|
Name |
Accession |
Description |
Interval |
E-value |
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
5-705 |
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: 852.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 5 EEALEDYFMKELRGMGWNDIPAAELGRDDPENPliesELIDSIRRINQYIEDDDIQQVIQELRGKAASIEGCKSILEYLK 84
Cdd:TIGR00348 1 EEEVEDLFIQRLKSLGWEYLKGSELNVEENEKQ----ELIEALKIINDHIEPERWDEVYKKITNKGDLYETNKIFYDYIK 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 85 NGVYIKSATTGEP-RKVKILDHDTPGHNSFTASRQVVFRRgdQTIRTDIMLFINGIPLVNIELKNpvgMSETWADAYRQI 163
Cdd:TIGR00348 77 NGVKIKESQKGEKkRIVKLIDFRNISQNIFQFANQVSFKG--HNIRPDVTLFVNGIPLVIIELKK---RSVTIREAFNQI 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 164 KDYEKTVPELYKYVQMGVAAEDFARYFPV-VPWLDEVPTFEWNETDGKLPpqsrkqdhehhTGLPAADILpLLRPERVLD 242
Cdd:TIGR00348 152 KRYEKEIPELFKYVQIFVISNGTDTRYYTgSDEDDFDFTFNWKESDNKLI-----------EDLKEFDIL-LLKKERLLD 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 243 FIRNYIYIRTEFGSTTKVIARHMQYHAAERIVERVLRNIRGEDKRnRGLIWHWQGSGKTLTMIFAASKLYrmKELENPTV 322
Cdd:TIGR00348 220 FIRNFIIFDKDTGLVTKPYQRYMQYRAVKKIVESITRKTWGKDER-GGLIWHTQGSGKTLTMLFAARKAL--ELLKNPKV 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 323 FFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDDyrgkRGLFITLIQKFTDKLdditAELREHGGetiMDRK 402
Cdd:TIGR00348 297 FFVVDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDD----GGIIITTIQKFDDKL----KEEEEKFP---VDRK 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 403 NVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRERDTYDRFAYPpEEKYIHQYFITDSIRDGFTVKITYQPR 482
Cdd:TIGR00348 366 EVVVIFDEAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFAYV-FGRYLHRYFITDAIRDGLTVKIDYEDR 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 483 LAGDvHLDRKHLEAFIGVEFEELPESIRKDVEESVKRKLDTIKTILENPRRIEIIAEDIAKHFKENIDGR-FKAMVVAPS 561
Cdd:TIGR00348 445 LPED-HLDKKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFkFKAMVVAIS 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 562 RRACVLYKRELDRHLPP--EYSEIVMTYTPRDEEIIRAYEEELMDKYHGRSHHEIKNLVLERFRDpDRNPRILIVTDMLL 639
Cdd:TIGR00348 524 RYACVEEKNALDEELNEkfEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKK-NENPKLLIVVDMLL 602
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1727833626 640 TGFDAPILQTMYLDKPLKEHRLLQAVARTNRPYRDVKEAGLIIDYIGVMgAELRRAFELYSKEEYE 705
Cdd:TIGR00348 603 TGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKDKTFGLIVDYRGLE-KSLIDALSLYGNEAIK 667
|
|
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
2-1008 |
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: 776.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 2 KLNEEALEDYFMKELRGMGWNDIPAAELGRDDPENPLIESELIDSIRRINQYIEDDDIQQVIQELRGKAAS--IEGCKSI 79
Cdd:COG0610 3 KFSEAALEQAIIELLQELGYEYLSGPDIAPEDESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNglLEANKGF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 80 LEYLKNGVYIKSATTGEPRKVKILDHDTPGHNSFTASRQVVFRRGDQTIRTDIMLFINGIPLVNIELKNPvGMSETWADA 159
Cdd:COG0610 83 YDLLRNGVKVEYDGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNP-LTQVTIKEA 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 160 YRQIKDYEKTVPELYKYVQMGVAAE-DFARYFpvVPWLDEVPTFEWNETDGKLPpqsrKQDHEHHTglpAADILPLLRPE 238
Cdd:COG0610 162 FNQIQRYRREIPGLFAYNQLFVISDgVEARYG--TNTAPFEFFLPWKDGDGNDL----NPDGITDL---DYLIEGLLSKE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 239 RVLDFIRNYIYIRTEFGSTTKVIARHMQYHAAERIVERVLRnirGEDKRNRGLIWHWQGSGKTLTMIFAASKLYRMKELE 318
Cdd:COG0610 233 RLLDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKE---AEGDGKGGVIWHTQGSGKSLTMVFLAQKLARLPDLD 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 319 NPTVFFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDDyrgkRGLFITLIQKFTDKLDDITAELrehggetI 398
Cdd:COG0610 310 NPTVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELLESDS----GGIIVTTIQKFPEALDEIKYPE-------L 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 399 MDRKNVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRERDTYDRFayppeEKYIHQYFITDSIRDGFTVKIT 478
Cdd:COG0610 379 SDRKNIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVF-----GDYIHTYTITQAIEDGATLPLL 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 479 YQPRLAgDVHLDRKHLEAfigvEFEELPESIRKDVEESVKRKLDTIKTILENPRRIEIIAEDIAKHFKENID-GRFKAMV 557
Cdd:COG0610 454 YEYRLA-KLKLDKEKIDE----EFDELTEGLDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRpGKGKAMV 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 558 VAPSRRACVLYKRELDRHLP-----PEYSEIVMTYTPRDEEiirayeEELmdKYHGRSHHEiKNLVlERFRDPDRNPRIL 632
Cdd:COG0610 529 VTSSREAAVRYYEAFDKLRPewgykPLKIAVVFSGSANDDP------EEL--KEHGNKEYE-KDLA-KRFKDPDDPLKLL 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 633 IVTDMLLTGFDAPILQTMYLDKPLKEHRLLQAVARTNRPYRDvKEAGLIIDYIGVMgAELRRAFELYSKEEYEGAVY-DM 711
Cdd:COG0610 599 IVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFPG-KPYGLIVDYRGIF-ENLKKALALYSEEDGKEDVLtDP 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 712 ESMKREYEELLRETLRIFS-DLEWDGMD----IEVLSDAVELITSDEELEKKFTENYRELRRLFELLS-DQPFIRHGLKD 785
Cdd:COG0610 677 EEALEELKEALDELRALFPeGVDFSAFDptekLEALDEAVERFLGDEEARKEFKKLFKELSRLYNLLSpDDEFGDLELEK 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 786 YRwltVIYTYYQRVVS--RKPSVEAETERYYQKTLKYIHRTtefreiesklpvIEFDSDYFENLRKvrdirdkaaltvyt 863
Cdd:COG0610 757 YR---DDVSFYLALRAklRKLGEKLDLKEYEEKIRQLLDEA------------IDLERKEIKPRIK-------------- 807
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 864 lnsyvlrngtRNPI-YESVAEKVERLLEQWREKTMDYEELYREGAAIIREIWKEERRMKELGLDEKEFAVLMTLrGRGIP 942
Cdd:COG0610 808 ----------QNPVqYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEEELAFYDAL-AENLG 876
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1727833626 943 EDKLKEYAVALTEEVDGNIFPGWTSQESVKRNVMRIIRVFLLRNLPKDapkrrqiADEAQEDLMKI 1008
Cdd:COG0610 877 DEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYPK-------QDEAVEEVYEQ 935
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
266-505 |
2.66e-78 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 255.05 E-value: 2.66e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 266 QYHAAERIVERVLRnirgEDKRNRGLIWHWQGSGKTLTMIFAASKLyrMKELENPTVFFIVDRRELEEQLYAELAALEIH 345
Cdd:pfam18766 2 QYFAVNKAVERVLE----DGDRRGGVIWHTQGSGKSLTMVFLARKL--RRELKNPTVVVVTDRNDLDDQLTKTFAACGRE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 346 QPERIESIAELKRTIasddyRGKRGLFITLIQKFTDKLDDitaelrehGGETIMDRKNVIVFIDEAHRSQYGLLAAQMKD 425
Cdd:pfam18766 76 VPVQAESRKDLRELL-----RGSGGIIFTTIQKFGETPDE--------GFPVLSDRRNIIVLVDEAHRSQYGGLAANMRD 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 426 MLRSAFFFGFTGTPISKRERDTYDRFayppeEKYIHQYFITDSIRDGFTVKITYQPRLAgDVHLDRKHLEAfigvEFEEL 505
Cdd:pfam18766 143 ALPNAAFIGFTGTPILKKDKNTRAVF-----GDYIDTYTIQDAVEDGATVPILYEGRLA-ELELDDEALDE----EFEEI 212
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
240-465 |
4.46e-69 |
|
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: 229.04 E-value: 4.46e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 240 VLDFIRNYIyIRTEFGSTTKVIARHMQYHAAERIVERVLRNIRGEDKRNRGLIWHWQGSGKTLTMIFAASKLYRMKelEN 319
Cdd:cd18030 1 LLDVLRNFI-VFDEDDDKTKKVARYYQYYAVEAALERIKTATNKDGDKKGGYIWHTQGSGKSLTMFKAAKLLIEDP--KN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 320 PTVFFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDdyrgKRGLFITLIQKFtdklDDITAELREHggeTIM 399
Cdd:cd18030 78 PKVVFVVDRKDLDYQTSSTFSRFAAEDVVRANSTKELKELLKNL----SGGIIVTTIQKF----NNAVKEESKP---VLI 146
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1727833626 400 DRKNVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRE-RDTYDRFAyppeeKYIHQYFI 465
Cdd:cd18030 147 YRKNIVVIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIFKEGdKTTEKVFG-----DYLHKYTI 208
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
271-451 |
7.92e-14 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 71.37 E-value: 7.92e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 271 ERIVERVLRNIRGedkrnrGLIWHWQGSGKTLTMIFAAskLYRMKELENPTVFFIVDRRELEEQLYAELAALEIHQPERI 350
Cdd:smart00487 14 KEAIEALLSGLRD------VILAAPTGSGKTLAALLPA--LEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 351 ESI--AELKRTIASDDYRGKRGLFITLIQKFTDKLDDITAELREHGgetimdrknvIVFIDEAHRSQYGLLAAQMKDMLR 428
Cdd:smart00487 86 VGLygGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVD----------LVILDEAHRLLDGGFGDQLEKLLK 155
|
170 180
....*....|....*....|....*..
gi 1727833626 429 ----SAFFFGFTGTPISKRERDTYDRF 451
Cdd:smart00487 156 llpkNVQLLLLSATPPEEIENLLELFL 182
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
878-985 |
1.76e-07 |
|
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: 54.46 E-value: 1.76e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 878 YESVAEKVERLLEQWREKTMDYEELYREGAAIIREIWKEERRMKELGLDEKEFA---VLMTLR--GRGIPEDKLKEYAVA 952
Cdd:pfam11867 194 SKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELGLSEEELAfydALAENEsaVEVMGDDKLKEIARE 273
|
90 100 110
....*....|....*....|....*....|...
gi 1727833626 953 LTEEVDGNIFPGWTSQESVKRNVMRIIRVfLLR 985
Cdd:pfam11867 274 LVETVRKNATVDWTKREDVRAKLRVAVKR-LLR 305
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
5-705 |
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: 852.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 5 EEALEDYFMKELRGMGWNDIPAAELGRDDPENPliesELIDSIRRINQYIEDDDIQQVIQELRGKAASIEGCKSILEYLK 84
Cdd:TIGR00348 1 EEEVEDLFIQRLKSLGWEYLKGSELNVEENEKQ----ELIEALKIINDHIEPERWDEVYKKITNKGDLYETNKIFYDYIK 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 85 NGVYIKSATTGEP-RKVKILDHDTPGHNSFTASRQVVFRRgdQTIRTDIMLFINGIPLVNIELKNpvgMSETWADAYRQI 163
Cdd:TIGR00348 77 NGVKIKESQKGEKkRIVKLIDFRNISQNIFQFANQVSFKG--HNIRPDVTLFVNGIPLVIIELKK---RSVTIREAFNQI 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 164 KDYEKTVPELYKYVQMGVAAEDFARYFPV-VPWLDEVPTFEWNETDGKLPpqsrkqdhehhTGLPAADILpLLRPERVLD 242
Cdd:TIGR00348 152 KRYEKEIPELFKYVQIFVISNGTDTRYYTgSDEDDFDFTFNWKESDNKLI-----------EDLKEFDIL-LLKKERLLD 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 243 FIRNYIYIRTEFGSTTKVIARHMQYHAAERIVERVLRNIRGEDKRnRGLIWHWQGSGKTLTMIFAASKLYrmKELENPTV 322
Cdd:TIGR00348 220 FIRNFIIFDKDTGLVTKPYQRYMQYRAVKKIVESITRKTWGKDER-GGLIWHTQGSGKTLTMLFAARKAL--ELLKNPKV 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 323 FFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDDyrgkRGLFITLIQKFTDKLdditAELREHGGetiMDRK 402
Cdd:TIGR00348 297 FFVVDRRELDYQLMKEFQSLQKDCAERIESIAELKELLEKDD----GGIIITTIQKFDDKL----KEEEEKFP---VDRK 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 403 NVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRERDTYDRFAYPpEEKYIHQYFITDSIRDGFTVKITYQPR 482
Cdd:TIGR00348 366 EVVVIFDEAHRSQYGELAKNLKKALKNASFFGFTGTPIFKKDRDTSLTFAYV-FGRYLHRYFITDAIRDGLTVKIDYEDR 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 483 LAGDvHLDRKHLEAFIGVEFEELPESIRKDVEESVKRKLDTIKTILENPRRIEIIAEDIAKHFKENIDGR-FKAMVVAPS 561
Cdd:TIGR00348 445 LPED-HLDKKKLDAFFDEIFELLPERIREITKESLKEKLQKTKKILFNEDRLESIAKDIAEHYAKFKELFkFKAMVVAIS 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 562 RRACVLYKRELDRHLPP--EYSEIVMTYTPRDEEIIRAYEEELMDKYHGRSHHEIKNLVLERFRDpDRNPRILIVTDMLL 639
Cdd:TIGR00348 524 RYACVEEKNALDEELNEkfEASAIVMTGKESDDAEIRDYNKHIRTKFDKSDGFEIYYKDLERFKK-NENPKLLIVVDMLL 602
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1727833626 640 TGFDAPILQTMYLDKPLKEHRLLQAVARTNRPYRDVKEAGLIIDYIGVMgAELRRAFELYSKEEYE 705
Cdd:TIGR00348 603 TGFDAPILNTLYLDKPLKYHGLLQAIARTNRIDGKDKTFGLIVDYRGLE-KSLIDALSLYGNEAIK 667
|
|
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
2-1008 |
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: 776.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 2 KLNEEALEDYFMKELRGMGWNDIPAAELGRDDPENPLIESELIDSIRRINQYIEDDDIQQVIQELRGKAAS--IEGCKSI 79
Cdd:COG0610 3 KFSEAALEQAIIELLQELGYEYLSGPDIAPEDESEVLLEDNLRAALERLNPGLSDDEIERALRELTKPESNglLEANKGF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 80 LEYLKNGVYIKSATTGEPRKVKILDHDTPGHNSFTASRQVVFRRGDQTIRTDIMLFINGIPLVNIELKNPvGMSETWADA 159
Cdd:COG0610 83 YDLLRNGVKVEYDGEEKTKTVRLIDFKNPENNDFLVVNQFTVSGGNYKRRPDVVLFVNGLPLVVIELKNP-LTQVTIKEA 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 160 YRQIKDYEKTVPELYKYVQMGVAAE-DFARYFpvVPWLDEVPTFEWNETDGKLPpqsrKQDHEHHTglpAADILPLLRPE 238
Cdd:COG0610 162 FNQIQRYRREIPGLFAYNQLFVISDgVEARYG--TNTAPFEFFLPWKDGDGNDL----NPDGITDL---DYLIEGLLSKE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 239 RVLDFIRNYIYIRTEFGSTTKVIARHMQYHAAERIVERVLRnirGEDKRNRGLIWHWQGSGKTLTMIFAASKLYRMKELE 318
Cdd:COG0610 233 RLLDIIRNFIVFDEDEGGLIKIVARYHQYFAVRKAVERVKE---AEGDGKGGVIWHTQGSGKSLTMVFLAQKLARLPDLD 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 319 NPTVFFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDDyrgkRGLFITLIQKFTDKLDDITAELrehggetI 398
Cdd:COG0610 310 NPTVVVVTDRKDLDDQLFDTFKAFGRESVVQAESRADLRELLESDS----GGIIVTTIQKFPEALDEIKYPE-------L 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 399 MDRKNVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRERDTYDRFayppeEKYIHQYFITDSIRDGFTVKIT 478
Cdd:COG0610 379 SDRKNIIVIVDEAHRSQYGGLAKNMRDALPNASFFGFTGTPIFKEDRTTLEVF-----GDYIHTYTITQAIEDGATLPLL 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 479 YQPRLAgDVHLDRKHLEAfigvEFEELPESIRKDVEESVKRKLDTIKTILENPRRIEIIAEDIAKHFKENID-GRFKAMV 557
Cdd:COG0610 454 YEYRLA-KLKLDKEKIDE----EFDELTEGLDDEEKEKLKAKWALLEEVLGAPERIEQIAEDIVEHFEERTRpGKGKAMV 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 558 VAPSRRACVLYKRELDRHLP-----PEYSEIVMTYTPRDEEiirayeEELmdKYHGRSHHEiKNLVlERFRDPDRNPRIL 632
Cdd:COG0610 529 VTSSREAAVRYYEAFDKLRPewgykPLKIAVVFSGSANDDP------EEL--KEHGNKEYE-KDLA-KRFKDPDDPLKLL 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 633 IVTDMLLTGFDAPILQTMYLDKPLKEHRLLQAVARTNRPYRDvKEAGLIIDYIGVMgAELRRAFELYSKEEYEGAVY-DM 711
Cdd:COG0610 599 IVVDMLLTGFDAPSLHTLYVDKPLKGHNLMQAISRVNRVFPG-KPYGLIVDYRGIF-ENLKKALALYSEEDGKEDVLtDP 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 712 ESMKREYEELLRETLRIFS-DLEWDGMD----IEVLSDAVELITSDEELEKKFTENYRELRRLFELLS-DQPFIRHGLKD 785
Cdd:COG0610 677 EEALEELKEALDELRALFPeGVDFSAFDptekLEALDEAVERFLGDEEARKEFKKLFKELSRLYNLLSpDDEFGDLELEK 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 786 YRwltVIYTYYQRVVS--RKPSVEAETERYYQKTLKYIHRTtefreiesklpvIEFDSDYFENLRKvrdirdkaaltvyt 863
Cdd:COG0610 757 YR---DDVSFYLALRAklRKLGEKLDLKEYEEKIRQLLDEA------------IDLERKEIKPRIK-------------- 807
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 864 lnsyvlrngtRNPI-YESVAEKVERLLEQWREKTMDYEELYREGAAIIREIWKEERRMKELGLDEKEFAVLMTLrGRGIP 942
Cdd:COG0610 808 ----------QNPVqYRKFSELLEEIIEEYNNGALDADEVLEELEELAKEVKEEEERAEEEGLNEEELAFYDAL-AENLG 876
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1727833626 943 EDKLKEYAVALTEEVDGNIFPGWTSQESVKRNVMRIIRVFLLRNLPKDapkrrqiADEAQEDLMKI 1008
Cdd:COG0610 877 DEKLKELAKELDDLLKKNVTVDWRKRESVRAKLRDAIKRLLRKYGYPK-------QDEAVEEVYEQ 935
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
266-505 |
2.66e-78 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 255.05 E-value: 2.66e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 266 QYHAAERIVERVLRnirgEDKRNRGLIWHWQGSGKTLTMIFAASKLyrMKELENPTVFFIVDRRELEEQLYAELAALEIH 345
Cdd:pfam18766 2 QYFAVNKAVERVLE----DGDRRGGVIWHTQGSGKSLTMVFLARKL--RRELKNPTVVVVTDRNDLDDQLTKTFAACGRE 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 346 QPERIESIAELKRTIasddyRGKRGLFITLIQKFTDKLDDitaelrehGGETIMDRKNVIVFIDEAHRSQYGLLAAQMKD 425
Cdd:pfam18766 76 VPVQAESRKDLRELL-----RGSGGIIFTTIQKFGETPDE--------GFPVLSDRRNIIVLVDEAHRSQYGGLAANMRD 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 426 MLRSAFFFGFTGTPISKRERDTYDRFayppeEKYIHQYFITDSIRDGFTVKITYQPRLAgDVHLDRKHLEAfigvEFEEL 505
Cdd:pfam18766 143 ALPNAAFIGFTGTPILKKDKNTRAVF-----GDYIDTYTIQDAVEDGATVPILYEGRLA-ELELDDEALDE----EFEEI 212
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
240-465 |
4.46e-69 |
|
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: 229.04 E-value: 4.46e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 240 VLDFIRNYIyIRTEFGSTTKVIARHMQYHAAERIVERVLRNIRGEDKRNRGLIWHWQGSGKTLTMIFAASKLYRMKelEN 319
Cdd:cd18030 1 LLDVLRNFI-VFDEDDDKTKKVARYYQYYAVEAALERIKTATNKDGDKKGGYIWHTQGSGKSLTMFKAAKLLIEDP--KN 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 320 PTVFFIVDRRELEEQLYAELAALEIHQPERIESIAELKRTIASDdyrgKRGLFITLIQKFtdklDDITAELREHggeTIM 399
Cdd:cd18030 78 PKVVFVVDRKDLDYQTSSTFSRFAAEDVVRANSTKELKELLKNL----SGGIIVTTIQKF----NNAVKEESKP---VLI 146
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1727833626 400 DRKNVIVFIDEAHRSQYGLLAAQMKDMLRSAFFFGFTGTPISKRE-RDTYDRFAyppeeKYIHQYFI 465
Cdd:cd18030 147 YRKNIVVIVDEAHRSQFGELAKALKKALPNATFIGFTGTPIFKEGdKTTEKVFG-----DYLHKYTI 208
|
|
| HsdR_N |
cd22332 |
N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and ... |
4-246 |
2.66e-43 |
|
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: 157.04 E-value: 2.66e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 4 NEEALEDYFMKELRGMGWNDIPAAELGRDdPENPLIESELIDSIRRINQYI------EDDDIQQVIQELRGKAASIEGCK 77
Cdd:cd22332 1 TESQLEEALIELLQELGYEYLPGPELERD-KTEVLLEDNLREALERLNPDIpsgvplTDNEFNQLLLELGRDVTPLLTLD 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 78 SileylkngvyiksATTGEPRKVKILDHDTPGHNSFTASRQVVFRRGDQTIRTDIMLFINGIPLVNIELKNPvgmSETWA 157
Cdd:cd22332 80 D-------------DGGKEKTRVILIDFENPENNDFQVVNQFTVEGGKHNRRPDVVLFVNGLPLVVIELKNP---GVTIR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 158 DAYRQIKDYEK--TVPELYKYVQMGVAA-EDFARYFPVVPWLD---EVPTFEWNETDGKLPPQsrkQDHEHHTglpaadi 231
Cdd:cd22332 144 EAYNQIKRYYKeiFIPGLFKYNQLFVISnGTETRYGANTAPYErfnEWFTFDWADEDNEPITD---LETFIKG------- 213
|
250
....*....|....*
gi 1727833626 232 lpLLRPERVLDFIRN 246
Cdd:cd22332 214 --LLSKERLLDLIRN 226
|
|
| SF2_C_EcoR124I-like |
cd18800 |
C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases; This ... |
554-684 |
2.65e-29 |
|
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: 111.50 E-value: 2.65e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 554 KAMVVAPSRRACVLYKRELDrhlppeyseivmtytprdeeiirayeeelmdkyhgrshheiknlvlerfrdpdrnprILI 633
Cdd:cd18800 8 KAMVVTSSRRAAVRYYKALD---------------------------------------------------------LLI 30
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1727833626 634 VTDMLLTGFDAPILQTMYLDKPLKEHRLLQAVARTNRPYRDVKEAGLIIDY 684
Cdd:cd18800 31 VVDMLLTGFDAPSLNTLYVDKPLKYHGLIQAIARVNRVYKDEKEFGLIVDY 81
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
263-440 |
5.57e-23 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 96.59 E-value: 5.57e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 263 RHMQYHAAERIVERVLRNirgedkRNRGLIWHWQGSGKTLTMIFAAskLYRMKELENPTVFFIVDRRELEEQLYAELAAL 342
Cdd:pfam04851 5 RPYQIEAIENLLESIKNG------QKRGLIVMATGSGKTLTAAKLI--ARLFKKGPIKKVLFLVPRKDLLEQALEEFKKF 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 343 EIHQPERIESIAELKRTIASDDYRgkrgLFITLIQKftdklddITAELREHGGETIMDRKNVIVfIDEAHRSQYGlLAAQ 422
Cdd:pfam04851 77 LPNYVEIGEIISGDKKDESVDDNK----IVVTTIQS-------LYKALELASLELLPDFFDVII-IDEAHRSGAS-SYRN 143
|
170
....*....|....*...
gi 1727833626 423 MKDMLRSAFFFGFTGTPI 440
Cdd:pfam04851 144 ILEYFKPAFLLGLTATPE 161
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
297-812 |
4.09e-19 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 92.40 E-value: 4.09e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 297 GSGKTLTMIFAASKLYRmkeleNPTVFFIVDRRELEEQLYaelaaleihqpERIESIAELKRTIASDDYRGKRGLFITlI 376
Cdd:COG1061 110 GTGKTVLALALAAELLR-----GKRVLVLVPRRELLEQWA-----------EELRRFLGDPLAGGGKKDSDAPITVAT-Y 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 377 QKFTDKLDDitaelrehggETIMDRKNVIVfIDEAHR---SQYGLLAaqmkDMLRSAFFFGFTGTPISKRERDTY-DRFA 452
Cdd:COG1061 173 QSLARRAHL----------DELGDRFGLVI-IDEAHHagaPSYRRIL----EAFPAAYRLGLTATPFRSDGREILlFLFD 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 453 YPpeekyIHQYFITDSIRDGFTVKITYQPRlagDVHLDRKhleafiGVEFEELPESIRKDVEESVKRKLDTIKTILEnpr 532
Cdd:COG1061 238 GI-----VYEYSLKEAIEDGYLAPPEYYGI---RVDLTDE------RAEYDALSERLREALAADAERKDKILRELLR--- 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 533 rieiiaediakhfkENIDGRfKAMVVAPSRRACVLYKRELDRHlppeyseivmtytprDEEIIRayeeelmdkYHGRSHH 612
Cdd:COG1061 301 --------------EHPDDR-KTLVFCSSVDHAEALAELLNEA---------------GIRAAV---------VTGDTPK 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 613 EIKNLVLERFRDpdRNPRILIVTDMLLTGFDAPILQTMYLDKPLKEHRL-LQAVARTNRPYRDvKEAGLIIDYIGV---- 687
Cdd:COG1061 342 KEREEILEAFRD--GELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREfIQRLGRGLRPAPG-KEDALVYDFVGNdvpv 418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 688 ---------MGAELRRAFELYSKEEYEGAVYDMESMKREYEELLRETLRIFSDLEWDGMDIEVLSDAVELITSDEELEKK 758
Cdd:COG1061 419 leelakdlrDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLEL 498
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....
gi 1727833626 759 FTENYRELRRLFELLSDQPFIRHGLKDYRWLTVIYTYYQRVVSRKPSVEAETER 812
Cdd:COG1061 499 AKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLELLELLAALLRLEELA 552
|
|
| HSDR_N |
pfam04313 |
Type I restriction enzyme R protein N terminus (HSDR_N); This family consists of a number of N ... |
2-195 |
1.01e-16 |
|
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: 78.12 E-value: 1.01e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 2 KLNEEALEDYF-MKELRGMGWNDIpaaELGRDDPENPLIESelidsirrinqyiedddiqqviqelrgkaasIEGCKSIL 80
Cdd:pfam04313 1 ILSEEEVEQKLiLPLLKALGYDVL---NEVRGIKAEVILEK-------------------------------LDGNEAFY 46
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 81 EYLKNGVYIKSATTGeprkvkildhdtpgHNSFTASRQVVFRrGDQTIRTDIMLFINGIPLVNIELKNPVGMsetwaDAY 160
Cdd:pfam04313 47 RLLKYGVTDGITKTE--------------NNSFQVANQVEVK-GVQKRRPDYVLFVNGLPLAVIELKRPGTE-----EAI 106
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1727833626 161 RQIKDYEKT----VPELYKYV--QMGVAAEDFARYFPVVPW 195
Cdd:pfam04313 107 NQIRRYEKDsfnaIPQLFRYAnvQFGILSNGRETRFYTKTA 147
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
271-451 |
7.92e-14 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 71.37 E-value: 7.92e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 271 ERIVERVLRNIRGedkrnrGLIWHWQGSGKTLTMIFAAskLYRMKELENPTVFFIVDRRELEEQLYAELAALEIHQPERI 350
Cdd:smart00487 14 KEAIEALLSGLRD------VILAAPTGSGKTLAALLPA--LEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 351 ESI--AELKRTIASDDYRGKRGLFITLIQKFTDKLDDITAELREHGgetimdrknvIVFIDEAHRSQYGLLAAQMKDMLR 428
Cdd:smart00487 86 VGLygGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVD----------LVILDEAHRLLDGGFGDQLEKLLK 155
|
170 180
....*....|....*....|....*..
gi 1727833626 429 ----SAFFFGFTGTPISKRERDTYDRF 451
Cdd:smart00487 156 llpkNVQLLLLSATPPEEIENLLELFL 182
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
263-755 |
3.35e-13 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 74.11 E-value: 3.35e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 263 RHMQYHAAERIVERVlrnirgEDKRNRGLIwhwQ---GSGKTLTMIFAASKLYRMKELENptVFFIVDRRELEEQLYAEL 339
Cdd:COG4096 160 RYYQIEAIRRVEEAI------AKGQRRALL---VmatGTGKTRTAIALIYRLLKAGRAKR--ILFLADRNALVDQAKNAF 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 340 AALEIHQPERIEsIAELKRTIAsDDYRgkrgLFITLIQKFTDKLDditaelrehGGETIMDRKNV------IVFIDEAHR 413
Cdd:COG4096 229 KPFLPDLDAFTK-LYNKSKDID-KSAR----VYFSTYQTMMNRID---------GEEEEPGYRQFppdffdLIIIDECHR 293
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 414 SQYGLlaaqMKDMLR--SAFFFGFTGTPISKRERDTYDRFAYPPeekyIHQYFITDSIRDGFTVK--------------I 477
Cdd:COG4096 294 GIYSK----WRAILDyfDALQIGLTATPKDTIDRNTYEYFNGNP----VYTYSLEQAVADGFLVPykviridtkfdregI 365
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 478 TYQprlAGDVHLDRKHLEafigVEFEELPESIRKDVEEsvkrkldtIKTILENPRRIEIIAEDIAKHFKENIDGRF-KAM 556
Cdd:COG4096 366 RYD---AGEDLSDEEGEE----IELEELEEDREYEAKD--------FNRKVVNEDTTRKVLEELMEYLDKPGGDRLgKTI 430
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 557 VVAPSRRACVLYKRELDRHLPPEYSEIVMTYTPRDEEiirayeeelmdkyhGRSHheiknlvLERFRDPDRNPRILIVTD 636
Cdd:COG4096 431 IFAKNDDHADRIVQALRELYPELGGDFVKKITGDDDY--------------GKSL-------IDNFKNPEKYPRIAVTVD 489
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 637 MLLTGFDAPILQTMYLDKPLKEHRLL-QAV---ARTNRPYRDVKEAGLIIDYIGVmgaelrraFELYSKEEYEGAVYDME 712
Cdd:COG4096 490 MLDTGIDVPEVVNLVFMRPVKSRIKFeQMIgrgTRLCPDLFPGKTHFTIFDFVGN--------TELFADPSFPLRIFEPR 561
|
490 500 510 520
....*....|....*....|....*....|....*....|....*....
gi 1727833626 713 SMKREYEELL----RETL--RIFSDLEWDGMDIEVLSDAVELITSDEEL 755
Cdd:COG4096 562 REREKFWDLLggedPAKLavHLADALDPDKVTIPVVAEAVQLLDDVPDL 610
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
278-439 |
7.34e-13 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 66.95 E-value: 7.34e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 278 LRNIRGEDKRNRGLIWHWQGSGKTLTMIFAASKLYRMKelenptVFFIVDRRELEEQLYAELAA-LEIHQPERIESiael 356
Cdd:cd17926 9 LEAWLAHKNNRRGILVLPTGSGKTLTALALIAYLKELR------TLIVVPTDALLDQWKERFEDfLGDSSIGLIGG---- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 357 KRTIASDDyrgkRGLFITLIQKftdkldditAELREHGGETIMDRKNVIVFiDEAHRSQyGLLAAQMKDMLRSAFFFGFT 436
Cdd:cd17926 79 GKKKDFDD----ANVVVATYQS---------LSNLAEEEKDLFDQFGLLIV-DEAHHLP-AKTFSEILKELNAKYRLGLT 143
|
...
gi 1727833626 437 GTP 439
Cdd:cd17926 144 ATP 146
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
263-451 |
1.43e-11 |
|
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: 63.73 E-value: 1.43e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 263 RHMQYHAAERIVERVlrnirgEDKRNRGLIWHWQGSGKTLTMIFAASKLyrMKELENPTVFFIVDRRELEEQlyaelAAL 342
Cdd:cd18032 2 RYYQQEAIEALEEAR------EKGQRRALLVMATGTGKTYTAAFLIKRL--LEANRKKRILFLAHREELLEQ-----AER 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 343 EIHQPERIESIAELKR-TIASDDYRgkrgLFITLIQKFTDkldditaelREHGGETIMDRKNVIVfIDEAHRSQYG---- 417
Cdd:cd18032 69 SFKEVLPDGSFGNLKGgKKKPDDAR----VVFATVQTLNK---------RKRLEKFPPDYFDLII-IDEAHHAIASsyrk 134
|
170 180 190
....*....|....*....|....*....|....
gi 1727833626 418 LLaaqmkDMLRSAFFFGFTGTPISKRERDTYDRF 451
Cdd:cd18032 135 IL-----EYFEPAFLLGLTATPERTDGLDTYELF 163
|
|
| DUF3387 |
pfam11867 |
Domain of unknown function (DUF3387); This domain is functionally uncharacterized. This domain ... |
878-985 |
1.76e-07 |
|
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: 54.46 E-value: 1.76e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 878 YESVAEKVERLLEQWREKTMDYEELYREGAAIIREIWKEERRMKELGLDEKEFA---VLMTLR--GRGIPEDKLKEYAVA 952
Cdd:pfam11867 194 SKKFSERLEEAINRYNNRALTTAEVIEELIELAKEIREEDKRGEELGLSEEELAfydALAENEsaVEVMGDDKLKEIARE 273
|
90 100 110
....*....|....*....|....*....|...
gi 1727833626 953 LTEEVDGNIFPGWTSQESVKRNVMRIIRVfLLR 985
Cdd:pfam11867 274 LVETVRKNATVDWTKREDVRAKLRVAVKR-LLR 305
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
290-425 |
1.38e-05 |
|
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: 45.86 E-value: 1.38e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 290 GLIWHWQGSGKTLT-MIFAASKLyrmkELENPTVFFIVDRRELEEQLYAELAALEIHqPERIESI-----AELKRTIASD 363
Cdd:cd00046 4 VLITAPTGSGKTLAaLLAALLLL----LKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLvggssAEEREKNKLG 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1727833626 364 DYRgkrgLFITLIQKFtdkLDDITAELREHggetimDRKNVIVFIDEAHRSQYGLLAAQMKD 425
Cdd:cd00046 79 DAD----IIIATPDML---LNLLLREDRLF------LKDLKLIIVDEAHALLIDSRGALILD 127
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
593-685 |
3.35e-04 |
|
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: 41.39 E-value: 3.35e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 593 EIIRAYEEELMDKYHGRSHHEIKNLVLERFRDPDRNPRILIVTDMLLTGFDAPILQTMYLDKPLKEHRL-LQAVARTNRP 671
Cdd:cd18799 24 EAFNEAGIDAVALNSDYSDRERGDEALILLFFGELKPPILVTVDLLTTGVDIPEVDNVVFLRPTESRTLfLQMLGRGLRL 103
|
90
....*....|....
gi 1727833626 672 YRDvKEAGLIIDYI 685
Cdd:cd18799 104 HEG-KDFFTILDFI 116
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
605-671 |
2.46e-03 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 37.96 E-value: 2.46e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1727833626 605 KYHGRSHHEIKNLVLERFRDPDRnpRILIVTDMLLTGFDAPILQTM-YLDKPLKEHRLLQAVARTNRP 671
Cdd:smart00490 16 RLHGGLSQEEREEILDKFNNGKI--KVLVATDVAERGLDLPGVDLViIYDLPWSPASYIQRIGRAGRA 81
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
297-445 |
5.19e-03 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 38.76 E-value: 5.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 297 GSGKTLT-MIFAASKLYrmKELENPTVFFIVDRRELEEQLYAELAALEIHQPERIESI---AELKRTIasDDYRGKRGLF 372
Cdd:pfam00270 24 GSGKTLAfLLPALEALD--KLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLlggDSRKEQL--EKLKGPDILV 99
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1727833626 373 ITliqkfTDKLDDITAELREhggetiMDRKNVIVfIDEAHRSQYGLLAAQMKDMLR----SAFFFGFTGTPISKRER 445
Cdd:pfam00270 100 GT-----PGRLLDLLQERKL------LKNLKLLV-LDEAHRLLDMGFGPDLEEILRrlpkKRQILLLSATLPRNLED 164
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
591-670 |
6.46e-03 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 37.58 E-value: 6.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1727833626 591 DEEIIRAYEEELMDKYHGRSHHEIKNLVLERFRDPDRnpRILIVTDMLLTGFDAPILQTM-YLDKPLKEHRLLQAVARTN 669
Cdd:pfam00271 29 EAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKI--DVLVATDVAERGLDLPDVDLViNYDLPWNPASYIQRIGRAG 106
|
.
gi 1727833626 670 R 670
Cdd:pfam00271 107 R 107
|
|
| |
