|
Name |
Accession |
Description |
Interval |
E-value |
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
1-815 |
0e+00 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 696.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 1 MNEAQTKHDLIEPALRAAGWgsVEGSRLRLEFPITKGRLIGLNRRATPL---FADYILEYKNRR-IGVVEAKKKHSYYTD 76
Cdd:COG4096 2 LSEAETRKKLIDPALKEAGW--DVDDQILREVRPTAGRNVVIGEWPTRGgkgYADYVLFGDDGKpLAVVEAKRTSKDVSA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 77 GVGQAKDYAERLD-----IRFTYATNGLQIYGIDL--DEGTEGDVSKYPTPDELWEMtyptpkedYKVEIADWKERLFAI 149
Cdd:COG4096 80 GLQQAKLYADGLEkqygqVPFIFATNGREIWFWDDrdPYPREREVDGFPSPEELWEL--------LKRRKGTARKRLATE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 150 PFEDrggTWQPRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWnlrrdgsrSPRILFLADRNIL 229
Cdd:COG4096 152 PYND---GIALRYYQIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAIALIYRLLKAGR--------AKRILFLADRNAL 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 230 ADQAFNSFNAF--DEDALVRISPKEikkkGKVPKNGSVFFTIFQTFMTnanqeedekdeeneeenysiaaepAAKYNTDD 307
Cdd:COG4096 221 VDQAKNAFKPFlpDLDAFTKLYNKS----KDIDKSARVYFSTYQTMMN------------------------RIDGEEEE 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 308 FNFGQYPKDFFDLIIIDECHRGGSrdeSSWRAIMEHFSpAVQLGLTATPKRDINGDTYDYF-GEPVYTYKLKDGINDGFL 386
Cdd:COG4096 273 PGYRQFPPDFFDLIIIDECHRGIY---SKWRAILDYFD-ALQIGLTATPKDTIDRNTYEYFnGNPVYTYSLEQAVADGFL 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 387 TPFKVKEISTTIDEY----------VHTSGDEVD-GEIEEGKTYSESDFNRIIAIKAREEYRVKLFMDSI-----NQNQK 450
Cdd:COG4096 349 VPYKVIRIDTKFDREgirydagedlSDEEGEEIElEELEEDREYEAKDFNRKVVNEDTTRKVLEELMEYLdkpggDRLGK 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 451 TLVFCATQIHAATVRDLINQYATSKSINYCHRVTADDGQiGEQHLRDFQDNEKsIPTILTTSQKLSTGVDAPEIRNIVLM 530
Cdd:COG4096 429 TIIFAKNDDHADRIVQALRELYPELGGDFVKKITGDDDY-GKSLIDNFKNPEK-YPRIAVTVDMLDTGIDVPEVVNLVFM 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 531 RPVNSMVEFKQIVGRGTRL----FDGKDYFTVFDFVDAHHHFQDPEWdgdPLEPKRPTEGGAPGDCNICSETP------- 599
Cdd:COG4096 507 RPVKSRIKFEQMIGRGTRLcpdlFPGKTHFTIFDFVGNTELFADPSF---PLRIFEPRREREKFWDLLGGEDPaklavhl 583
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 600 -------CVCQKPPEEACP---KCENIPCVCETPPRAMISVRLSDNQvreiDSMVKTSFWspSGKPISSQEFITQLFGDL 669
Cdd:COG4096 584 adaldpdKVTIPVVAEAVQlldDVPDLRDLLKFIDKDKRQIIYTDFE----DELLEAEEG--YGKKLKAEDYRDKFEAFL 657
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 670 P--SFFNNEEQLRTLWSvPSTRKKLLTELSEKGYTNSQLEDLRHLIHGEDSDLFDVLSYVAYH-KELVPRLERASRAK-- 744
Cdd:COG4096 658 RehKEIPALQKLRNRLT-REDLKELEEELEEQGLGEEDLAEAYGEVGNELADLIDLIRHIAGLdQPLLTRRERVERAFkr 736
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504838941 745 -IQMNSYNVKQQEFLNFVLDQYVREGVDELDDSKLPdllELKYK-AIADAKKELGDTKSIRDTFIGFQQHLYQ 815
Cdd:COG4096 737 fLAGHKYTEEQREFLERILDHLADNGVIELEDLDEA---PFTQDgGPGGIDGLFGGVDELDEALEELNEALYA 806
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
1-570 |
1.48e-60 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 222.90 E-value: 1.48e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 1 MNEAQTKHdLIEPALRAAGWgsvEGSRLRLEF-----PiTKGRLIGLNRRATPL--FADYILEYKNRRIGVVEAKKKHSY 73
Cdd:PRK11448 231 LSEEETRI-LIDQQLRKAGW---EADSKTLRFskgarP-EKGRNLAIAEWPTGKtgRADYALFIGLKPVGVVEAKRKNKD 305
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 74 YTDGVGQAKDYAERLDIR---------------------FTYATNG------LQ----IYGIDLDEGTEGDVS--KYPTP 120
Cdd:PRK11448 306 VASKLNQAKRYSKGFDVAeevpeyggpwqdtsggrykvpFVFSTNGrpylkqLKtksgIWFRDVRKPTNHPRAlqGWHTP 385
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 121 DELWEMTyptpkedyKVEIADWKERLFAIPFEDRGGTwqpRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIA 200
Cdd:PRK11448 386 EGLLDLL--------ESDIEAANQWLADEPFDYGLGL---RYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM 454
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 201 WKLFHAKwnlrrdgsRSPRILFLADRNILADQAFNSFnafdedalvrispKEIKKKGkvpkngsvfftiFQTFmtnanqe 280
Cdd:PRK11448 455 YRLLKAK--------RFRRILFLVDRSALGEQAEDAF-------------KDTKIEG------------DQTF------- 494
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 281 edekdeeneEENYSI------AAEPAAK--------------YNTDdfNFGQYPKDFFDLIIIDECHRG----------- 329
Cdd:PRK11448 495 ---------ASIYDIkgledkFPEDETKvhvatvqgmvkrilYSDD--PMDKPPVDQYDCIIVDEAHRGytldkemsege 563
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 330 -GSRDE----SSWRAIMEHFSpAVQLGLTATPKRDingdTYDYFGEPVYTYKLKDGINDGFLT----PFKVK-------- 392
Cdd:PRK11448 564 lQFRDQldyvSKYRRVLDYFD-AVKIGLTATPALH----TTEIFGEPVYTYSYREAVIDGYLIdhepPIRIEtrlsqegi 638
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 393 --EISTTIDEYVHTSG--------DEVDGEIEE--GKTYSESdFNRIIAikareEYRVKlFMDSINQnQKTLVFCATQIH 460
Cdd:PRK11448 639 hfEKGEEVEVINTQTGeidlatleDEVDFEVEDfnRRVITES-FNRVVC-----EELAK-YLDPTGE-GKTLIFAATDAH 710
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 461 AATVRDLINQYATSKSINYCH----RVTaddGQIG--EQHLRDFQdNEKsIPTILTTSQKLSTGVDAPEIRNIVLMRPVN 534
Cdd:PRK11448 711 ADMVVRLLKEAFKKKYGQVEDdaviKIT---GSIDkpDQLIRRFK-NER-LPNIVVTVDLLTTGIDVPSICNLVFLRRVR 785
|
650 660 670
....*....|....*....|....*....|....*...
gi 504838941 535 SMVEFKQIVGRGTRLFD--GKDYFTVFDFVDAHHHFQD 570
Cdd:PRK11448 786 SRILYEQMLGRATRLCPeiGKTHFRIFDAVDIYEALES 823
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
160-368 |
3.85e-59 |
|
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: 198.17 E-value: 3.85e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 160 PRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWNlrrdgsrsPRILFLADRNILADQAFNSFNA 239
Cdd:cd18032 1 PRYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRK--------KRILFLAHREELLEQAERSFKE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 240 FdedaLVRISPKEIKKKGKVPKNGSVFFTIFQTFMTNANQEedekdeeneeenysiaaepaakyntddfnfgQYPKDFFD 319
Cdd:cd18032 73 V----LPDGSFGNLKGGKKKPDDARVVFATVQTLNKRKRLE-------------------------------KFPPDYFD 117
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 504838941 320 LIIIDECHRGGSrdeSSWRAIMEHFSPAVQLGLTATPKRDINGDTYDYF 368
Cdd:cd18032 118 LIIIDEAHHAIA---SSYRKILEYFEPAFLLGLTATPERTDGLDTYELF 163
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
159-358 |
1.15e-40 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 146.66 E-value: 1.15e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWNlrrdgsrsPRILFLADRNILADQAFNSFN 238
Cdd:pfam04851 3 ELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPI--------KKVLFLVPRKDLLEQALEEFK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AFDEDALVRISPKEIKKKGKVPKNGSVFFTIFQTFMTNANQEEDekdeeneeenysiaaepaakyntddfnfgQYPKDFF 318
Cdd:pfam04851 75 KFLPNYVEIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASL-----------------------------ELLPDFF 125
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 504838941 319 DLIIIDECHRGGSrdeSSWRAIMEHFSPAVQLGLTATPKR 358
Cdd:pfam04851 126 DVIIIDEAHRSGA---SSYRNILEYFKPAFLLGLTATPER 162
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
159-394 |
2.84e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 81.00 E-value: 2.84e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVLEAISekkdRLLLTLATGTGKTAIAFQIAWKLFHAKwnlrrdgsRSPRILFLADRNILADQAFNSFN 238
Cdd:smart00487 8 PLRPYQKEAIEALLSGLR----DVILAAPTGSGKTLAALLPALEALKRG--------KGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AFDEDALVR----ISPKEIKKKGKVPKNGS--VFFTIFQTFMtnanqeedekdeeneeenysiaaepaakyntDDFNFGQ 312
Cdd:smart00487 76 KLGPSLGLKvvglYGGDSKREQLRKLESGKtdILVTTPGRLL-------------------------------DLLENDK 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 313 YPKDFFDLIIIDECHRGGSRD-ESSWRAIMEHFSPAVQ-LGLTATPKRDINGDTYDYFGEPVYtyklkdgINDGFLTPFK 390
Cdd:smart00487 125 LSLSNVDLVILDEAHRLLDGGfGDQLEKLLKLLPKNVQlLLLSATPPEEIENLLELFLNDPVF-------IDVGFTPLEP 197
|
....
gi 504838941 391 VKEI 394
Cdd:smart00487 198 IEQF 201
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
1-815 |
0e+00 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 696.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 1 MNEAQTKHDLIEPALRAAGWgsVEGSRLRLEFPITKGRLIGLNRRATPL---FADYILEYKNRR-IGVVEAKKKHSYYTD 76
Cdd:COG4096 2 LSEAETRKKLIDPALKEAGW--DVDDQILREVRPTAGRNVVIGEWPTRGgkgYADYVLFGDDGKpLAVVEAKRTSKDVSA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 77 GVGQAKDYAERLD-----IRFTYATNGLQIYGIDL--DEGTEGDVSKYPTPDELWEMtyptpkedYKVEIADWKERLFAI 149
Cdd:COG4096 80 GLQQAKLYADGLEkqygqVPFIFATNGREIWFWDDrdPYPREREVDGFPSPEELWEL--------LKRRKGTARKRLATE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 150 PFEDrggTWQPRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWnlrrdgsrSPRILFLADRNIL 229
Cdd:COG4096 152 PYND---GIALRYYQIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAIALIYRLLKAGR--------AKRILFLADRNAL 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 230 ADQAFNSFNAF--DEDALVRISPKEikkkGKVPKNGSVFFTIFQTFMTnanqeedekdeeneeenysiaaepAAKYNTDD 307
Cdd:COG4096 221 VDQAKNAFKPFlpDLDAFTKLYNKS----KDIDKSARVYFSTYQTMMN------------------------RIDGEEEE 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 308 FNFGQYPKDFFDLIIIDECHRGGSrdeSSWRAIMEHFSpAVQLGLTATPKRDINGDTYDYF-GEPVYTYKLKDGINDGFL 386
Cdd:COG4096 273 PGYRQFPPDFFDLIIIDECHRGIY---SKWRAILDYFD-ALQIGLTATPKDTIDRNTYEYFnGNPVYTYSLEQAVADGFL 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 387 TPFKVKEISTTIDEY----------VHTSGDEVD-GEIEEGKTYSESDFNRIIAIKAREEYRVKLFMDSI-----NQNQK 450
Cdd:COG4096 349 VPYKVIRIDTKFDREgirydagedlSDEEGEEIElEELEEDREYEAKDFNRKVVNEDTTRKVLEELMEYLdkpggDRLGK 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 451 TLVFCATQIHAATVRDLINQYATSKSINYCHRVTADDGQiGEQHLRDFQDNEKsIPTILTTSQKLSTGVDAPEIRNIVLM 530
Cdd:COG4096 429 TIIFAKNDDHADRIVQALRELYPELGGDFVKKITGDDDY-GKSLIDNFKNPEK-YPRIAVTVDMLDTGIDVPEVVNLVFM 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 531 RPVNSMVEFKQIVGRGTRL----FDGKDYFTVFDFVDAHHHFQDPEWdgdPLEPKRPTEGGAPGDCNICSETP------- 599
Cdd:COG4096 507 RPVKSRIKFEQMIGRGTRLcpdlFPGKTHFTIFDFVGNTELFADPSF---PLRIFEPRREREKFWDLLGGEDPaklavhl 583
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 600 -------CVCQKPPEEACP---KCENIPCVCETPPRAMISVRLSDNQvreiDSMVKTSFWspSGKPISSQEFITQLFGDL 669
Cdd:COG4096 584 adaldpdKVTIPVVAEAVQlldDVPDLRDLLKFIDKDKRQIIYTDFE----DELLEAEEG--YGKKLKAEDYRDKFEAFL 657
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 670 P--SFFNNEEQLRTLWSvPSTRKKLLTELSEKGYTNSQLEDLRHLIHGEDSDLFDVLSYVAYH-KELVPRLERASRAK-- 744
Cdd:COG4096 658 RehKEIPALQKLRNRLT-REDLKELEEELEEQGLGEEDLAEAYGEVGNELADLIDLIRHIAGLdQPLLTRRERVERAFkr 736
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 504838941 745 -IQMNSYNVKQQEFLNFVLDQYVREGVDELDDSKLPdllELKYK-AIADAKKELGDTKSIRDTFIGFQQHLYQ 815
Cdd:COG4096 737 fLAGHKYTEEQREFLERILDHLADNGVIELEDLDEA---PFTQDgGPGGIDGLFGGVDELDEALEELNEALYA 806
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
133-567 |
1.73e-69 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 239.93 E-value: 1.73e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 133 EDYKVEIADWKERLFAIPFEDRGGTWQPRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKwnlrr 212
Cdd:COG1061 54 PEEDTERELAEAEALEAGDEASGTSFELRPYQQEALEALLAALERGGGRGLVVAPTGTGKTVLALALAAELLRGK----- 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 213 dgsrspRILFLADRNILADQAFNSFNAFDEDALVRISPKEIKKKgkvpkngsVFFTIFQTFMTNANqeedekdeeneeen 292
Cdd:COG1061 129 ------RVLVLVPRRELLEQWAEELRRFLGDPLAGGGKKDSDAP--------ITVATYQSLARRAH-------------- 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 293 ysiaaepaakynTDDFnfgqypKDFFDLIIIDECHRGGSrdeSSWRAIMEHFSPAVQLGLTATPKRDINGDTY-DYFGEP 371
Cdd:COG1061 181 ------------LDEL------GDRFGLVIIDEAHHAGA---PSYRRILEAFPAAYRLGLTATPFRSDGREILlFLFDGI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 372 VYTYKLKDGINDGFLTPFKVKEISttideyvhtsgDEVDGEIEEGKTYSESDFNRIIAIKAREEYRVKLFMDSINQNQKT 451
Cdd:COG1061 240 VYEYSLKEAIEDGYLAPPEYYGIR-----------VDLTDERAEYDALSERLREALAADAERKDKILRELLREHPDDRKT 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 452 LVFCATQIHAATVRDLINQYATSksinyCHRVTADDGQIG-EQHLRDFQDNEKsipTILTTSQKLSTGVDAPEIRNIVLM 530
Cdd:COG1061 309 LVFCSSVDHAEALAELLNEAGIR-----AAVVTGDTPKKErEEILEAFRDGEL---RILVTVDVLNEGVDVPRLDVAILL 380
|
410 420 430
....*....|....*....|....*....|....*..
gi 504838941 531 RPVNSMVEFKQIVGRGTRLFDGKDYFTVFDFVDAHHH 567
Cdd:COG1061 381 RPTGSPREFIQRLGRGLRPAPGKEDALVYDFVGNDVP 417
|
|
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
1-570 |
1.48e-60 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 222.90 E-value: 1.48e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 1 MNEAQTKHdLIEPALRAAGWgsvEGSRLRLEF-----PiTKGRLIGLNRRATPL--FADYILEYKNRRIGVVEAKKKHSY 73
Cdd:PRK11448 231 LSEEETRI-LIDQQLRKAGW---EADSKTLRFskgarP-EKGRNLAIAEWPTGKtgRADYALFIGLKPVGVVEAKRKNKD 305
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 74 YTDGVGQAKDYAERLDIR---------------------FTYATNG------LQ----IYGIDLDEGTEGDVS--KYPTP 120
Cdd:PRK11448 306 VASKLNQAKRYSKGFDVAeevpeyggpwqdtsggrykvpFVFSTNGrpylkqLKtksgIWFRDVRKPTNHPRAlqGWHTP 385
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 121 DELWEMTyptpkedyKVEIADWKERLFAIPFEDRGGTwqpRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIA 200
Cdd:PRK11448 386 EGLLDLL--------ESDIEAANQWLADEPFDYGLGL---RYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALM 454
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 201 WKLFHAKwnlrrdgsRSPRILFLADRNILADQAFNSFnafdedalvrispKEIKKKGkvpkngsvfftiFQTFmtnanqe 280
Cdd:PRK11448 455 YRLLKAK--------RFRRILFLVDRSALGEQAEDAF-------------KDTKIEG------------DQTF------- 494
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 281 edekdeeneEENYSI------AAEPAAK--------------YNTDdfNFGQYPKDFFDLIIIDECHRG----------- 329
Cdd:PRK11448 495 ---------ASIYDIkgledkFPEDETKvhvatvqgmvkrilYSDD--PMDKPPVDQYDCIIVDEAHRGytldkemsege 563
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 330 -GSRDE----SSWRAIMEHFSpAVQLGLTATPKRDingdTYDYFGEPVYTYKLKDGINDGFLT----PFKVK-------- 392
Cdd:PRK11448 564 lQFRDQldyvSKYRRVLDYFD-AVKIGLTATPALH----TTEIFGEPVYTYSYREAVIDGYLIdhepPIRIEtrlsqegi 638
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 393 --EISTTIDEYVHTSG--------DEVDGEIEE--GKTYSESdFNRIIAikareEYRVKlFMDSINQnQKTLVFCATQIH 460
Cdd:PRK11448 639 hfEKGEEVEVINTQTGeidlatleDEVDFEVEDfnRRVITES-FNRVVC-----EELAK-YLDPTGE-GKTLIFAATDAH 710
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 461 AATVRDLINQYATSKSINYCH----RVTaddGQIG--EQHLRDFQdNEKsIPTILTTSQKLSTGVDAPEIRNIVLMRPVN 534
Cdd:PRK11448 711 ADMVVRLLKEAFKKKYGQVEDdaviKIT---GSIDkpDQLIRRFK-NER-LPNIVVTVDLLTTGIDVPSICNLVFLRRVR 785
|
650 660 670
....*....|....*....|....*....|....*...
gi 504838941 535 SMVEFKQIVGRGTRLFD--GKDYFTVFDFVDAHHHFQD 570
Cdd:PRK11448 786 SRILYEQMLGRATRLCPeiGKTHFRIFDAVDIYEALES 823
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
160-368 |
3.85e-59 |
|
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: 198.17 E-value: 3.85e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 160 PRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWNlrrdgsrsPRILFLADRNILADQAFNSFNA 239
Cdd:cd18032 1 PRYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRK--------KRILFLAHREELLEQAERSFKE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 240 FdedaLVRISPKEIKKKGKVPKNGSVFFTIFQTFMTNANQEedekdeeneeenysiaaepaakyntddfnfgQYPKDFFD 319
Cdd:cd18032 73 V----LPDGSFGNLKGGKKKPDDARVVFATVQTLNKRKRLE-------------------------------KFPPDYFD 117
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 504838941 320 LIIIDECHRGGSrdeSSWRAIMEHFSPAVQLGLTATPKRDINGDTYDYF 368
Cdd:cd18032 118 LIIIDEAHHAIA---SSYRKILEYFEPAFLLGLTATPERTDGLDTYELF 163
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
159-358 |
1.15e-40 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 146.66 E-value: 1.15e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVLEAISEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKWNlrrdgsrsPRILFLADRNILADQAFNSFN 238
Cdd:pfam04851 3 ELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPI--------KKVLFLVPRKDLLEQALEEFK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AFDEDALVRISPKEIKKKGKVPKNGSVFFTIFQTFMTNANQEEDekdeeneeenysiaaepaakyntddfnfgQYPKDFF 318
Cdd:pfam04851 75 KFLPNYVEIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASL-----------------------------ELLPDFF 125
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 504838941 319 DLIIIDECHRGGSrdeSSWRAIMEHFSPAVQLGLTATPKR 358
Cdd:pfam04851 126 DVIIIDEAHRSGA---SSYRNILEYFKPAFLLGLTATPER 162
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
449-562 |
3.15e-35 |
|
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: 129.60 E-value: 3.15e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 449 QKTLVFCATQIHAATVRDLINQY---ATSKSINYCHRVTADDGqigeqhLRDFQDNEKSiPTILTTSQKLSTGVDAPEIR 525
Cdd:cd18799 7 IKTLIFCVSIEHAEFMAEAFNEAgidAVALNSDYSDRERGDEA------LILLFFGELK-PPILVTVDLLTTGVDIPEVD 79
|
90 100 110
....*....|....*....|....*....|....*..
gi 504838941 526 NIVLMRPVNSMVEFKQIVGRGTRLFDGKDYFTVFDFV 562
Cdd:cd18799 80 NVVFLRPTESRTLFLQMLGRGLRLHEGKDFFTILDFI 116
|
|
| EcoEI_R_C |
pfam08463 |
EcoEI R protein C-terminal; The restriction enzyme EcoEI recognizes 5'-GAGN(7)ATGC-3' and is ... |
661-813 |
1.63e-30 |
|
EcoEI R protein C-terminal; The restriction enzyme EcoEI recognizes 5'-GAGN(7)ATGC-3' and is composed of the three proteins R, M, and S. The domain described here is found at the C-terminus of the R protein (HsdR) which is required for both nuclease and ATPase activity.
Pssm-ID: 462485 [Multi-domain] Cd Length: 159 Bit Score: 117.73 E-value: 1.63e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 661 FITQLFGDLPSFFNNEEQLRTLWSVPSTRKKLLTELSEK----GYTNSQLEDLRHLIHGEDSDLFDVLSYVAYH-KELVP 735
Cdd:pfam08463 1 YLDYFRAFIRENFDEIDALRKLWNNRELTRADLKELEEKldqpGFTEEQLWEAYEILKSNQADLFDLIRHIAGLdQPLLT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 736 RLERASRAK---IQMNSYNVKQQEFLNFVLDQYVREGVDELDdsklpDLLELKYKAI---ADAKKELGDTKSIRDTFIGF 809
Cdd:pfam08463 81 RRERAERAFkrwLAQHNFTEEQREFLERILDHYAENGVIELD-----DLLELPFKDLgglGKIIKLFGGKKELDEIIDEL 155
|
....
gi 504838941 810 QQHL 813
Cdd:pfam08463 156 NEEL 159
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
160-356 |
2.09e-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: 105.47 E-value: 2.09e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 160 PRYYQQNAIAKVLeaISEKKDRLLLTLATGTGKTAIAFQIAWKLfhakwnlrrdgsRSPRILFLADRNILADQAFNSFNA 239
Cdd:cd17926 1 LRPYQEEALEAWL--AHKNNRRGILVLPTGSGKTLTALALIAYL------------KELRTLIVVPTDALLDQWKERFED 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 240 FDEDALVRISPKEIKKKgkvPKNGSVFFTIFQtfmtnanqeedekdeeneeenySIAAEPAAkyntddfnfGQYPKDFFD 319
Cdd:cd17926 67 FLGDSSIGLIGGGKKKD---FDDANVVVATYQ----------------------SLSNLAEE---------EKDLFDQFG 112
|
170 180 190
....*....|....*....|....*....|....*..
gi 504838941 320 LIIIDECHRGGSRdesSWRAIMEHFSPAVQLGLTATP 356
Cdd:cd17926 113 LLIVDEAHHLPAK---TFSEILKELNAKYRLGLTATP 146
|
|
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
160-436 |
9.04e-20 |
|
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: 94.93 E-value: 9.04e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 160 PRYYQ----QNAIAKVLEAISEKKDRLLL-TlaTGTGKTAIAFQIAWKLfhakwnLRRDGSRSPRILFLADRNILADQAF 234
Cdd:COG0610 256 ARYHQyfavRKAVERVKEAEGDGKGGVIWhT--QGSGKSLTMVFLAQKL------ARLPDLDNPTVVVVTDRKDLDDQLF 327
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 235 NSFNAFDEDALVRI-SPKEIKKKGKVPKNGsVFFTIFQTFMTNanqeedekdeeneeenysIAAEPAAKYNTDdfnfgqy 313
Cdd:COG0610 328 DTFKAFGRESVVQAeSRADLRELLESDSGG-IIVTTIQKFPEA------------------LDEIKYPELSDR------- 381
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 314 pKDFFdlIIIDECHR---GGSRdesswRAIMEHFSPAVQLGLTATPKRDINGDTYDYFGEPVYTYKLKDGINDGFLTPFK 390
Cdd:COG0610 382 -KNII--VIVDEAHRsqyGGLA-----KNMRDALPNASFFGFTGTPIFKEDRTTLEVFGDYIHTYTITQAIEDGATLPLL 453
|
250 260 270 280
....*....|....*....|....*....|....*....|....*..
gi 504838941 391 VKeiSTTIDeyVHTSGDEVDGEIEE-GKTYSESDFNRIIAIKAREEY 436
Cdd:COG0610 454 YE--YRLAK--LKLDKEKIDEEFDElTEGLDDEEKEKLKAKWALLEE 496
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
159-394 |
2.84e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 81.00 E-value: 2.84e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVLEAISekkdRLLLTLATGTGKTAIAFQIAWKLFHAKwnlrrdgsRSPRILFLADRNILADQAFNSFN 238
Cdd:smart00487 8 PLRPYQKEAIEALLSGLR----DVILAAPTGSGKTLAALLPALEALKRG--------KGGRVLVLVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AFDEDALVR----ISPKEIKKKGKVPKNGS--VFFTIFQTFMtnanqeedekdeeneeenysiaaepaakyntDDFNFGQ 312
Cdd:smart00487 76 KLGPSLGLKvvglYGGDSKREQLRKLESGKtdILVTTPGRLL-------------------------------DLLENDK 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 313 YPKDFFDLIIIDECHRGGSRD-ESSWRAIMEHFSPAVQ-LGLTATPKRDINGDTYDYFGEPVYtyklkdgINDGFLTPFK 390
Cdd:smart00487 125 LSLSNVDLVILDEAHRLLDGGfGDQLEKLLKLLPKNVQlLLLSATPPEEIENLLELFLNDPVF-------IDVGFTPLEP 197
|
....
gi 504838941 391 VKEI 394
Cdd:smart00487 198 IEQF 201
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
131-563 |
5.36e-11 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 65.80 E-value: 5.36e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 131 PKEDYKVEI--ADWKERLFAIPFEDRGGTWQPRYYQQNAIAKVLeaiseKKDRLLLTLATGTGKTAIAFQIAwklfhaKW 208
Cdd:PHA02558 84 PRIEENEDIsrEDFDEWVSSLEIYSGNKKIEPHWYQYDAVYEGL-----KNNRRLLNLPTSAGKSLIQYLLS------RY 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 209 NLRRdgsRSPRILFLADRNILADQAFNSFNAFdedalvRISPKE--IKKKGKVPKNGS--VFFTIFQtfmtnanqeedek 284
Cdd:PHA02558 153 YLEN---YEGKVLIIVPTTSLVTQMIDDFVDY------RLFPREamHKIYSGTAKDTDapIVVSTWQ------------- 210
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 285 deeneeenySIAAEPAaKYntddfnFGQypkdfFDLIIIDECHRGGSRDESSwraIMEHFSPAVQ-LGLTATPkRDINGD 363
Cdd:PHA02558 211 ---------SAVKQPK-EW------FDQ-----FGMVIVDECHLFTGKSLTS---IITKLDNCKFkFGLTGSL-RDGKAN 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 364 TYDY---FGE---PVYTYKLkdgINDGFLTPFKVKEISTTideyvHTSGDEVDgeiEEGKTY-SESDFnrIIAIKAREEY 436
Cdd:PHA02558 266 ILQYvglFGDifkPVTTSQL---MEEGQVTDLKINSIFLR-----YPDEDRVK---LKGEDYqEEIKY--ITSHTKRNKW 332
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 437 RVKLFMDSINQNQKTLVFCATQIHAATVRDLINqyATSKSINYCH-RVTADDgqigEQHLRDFQDNEKSIpTILTTSQKL 515
Cdd:PHA02558 333 IANLALKLAKKGENTFVMFKYVEHGKPLYEMLK--KVYDKVYYVSgEVDTED----RNEMKKIAEGGKGI-IIVASYGVF 405
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 504838941 516 STGVDAPEIRNIVLMRPVNSMVEFKQIVGRGTRLFDGKDYFTVFDFVD 563
Cdd:PHA02558 406 STGISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSKSIATVWDIID 453
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
188-415 |
1.27e-10 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 62.06 E-value: 1.27e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 188 TGTGKTAIAFqiawklFHAKWnLRRDgSRSPRILFLADRNILADQAFNSFNAFDEDALVRI-SPKEIKKKgkVPKNGSVF 266
Cdd:pfam18766 28 QGSGKSLTMV------FLARK-LRRE-LKNPTVVVVTDRNDLDDQLTKTFAACGREVPVQAeSRKDLREL--LRGSGGII 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 267 FTIFQTFMTNanqeedekdeeneeenysiaaePAAKYN--TDDFNFgqypkdffdLIIIDECHR---GGSRdesswRAIM 341
Cdd:pfam18766 98 FTTIQKFGET----------------------PDEGFPvlSDRRNI---------IVLVDEAHRsqyGGLA-----ANMR 141
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 504838941 342 EHFSPAVQLGLTATP--KRDINgdTYDYFGEPVYTYKLKDGINDGFLTPfkVKEISTTIDeyVHTSGDEVDGEIEE 415
Cdd:pfam18766 142 DALPNAAFIGFTGTPilKKDKN--TRAVFGDYIDTYTIQDAVEDGATVP--ILYEGRLAE--LELDDEALDEEFEE 211
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
507-562 |
4.55e-10 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The 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: 350172 [Multi-domain] Cd Length: 77 Bit Score: 56.56 E-value: 4.55e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 504838941 507 TILTTSQKLSTGVDAPEIRNIVLMRPVNSMVEFKQIVGRGTRLfdGKDYFTVFDFV 562
Cdd:cd18785 24 EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRG--GKDEGEVILFV 77
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
169-360 |
2.31e-07 |
|
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: 51.47 E-value: 2.31e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 169 AKVLEAISEKKDrLLLTLATGTGKTAIAFQIAWKLFHAKWNlrrdgsrSPRILFLADRNILADQAFNSFNAFDEDALVR- 247
Cdd:pfam00270 5 AEAIPAILEGRD-VLVQAPTGSGKTLAFLLPALEALDKLDN-------GPQALVLAPTRELAEQIYEELKKLGKGLGLKv 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 248 ---ISPKEIKKKGKVPKNGSVFFTIFQTFMtnanqeedekdeeneeenysiaaepaakyntDDFNFGQYPKDFfDLIIID 324
Cdd:pfam00270 77 aslLGGDSRKEQLEKLKGPDILVGTPGRLL-------------------------------DLLQERKLLKNL-KLLVLD 124
|
170 180 190
....*....|....*....|....*....|....*...
gi 504838941 325 ECHRGGSRD-ESSWRAIMEHFSPAVQ-LGLTATPKRDI 360
Cdd:pfam00270 125 EAHRLLDMGfGPDLEEILRRLPKKRQiLLLSATLPRNL 162
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
159-360 |
1.99e-06 |
|
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef 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: 350793 [Multi-domain] Cd Length: 181 Bit Score: 49.05 E-value: 1.99e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVleaiseKKDRLLLTLATGTGKTAIAFQIawklfhAKWNLRRDGSrspRILFLADRNILADQAFNSFN 238
Cdd:cd18035 2 ERRLYQVLIAAVA------LNGNTLIVLPTGLGKTIIAILV------AADRLTKKGG---KVLILAPSRPLVEQHAENLK 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AF--DEDALVRIS-PKEIKKKGKVPKNGSVFFTIFQTFMTNAnqeedekdeeneeenysiaaePAAKYNTDDFNfgqypk 315
Cdd:cd18035 67 RVlnIPDKITSLTgEVKPEERAERWDASKIIVATPQVIENDL---------------------LAGRITLDDVS------ 119
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 504838941 316 dffdLIIIDECHRggSRDESSWRAIMEHFSPAVQ----LGLTATPKRDI 360
Cdd:cd18035 120 ----LLIFDEAHH--AVGNYAYVYIAHRYKREANnpliLGLTASPGSDK 162
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
182-355 |
2.25e-06 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 48.17 E-value: 2.25e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 182 LLLTLATGTGKTAIAFQIAwklfhakwnLRRDGSRSPRILFLADRNILADQAFNSFNA-FDEDALVRI----SPKEIKKK 256
Cdd:cd00046 4 VLITAPTGSGKTLAALLAA---------LLLLLKKGKKVLVLVPTKALALQTAERLRElFGPGIRVAVlvggSSAEEREK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 257 GKVPKNGSVFFTIFQTFMtnanqeedekdeeneeenysiAAEPAAKYNTDDfnfgqypkdfFDLIIIDECHRGGSRDESS 336
Cdd:cd00046 75 NKLGDADIIIATPDMLLN---------------------LLLREDRLFLKD----------LKLIIVDEAHALLIDSRGA 123
|
170 180
....*....|....*....|...
gi 504838941 337 WRA----IMEHFSPAVQLGLTAT 355
Cdd:cd00046 124 LILdlavRKAGLKNAQVILLSAT 146
|
|
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
159-555 |
2.78e-06 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 51.11 E-value: 2.78e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 159 QPRYYQQNAIAKVLEAIsEKKDRLLLTLATGTGKTAIAFQIAWKLFHAKwnlrrdgsrsPRILFLADRNILADQAFNSFN 238
Cdd:COG4889 169 TLRPHQQEAIEAVLAGF-KTHDRGKLIMACGTGKTFTSLRIAEELAGKG----------GRVLFLVPSISLLSQTLREWT 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 239 AfdeDALVRISPKEI---KKKGKVPKNGSVfftifQTFM--------TNANqeedekdeeneeenySIAAEPAAKYNTDD 307
Cdd:COG4889 238 A---ESEVPLRSFAVcsdSKVGKRRKKDDE-----DTSAhdlaypatTDAE---------------KLAAAAQKRHDADR 294
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 308 FN--FGQY----------PKDF--FDLIIIDECHR-----GGSRDESSWRAImeHFSPAVQ----LGLTATPKrdINGDT 364
Cdd:COG4889 295 MTvvFSTYqsidvvadaqKLGLpeFDLIICDEAHRttgatLAGEDESAFVRV--HDNDYIKakkrLYMTATPR--IYGDD 370
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 365 Y-----------------DYFGEPVYTYKLKDGINDGFLTPFKVkeISTTIDEYvHTSGDEVDGEIEEGKTYSESDFNRI 427
Cdd:COG4889 371 AkkkakeasavlasmddeALFGPEFHRLGFGEAVERGLLTDYKV--IVLAVDES-HVSRRLQQLLADNGNELKLDDAAKI 447
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 428 I-AIKAREEYRVKlfMDSINQNQ--KTLV-FCAT-----QIHAATVRdLINQYATSKS---INYCHRVTAD----DGQIG 491
Cdd:COG4889 448 VgCWNGLAKRGGE--EDGTDDPApmKRAVaFCQTikeskRIAEHFVS-VVNIYLMFQDdeaEEDAPSLRCEaehvDGTMN 524
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 504838941 492 ----EQHLRDFQDN-EKSIPTILTTSQKLSTGVDAPEIRNIVLMRPVNSMVEFKQIVGRGTRLFDGKDY 555
Cdd:COG4889 525 alerNEKLDWLKAEtPENTCRILSNARCLSEGVDVPALDAVLFLTPRKSQVDVVQSVGRVMRKAPGKKY 593
|
|
| COG2810 |
COG2810 |
Predicted type IV restriction endonuclease [Defense mechanisms]; |
2-110 |
6.51e-06 |
|
Predicted type IV restriction endonuclease [Defense mechanisms];
Pssm-ID: 442059 [Multi-domain] Cd Length: 340 Bit Score: 49.21 E-value: 6.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 2 NEAQTKHDLIEPALRAAGWgSVEGSR-LRLEFPITKGRliglnrratplfADYILEYKNRRIGVVEAKK-KHSYYTDGVG 79
Cdd:COG2810 27 NEAATRQEFIDPLLEALGW-DIDNPEeVIPEERVEGGR------------PDYALRLNGKRKLFVEAKKpGVNLKDKPAR 93
|
90 100 110
....*....|....*....|....*....|.
gi 504838941 80 QAKDYAERLDIRFTYATNGLQIYGIDLDEGT 110
Cdd:COG2810 94 QARSYAWSSGVRWAILTNGREWRVYDAQEKT 124
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
156-360 |
2.07e-05 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 48.33 E-value: 2.07e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 156 GTWQPRYYQQNAIAKVLEAISekkdrlLLTLATGTGKTAIA-FQIAWKLfhakwnLRRDGsrspRILFLADRNILADQAF 234
Cdd:PRK13766 12 NTIEARLYQQLLAATALKKNT------LVVLPTGLGKTAIAlLVIAERL------HKKGG----KVLILAPTKPLVEQHA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 235 NSFNAF----DEDALV---RISPKeikKKGKVPKNGSVFFTIFQTfMTNanqeedekdeeneeenySIAAEpaaKYNTDD 307
Cdd:PRK13766 76 EFFRKFlnipEEKIVVftgEVSPE---KRAELWEKAKVIVATPQV-IEN-----------------DLIAG---RISLED 131
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 504838941 308 FNfgqypkdffdLIIIDECHRG-GSRdesSWRAIMEHF-----SPAVqLGLTATPKRDI 360
Cdd:PRK13766 132 VS----------LLIFDEAHRAvGNY---AYVYIAERYhedakNPLV-LGLTASPGSDE 176
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
446-545 |
1.09e-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: 39.50 E-value: 1.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504838941 446 NQNQKTLVFCATQIHAAtvrdlINQYATSKSINYChRVTADDGQIG-EQHLRDFQDNEKSIptILTTSQkLSTGVDAPEI 524
Cdd:pfam00271 13 ERGGKVLIFSQTKKTLE-----AELLLEKEGIKVA-RLHGDLSQEErEEILEDFRKGKIDV--LVATDV-AERGLDLPDV 83
|
90 100
....*....|....*....|.
gi 504838941 525 RNIVLMRPVNSMVEFKQIVGR 545
Cdd:pfam00271 84 DLVINYDLPWNPASYIQRIGR 104
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
495-548 |
9.55e-03 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 36.04 E-value: 9.55e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 504838941 495 LRDFQDNEKSIptiLTTSQKLSTGVDAPEIRNIVLMRPVNSMVEFKQIVGRGTR 548
Cdd:smart00490 30 LDKFNNGKIKV---LVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
|
|
| |
