAYGRTSVVKSQKFSEMLQNTLNAYLNGMLTNAQVIEELVNMAKEIMKDRDDAQKLGLSDEE 949
Cdd:pfam11867 166 KQKNLAIELLRKLLNDEIKARSRTNLVQSKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELGLSEEE 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 950 MAFYDAITQPQAVKDFYDNDQLVSIARELTDAMRSNATIDWQKKESARAGMRRAIKRLLRKYKYPPEGVEDAMKTVMEQC 1029
Cdd:pfam11867 246 LAFYDALAENESAVEVMGDDKLKEIARELVETVRKNATVDWTKREDVRAKLRVAVKRLLRKYGYPPDKQEEAVELVLEQA 325
|
....*
gi 386414507 1030 ELWAD 1034
Cdd:pfam11867 326 ELLAK 330
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
284-520 |
4.05e-105 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 327.47 E-value: 4.05e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 284 HQYFAVRKAIVRAEEavNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDRNDLDDQLFGQFSRCarfLRQ 363
Cdd:pfam18766 1 QQYFAVNKAVERVLE--DGDRRGGVIWHTQGSGKSLTMVFLARKLRRELKNPTVVVVTDRNDLDDQLTKTFAAC---GRE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 364 KAVQAESRRNLQELLegREANGIIFTTMQKFSDGDE----PLCDRSNVVVMVDEAHRGQYGlterinadghvsvGAARVV 439
Cdd:pfam18766 76 VPVQAESRKDLRELL--RGSGGIIFTTIQKFGETPDegfpVLSDRRNIIVLVDEAHRSQYG-------------GLAANM 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 440 RKALPNASYIGFTGTPISTDDRNTREIFGDYIDVYDMTQSVEDESTKPVYYESRVVSLHLDENAlgrIDAVYKE-FADQA 518
Cdd:pfam18766 141 RDALPNAAFIGFTGTPILKKDKNTRAVFGDYIDTYTIQDAVEDGATVPILYEGRLAELELDDEA---LDEEFEEiTEDLE 217
|
..
gi 386414507 519 DE 520
Cdd:pfam18766 218 DE 219
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
259-476 |
5.33e-81 |
|
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: 262.16 E-value: 5.33e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 259 LLDIIQNFVCFnDSSEKVVKIIAAYHQYFAVRKAIVRAEEAVNGDG--RIGVFWHTQGSGKSLSMVFFAHLLQRYLESPT 336
Cdd:cd18030 1 LLDVLRNFIVF-DEDDDKTKKVARYYQYYAVEAALERIKTATNKDGdkKGGYIWHTQGSGKSLTMFKAAKLLIEDPKNPK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 337 IVVITDRNDLDDQLFGQFSRCArflRQKAVQAESRRNLQELLEGrEANGIIFTTMQKF-----SDGDEPLCDRSNVVVMV 411
Cdd:cd18030 80 VVFVVDRKDLDYQTSSTFSRFA---AEDVVRANSTKELKELLKN-LSGGIIVTTIQKFnnavkEESKPVLIYRKNIVVIV 155
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 386414507 412 DEAHRGQYGlterinadghvsvGAARVVRKALPNASYIGFTGTPI-STDDRNTREIFGDYIDVYDM 476
Cdd:cd18030 156 DEAHRSQFG-------------ELAKALKKALPNATFIGFTGTPIfKEGDKTTEKVFGDYLHKYTI 208
|
|
| HsdR_N |
cd22332 |
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and ... |
26-265 |
4.29e-61 |
|
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: 207.89 E-value: 4.29e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 26 NEEWYENLIVEHLTEkLGYEHLYGPDVRRtddSYRDVFLPDILPDALRRINRNLPEaaveeaIRKIQNVEIgsleqrNEI 105
Cdd:cd22332 1 TESQLEEALIELLQE-LGYEYLPGPELER---DKTEVLLEDNLREALERLNPDIPS------GVPLTDNEF------NQL 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 106 FNDYLQSGVEVHFFDGKEERD-DIVRLLDFDDPENNDFHVVNQWTFVE-YSEKRPDVIIFVNGMPLVLFELKSPSreeTD 183
Cdd:cd22332 65 LLELGRDVTPLLTLDDDGGKEkTRVILIDFENPENNDFQVVNQFTVEGgKHNRRPDVVLFVNGLPLVVIELKNPG---VT 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 184 ASHAYLQLRQYMK--QIPSMFVPNVFCVMSDMTQTRVGTITSDEDRYVAWKSADG-DYSGTKAAAWSTMIDGMLPKERLL 260
Cdd:cd22332 142 IREAYNQIKRYYKeiFIPGLFKYNQLFVISNGTETRYGANTAPYERFNEWFTFDWaDEDNEPITDLETFIKGLLSKERLL 221
|
....*
gi 386414507 261 DIIQN 265
Cdd:cd22332 222 DLIRN 226
|
|
| SF2_C_EcoR124I-like |
cd18800 |
C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases; This ... |
619-686 |
4.64e-27 |
|
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: 105.34 E-value: 4.64e-27
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386414507 619 KEMERRFKDDsdsLKIAIVVDMWLTGFDVPSLSTMYVFKPMKGHNLMQAIARVNRVCKG-KEGGLVVDY 686
Cdd:cd18800 16 RRAAVRYYKA---LDLLIVVDMLLTGFDAPSLNTLYVDKPLKYHGLIQAIARVNRVYKDeKEFGLIVDY 81
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
290-775 |
2.26e-21 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 99.71 E-value: 2.26e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 290 RKAIVRAEEAVNGDGRIGVFWHTQGSGKSlsmVFFAHLLQRYLESPTIVVITDRNDLDDQLFGQFSRcaRFLRQKAVQAE 369
Cdd:COG1061 86 QEALEALLAALERGGGRGLVVAPTGTGKT---VLALALAAELLRGKRVLVLVPRRELLEQWAEELRR--FLGDPLAGGGK 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 370 SRRNLQellegreangIIFTTMQKFS--DGDEPLCDRSNVVVmVDEAHrgqyglterinadgHVSVGAARVVRKALPNAS 447
Cdd:COG1061 161 KDSDAP----------ITVATYQSLArrAHLDELGDRFGLVI-IDEAH--------------HAGAPSYRRILEAFPAAY 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 448 YIGFTGTPISTDDRNtrEIFGDYIDV---YDMTQSVEDESTKPVYYESRVVSLHLDENAlgridavYKEFADQADEAsve 524
Cdd:COG1061 216 RLGLTATPFRSDGRE--ILLFLFDGIvyeYSLKEAIEDGYLAPPEYYGIRVDLTDERAE-------YDALSERLREA--- 283
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 525 kskhdlggldaIFDTPETIDALCRDIVDHYENNRadvlagKALIVAYSRPIAmkiyYRIMELRPEWKDKVGVVmtmSNQD 604
Cdd:COG1061 284 -----------LAADAERKDKILRELLREHPDDR------KTLVFCSSVDHA----EALAELLNEAGIRAAVV---TGDT 339
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 605 PEEwfdvcggttHKKEMERRFKDDSdsLKIAIVVDMWLTGFDVPSLSTMYVFKPMKGHNLM-QAIARVNRVCKGKEGGLV 683
Cdd:COG1061 340 PKK---------EREEILEAFRDGE--LRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFiQRLGRGLRPAPGKEDALV 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 684 VDYIGIAGALKRAMkdYTSRDQHNYGDMNIAETAYPKFLEKLDVCRDLMYGFDYRKLIFQNSREALADAIAEGTDWLLDP 763
Cdd:COG1061 409 YDFVGNDVPVLEEL--AKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLL 486
|
490
....*....|..
gi 386414507 764 ERHEDMESFLKQ 775
Cdd:COG1061 487 ELLALALELLEL 498
|
|
| HSDR_N |
pfam04313 |
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
84-227 |
3.98e-19 |
|
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: 85.05 E-value: 3.98e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 84 VEEAIRKIQNVEIGSLEQRNEIFNDYLQSGVEVHFfdgkeerddivrlldfDDPENNDFHVVNQWTFVEYSEKRPDVIIF 163
Cdd:pfam04313 23 VLNEVRGIKAEVILEKLDGNEAFYRLLKYGVTDGI----------------TKTENNSFQVANQVEVKGVQKRRPDYVLF 86
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 164 VNGMPLVLFELKSPSREEtdashAYLQLRQYMKQ----IPSMFVPNV--FCVMSDMTQTRVGTITSDEDR 227
Cdd:pfam04313 87 VNGLPLAVIELKRPGTEE-----AINQIRRYEKDsfnaIPQLFRYANvqFGILSNGRETRFYTKTAKENR 151
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
283-456 |
9.63e-17 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 78.48 E-value: 9.63e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 283 YHQyfavRKAIVRAEEAVNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDRNDLDDQLFGQFSRCARFLR 362
Cdd:pfam04851 6 PYQ----IEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNYV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 363 QKAVQAESRRNLQELLEGReangIIFTTMQKFS-----DGDEPLCDRSNVVVmVDEAHRGQYGLTERINadghvsvgaar 437
Cdd:pfam04851 82 EIGEIISGDKKDESVDDNK----IVVTTIQSLYkalelASLELLPDFFDVII-IDEAHRSGASSYRNIL----------- 145
|
170
....*....|....*....
gi 386414507 438 vvrKALPNASYIGFTGTPI 456
Cdd:pfam04851 146 ---EYFKPAFLLGLTATPE 161
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
286-482 |
3.03e-13 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 69.83 E-value: 3.03e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 286 YFAVRKAIVRAEEAVNGDGRIGVFWHTQGSGKSLSMVFFAHLLQRYLESPTIVVITDRNDLDDQLFGQFSRCARFLRQKA 365
Cdd:smart00487 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 366 VQAESRRNLQELLE--GREANGIIFTTMQKFSD-GDEPLCDRSNV-VVMVDEAHR-GQYGLTERInadghvsvgaARVVR 440
Cdd:smart00487 86 VGLYGGDSKREQLRklESGKTDILVTTPGRLLDlLENDKLSLSNVdLVILDEAHRlLDGGFGDQL----------EKLLK 155
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 386414507 441 KALPNASYIGFTGTPISTDDRNTREIFGDYIDVYDMTQSVED 482
Cdd:smart00487 156 LLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
409-689 |
2.70e-10 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 64.48 E-value: 2.70e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 409 VMVDEAHRGQYGLTERInadghvsvgaarvvrkaLP--NASYIGFTGTPISTDDRNTREIF-GDYIDVYDMTQSVEDEst 485
Cdd:COG4096 286 IIIDECHRGIYSKWRAI-----------------LDyfDALQIGLTATPKDTIDRNTYEYFnGNPVYTYSLEQAVADG-- 346
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 486 kpvY---YESRVVSLHLDENAlGRIDAVYK---------EFADQADEASVEKSKhdlggLDAIFDTPETIDALCRDIVDH 553
Cdd:COG4096 347 ---FlvpYKVIRIDTKFDREG-IRYDAGEDlsdeegeeiELEELEEDREYEAKD-----FNRKVVNEDTTRKVLEELMEY 417
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 554 YENNRADVLaGKALIVAYSRPIAMKIYYRIMELRPEWKDKVGVVMTMSNQDPEEWFDvcggtthkkemerRFKDDSDSLK 633
Cdd:COG4096 418 LDKPGGDRL-GKTIIFAKNDDHADRIVQALRELYPELGGDFVKKITGDDDYGKSLID-------------NFKNPEKYPR 483
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 386414507 634 IAIVVDMWLTGFDVPSLSTMYVFKPMKGHNL-MQAIARVNRVCK----GKEGGLVVDYIGI 689
Cdd:COG4096 484 IAVTVDMLDTGIDVPEVVNLVFMRPVKSRIKfEQMIGRGTRLCPdlfpGKTHFTIFDFVGN 544
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
290-455 |
9.92e-09 |
|
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: 55.00 E-value: 9.92e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 290 RKAIVRAEEAVNGDGriGVFWHTQGSGKSLSMVffahLLQRYLESPTIVVITDRNDLDDQLFGQFsrcARFLRQKAVQAE 369
Cdd:cd17926 6 EEALEAWLAHKNNRR--GILVLPTGSGKTLTAL----ALIAYLKELRTLIVVPTDALLDQWKERF---EDFLGDSSIGLI 76
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 370 SRRNlQELLEGREangIIFTTMQKFSDGDEPLCDRSN--VVVMVDEAHrgqyglteRINADGhvsvgaARVVRKALpNAS 447
Cdd:cd17926 77 GGGK-KKDFDDAN---VVVATYQSLSNLAEEEKDLFDqfGLLIVDEAH--------HLPAKT------FSEILKEL-NAK 137
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....*....
gi 386414507 448 Y-IGFTGTP 455
Cdd:cd17926 138 YrLGLTATP 146
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| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
292-467 |
2.53e-07 |
|
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: 51.41 E-value: 2.53e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 292 AIVRAEEAV-NGDGRIGVFWHTqGSGKSlsMVFFAhLLQRYLES---PTIVVITDRNDLDDQLFGQFsrcARFLRQKavq 367
Cdd:cd18032 8 AIEALEEAReKGQRRALLVMAT-GTGKT--YTAAF-LIKRLLEAnrkKRILFLAHREELLEQAERSF---KEVLPDG--- 77
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 368 aesrrNLQELLEGREANG---IIFTTMQKFS---DGDEPLCDRSNVVVmVDEAHRGqyglterinadghvsvgAARVVRK 441
Cdd:cd18032 78 -----SFGNLKGGKKKPDdarVVFATVQTLNkrkRLEKFPPDYFDLII-IDEAHHA-----------------IASSYRK 134
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170 180
....*....|....*....|....*....
gi 386414507 442 AL---PNASYIGFTGTPISTDDRNTREIF 467
Cdd:cd18032 135 ILeyfEPAFLLGLTATPERTDGLDTYELF 163
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| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
310-454 |
1.36e-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: 48.94 E-value: 1.36e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386414507 310 WHTQGSGKSLsmVFFAHLLQRYLES-PTIVVITDRNDLDDQlfgQFSRCARFLRQKA----VQAESRRNLQELLEGREAN 384
Cdd:cd00046 7 TAPTGSGKTL--AALLAALLLLLKKgKKVLVLVPTKALALQ---TAERLRELFGPGIrvavLVGGSSAEEREKNKLGDAD 81
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90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 386414507 385 gIIFTTMQKFSD---GDEPLCDRSNVVVMVDEAHRGQyglterINADGHVSVgAARVVRKALPNASYIGFTGT 454
Cdd:cd00046 82 -IIIATPDMLLNlllREDRLFLKDLKLIIVDEAHALL------IDSRGALIL-DLAVRKAGLKNAQVILLSAT 146
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| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
620-687 |
4.16e-06 |
|
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: 46.78 E-value: 4.16e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 386414507 620 EMERRFKDDSDSLKIAIVVDMWLTGFDVPSLSTMYVFKPMKGHNL-MQAIARVNRVCKGKEGGLVVDYI 687
Cdd:cd18799 48 EALILLFFGELKPPILVTVDLLTTGVDIPEVDNVVFLRPTESRTLfLQMLGRGLRLHEGKDFFTILDFI 116
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