|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
5-979 |
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: 636.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 5 ESTIEQELVEKLGGLKYT--LRADI----RSRAALEANFRKHFEELNRvALTNAEFQRLLEEV---VTADVFKAAHT--- 72
Cdd:COG0610 6 EAALEQAIIELLQELGYEylSGPDIapedESEVLLEDNLRAALERLNP-GLSDDEIERALRELtkpESNGLLEANKGfyd 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 73 -LRHRNAFTRDDGT-PLNYTLVNINDWCKNTFEVASQLRINTDDSHHRYDVILLINGVPAVQIELKT--LGINPRRAIEQ 148
Cdd:COG0610 85 lLRNGVKVEYDGEEkTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNplTQVTIKEAFNQ 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 149 IVEYKHDVgngytRTLLCFIQLFIVSNRDATYYFANNNArhfafnaDERFLPiyqYAAPDN-----SKISGLDAFADAFL 223
Cdd:COG0610 165 IQRYRREI-----PGLFAYNQLFVISDGVEARYGTNTAP-------FEFFLP---WKDGDGndlnpDGITDLDYLIEGLL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 224 PKCTLGQIISRYMVLVASE--QKLLMMRPYQIYAVKNIVECIDKNLG---NGYIWHTTGSGKTLTSFKASTLLKANPAIE 298
Cdd:COG0610 230 SKERLLDIIRNFIVFDEDEggLIKIVARYHQYFAVRKAVERVKEAEGdgkGGVIWHTQGSGKSLTMVFLAQKLARLPDLD 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 299 K--CLFVVDRKDLDRQTREEFNRFQEGCVEENTNTESMVRRLvsDDAADKVIVTTIQKLGRALDPARadyrqHLEPLRDQ 376
Cdd:COG0610 310 NptVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELL--ESDSGGIIVTTIQKFPEALDEIK-----YPELSDRK 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 377 RMVFIFDECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFEDNasyrriegdeqtlKTTEDLFQQSLHEYTITHAIEDRNV 456
Cdd:COG0610 383 NIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKED-------------RTTLEVFGDYIHTYTITQAIEDGAT 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 457 LRFHVDY-----------------YKPDGKNAPKPGETLAK--------------RAVVDAILSKHDAATGGRRFNALFA 505
Cdd:COG0610 450 LPLLYEYrlaklkldkekideefdELTEGLDDEEKEKLKAKwalleevlgaperiEQIAEDIVEHFEERTRPGKGKAMVV 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 506 TASINDAIEYvglFKAaqLEKQQADSGYVPLNIAAVFSPPgdisadvrqlQEDLPQEQADNRTdpdakkaalkaivadyn 585
Cdd:COG0610 530 TSSREAAVRY---YEA--FDKLRPEWGYKPLKIAVVFSGS----------ANDDPEELKEHGN----------------- 577
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 586 vrfgtnhrieefDAYYQDVQQRIKDQQfpnadlpmkgrEKLDIVIVVDMLLTGFDSKYLNTLYVDKNLKYHGLIQAFSRT 665
Cdd:COG0610 578 ------------KEYEKDLAKRFKDPD-----------DPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRV 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 666 NRVLNDtKPYGNILDFRSQQSAVDAAIALFSGakaEKAREIWLVDTaPVVIDKLQKARASLDSFLASQ------GLGGKP 739
Cdd:COG0610 635 NRVFPG-KPYGLIVDYRGIFENLKKALALYSE---EDGKEDVLTDP-EEALEELKEALDELRALFPEGvdfsafDPTEKL 709
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 740 EDI-----ANLKGTAAKVAFVKHFKDVQKLQTQLDQYTDLTAEQqaqveailpkdelrsfrgqylqkAEELRADQKKAGG 814
Cdd:COG0610 710 EALdeaveRFLGDEEARKEFKKLFKELSRLYNLLSPDDEFGDLE-----------------------LEKYRDDVSFYLA 766
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 815 LDDATRNDVEQLDFEFVLFASSTIDYDYImkliadysgkapgkaSMSREQLIGLIASD-AKFVDEREDISAYVRGLKAGE 893
Cdd:COG0610 767 LRAKLRKLGEKLDLKEYEEKIRQLLDEAI---------------DLERKEIKPRIKQNpVQYRKFSELLEEIIEEYNNGA 831
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 894 gLSEEAIRAGYEAFKAEKAAQEmtALSGRHGLPvADLQAFVDAvLARRIFDGE------RLTELLAP-LDLGWKARTQAE 966
Cdd:COG0610 832 -LDADEVLEELEELAKEVKEEE--ERAEEEGLN-EEELAFYDA-LAENLGDEKlkelakELDDLLKKnVTVDWRKRESVR 906
|
1050
....*....|...
gi 499346176 967 LALMRDLLPLLHK 979
Cdd:COG0610 907 AKLRDAIKRLLRK 919
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
83-696 |
1.60e-107 |
|
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: 348.62 E-value: 1.60e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 83 DGTPLNYTLVNIN----------DWCKNTFEVASQLRINTDDShhRYDVILLINGVPAVQIELKTLGINPRRAIEQIVEY 152
Cdd:TIGR00348 77 NGVKIKESQKGEKkrivklidfrNISQNIFQFANQVSFKGHNI--RPDVTLFVNGIPLVIIELKKRSVTIREAFNQIKRY 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 153 KHDVgngytRTLLCFIQLFIVSNRDATYYFANNNArhfafnadERFLPIYQYAAPDNSKISGLDAFADAFLPKCTLGQII 232
Cdd:TIGR00348 155 EKEI-----PELFKYVQIFVISNGTDTRYYTGSDE--------DDFDFTFNWKESDNKLIEDLKEFDILLLKKERLLDFI 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 233 SRYMVLvaSEQKLLMMRPYQIY----AVKNIVECIDKNLGN-----GYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFV 303
Cdd:TIGR00348 222 RNFIIF--DKDTGLVTKPYQRYmqyrAVKKIVESITRKTWGkdergGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFV 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 304 VDRKDLDRQTREEFNRFQEGCVEENTNTESMVRRLVSDDAadKVIVTTIQKLGRALDPARADYrqhlePLRDQRMVFIFD 383
Cdd:TIGR00348 300 VDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDDG--GIIITTIQKFDDKLKEEEEKF-----PVDRKEVVVIFD 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 384 ECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFEDNASyrriegdeqTLKTTEDLFQQSLHEYTITHAIEDRNVLRFHVDY 463
Cdd:TIGR00348 373 EAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRD---------TSLTFAYVFGRYLHRYFITDAIRDGLTVKIDYED 443
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 464 YKPDGKNAPKPGET-LAKRAVVDA---------ILSKHDAATGGRRFNALFATASINDAIEYVGLFKAAQlekqqadsgY 533
Cdd:TIGR00348 444 RLPEDHLDKKKLDAfFDEIFELLPerireitkeSLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELF---------K 514
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 534 VPLNIAAVFSppgdiSADV---RQLQEDLPQEQADNRTDPDAKKAaLKAIVADYNVRFGTN-HRIEEFDAYYQDVQQRIK 609
Cdd:TIGR00348 515 FKAMVVAISR-----YACVeekNALDEELNEKFEASAIVMTGKES-DDAEIRDYNKHIRTKfDKSDGFEIYYKDLERFKK 588
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 610 DqqfpnadlpmkgrEKLDIVIVVDMLLTGFDSKYLNTLYVDKNLKYHGLIQAFSRTNRVLNDTKPYGNILDFRSQQSAVD 689
Cdd:TIGR00348 589 N-------------ENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKDKTFGLIVDYRGLEKSLI 655
|
....*..
gi 499346176 690 AAIALFS 696
Cdd:TIGR00348 656 DALSLYG 662
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
228-447 |
3.84e-65 |
|
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: 218.25 E-value: 3.84e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 228 LGQIISRYMVLVASEQKLLM-MRPYQIYAVKNIVECIDKNLGN------GYIWHTTGSGKTLTSFKASTLLKANPAIEKC 300
Cdd:cd18030 1 LLDVLRNFIVFDEDDDKTKKvARYYQYYAVEAALERIKTATNKdgdkkgGYIWHTQGSGKSLTMFKAAKLLIEDPKNPKV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 301 LFVVDRKDLDRQTREEFNRFQ-EGCVeeNTNTESMVRRLVSDDAAdKVIVTTIQKLGRAldparADYRQHLEPLRDQRMV 379
Cdd:cd18030 81 VFVVDRKDLDYQTSSTFSRFAaEDVV--RANSTKELKELLKNLSG-GIIVTTIQKFNNA-----VKEESKPVLIYRKNIV 152
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499346176 380 FIFDECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFednasyrriegdEQTLKTTEDLFQQSLHEYTI 447
Cdd:cd18030 153 VIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIF------------KEGDKTTEKVFGDYLHKYTI 208
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
251-458 |
4.70e-63 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 213.06 E-value: 4.70e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 251 YQIYAVKNIVECIDKNLG--NGYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFVVDRKDLDRQTREEFNRFQEGCVEEN 328
Cdd:pfam18766 1 QQYFAVNKAVERVLEDGDrrGGVIWHTQGSGKSLTMVFLARKLRRELKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 329 TNTESMVRRLvsdDAADKVIVTTIQKLGRALDparadyrQHLEPLRDQR-MVFIFDECHRSQFGENHQAIKEFFPKAQLF 407
Cdd:pfam18766 81 ESRKDLRELL---RGSGGIIFTTIQKFGETPD-------EGFPVLSDRRnIIVLVDEAHRSQYGGLAANMRDALPNAAFI 150
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 499346176 408 GFTGTPIFEDNasyrriegdeqtlKTTEDLFQQSLHEYTITHAIEDRNVLR 458
Cdd:pfam18766 151 GFTGTPILKKD-------------KNTRAVFGDYIDTYTIQDAVEDGATVP 188
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
248-414 |
1.63e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 82.15 E-value: 1.63e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 248 MRPYQIYAVKNIVEcidkNLGNGYIWHTTGSGKTLTSFK-ASTLLKANPAIeKCLFVVDRKDLDRQTREEFNRF------ 320
Cdd:smart00487 9 LRPYQKEAIEALLS----GLRDVILAAPTGSGKTLAALLpALEALKRGKGG-RVLVLVPTRELAEQWAEELKKLgpslgl 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 321 QEGCVEENTNTESMVRRLVSDDAadKVIVTTIQKLgraldpaRADYRQHLEPLRDQRMVfIFDECHR---SQFGEN-HQA 396
Cdd:smart00487 84 KVVGLYGGDSKREQLRKLESGKT--DILVTTPGRL-------LDLLENDKLSLSNVDLV-ILDEAHRlldGGFGDQlEKL 153
|
170
....*....|....*...
gi 499346176 397 IKEFFPKAQLFGFTGTPI 414
Cdd:smart00487 154 LKLLPKNVQLLLLSATPP 171
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
240-387 |
3.41e-05 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 48.02 E-value: 3.41e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 240 ASEQKL--------LMMRPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTS----FKastLLKANPAiEKCLFVVDRK 307
Cdd:PRK11448 398 AANQWLadepfdygLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAialmYR---LLKAKRF-RRILFLVDRS 473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 308 DLDRQTREEFnrfqegcveENTNTESM--------VRRL--VSDDAADKVIVTTIQKL-GRALDPARADYRqhlePLRDQ 376
Cdd:PRK11448 474 ALGEQAEDAF---------KDTKIEGDqtfasiydIKGLedKFPEDETKVHVATVQGMvKRILYSDDPMDK----PPVDQ 540
|
170
....*....|.
gi 499346176 377 RMVFIFDECHR 387
Cdd:PRK11448 541 YDCIIVDEAHR 551
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
5-979 |
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: 636.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 5 ESTIEQELVEKLGGLKYT--LRADI----RSRAALEANFRKHFEELNRvALTNAEFQRLLEEV---VTADVFKAAHT--- 72
Cdd:COG0610 6 EAALEQAIIELLQELGYEylSGPDIapedESEVLLEDNLRAALERLNP-GLSDDEIERALRELtkpESNGLLEANKGfyd 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 73 -LRHRNAFTRDDGT-PLNYTLVNINDWCKNTFEVASQLRINTDDSHHRYDVILLINGVPAVQIELKT--LGINPRRAIEQ 148
Cdd:COG0610 85 lLRNGVKVEYDGEEkTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNplTQVTIKEAFNQ 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 149 IVEYKHDVgngytRTLLCFIQLFIVSNRDATYYFANNNArhfafnaDERFLPiyqYAAPDN-----SKISGLDAFADAFL 223
Cdd:COG0610 165 IQRYRREI-----PGLFAYNQLFVISDGVEARYGTNTAP-------FEFFLP---WKDGDGndlnpDGITDLDYLIEGLL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 224 PKCTLGQIISRYMVLVASE--QKLLMMRPYQIYAVKNIVECIDKNLG---NGYIWHTTGSGKTLTSFKASTLLKANPAIE 298
Cdd:COG0610 230 SKERLLDIIRNFIVFDEDEggLIKIVARYHQYFAVRKAVERVKEAEGdgkGGVIWHTQGSGKSLTMVFLAQKLARLPDLD 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 299 K--CLFVVDRKDLDRQTREEFNRFQEGCVEENTNTESMVRRLvsDDAADKVIVTTIQKLGRALDPARadyrqHLEPLRDQ 376
Cdd:COG0610 310 NptVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELL--ESDSGGIIVTTIQKFPEALDEIK-----YPELSDRK 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 377 RMVFIFDECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFEDNasyrriegdeqtlKTTEDLFQQSLHEYTITHAIEDRNV 456
Cdd:COG0610 383 NIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKED-------------RTTLEVFGDYIHTYTITQAIEDGAT 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 457 LRFHVDY-----------------YKPDGKNAPKPGETLAK--------------RAVVDAILSKHDAATGGRRFNALFA 505
Cdd:COG0610 450 LPLLYEYrlaklkldkekideefdELTEGLDDEEKEKLKAKwalleevlgaperiEQIAEDIVEHFEERTRPGKGKAMVV 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 506 TASINDAIEYvglFKAaqLEKQQADSGYVPLNIAAVFSPPgdisadvrqlQEDLPQEQADNRTdpdakkaalkaivadyn 585
Cdd:COG0610 530 TSSREAAVRY---YEA--FDKLRPEWGYKPLKIAVVFSGS----------ANDDPEELKEHGN----------------- 577
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 586 vrfgtnhrieefDAYYQDVQQRIKDQQfpnadlpmkgrEKLDIVIVVDMLLTGFDSKYLNTLYVDKNLKYHGLIQAFSRT 665
Cdd:COG0610 578 ------------KEYEKDLAKRFKDPD-----------DPLKLLIVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRV 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 666 NRVLNDtKPYGNILDFRSQQSAVDAAIALFSGakaEKAREIWLVDTaPVVIDKLQKARASLDSFLASQ------GLGGKP 739
Cdd:COG0610 635 NRVFPG-KPYGLIVDYRGIFENLKKALALYSE---EDGKEDVLTDP-EEALEELKEALDELRALFPEGvdfsafDPTEKL 709
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 740 EDI-----ANLKGTAAKVAFVKHFKDVQKLQTQLDQYTDLTAEQqaqveailpkdelrsfrgqylqkAEELRADQKKAGG 814
Cdd:COG0610 710 EALdeaveRFLGDEEARKEFKKLFKELSRLYNLLSPDDEFGDLE-----------------------LEKYRDDVSFYLA 766
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 815 LDDATRNDVEQLDFEFVLFASSTIDYDYImkliadysgkapgkaSMSREQLIGLIASD-AKFVDEREDISAYVRGLKAGE 893
Cdd:COG0610 767 LRAKLRKLGEKLDLKEYEEKIRQLLDEAI---------------DLERKEIKPRIKQNpVQYRKFSELLEEIIEEYNNGA 831
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 894 gLSEEAIRAGYEAFKAEKAAQEmtALSGRHGLPvADLQAFVDAvLARRIFDGE------RLTELLAP-LDLGWKARTQAE 966
Cdd:COG0610 832 -LDADEVLEELEELAKEVKEEE--ERAEEEGLN-EEELAFYDA-LAENLGDEKlkelakELDDLLKKnVTVDWRKRESVR 906
|
1050
....*....|...
gi 499346176 967 LALMRDLLPLLHK 979
Cdd:COG0610 907 AKLRDAIKRLLRK 919
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
83-696 |
1.60e-107 |
|
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: 348.62 E-value: 1.60e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 83 DGTPLNYTLVNIN----------DWCKNTFEVASQLRINTDDShhRYDVILLINGVPAVQIELKTLGINPRRAIEQIVEY 152
Cdd:TIGR00348 77 NGVKIKESQKGEKkrivklidfrNISQNIFQFANQVSFKGHNI--RPDVTLFVNGIPLVIIELKKRSVTIREAFNQIKRY 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 153 KHDVgngytRTLLCFIQLFIVSNRDATYYFANNNArhfafnadERFLPIYQYAAPDNSKISGLDAFADAFLPKCTLGQII 232
Cdd:TIGR00348 155 EKEI-----PELFKYVQIFVISNGTDTRYYTGSDE--------DDFDFTFNWKESDNKLIEDLKEFDILLLKKERLLDFI 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 233 SRYMVLvaSEQKLLMMRPYQIY----AVKNIVECIDKNLGN-----GYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFV 303
Cdd:TIGR00348 222 RNFIIF--DKDTGLVTKPYQRYmqyrAVKKIVESITRKTWGkdergGLIWHTQGSGKTLTMLFAARKALELLKNPKVFFV 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 304 VDRKDLDRQTREEFNRFQEGCVEENTNTESMVRRLVSDDAadKVIVTTIQKLGRALDPARADYrqhlePLRDQRMVFIFD 383
Cdd:TIGR00348 300 VDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDDG--GIIITTIQKFDDKLKEEEEKF-----PVDRKEVVVIFD 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 384 ECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFEDNASyrriegdeqTLKTTEDLFQQSLHEYTITHAIEDRNVLRFHVDY 463
Cdd:TIGR00348 373 EAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRD---------TSLTFAYVFGRYLHRYFITDAIRDGLTVKIDYED 443
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 464 YKPDGKNAPKPGET-LAKRAVVDA---------ILSKHDAATGGRRFNALFATASINDAIEYVGLFKAAQlekqqadsgY 533
Cdd:TIGR00348 444 RLPEDHLDKKKLDAfFDEIFELLPerireitkeSLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELF---------K 514
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 534 VPLNIAAVFSppgdiSADV---RQLQEDLPQEQADNRTDPDAKKAaLKAIVADYNVRFGTN-HRIEEFDAYYQDVQQRIK 609
Cdd:TIGR00348 515 FKAMVVAISR-----YACVeekNALDEELNEKFEASAIVMTGKES-DDAEIRDYNKHIRTKfDKSDGFEIYYKDLERFKK 588
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 610 DqqfpnadlpmkgrEKLDIVIVVDMLLTGFDSKYLNTLYVDKNLKYHGLIQAFSRTNRVLNDTKPYGNILDFRSQQSAVD 689
Cdd:TIGR00348 589 N-------------ENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKDKTFGLIVDYRGLEKSLI 655
|
....*..
gi 499346176 690 AAIALFS 696
Cdd:TIGR00348 656 DALSLYG 662
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
228-447 |
3.84e-65 |
|
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: 218.25 E-value: 3.84e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 228 LGQIISRYMVLVASEQKLLM-MRPYQIYAVKNIVECIDKNLGN------GYIWHTTGSGKTLTSFKASTLLKANPAIEKC 300
Cdd:cd18030 1 LLDVLRNFIVFDEDDDKTKKvARYYQYYAVEAALERIKTATNKdgdkkgGYIWHTQGSGKSLTMFKAAKLLIEDPKNPKV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 301 LFVVDRKDLDRQTREEFNRFQ-EGCVeeNTNTESMVRRLVSDDAAdKVIVTTIQKLGRAldparADYRQHLEPLRDQRMV 379
Cdd:cd18030 81 VFVVDRKDLDYQTSSTFSRFAaEDVV--RANSTKELKELLKNLSG-GIIVTTIQKFNNA-----VKEESKPVLIYRKNIV 152
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499346176 380 FIFDECHRSQFGENHQAIKEFFPKAQLFGFTGTPIFednasyrriegdEQTLKTTEDLFQQSLHEYTI 447
Cdd:cd18030 153 VIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIF------------KEGDKTTEKVFGDYLHKYTI 208
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
251-458 |
4.70e-63 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 213.06 E-value: 4.70e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 251 YQIYAVKNIVECIDKNLG--NGYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFVVDRKDLDRQTREEFNRFQEGCVEEN 328
Cdd:pfam18766 1 QQYFAVNKAVERVLEDGDrrGGVIWHTQGSGKSLTMVFLARKLRRELKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 329 TNTESMVRRLvsdDAADKVIVTTIQKLGRALDparadyrQHLEPLRDQR-MVFIFDECHRSQFGENHQAIKEFFPKAQLF 407
Cdd:pfam18766 81 ESRKDLRELL---RGSGGIIFTTIQKFGETPD-------EGFPVLSDRRnIIVLVDEAHRSQYGGLAANMRDALPNAAFI 150
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 499346176 408 GFTGTPIFEDNasyrriegdeqtlKTTEDLFQQSLHEYTITHAIEDRNVLR 458
Cdd:pfam18766 151 GFTGTPILKKD-------------KNTRAVFGDYIDTYTIQDAVEDGATVP 188
|
|
| HsdR_N |
cd22332 |
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and ... |
5-234 |
2.46e-53 |
|
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: 185.93 E-value: 2.46e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 5 ESTIEQELVEKLGGLKYTLRADI-----RSRAALEANFRKHFEELNR-----VALTNAEFQRLLEEVVTADVFKaahtlr 74
Cdd:cd22332 2 ESQLEEALIELLQELGYEYLPGPelerdKTEVLLEDNLREALERLNPdipsgVPLTDNEFNQLLLELGRDVTPL------ 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 75 hrnaFTRDDGTPLNYTLVNINDW---CKNTFEVASQLRINTDDSHHRYDVILLINGVPAVQIELKTLGINPRRAIEQIVE 151
Cdd:cd22332 76 ----LTLDDDGGKEKTRVILIDFenpENNDFQVVNQFTVEGGKHNRRPDVVLFVNGLPLVVIELKNPGVTIREAYNQIKR 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 152 YKHDvgnGYTRTLLCFIQLFIVSNRDATYYFANNNAR---HFAFNADERFLpiyqyaapDNSKISGLDAFADAFLPKCTL 228
Cdd:cd22332 152 YYKE---IFIPGLFKYNQLFVISNGTETRYGANTAPYerfNEWFTFDWADE--------DNEPITDLETFIKGLLSKERL 220
|
....*.
gi 499346176 229 GQIISR 234
Cdd:cd22332 221 LDLIRN 226
|
|
| EcoR124_C |
pfam12008 |
Type I restriction and modification enzyme - subunit R C terminal; This enzyme has been ... |
707-944 |
2.83e-51 |
|
Type I restriction and modification enzyme - subunit R C terminal; This enzyme has been characterized and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit.
Pssm-ID: 432259 Cd Length: 232 Bit Score: 180.13 E-value: 2.83e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 707 WLVDTAPVVIDKLQKARASLDSFLASqglggkPEDIANLKGTAAKVAFVKHFKDVQKLQTQLDQYTDLTAEQQaqVEAIL 786
Cdd:pfam12008 1 VLVKPYEEYLEKFKDAVEELKELFPT------PESVDNLKSEEEKKEFIKLFRELLRLLNILKQYDEFTGDKS--DLEYL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 787 PKDELRSFRGQYLQKAEELRADQKkagglDDATRNDVEQLDFEFVLFASSTIDYDYIMKLIADYSGKAPGKASMSREQLI 866
Cdd:pfam12008 73 TEREFEDYRSKYLDLYDELRKKEG-----EKEKESILDDIDFELELIKSDEINYDYILELIAKYLKQDMTDDKEEREEII 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 867 GLIASDAKFVDEREDISAYVRGLKAGEGL--SEEAIRAGYEAFKAEKAAQEMTALSGRHGLPVADLQAFVDAVLARRIFD 944
Cdd:pfam12008 148 RALDSSAKLRSKKDLIEAFINDLNPGEGKidDEKDIRDYFEEFKAEEKEKELEELIEEEGLDEEALRKFIDNILRRGRFD 227
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
245-415 |
3.64e-50 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 174.40 E-value: 3.64e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 245 LLMMRPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFVVDRKDLDRQTREEFNRFQEGC 324
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 325 VEENTNTESmvRRLVSDDAADKVIVTTIQKLGRALDparadyRQHLEPLRDQRMVFIFDECHRSQFgENHQAIKEFFPKA 404
Cdd:pfam04851 81 VEIGEIISG--DKKDESVDDNKIVVTTIQSLYKALE------LASLELLPDFFDVIIIDEAHRSGA-SSYRNILEYFKPA 151
|
170
....*....|.
gi 499346176 405 QLFGFTGTPIF 415
Cdd:pfam04851 152 FLLGLTATPER 162
|
|
| SF2_C_EcoR124I-like |
cd18800 |
C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases; This ... |
621-682 |
2.67e-32 |
|
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: 120.36 E-value: 2.67e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499346176 621 KGREKLDIVIVVDMLLTGFDSKYLNTLYVDKNLKYHGLIQAFSRTNRVLNDTKPYGNILDFR 682
Cdd:cd18800 21 RYYKALDLLIVVDMLLTGFDAPSLNTLYVDKPLKYHGLIQAIARVNRVYKDEKEFGLIVDYR 82
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
248-413 |
7.10e-26 |
|
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: 104.31 E-value: 7.10e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 248 MRPYQIYAVKNIVecIDKNLGNGYIWHTTGSGKTLTSFKASTLLKAnpaiEKCLFVVDRKDLDRQTREEFNRFqegcvee 327
Cdd:cd17926 1 LRPYQEEALEAWL--AHKNNRRGILVLPTGSGKTLTALALIAYLKE----LRTLIVVPTDALLDQWKERFEDF------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 328 ntNTESMVRRLVSDDAADK----VIVTTIQKLGRALDPARadyrqhlePLRDQRMVFIFDECHR---SQFGEnhqAIKEF 400
Cdd:cd17926 68 --LGDSSIGLIGGGKKKDFddanVVVATYQSLSNLAEEEK--------DLFDQFGLLIVDEAHHlpaKTFSE---ILKEL 134
|
170
....*....|...
gi 499346176 401 FPKAQLfGFTGTP 413
Cdd:cd17926 135 NAKYRL-GLTATP 146
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
248-525 |
2.43e-22 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 102.41 E-value: 2.43e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 248 MRPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTsfkASTLLKANPAIEKCLFVVDRKDLDRQTREEFNRFqEGCVEE 327
Cdd:COG1061 81 LRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVL---ALALAAELLRGKRVLVLVPRRELLEQWAEELRRF-LGDPLA 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 328 NTNtesmvrrlvSDDAADKVIVTTIQKLGRaldparadyRQHLEPLRDQRMVFIFDECHRSqFGENHQAIKEFFPKAQLF 407
Cdd:COG1061 157 GGG---------KKDSDAPITVATYQSLAR---------RAHLDELGDRFGLVIIDEAHHA-GAPSYRRILEAFPAAYRL 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 408 GFTGTPIFEDNasyRRIEgdeqtlkttEDLFQQSLHEYTITHAIEDRNVLRFHV----DYYKPDGKNAPKPGETL----- 478
Cdd:COG1061 218 GLTATPFRSDG---REIL---------LFLFDGIVYEYSLKEAIEDGYLAPPEYygirVDLTDERAEYDALSERLreala 285
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|.
gi 499346176 479 ----AKRAVVDAILSKHdaatgGRRFNALFATASINDAIEYVGLFKAAQLE 525
Cdd:COG1061 286 adaeRKDKILRELLREH-----PDDRKTLVFCSSVDHAEALAELLNEAGIR 331
|
|
| HSDR_N |
pfam04313 |
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
4-190 |
1.96e-18 |
|
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: 83.12 E-value: 1.96e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 4 RESTIEQELV-EKLGGLKYTLRADIRsraaleanfrkhfEELNRVALTNAefqrlleevvtaDVFKAAHTLRHRNAftrD 82
Cdd:pfam04313 3 SEEEVEQKLIlPLLKALGYDVLNEVR-------------GIKAEVILEKL------------DGNEAFYRLLKYGV---T 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 83 DGTPLNytlvnindwCKNTFEVASQLRInTDDSHHRYDVILLINGVPAVQIELKTLGinPRRAIEQIVEYKHDVGNGYTR 162
Cdd:pfam04313 55 DGITKT---------ENNSFQVANQVEV-KGVQKRRPDYVLFVNGLPLAVIELKRPG--TEEAINQIRRYEKDSFNAIPQ 122
|
170 180 190
....*....|....*....|....*....|
gi 499346176 163 tLLCFI--QLFIVSNRDATYYFANNNARHF 190
Cdd:pfam04313 123 -LFRYAnvQFGILSNGRETRFYTKTAKENR 151
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
248-414 |
1.63e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 82.15 E-value: 1.63e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 248 MRPYQIYAVKNIVEcidkNLGNGYIWHTTGSGKTLTSFK-ASTLLKANPAIeKCLFVVDRKDLDRQTREEFNRF------ 320
Cdd:smart00487 9 LRPYQKEAIEALLS----GLRDVILAAPTGSGKTLAALLpALEALKRGKGG-RVLVLVPTRELAEQWAEELKKLgpslgl 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 321 QEGCVEENTNTESMVRRLVSDDAadKVIVTTIQKLgraldpaRADYRQHLEPLRDQRMVfIFDECHR---SQFGEN-HQA 396
Cdd:smart00487 84 KVVGLYGGDSKREQLRKLESGKT--DILVTTPGRL-------LDLLENDKLSLSNVDLV-ILDEAHRlldGGFGDQlEKL 153
|
170
....*....|....*...
gi 499346176 397 IKEFFPKAQLFGFTGTPI 414
Cdd:smart00487 154 LKLLPKNVQLLLLSATPP 171
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
249-420 |
2.37e-17 |
|
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: 80.30 E-value: 2.37e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 249 RPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTSFKASTLLKANPAIEKCLFVVDRKDLDRQTREEFNRFQegcvEEN 328
Cdd:cd18032 2 RYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEVL----PDG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 329 TNTESMVRRLVSDDAadKVIVTTIQKLGR-----ALDPARADYrqhleplrdqrmvFIFDECHRSQFGeNHQAIKEFFPK 403
Cdd:cd18032 78 SFGNLKGGKKKPDDA--RVVFATVQTLNKrkrleKFPPDYFDL-------------IIIDEAHHAIAS-SYRKILEYFEP 141
|
170
....*....|....*..
gi 499346176 404 AQLFGFTGTPIFEDNAS 420
Cdd:cd18032 142 AFLLGLTATPERTDGLD 158
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
269-412 |
7.41e-16 |
|
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: 75.52 E-value: 7.41e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 269 NGYIWHTTGSGKTLTSFKAStLLKANPAIEKCLFVVDRKDLDRQTREEF-NRFQEGC-VEENTNTESMVRRLVSDDAADK 346
Cdd:cd00046 3 NVLITAPTGSGKTLAALLAA-LLLLLKKGKKVLVLVPTKALALQTAERLrELFGPGIrVAVLVGGSSAEEREKNKLGDAD 81
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499346176 347 VIVTTIQKLGRALDPARADYrqhlepLRDQRmVFIFDECHRSQFGE------NHQAIKEFFPKAQLFGFTGT 412
Cdd:cd00046 82 IIIATPDMLLNLLLREDRLF------LKDLK-LIIVDEAHALLIDSrgalilDLAVRKAGLKNAQVILLSAT 146
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
249-463 |
1.96e-12 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 71.41 E-value: 1.96e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 249 RPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTSFkAST--LLKANPAiEKCLFVVDRKDLDRQTREEFNRFQegcve 326
Cdd:COG4096 160 RYYQIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAI-ALIyrLLKAGRA-KRILFLADRNALVDQAKNAFKPFL----- 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 327 enTNTESMVrRLVSD----DAADKVIVTTIQKLGRALDPARAD--YRQhlePLRDQrmvF---IFDECHRSQFGeNHQAI 397
Cdd:COG4096 233 --PDLDAFT-KLYNKskdiDKSARVYFSTYQTMMNRIDGEEEEpgYRQ---FPPDF---FdliIIDECHRGIYS-KWRAI 302
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499346176 398 KEFFpKAQLFGFTGTPIFEDNASyrriegdeqtlktTEDLFQQSL-HEYTITHAIEDrnvlRFHVDY 463
Cdd:COG4096 303 LDYF-DALQIGLTATPKDTIDRN-------------TYEYFNGNPvYTYSLEQAVAD----GFLVPY 351
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
240-387 |
3.41e-05 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 48.02 E-value: 3.41e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 240 ASEQKL--------LMMRPYQIYAVKNIVECIDKNLGNGYIWHTTGSGKTLTS----FKastLLKANPAiEKCLFVVDRK 307
Cdd:PRK11448 398 AANQWLadepfdygLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAialmYR---LLKAKRF-RRILFLVDRS 473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 308 DLDRQTREEFnrfqegcveENTNTESM--------VRRL--VSDDAADKVIVTTIQKL-GRALDPARADYRqhlePLRDQ 376
Cdd:PRK11448 474 ALGEQAEDAF---------KDTKIEGDqtfasiydIKGLedKFPEDETKVHVATVQGMvKRILYSDDPMDK----PPVDQ 540
|
170
....*....|.
gi 499346176 377 RMVFIFDECHR 387
Cdd:PRK11448 541 YDCIIVDEAHR 551
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
248-414 |
4.67e-05 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 45.25 E-value: 4.67e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 248 MRPYQIYAVKNIVECIDKNLGnGYIWHTTGSGKTL--TSFkASTLLKANPAIEKCLFVVDrKDLDRQTREEFNRFQEGC- 324
Cdd:cd17919 1 LRPYQLEGLNFLLELYENGPG-GILADEMGLGKTLqaIAF-LAYLLKEGKERGPVLVVCP-LSVLENWEREFEKWTPDLr 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 325 ---VEENTNTESMVRRLVSDDAADkVIVTTIQKLGRaldparadYRQHLEPLRdQRMVfIFDECHR-----SQFgenHQA 396
Cdd:cd17919 78 vvvYHGSQRERAQIRAKEKLDKFD-VVLTTYETLRR--------DKASLRKFR-WDLV-VVDEAHRlknpkSQL---SKA 143
|
170
....*....|....*...
gi 499346176 397 IKEFFPKAQLfGFTGTPI 414
Cdd:cd17919 144 LKALRAKRRL-LLTGTPL 160
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
276-414 |
6.73e-05 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 44.54 E-value: 6.73e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 276 TGSGKTLTSFKA--STLLKANPAIeKCLFVVDRKDLDRQTREEFNRF------QEGCVEENTNTESMVRRLVSDDaadkV 347
Cdd:pfam00270 23 TGSGKTLAFLLPalEALDKLDNGP-QALVLAPTRELAEQIYEELKKLgkglglKVASLLGGDSRKEQLEKLKGPD----I 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499346176 348 IVTTIQKLgraldparADYRQHLEPLRDQRMVfIFDECHR---SQFGENHQAIKEFFP-KAQLFGFTGTPI 414
Cdd:pfam00270 98 LVGTPGRL--------LDLLQERKLLKNLKLL-VLDEAHRlldMGFGPDLEEILRRLPkKRQILLLSATLP 159
|
|
| DEAD-like_helicase_C |
cd09300 |
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ... |
628-667 |
6.31e-04 |
|
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain] Cd Length: 59 Bit Score: 38.68 E-value: 6.31e-04
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 499346176 628 IVIVVDMLLTGFDSKYLNTLYVDKNLK-YHGLIQAFSRTNR 667
Cdd:cd09300 8 VLIAVN*ALTGFDAPELNTIIVDKNLRsYRGLNQAFGRANR 48
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
246-413 |
6.32e-04 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 42.08 E-value: 6.32e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 246 LMMRPYQIYAVKNIVECIdknlgNGYIWHTTGSGKTLTSFKAST--LLKANPAIE--KCLFVVDRKDLDRQTREEFNRFQ 321
Cdd:cd18036 1 LELRNYQLELVLPALRGK-----NTIICAPTGSGKTRVAVYICRhhLEKRRSAGEkgRVVVLVNKVPLVEQQLEKFFKYF 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 322 EGCVEEN-----TNTESMVRRLVSddaADKVIVTTIQKLGRALDPARADYRQHLEplrDQRMVfIFDECHRSQfgENH-- 394
Cdd:cd18036 76 RKGYKVTglsgdSSHKVSFGQIVK---ASDVIICTPQILINNLLSGREEERVYLS---DFSLL-IFDECHHTQ--KEHpy 146
|
170 180
....*....|....*....|....*...
gi 499346176 395 ---------QAIKEFFPKAQLFGFTGTP 413
Cdd:cd18036 147 nkimrmyldKKLSSQGPLPQILGLTASP 174
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
249-413 |
5.28e-03 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 39.34 E-value: 5.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 249 RPYQIYAVKNIVEciDKNLgngYIWHTTGSGKTLTS-FKASTLLKANPAIE--KCLFVVDRKDLDRQTREEFNR------ 319
Cdd:cd17927 4 RNYQLELAQPALK--GKNT---IICLPTGSGKTFVAvLICEHHLKKFPAGRkgKVVFLANKVPLVEQQKEVFRKhferpg 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499346176 320 FQEGCVEENTNTESMVRRLVSDDaadKVIVTTIQKLGRALDPARadyrqhlEPLRDQRMVFIFDECHRSQfgENH----- 394
Cdd:cd17927 79 YKVTGLSGDTSENVSVEQIVESS---DVIIVTPQILVNDLKSGT-------IVSLSDFSLLVFDECHNTT--KNHpynei 146
|
170 180
....*....|....*....|....*
gi 499346176 395 ------QAIKEFFPKAQLFGFTGTP 413
Cdd:cd17927 147 mfryldQKLGSSGPLPQILGLTASP 171
|
|
| |
