|
Name |
Accession |
Description |
Interval |
E-value |
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
1-1071 |
0e+00 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 1564.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 1 MSNFQTSENNYQEYAQLASSAESLIYSDPRSSLTVFGTFGEQLTKEIMHLDDIVDWELNQKQRIEKLALSRNEYPAVVLT 80
Cdd:PRK11448 3 KSNFEFLKGHDPVLAALACLAERNFYDDPNTTLIKLRQFGEALAKHIAALLGIYEPPCENQHDLLRRLGKEGFLPDEILD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 81 ALNEIRFKRNKATHddQFIATKSDALAIDQKAYLVWKWFLEVYSLD---QVADYKKPIDQRAVLQNQ------------- 144
Cdd:PRK11448 83 VFHKLRKIGNKAVH--EFHGDHREALMGLKLAFRLAVWFHRTYGKDwdfKPGPFVPPEDPENLLHALqqevltlkqqlel 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 145 -----------------------------EDKIKALEAKIKELQANRPQKvtvTPEERVRRHEINIQFAKKHKLTEAETR 195
Cdd:PRK11448 161 qarekaqsqalaeaqqqelvaleglaaelEEKQQELEAQLEQLQEKAAET---SQERKQKRKEITDQAAKRLELSEEETR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 196 QLIDQQLRSAGWEVDTERLNnWKNQTQPQRGHNMAIAEWVLPNDQRADYALFKGLDFYGIVEAKKWDEDIAGQMAQPKEY 275
Cdd:PRK11448 238 ILIDQQLRKAGWEADSKTLR-FSKGARPEKGRNLAIAEWPTGKTGRADYALFIGLKPVGVVEAKRKNKDVASKLNQAKRY 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 276 AKEVPYQSNYYLLSNQMGD-----YKVPFIYTANGRPYLKQYQEKSGIWFWDARNPKENAYALEEFHKPDDLaLKLTAKN 350
Cdd:PRK11448 317 SKGFDVAEEVPEYGGPWQDtsggrYKVPFVFSTNGRPYLKQLKTKSGIWFRDVRKPTNHPRALQGWHTPEGL-LDLLESD 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 351 KIEADNDLVDDHDYPKFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSL 430
Cdd:PRK11448 396 IEAANQWLADEPFDYGLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSAL 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 431 GRQTANAIKDNKIGTM-SISSIYGLKELSDKVPDASTKIQIATVQGMIKRLFFSDDNSEKPSVGQYDFIIVDEAHRGYAE 509
Cdd:PRK11448 476 GEQAEDAFKDTKIEGDqTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTL 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 510 DKELSDNEYQFYNQEEYVSQYRRVVDYFDATAIGMTATPALQTTEIFGDPVYTYSYQQAVLDGYLVNHDAPVIIKTKLAK 589
Cdd:PRK11448 556 DKEMSEGELQFRDQLDYVSKYRRVLDYFDAVKIGLTATPALHTTEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQ 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 590 EGIHFKKGTEVDIFDQDEKTINKEKLPDNMNFDVKDFNHRVITRNFNKVVCDELVkKYLDPTDPylGKTLIFAATDAHAD 669
Cdd:PRK11448 636 EGIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELA-KYLDPTGE--GKTLIFAATDAHAD 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 670 MVVDLLKQAFKEQGRSVDDDAIEKITGSIRHPNQEIKNFKNEENPNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYEQ 749
Cdd:PRK11448 713 MVVRLLKEAFKKKYGQVEDDAVIKITGSIDKPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQ 792
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 750 MLGRATRLCPEIHKEKFTIFDAVGIYDAMNKVTNMKPVVKNPGHNVHYFLSHKNYFETNEDTNQYQVDMAGAVERKIKRW 829
Cdd:PRK11448 793 MLGRATRLCPEIGKTHFRIFDAVDIYEALESVTTMKPVVVNPNISLEQLVNELTDADGESHAEHVREQLIAKLQRKLRKA 872
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 830 DDQRRKEFERLAEI----KSVDN---WARKLSKLTKTDFLKEWPKFV-QLDH---INPARPKQFISDAPDEVVDVSRGYG 898
Cdd:PRK11448 873 TDNAERSFEILAQLrragVTPEEfasRLKELGPHEAAEWLNKHPSLIeQLDElktINGLDDAPIISDHDDEVVSVERGYG 952
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 899 sGNQKPEDYIDSFNNFIKQNVNTIPALQVVATRPKDLTFDELKEIKLKLEQNGFKEKDLQTAWKNAKHVQTTADIISFIR 978
Cdd:PRK11448 953 -DADKPEDYLEAFDAFVRENINQIPALQVVVNRPRDLTRKELKELRLLLDQQGFSEASLRSAWKETKNEDIAASIIGFIR 1031
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 979 QVAAGSELVDHDVRIHNAMQKVYGMADWSISQRKWLKRIENQLMSSTVLGpnaEEAFNDNfYFKRQGGYKQIKKIFPEYA 1058
Cdd:PRK11448 1032 QAALGDALVPFEERVDHAMQKIYAERDWTPVQRKWLERIAKQLKEEVVLD---RDAFDTG-PFKRRGGFKRLNKVFDGNL 1107
|
1130
....*....|...
gi 1993121499 1059 DQIIYVLNENLYV 1071
Cdd:PRK11448 1108 DQILDKINEYLWD 1120
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
189-1071 |
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: 789.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 189 LTEAETR-QLIDQQLRSAGWEVDTERLNnwknQTQPQRGHNMAIAEWVLPNDQ-RADYALFKGLDF-YGIVEAKKWDEDI 265
Cdd:COG4096 2 LSEAETRkKLIDPALKEAGWDVDDQILR----EVRPTAGRNVVIGEWPTRGGKgYADYVLFGDDGKpLAVVEAKRTSKDV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 266 AGQMAQPKEYAKEVPYQSNyyllsnqmgdyKVPFIYTANGRPylkqyqeksgIWFWDARNPKENAYALEEFHKPDDLALK 345
Cdd:COG4096 78 SAGLQQAKLYADGLEKQYG-----------QVPFIFATNGRE----------IWFWDDRDPYPREREVDGFPSPEELWEL 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 346 LtAKNKIEADNDLVDDHDYPKFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLV 425
Cdd:COG4096 137 L-KRRKGTARKRLATEPYNDGIALRYYQIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAIALIYRLLKAGRAKRILFLA 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 426 DRNSLGRQTANAIKDNKIGTMSISSIYGlkelSDKVPDASTKIQIATVQGMIKRLFFSDDNSE--KPSVGQYDFIIVDEA 503
Cdd:COG4096 216 DRNALVDQAKNAFKPFLPDLDAFTKLYN----KSKDIDKSARVYFSTYQTMMNRIDGEEEEPGyrQFPPDFFDLIIIDEC 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 504 HRGYAedkelsdneyqfynqeeyvSQYRRVVDYFDATAIGMTATPAL----QTTEIF-GDPVYTYSYQQAVLDGYLVNHD 578
Cdd:COG4096 292 HRGIY-------------------SKWRAILDYFDALQIGLTATPKDtidrNTYEYFnGNPVYTYSLEQAVADGFLVPYK 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 579 aPVIIKTKLAKEGIHFKKGteVDIFDQDEKTINKEKLPDNMNFDVKDFNHRVITRNFNKVVCDELVKKYLDPTDPYLGKT 658
Cdd:COG4096 353 -VIRIDTKFDREGIRYDAG--EDLSDEEGEEIELEELEEDREYEAKDFNRKVVNEDTTRKVLEELMEYLDKPGGDRLGKT 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 659 LIFAATDAHADMVVDLLKQAFKEQGrsvdDDAIEKITGSIRHPNQEIKNFKNEE-NPNIVVTVDLLTTGIDVPRITNIVF 737
Cdd:COG4096 430 IIFAKNDDHADRIVQALRELYPELG----GDFVKKITGDDDYGKSLIDNFKNPEkYPRIAVTVDMLDTGIDVPEVVNLVF 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 738 LRRVQSRILYEQMLGRATRLCPEI--HKEKFTIFDAVGIYDAMNKVTnmKPVVKnpghnvhyflshknyFETNEDTNQYQ 815
Cdd:COG4096 506 MRPVKSRIKFEQMIGRGTRLCPDLfpGKTHFTIFDFVGNTELFADPS--FPLRI---------------FEPRREREKFW 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 816 VDMAGAVERKIKrwddqrrkefERLAEIKSVDNWARKLSKlTKTDFLKEWPKFV-QLDHINPARPKQFISDAPDEVVDVS 894
Cdd:COG4096 569 DLLGGEDPAKLA----------VHLADALDPDKVTIPVVA-EAVQLLDDVPDLRdLLKFIDKDKRQIIYTDFEDELLEAE 637
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 895 RGYGSGnQKPEDYIDSFNNFIKQNVNtIPALQVVATRpkdLTFDELKEIKLKLEQNGFKEKDLQTAWKNAKhvQTTADII 974
Cdd:COG4096 638 EGYGKK-LKAEDYRDKFEAFLREHKE-IPALQKLRNR---LTREDLKELEEELEEQGLGEEDLAEAYGEVG--NELADLI 710
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 975 SFIRQVA-AGSELVDHDVRIHNAMQKVYGMADWSISQRKWLKRIENQLMSSTVLGPnaeeafnDNFY---FKRQGGYKQI 1050
Cdd:COG4096 711 DLIRHIAgLDQPLLTRRERVERAFKRFLAGHKYTEEQREFLERILDHLADNGVIEL-------EDLDeapFTQDGGPGGI 783
|
890 900
....*....|....*....|...
gi 1993121499 1051 KKIFPEYA--DQIIYVLNENLYV 1071
Cdd:COG4096 784 DGLFGGVDelDEALEELNEALYA 806
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
370-556 |
4.35e-54 |
|
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: 185.46 E-value: 4.35e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNkigtMSIS 449
Cdd:cd18032 2 RYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEV----LPDG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 450 SIYGLKELSDKvpDASTKIQIATVQGMIKRlffsdDNSEKPSVGQYDFIIVDEAHRGYAedkelsdneyqfynqeeyvSQ 529
Cdd:cd18032 78 SFGNLKGGKKK--PDDARVVFATVQTLNKR-----KRLEKFPPDYFDLIIIDEAHHAIA-------------------SS 131
|
170 180 190
....*....|....*....|....*....|..
gi 1993121499 530 YRRVVDYF-DATAIGMTATPA----LQTTEIF 556
Cdd:cd18032 132 YRKILEYFePAFLLGLTATPErtdgLDTYELF 163
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
366-548 |
2.12e-37 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 137.80 E-value: 2.12e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 366 KFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNKIGT 445
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 MSISSIYglKELSDKVPDASTKIQIATVQGMIKRLffsDDNSEKPSVGQYDFIIVDEAHRGYAEdkelsdneyqfynqee 525
Cdd:pfam04851 81 VEIGEII--SGDKKDESVDDNKIVVTTIQSLYKAL---ELASLELLPDFFDVIIIDEAHRSGAS---------------- 139
|
170 180
....*....|....*....|....
gi 1993121499 526 yvsQYRRVVDYFD-ATAIGMTATP 548
Cdd:pfam04851 140 ---SYRNILEYFKpAFLLGLTATP 160
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
370-548 |
1.55e-19 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 87.93 E-value: 1.55e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEdaikNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIK----DNKIGT 445
Cdd:smart00487 10 RPYQKEAIEALL----SGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKklgpSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 MSISSIYGLKELSDKVPDASTKIQIATVQGMIKRLffsddNSEKPSVGQYDFIIVDEAHRgyaedkeLSDNEYQfynqee 525
Cdd:smart00487 86 VGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL-----ENDKLSLSNVDLVILDEAHR-------LLDGGFG------ 147
|
170 180
....*....|....*....|....*
gi 1993121499 526 yvSQYRRVVDYFDATA--IGMTATP 548
Cdd:smart00487 148 --DQLEKLLKLLPKNVqlLLLSATP 170
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
254-784 |
9.37e-12 |
|
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: 69.35 E-value: 9.37e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 254 GIVEAKKWDEDIAGQMAQPKEYAKEVPYQSNYyllsNQMGdykvpfiYTANGRPYLKQYQEKSGIWF----WDARNPKeN 329
Cdd:TIGR00348 133 VIIELKKRSVTIREAFNQIKRYEKEIPELFKY----VQIF-------VISNGTDTRYYTGSDEDDFDftfnWKESDNK-L 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 330 AYALEEFHKpdDLALKLTAKNKIEadNDLVDDHDYPKFAdRPYQI----DAINAMEDAIKN-----GKKRILLAMATGTG 400
Cdd:TIGR00348 201 IEDLKEFDI--LLLKKERLLDFIR--NFIIFDKDTGLVT-KPYQRymqyRAVKKIVESITRktwgkDERGGLIWHTQGSG 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 401 KTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNKIGTM-SISSIYGLKELSDKVPDastKIQIATVQGMIKR 479
Cdd:TIGR00348 276 KTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQKDCAeRIESIAELKELLEKDDG---GIIITTIQKFDDK 352
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 480 LffSDDNSEKPSVGQYDFIIVDEAHRgyaedkelsdNEYQFYNQeeyvsQYRRVVDyfDATAIGMTATP--------ALQ 551
Cdd:TIGR00348 353 L--KEEEEKFPVDRKEVVVIFDEAHR----------SQYGELAK-----NLKKALK--NASFFGFTGTPifkkdrdtSLT 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 552 TTEIFGDPVYTYSYQQAVLDGYLVNHD-APVIIKTKLAKEgihfkkgtEVDIFDQDEKTINKEKLPDNMNFDVKDFNHRV 630
Cdd:TIGR00348 414 FAYVFGRYLHRYFITDAIRDGLTVKIDyEDRLPEDHLDKK--------KLDAFFDEIFELLPERIREITKESLKEKLQKT 485
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 631 ITRNFNKV----VCDELVKKYLDPTDPYLGKTLIFA----ATDAHADMVVDLLKQAFKE-----QGRSVDDDAIE----- 692
Cdd:TIGR00348 486 KKILFNEDrlesIAKDIAEHYAKFKELFKFKAMVVAisryACVEEKNALDEELNEKFEAsaivmTGKESDDAEIRdynkh 565
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 693 ---KITGSIRHPNQE--IKNFKNEENPNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYeQMLGRATRLCPEIhKEKFT 767
Cdd:TIGR00348 566 irtKFDKSDGFEIYYkdLERFKKNENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLL-QAIARTNRIDGKD-KTFGL 643
|
570
....*....|....*..
gi 1993121499 768 IFDAVGIYDAMNKVTNM 784
Cdd:TIGR00348 644 IVDYRGLEKSLIDALSL 660
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| hsdR |
PRK11448 |
type I restriction enzyme EcoKI subunit R; Provisional |
1-1071 |
0e+00 |
|
type I restriction enzyme EcoKI subunit R; Provisional
Pssm-ID: 236912 [Multi-domain] Cd Length: 1123 Bit Score: 1564.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 1 MSNFQTSENNYQEYAQLASSAESLIYSDPRSSLTVFGTFGEQLTKEIMHLDDIVDWELNQKQRIEKLALSRNEYPAVVLT 80
Cdd:PRK11448 3 KSNFEFLKGHDPVLAALACLAERNFYDDPNTTLIKLRQFGEALAKHIAALLGIYEPPCENQHDLLRRLGKEGFLPDEILD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 81 ALNEIRFKRNKATHddQFIATKSDALAIDQKAYLVWKWFLEVYSLD---QVADYKKPIDQRAVLQNQ------------- 144
Cdd:PRK11448 83 VFHKLRKIGNKAVH--EFHGDHREALMGLKLAFRLAVWFHRTYGKDwdfKPGPFVPPEDPENLLHALqqevltlkqqlel 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 145 -----------------------------EDKIKALEAKIKELQANRPQKvtvTPEERVRRHEINIQFAKKHKLTEAETR 195
Cdd:PRK11448 161 qarekaqsqalaeaqqqelvaleglaaelEEKQQELEAQLEQLQEKAAET---SQERKQKRKEITDQAAKRLELSEEETR 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 196 QLIDQQLRSAGWEVDTERLNnWKNQTQPQRGHNMAIAEWVLPNDQRADYALFKGLDFYGIVEAKKWDEDIAGQMAQPKEY 275
Cdd:PRK11448 238 ILIDQQLRKAGWEADSKTLR-FSKGARPEKGRNLAIAEWPTGKTGRADYALFIGLKPVGVVEAKRKNKDVASKLNQAKRY 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 276 AKEVPYQSNYYLLSNQMGD-----YKVPFIYTANGRPYLKQYQEKSGIWFWDARNPKENAYALEEFHKPDDLaLKLTAKN 350
Cdd:PRK11448 317 SKGFDVAEEVPEYGGPWQDtsggrYKVPFVFSTNGRPYLKQLKTKSGIWFRDVRKPTNHPRALQGWHTPEGL-LDLLESD 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 351 KIEADNDLVDDHDYPKFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSL 430
Cdd:PRK11448 396 IEAANQWLADEPFDYGLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSAL 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 431 GRQTANAIKDNKIGTM-SISSIYGLKELSDKVPDASTKIQIATVQGMIKRLFFSDDNSEKPSVGQYDFIIVDEAHRGYAE 509
Cdd:PRK11448 476 GEQAEDAFKDTKIEGDqTFASIYDIKGLEDKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTL 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 510 DKELSDNEYQFYNQEEYVSQYRRVVDYFDATAIGMTATPALQTTEIFGDPVYTYSYQQAVLDGYLVNHDAPVIIKTKLAK 589
Cdd:PRK11448 556 DKEMSEGELQFRDQLDYVSKYRRVLDYFDAVKIGLTATPALHTTEIFGEPVYTYSYREAVIDGYLIDHEPPIRIETRLSQ 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 590 EGIHFKKGTEVDIFDQDEKTINKEKLPDNMNFDVKDFNHRVITRNFNKVVCDELVkKYLDPTDPylGKTLIFAATDAHAD 669
Cdd:PRK11448 636 EGIHFEKGEEVEVINTQTGEIDLATLEDEVDFEVEDFNRRVITESFNRVVCEELA-KYLDPTGE--GKTLIFAATDAHAD 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 670 MVVDLLKQAFKEQGRSVDDDAIEKITGSIRHPNQEIKNFKNEENPNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYEQ 749
Cdd:PRK11448 713 MVVRLLKEAFKKKYGQVEDDAVIKITGSIDKPDQLIRRFKNERLPNIVVTVDLLTTGIDVPSICNLVFLRRVRSRILYEQ 792
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 750 MLGRATRLCPEIHKEKFTIFDAVGIYDAMNKVTNMKPVVKNPGHNVHYFLSHKNYFETNEDTNQYQVDMAGAVERKIKRW 829
Cdd:PRK11448 793 MLGRATRLCPEIGKTHFRIFDAVDIYEALESVTTMKPVVVNPNISLEQLVNELTDADGESHAEHVREQLIAKLQRKLRKA 872
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 830 DDQRRKEFERLAEI----KSVDN---WARKLSKLTKTDFLKEWPKFV-QLDH---INPARPKQFISDAPDEVVDVSRGYG 898
Cdd:PRK11448 873 TDNAERSFEILAQLrragVTPEEfasRLKELGPHEAAEWLNKHPSLIeQLDElktINGLDDAPIISDHDDEVVSVERGYG 952
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 899 sGNQKPEDYIDSFNNFIKQNVNTIPALQVVATRPKDLTFDELKEIKLKLEQNGFKEKDLQTAWKNAKHVQTTADIISFIR 978
Cdd:PRK11448 953 -DADKPEDYLEAFDAFVRENINQIPALQVVVNRPRDLTRKELKELRLLLDQQGFSEASLRSAWKETKNEDIAASIIGFIR 1031
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 979 QVAAGSELVDHDVRIHNAMQKVYGMADWSISQRKWLKRIENQLMSSTVLGpnaEEAFNDNfYFKRQGGYKQIKKIFPEYA 1058
Cdd:PRK11448 1032 QAALGDALVPFEERVDHAMQKIYAERDWTPVQRKWLERIAKQLKEEVVLD---RDAFDTG-PFKRRGGFKRLNKVFDGNL 1107
|
1130
....*....|...
gi 1993121499 1059 DQIIYVLNENLYV 1071
Cdd:PRK11448 1108 DQILDKINEYLWD 1120
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
189-1071 |
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: 789.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 189 LTEAETR-QLIDQQLRSAGWEVDTERLNnwknQTQPQRGHNMAIAEWVLPNDQ-RADYALFKGLDF-YGIVEAKKWDEDI 265
Cdd:COG4096 2 LSEAETRkKLIDPALKEAGWDVDDQILR----EVRPTAGRNVVIGEWPTRGGKgYADYVLFGDDGKpLAVVEAKRTSKDV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 266 AGQMAQPKEYAKEVPYQSNyyllsnqmgdyKVPFIYTANGRPylkqyqeksgIWFWDARNPKENAYALEEFHKPDDLALK 345
Cdd:COG4096 78 SAGLQQAKLYADGLEKQYG-----------QVPFIFATNGRE----------IWFWDDRDPYPREREVDGFPSPEELWEL 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 346 LtAKNKIEADNDLVDDHDYPKFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLV 425
Cdd:COG4096 137 L-KRRKGTARKRLATEPYNDGIALRYYQIEAIRRVEEAIAKGQRRALLVMATGTGKTRTAIALIYRLLKAGRAKRILFLA 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 426 DRNSLGRQTANAIKDNKIGTMSISSIYGlkelSDKVPDASTKIQIATVQGMIKRLFFSDDNSE--KPSVGQYDFIIVDEA 503
Cdd:COG4096 216 DRNALVDQAKNAFKPFLPDLDAFTKLYN----KSKDIDKSARVYFSTYQTMMNRIDGEEEEPGyrQFPPDFFDLIIIDEC 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 504 HRGYAedkelsdneyqfynqeeyvSQYRRVVDYFDATAIGMTATPAL----QTTEIF-GDPVYTYSYQQAVLDGYLVNHD 578
Cdd:COG4096 292 HRGIY-------------------SKWRAILDYFDALQIGLTATPKDtidrNTYEYFnGNPVYTYSLEQAVADGFLVPYK 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 579 aPVIIKTKLAKEGIHFKKGteVDIFDQDEKTINKEKLPDNMNFDVKDFNHRVITRNFNKVVCDELVKKYLDPTDPYLGKT 658
Cdd:COG4096 353 -VIRIDTKFDREGIRYDAG--EDLSDEEGEEIELEELEEDREYEAKDFNRKVVNEDTTRKVLEELMEYLDKPGGDRLGKT 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 659 LIFAATDAHADMVVDLLKQAFKEQGrsvdDDAIEKITGSIRHPNQEIKNFKNEE-NPNIVVTVDLLTTGIDVPRITNIVF 737
Cdd:COG4096 430 IIFAKNDDHADRIVQALRELYPELG----GDFVKKITGDDDYGKSLIDNFKNPEkYPRIAVTVDMLDTGIDVPEVVNLVF 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 738 LRRVQSRILYEQMLGRATRLCPEI--HKEKFTIFDAVGIYDAMNKVTnmKPVVKnpghnvhyflshknyFETNEDTNQYQ 815
Cdd:COG4096 506 MRPVKSRIKFEQMIGRGTRLCPDLfpGKTHFTIFDFVGNTELFADPS--FPLRI---------------FEPRREREKFW 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 816 VDMAGAVERKIKrwddqrrkefERLAEIKSVDNWARKLSKlTKTDFLKEWPKFV-QLDHINPARPKQFISDAPDEVVDVS 894
Cdd:COG4096 569 DLLGGEDPAKLA----------VHLADALDPDKVTIPVVA-EAVQLLDDVPDLRdLLKFIDKDKRQIIYTDFEDELLEAE 637
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 895 RGYGSGnQKPEDYIDSFNNFIKQNVNtIPALQVVATRpkdLTFDELKEIKLKLEQNGFKEKDLQTAWKNAKhvQTTADII 974
Cdd:COG4096 638 EGYGKK-LKAEDYRDKFEAFLREHKE-IPALQKLRNR---LTREDLKELEEELEEQGLGEEDLAEAYGEVG--NELADLI 710
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 975 SFIRQVA-AGSELVDHDVRIHNAMQKVYGMADWSISQRKWLKRIENQLMSSTVLGPnaeeafnDNFY---FKRQGGYKQI 1050
Cdd:COG4096 711 DLIRHIAgLDQPLLTRRERVERAFKRFLAGHKYTEEQREFLERILDHLADNGVIEL-------EDLDeapFTQDGGPGGI 783
|
890 900
....*....|....*....|...
gi 1993121499 1051 KKIFPEYA--DQIIYVLNENLYV 1071
Cdd:COG4096 784 DGLFGGVDelDEALEELNEALYA 806
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
319-864 |
1.01e-55 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 203.72 E-value: 1.01e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 319 WFWDARNPKENAYALEEFHKPDDLALKLTAKNKIEADndlvDDHDYPKFADRPYQIDAINAMEDAIKNGKKRILLAMATG 398
Cdd:COG1061 35 VEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAG----DEASGTSFELRPYQQEALEALLAALERGGGRGLVVAPTG 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 399 TGKTRTAISLMYRLLkhkRARRILYLVDRNSLGRQTANAIKdnkigtmsisSIYGLKELSDKVPDASTKIQIATVQGMIK 478
Cdd:COG1061 111 TGKTVLALALAAELL---RGKRVLVLVPRRELLEQWAEELR----------RFLGDPLAGGGKKDSDAPITVATYQSLAR 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 479 RLF---FSDDnsekpsvgqYDFIIVDEAHRGYAEdkelsdneyqfynqeeyvsQYRRVVDYFDATAI-GMTATP-----A 549
Cdd:COG1061 178 RAHldeLGDR---------FGLVIIDEAHHAGAP-------------------SYRRILEAFPAAYRlGLTATPfrsdgR 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 550 LQTTEIFGDPVYTYSYQQAVLDGYLVNHDApVIIKTKLAKEGIHFKKGTEVDIFDQDEKTINKEKlpdnmnfdvkdfnhr 629
Cdd:COG1061 230 EILLFLFDGIVYEYSLKEAIEDGYLAPPEY-YGIRVDLTDERAEYDALSERLREALAADAERKDK--------------- 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 630 vitrnfnkvVCDELVKKYLDPtdpylGKTLIFAATDAHADMVVDLLKQAfkeqgrsvdDDAIEKITGSIRHPNQE--IKN 707
Cdd:COG1061 294 ---------ILRELLREHPDD-----RKTLVFCSSVDHAEALAELLNEA---------GIRAAVVTGDTPKKEREeiLEA 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 708 FKNEEnPNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYEQMLGRATRLCPEihKEKFTIFDAVGiydamNKVTNMKPV 787
Cdd:COG1061 351 FRDGE-LRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPG--KEDALVYDFVG-----NDVPVLEEL 422
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1993121499 788 VKNPGHNVHYFLSHKNYFETNEDTNQYQVDMAGAVERKIKRWDDQRRKEFERLAEIKSVDNWARKLSKLTKTDFLKE 864
Cdd:COG1061 423 AKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLELA 499
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
370-556 |
4.35e-54 |
|
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: 185.46 E-value: 4.35e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNkigtMSIS 449
Cdd:cd18032 2 RYYQQEAIEALEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRKKRILFLAHREELLEQAERSFKEV----LPDG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 450 SIYGLKELSDKvpDASTKIQIATVQGMIKRlffsdDNSEKPSVGQYDFIIVDEAHRGYAedkelsdneyqfynqeeyvSQ 529
Cdd:cd18032 78 SFGNLKGGKKK--PDDARVVFATVQTLNKR-----KRLEKFPPDYFDLIIIDEAHHAIA-------------------SS 131
|
170 180 190
....*....|....*....|....*....|..
gi 1993121499 530 YRRVVDYF-DATAIGMTATPA----LQTTEIF 556
Cdd:cd18032 132 YRKILEYFePAFLLGLTATPErtdgLDTYELF 163
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
657-772 |
8.36e-42 |
|
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: 148.86 E-value: 8.36e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 657 KTLIFAATDAHADMVVDLLKQAFKEQGRSVDDDAIEkitgsIRHPNQEIKNFKNEENPNIVVTVDLLTTGIDVPRITNIV 736
Cdd:cd18799 8 KTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDR-----ERGDEALILLFFGELKPPILVTVDLLTTGVDIPEVDNVV 82
|
90 100 110
....*....|....*....|....*....|....*.
gi 1993121499 737 FLRRVQSRILYEQMLGRATRLCPEihKEKFTIFDAV 772
Cdd:cd18799 83 FLRPTESRTLFLQMLGRGLRLHEG--KDFFTILDFI 116
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
366-548 |
2.12e-37 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 137.80 E-value: 2.12e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 366 KFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNKIGT 445
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKNGQKRGLIVMATGSGKTLTAAKLIARLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPNY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 MSISSIYglKELSDKVPDASTKIQIATVQGMIKRLffsDDNSEKPSVGQYDFIIVDEAHRGYAEdkelsdneyqfynqee 525
Cdd:pfam04851 81 VEIGEII--SGDKKDESVDDNKIVVTTIQSLYKAL---ELASLELLPDFFDVIIIDEAHRSGAS---------------- 139
|
170 180
....*....|....*....|....
gi 1993121499 526 yvsQYRRVVDYFD-ATAIGMTATP 548
Cdd:pfam04851 140 ---SYRNILEYFKpAFLLGLTATP 160
|
|
| EcoEI_R_C |
pfam08463 |
EcoEI R protein C-terminal; The restriction enzyme EcoEI recognizes 5'-GAGN(7)ATGC-3' and is ... |
907-1069 |
4.98e-29 |
|
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: 113.88 E-value: 4.98e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 907 YIDSFNNFIKQNVNTIPALQVVATRPkDLTFDELKEIKLKLEQNGFKEKDLQTAWKNAKHVQttADIISFIRQVAAGSE- 985
Cdd:pfam08463 1 YLDYFRAFIRENFDEIDALRKLWNNR-ELTRADLKELEEKLDQPGFTEEQLWEAYEILKSNQ--ADLFDLIRHIAGLDQp 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 986 LVDHDVRIHNAMQKVYGMADWSISQRKWLKRIENQLMSSTVLGPnaeEAFNDNfYFKRQGGYKQIKKIFPEYA--DQIIY 1063
Cdd:pfam08463 78 LLTRRERAERAFKRWLAQHNFTEEQREFLERILDHYAENGVIEL---DDLLEL-PFKDLGGLGKIIKLFGGKKelDEIID 153
|
....*.
gi 1993121499 1064 VLNENL 1069
Cdd:pfam08463 154 ELNEEL 159
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
370-548 |
2.59e-23 |
|
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: 96.99 E-value: 2.59e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMedAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHkrarRILYLVDRNSLGRQTANAIKDnkigTMSIS 449
Cdd:cd17926 2 RPYQEEALEAW--LAHKNNRRGILVLPTGSGKTLTALALIAYLKEL----RTLIVVPTDALLDQWKERFED----FLGDS 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 450 SIYGLKELSDKVPDaSTKIQIATVQgmikrLFFSDDNSEKPSVGQYDFIIVDEAHRGYAEdkelsdneyqfynqeeyvsQ 529
Cdd:cd17926 72 SIGLIGGGKKKDFD-DANVVVATYQ-----SLSNLAEEEKDLFDQFGLLIVDEAHHLPAK-------------------T 126
|
170 180
....*....|....*....|
gi 1993121499 530 YRRVVDYFDAT-AIGMTATP 548
Cdd:cd17926 127 FSEILKELNAKyRLGLTATP 146
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
370-548 |
1.55e-19 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 87.93 E-value: 1.55e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEdaikNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIK----DNKIGT 445
Cdd:smart00487 10 RPYQKEAIEALL----SGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKklgpSLGLKV 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 MSISSIYGLKELSDKVPDASTKIQIATVQGMIKRLffsddNSEKPSVGQYDFIIVDEAHRgyaedkeLSDNEYQfynqee 525
Cdd:smart00487 86 VGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLL-----ENDKLSLSNVDLVILDEAHR-------LLDGGFG------ 147
|
170 180
....*....|....*....|....*
gi 1993121499 526 yvSQYRRVVDYFDATA--IGMTATP 548
Cdd:smart00487 148 --DQLEKLLKLLPKNVqlLLLSATP 170
|
|
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
366-841 |
2.37e-18 |
|
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: 91.08 E-value: 2.37e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 366 KFAdRPYQIDAINAMEDAIK--NGKKRI-LLAMATGTGKTRTAISLMYRLLKHKRAR--RILYLVDRNSLGRQTANAIkd 440
Cdd:COG0610 254 IVA-RYHQYFAVRKAVERVKeaEGDGKGgVIWHTQGSGKSLTMVFLAQKLARLPDLDnpTVVVVTDRKDLDDQLFDTF-- 330
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 441 NKIGTMSISSIYGLKELSDKVPDASTKIQIATVQgmiKrlFFSDDNSEKPSVGQYD---FIIVDEAHRgyaedkelsdne 517
Cdd:COG0610 331 KAFGRESVVQAESRADLRELLESDSGGIIVTTIQ---K--FPEALDEIKYPELSDRkniIVIVDEAHR------------ 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 518 yqfynqeeyvSQY----RRVVDYF-DATAIGMTATPALQ----TTEIFGDPVYTYSYQQAVLDGYLVnhdaPVIIKTKLA 588
Cdd:COG0610 394 ----------SQYgglaKNMRDALpNASFFGFTGTPIFKedrtTLEVFGDYIHTYTITQAIEDGATL----PLLYEYRLA 459
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 589 KegIHFKKGTEVDIFDQ------DEKTINKEKLPDNMNFDVKDfNHRVitrnfnKVVCDELVKKYLDPTDPYLGKTLIFA 662
Cdd:COG0610 460 K--LKLDKEKIDEEFDEltegldDEEKEKLKAKWALLEEVLGA-PERI------EQIAEDIVEHFEERTRPGKGKAMVVT 530
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 663 ATDAHA----DMVVDLLKQAFKEQGRSV------DDDAIEKITgsiRHPNQE-----IKNFKNEENP-NIVVTVDLLTTG 726
Cdd:COG0610 531 SSREAAvryyEAFDKLRPEWGYKPLKIAvvfsgsANDDPEELK---EHGNKEyekdlAKRFKDPDDPlKLLIVVDMLLTG 607
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 727 IDVPRIT-----------NIVflrrvqsrilyeQMLGRATRLCPEihKEKFTIFDAVGIYDAMNKVTNM-------KPVV 788
Cdd:COG0610 608 FDAPSLHtlyvdkplkghNLM------------QAISRVNRVFPG--KPYGLIVDYRGIFENLKKALALyseedgkEDVL 673
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1993121499 789 KNPGHNVHYFLSH----KNYFETNEDTNQYQV-----DMAGAVERKIKrwDDQRRKEFERLA 841
Cdd:COG0610 674 TDPEEALEELKEAldelRALFPEGVDFSAFDPtekleALDEAVERFLG--DEEARKEFKKLF 733
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
370-565 |
2.23e-12 |
|
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: 67.25 E-value: 2.23e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEDAIKNG------KKRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKD-NK 442
Cdd:cd18030 23 RYYQYYAVEAALERIKTAtnkdgdKKGGYIWHTQGSGKSLTMFKAAKLLIEDPKNPKVVFVVDRKDLDYQTSSTFSRfAA 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 443 IGTMSISSIYGLKELSDKvpdASTKIQIATVQ--GMIKRlffsDDNSEKPSVGQYDFIIVDEAHRGyaedkelsdneyQF 520
Cdd:cd18030 103 EDVVRANSTKELKELLKN---LSGGIIVTTIQkfNNAVK----EESKPVLIYRKNIVVIVDEAHRS------------QF 163
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|.
gi 1993121499 521 YNQEEYvsqyrrVVDYF-DATAIGMTATP-----ALQTTEIFGDPVYTYSY 565
Cdd:cd18030 164 GELAKA------LKKALpNATFIGFTGTPifkegDKTTEKVFGDYLHKYTI 208
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
389-547 |
4.98e-12 |
|
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: 64.73 E-value: 4.98e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 389 KRILLAMATGTGKTRTAISLMYRLLKhKRARRILYLVDRNSLGRQTANAIKD-----NKIGTMSISSIYGLKElSDKVPD 463
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLL-KKGKKVLVLVPTKALALQTAERLRElfgpgIRVAVLVGGSSAEERE-KNKLGD 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 464 AstKIQIATVQgmikrLFFSDDNSEKPSVG-QYDFIIVDEAHRgyaedkeLSDNEYQFYNQEEYVSQYRRvvdyFDATAI 542
Cdd:cd00046 80 A--DIIIATPD-----MLLNLLLREDRLFLkDLKLIIVDEAHA-------LLIDSRGALILDLAVRKAGL----KNAQVI 141
|
....*
gi 1993121499 543 GMTAT 547
Cdd:cd00046 142 LLSAT 146
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
372-572 |
8.80e-12 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 65.92 E-value: 8.80e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 372 YQIDAINAMEDAIKN-GKKRILLAMAT-GTGKTRTAISLMYRLLKHKRARRILYLVDRNSLGRQT----ANAIKDNKIGT 445
Cdd:pfam18766 1 QQYFAVNKAVERVLEdGDRRGGVIWHTqGSGKSLTMVFLARKLRRELKNPTVVVVTDRNDLDDQLtktfAACGREVPVQA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 msiSSIYGLKELSDKvpdaSTKIQIATVQgmiKrlFFSDDN------SEKPSVgqydFIIVDEAHRgyaedkelsdneyq 519
Cdd:pfam18766 81 ---ESRKDLRELLRG----SGGIIFTTIQ---K--FGETPDegfpvlSDRRNI----IVLVDEAHR-------------- 130
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1993121499 520 fynqeeyvSQY----RRVVDYF-DATAIGMTATPAL----QTTEIFGDPVYTYSYQQAVLDG 572
Cdd:pfam18766 131 --------SQYgglaANMRDALpNAAFIGFTGTPILkkdkNTRAVFGDYIDTYTIQDAVEDG 184
|
|
| hsdR |
TIGR00348 |
type I site-specific deoxyribonuclease, HsdR family; This gene is part of the type I ... |
254-784 |
9.37e-12 |
|
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: 69.35 E-value: 9.37e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 254 GIVEAKKWDEDIAGQMAQPKEYAKEVPYQSNYyllsNQMGdykvpfiYTANGRPYLKQYQEKSGIWF----WDARNPKeN 329
Cdd:TIGR00348 133 VIIELKKRSVTIREAFNQIKRYEKEIPELFKY----VQIF-------VISNGTDTRYYTGSDEDDFDftfnWKESDNK-L 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 330 AYALEEFHKpdDLALKLTAKNKIEadNDLVDDHDYPKFAdRPYQI----DAINAMEDAIKN-----GKKRILLAMATGTG 400
Cdd:TIGR00348 201 IEDLKEFDI--LLLKKERLLDFIR--NFIIFDKDTGLVT-KPYQRymqyRAVKKIVESITRktwgkDERGGLIWHTQGSG 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 401 KTRTAISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNKIGTM-SISSIYGLKELSDKVPDastKIQIATVQGMIKR 479
Cdd:TIGR00348 276 KTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQKDCAeRIESIAELKELLEKDDG---GIIITTIQKFDDK 352
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 480 LffSDDNSEKPSVGQYDFIIVDEAHRgyaedkelsdNEYQFYNQeeyvsQYRRVVDyfDATAIGMTATP--------ALQ 551
Cdd:TIGR00348 353 L--KEEEEKFPVDRKEVVVIFDEAHR----------SQYGELAK-----NLKKALK--NASFFGFTGTPifkkdrdtSLT 413
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 552 TTEIFGDPVYTYSYQQAVLDGYLVNHD-APVIIKTKLAKEgihfkkgtEVDIFDQDEKTINKEKLPDNMNFDVKDFNHRV 630
Cdd:TIGR00348 414 FAYVFGRYLHRYFITDAIRDGLTVKIDyEDRLPEDHLDKK--------KLDAFFDEIFELLPERIREITKESLKEKLQKT 485
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 631 ITRNFNKV----VCDELVKKYLDPTDPYLGKTLIFA----ATDAHADMVVDLLKQAFKE-----QGRSVDDDAIE----- 692
Cdd:TIGR00348 486 KKILFNEDrlesIAKDIAEHYAKFKELFKFKAMVVAisryACVEEKNALDEELNEKFEAsaivmTGKESDDAEIRdynkh 565
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 693 ---KITGSIRHPNQE--IKNFKNEENPNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYeQMLGRATRLCPEIhKEKFT 767
Cdd:TIGR00348 566 irtKFDKSDGFEIYYkdLERFKKNENPKLLIVVDMLLTGFDAPILNTLYLDKPLKYHGLL-QAIARTNRIDGKD-KTFGL 643
|
570
....*....|....*..
gi 1993121499 768 IFDAVGIYDAMNKVTNM 784
Cdd:TIGR00348 644 IVDYRGLEKSLIDALSL 660
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
370-555 |
9.04e-11 |
|
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: 61.49 E-value: 9.04e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAmedaIKNGKkRILLAMATGTGKTRTA-ISLMYRLLKHKRARRILYLVDRNSLGRQTANAIKDNKIGT-MS 447
Cdd:pfam00270 1 TPIQAEAIPA----ILEGR-DVLVQAPTGSGKTLAFlLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGLgLK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 448 ISSIYGLKELSDKVPD-ASTKIQIATvqgmIKRLFfsDDNSEKPSVGQYDFIIVDEAHRgyaedkelsdneyqfYNQEEY 526
Cdd:pfam00270 76 VASLLGGDSRKEQLEKlKGPDILVGT----PGRLL--DLLQERKLLKNLKLLVLDEAHR---------------LLDMGF 134
|
170 180 190
....*....|....*....|....*....|.
gi 1993121499 527 VSQYRRVVDYFDATA--IGMTATPALQTTEI 555
Cdd:pfam00270 135 GPDLEEILRRLPKKRqiLLLSATLPRNLEDL 165
|
|
| ResIII |
COG3421 |
Type III restriction endonuclease [Defense mechanisms]; |
339-767 |
9.58e-09 |
|
Type III restriction endonuclease [Defense mechanisms];
Pssm-ID: 442647 [Multi-domain] Cd Length: 883 Bit Score: 59.64 E-value: 9.58e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 339 PDDLALKLTAKNKIEADNDLVDDHDY----PKFADRPYQIDAI-----NAMEDAIKNGKKRILLAMATGTGKTRTAISLM 409
Cdd:COG3421 11 KRFLLLQKLDQSEIVLFAEEFPITITlnlnENIRKRLYEEEAFylknyIENEPFIKNKPKHLLFNMATGSGKTLIMAGLI 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 410 YRLLkHKRARRILYLVDRNSLGRQTanaiKDNKIGTMSISSIYG-----------LKELsDKVPDAST---KIQIATVQG 475
Cdd:COG3421 91 LYLY-KKGYRNFLFFVNTNNIIYKT----RENFLNPQSPKYLFNekieidgenvaIKEV-DNFPEADEndiNIKFTSIQK 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 476 MIKRLFFSDDNsekpSVGQYDF------IIVDEAHRGYAEDK-ELSDNEYQFYNQEEYVSQYRRvvDYFDATAIGMTATP 548
Cdd:COG3421 165 LHNDLNTPREN----SLTYEDFedkklvLISDEAHHLNASTKsKKKTEKEEEKSWEYTVNRILK--ANPDNILLEFTATI 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 549 ALQTTEIFGD----PVYTYSYQQAVLDGY-----LVNHDA--------PVII---KTKLAKE-GIHFK-----KGTEVDI 602
Cdd:COG3421 239 DLSNKEIYKKykdkIIYRYDLKQFREDGYskdvkRLQSDYedqermlnAVLLseyRRKLAERnGINIKpvilfKSKKIKE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 603 FDQDEKTINkeKLPDNMNFDvkDFNHRVITRNFNKVVCDELVKKYLDptdpylgktlIFAATDAHADMVVDLLKQAFKEQ 682
Cdd:COG3421 319 SKEAYDEFL--QLIKNLSAD--DIEKLIKFSTGKNENGSEILENAFD----------YFRKNDISLNSLVREIKRDFSEE 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 683 GR-SVDDDAIEKITGSIRhpnqeIKNFKNEENP-NIVVTVDLLTTGIDVPRITNIVFL---------RRVQSRILYEQML 751
Cdd:COG3421 385 NViNVNSKDDSEKEKQIL-----LNTLEDPDNPiRAIFAVDKLNEGWDVLNLFDIVRLydtrdgkggKPGKTTISEAQLI 459
|
490
....*....|....*....
gi 1993121499 752 GRATRLCP---EIHKEKFT 767
Cdd:COG3421 460 GRGARYYPfelEEGQDKFK 478
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
656-756 |
1.47e-08 |
|
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: 53.75 E-value: 1.47e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 656 GKTLIFAATDAHADMvvDLLKQAFKEQgrsvdddaIEKITGSIRHPNQE--IKNFKNEENpNIVVTVDLLTTGIDVPRIT 733
Cdd:pfam00271 16 GKVLIFSQTKKTLEA--ELLLEKEGIK--------VARLHGDLSQEEREeiLEDFRKGKI-DVLVATDVAERGLDLPDVD 84
|
90 100
....*....|....*....|...
gi 1993121499 734 NIVFLRRVQSRILYEQMLGRATR 756
Cdd:pfam00271 85 LVINYDLPWNPASYIQRIGRAGR 107
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
715-772 |
1.70e-08 |
|
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: 52.32 E-value: 1.70e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1993121499 715 NIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYEQMLGRATRlcpeIHKEKFTIFDAV 772
Cdd:cd18785 24 EILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGR----GGKDEGEVILFV 77
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
370-548 |
2.42e-08 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 55.37 E-value: 2.42e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINameDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRIL-------------YLVDRNSLGRQtan 436
Cdd:cd18011 2 LPHQIDAVL---RALRKPPVRLLLADEVGLGKTIEAGLIIKELLLRGDAKRVLilcpaslveqwqdELQDKFGLPFL--- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 437 aIKDnkigtmsiSSIYGLKELSDKVPDASTKIQIATVqGMIKRlffSDDNSEKPSVGQYDFIIVDEAHRGYAEDKELSDN 516
Cdd:cd18011 76 -ILD--------RETAAQLRRLIGNPFEEFPIVIVSL-DLLKR---SEERRGLLLSEEWDLVVVDEAHKLRNSGGGKETK 142
|
170 180 190
....*....|....*....|....*....|..
gi 1993121499 517 EYQFynqeeyVSQYRRVVDYFdataIGMTATP 548
Cdd:cd18011 143 RYKL------GRLLAKRARHV----LLLTATP 164
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
673-756 |
2.83e-08 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 51.83 E-value: 2.83e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 673 DLLKQAFKEQGRSVdddaiEKITGSIRHPNQE--IKNFKNEENpNIVVTVDLLTTGIDVPRITNIVFLRRVQSRILYEQM 750
Cdd:smart00490 1 EELAELLKELGIKV-----ARLHGGLSQEEREeiLDKFNNGKI-KVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQR 74
|
....*.
gi 1993121499 751 LGRATR 756
Cdd:smart00490 75 IGRAGR 80
|
|
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
365-576 |
7.16e-07 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 53.81 E-value: 7.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 365 PKFADRPYQIDAINAMEDAIKN---GKkrilLAMATGTGKTRTAISLMYRLLkhKRARRILYLVDRNSLGRQT------- 434
Cdd:COG4889 166 AKKTLRPHQQEAIEAVLAGFKThdrGK----LIMACGTGKTFTSLRIAEELA--GKGGRVLFLVPSISLLSQTlrewtae 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 435 ------ANAI-KDNKIGTMSISSIYGLKELSDKVPdASTKI--------QIATVQGMIkrLFFSDDNS-------EKPSV 492
Cdd:COG4889 240 sevplrSFAVcSDSKVGKRRKKDDEDTSAHDLAYP-ATTDAeklaaaaqKRHDADRMT--VVFSTYQSidvvadaQKLGL 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 493 GQYDFIIVDEAHR--GYAEDKElsdNEYQF--YNQEEYVSQYRRVvdYfdataigMTATPALQT---------------- 552
Cdd:COG4889 317 PEFDLIICDEAHRttGATLAGE---DESAFvrVHDNDYIKAKKRL--Y-------MTATPRIYGddakkkakeasavlas 384
|
250 260
....*....|....*....|....*..
gi 1993121499 553 ---TEIFGDPVYTYSYQQAVLDGYLVN 576
Cdd:COG4889 385 mddEALFGPEFHRLGFGEAVERGLLTD 411
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
370-505 |
1.26e-05 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 47.43 E-value: 1.26e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIdaiNAMEDAIKNgkKRILLAMATGTGKTRTAISLMYRLLKHKRAR---RILYLVDRNSLGRQTANAIKDN-KIGT 445
Cdd:cd17927 4 RNYQL---ELAQPALKG--KNTIICLPTGSGKTFVAVLICEHHLKKFPAGrkgKVVFLANKVPLVEQQKEVFRKHfERPG 78
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1993121499 446 MSISSIYGLKELSDKVPD--ASTKIQIATVQGMIKRLffsdDNSEKPSVGQYDFIIVDEAHR 505
Cdd:cd17927 79 YKVTGLSGDTSENVSVEQivESSDVIIVTPQILVNDL----KSGTIVSLSDFSLLVFDECHN 136
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
370-504 |
1.89e-05 |
|
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer 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: 350792 [Multi-domain] Cd Length: 200 Bit Score: 46.88 E-value: 1.89e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAmedAIKngkKRILLAMATGTGKTRTAISLMYRLLKHKRA-----RRILYLVDRNSLGRQTANAIKDN--- 441
Cdd:cd18034 4 RSYQLELFEA---ALK---RNTIVVLPTGSGKTLIAVMLIKEMGELNRKeknpkKRAVFLVPTVPLVAQQAEAIRSHtdl 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1993121499 442 KIGTMS-ISSIYGLKELSDKVPDASTKIQIATVQ---GMIKRLFFSDDNsekpsvgqYDFIIVDEAH 504
Cdd:cd18034 78 KVGEYSgEMGVDKWTKERWKEELEKYDVLVMTAQillDALRHGFLSLSD--------INLLIFDECH 136
|
|
| uvsW |
PHA02558 |
UvsW helicase; Provisional |
370-804 |
2.96e-05 |
|
UvsW helicase; Provisional
Pssm-ID: 222875 [Multi-domain] Cd Length: 501 Bit Score: 48.08 E-value: 2.96e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINameDAIKNgkKRILLAMATGTGKTRTAISLMYRLLKHKRARrILYLVDRNSLGRQTANAIKDnkIGTMSIS 449
Cdd:PHA02558 116 HWYQYDAVY---EGLKN--NRRLLNLPTSAGKSLIQYLLSRYYLENYEGK-VLIIVPTTSLVTQMIDDFVD--YRLFPRE 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 450 SIYGLKELSDKvpDASTKIQIATVQGMIK--RLFFSddnsekpsvgQYDFIIVDEAHRGYAED-----KELSDNEYQFyn 522
Cdd:PHA02558 188 AMHKIYSGTAK--DTDAPIVVSTWQSAVKqpKEWFD----------QFGMVIVDECHLFTGKSltsiiTKLDNCKFKF-- 253
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 523 qeeyvsqyrrvvdyfdataiGMTATP------ALQTTEIFGD---PVYTysyQQAVLDGYLVNHDAPVI-IKTKlakegi 592
Cdd:PHA02558 254 --------------------GLTGSLrdgkanILQYVGLFGDifkPVTT---SQLMEEGQVTDLKINSIfLRYP------ 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 593 hfkkgtevdifDQDEKTINKEKLPDNMNFdvkdfnhrvITRN--FNKVVCDeLVKKYLDPTdpylGKTLIFAATDAHADM 670
Cdd:PHA02558 305 -----------DEDRVKLKGEDYQEEIKY---------ITSHtkRNKWIAN-LALKLAKKG----ENTFVMFKYVEHGKP 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 671 VVDLLKQA-----FKEQGRSVDD-DAIEKITgsirhpnqeiknfKNEENPNIVVTVDLLTTGIDVPRITNIVFLRRVQSR 744
Cdd:PHA02558 360 LYEMLKKVydkvyYVSGEVDTEDrNEMKKIA-------------EGGKGIIIVASYGVFSTGISIKNLHHVIFAHPSKSK 426
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1993121499 745 ILYEQMLGRATRLcpeiH--KEKFTIFDavgIYDAMNkvtnmkpvVKNPGHNVHYFLSHKNY 804
Cdd:PHA02558 427 IIVLQSIGRVLRK----HgsKSIATVWD---IIDDLS--------VKPKSANAKKKYVHLNY 473
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
373-552 |
8.04e-05 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA 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: 350687 [Multi-domain] Cd Length: 178 Bit Score: 44.51 E-value: 8.04e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 373 QIDAINAMEDAiKNGKKRILLAMATGTGKTRTAISLMYRLLkhKRARRILYLVDRNSLGRQTANAIKD---NKIGTM--S 447
Cdd:cd17929 1 QRKAYEAIVSS-LGGFKTFLLHGVTGSGKTEVYIELIEKVL--AKGKQVLVLVPEISLTPQLIKRFKKrfgDKVAVLhsK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 448 ISSIYGLKELSdKVPDASTKIQIATvqgmikR--LFFSDDNsekpsvgqYDFIIVDEAHRG-YAEDKELSdneyqfYNQE 524
Cdd:cd17929 78 LSDKERADEWR-KIKRGEAKVVIGA------RsaLFAPFKN--------LGLIIVDEEHDSsYKQDSGPR------YHAR 136
|
170 180
....*....|....*....|....*...
gi 1993121499 525 EyVSQYRrvVDYFDATAIGMTATPALQT 552
Cdd:cd17929 137 D-VAIYR--AKLENAPVVLGSATPSLES 161
|
|
| DEXHc_ATRX-like |
cd18007 |
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ... |
370-505 |
9.57e-05 |
|
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They 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: 350765 [Multi-domain] Cd Length: 239 Bit Score: 44.98 E-value: 9.57e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAI-----NAMEDAIKNGKKR-ILLAMATGTGKTRTAISLMYRLLKH-KRARRILYLVDRNSL-------GRQTA 435
Cdd:cd18007 2 KPHQVEGVrflwsNLVGTDVGSDEGGgCILAHTMGLGKTLQVITFLHTYLAAaPRRSRPLVLCPASTLynwedefKKWLP 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 436 NAIKDNKIGTMSISSIYGLKELsDKVPDASTK--------------IQIATVQGMIKRLFFSDDNSEKPsvgqyDFIIVD 501
Cdd:cd18007 82 PDLRPLLVLVSLSASKRADARL-RKINKWHKEggvlligyelfrnlASNATTDPRLKQEFIAALLDPGP-----DLLVLD 155
|
....
gi 1993121499 502 EAHR 505
Cdd:cd18007 156 EGHR 159
|
|
| DEXHc_Hef |
cd18035 |
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ... |
370-548 |
1.75e-04 |
|
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: 43.66 E-value: 1.75e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAinamedAIKNGKKRILLAMATGTGKTRTAISLM-YRLLKHKraRRILYLVDRNSLGRQTANAIKDNKIGTMSI 448
Cdd:cd18035 4 RLYQVLI------AAVALNGNTLIVLPTGLGKTIIAILVAaDRLTKKG--GKVLILAPSRPLVEQHAENLKRVLNIPDKI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 449 SSIYGLKELSDKVPD-ASTKIQIATVQgmikrLFFSDDNSEKPSVGQYDFIIVDEAHRGyaedkeLSDNEYQFYnQEEYV 527
Cdd:cd18035 76 TSLTGEVKPEERAERwDASKIIVATPQ-----VIENDLLAGRITLDDVSLLIFDEAHHA------VGNYAYVYI-AHRYK 143
|
170 180
....*....|....*....|.
gi 1993121499 528 SQYRrvvdyfDATAIGMTATP 548
Cdd:cd18035 144 REAN------NPLILGLTASP 158
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
365-423 |
2.49e-04 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 45.07 E-value: 2.49e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 1993121499 365 PKFADRPYQIDAINAMEDAIKNGKKRILLAMATGTGKTRTAISLMYRLLKHKRARRILY 423
Cdd:COG1203 124 PRTPINPLQNEALELALEAAEEEPGLFILTAPTGGGKTEAALLFALRLAAKHGGRRIIY 182
|
|
| DinG |
COG1199 |
Rad3-related DNA helicase DinG [Replication, recombination and repair]; |
365-402 |
5.70e-04 |
|
Rad3-related DNA helicase DinG [Replication, recombination and repair];
Pssm-ID: 440812 [Multi-domain] Cd Length: 629 Bit Score: 43.76 E-value: 5.70e-04
10 20 30
....*....|....*....|....*....|....*....
gi 1993121499 365 PKFADRPYQIDAINAMEDAIKNGkkRILLAMA-TGTGKT 402
Cdd:COG1199 11 PGFEPRPGQREMAEAVARALAEG--RHLLIEAgTGTGKT 47
|
|
| DEXHc_Snf |
cd17919 |
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ... |
370-505 |
5.73e-04 |
|
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 42.17 E-value: 5.73e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMEDAIKNGKkRILLAMATGTGKTRTAISLMYRLLKH-KRARRILYLVDrNSLGRQTANAIKdnKI-GTMS 447
Cdd:cd17919 2 RPYQLEGLNFLLELYENGP-GGILADEMGLGKTLQAIAFLAYLLKEgKERGPVLVVCP-LSVLENWEREFE--KWtPDLR 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1993121499 448 ISSIYGLKE----LSDKVPDASTKIQIATVQgMIKRlffsddNSEKPSVGQYDFIIVDEAHR 505
Cdd:cd17919 78 VVVYHGSQReraqIRAKEKLDKFDVVLTTYE-TLRR------DKASLRKFRWDLVVVDEAHR 132
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
370-550 |
5.76e-04 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350794 [Multi-domain] Cd Length: 204 Bit Score: 42.46 E-value: 5.76e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQIDAINAMedaiKNGKKRILLAmATGTGKTRTAISLMYRLLKHKRAR----RILYLVDRNSLGRQTANAIKDNKIGT 445
Cdd:cd18036 4 RNYQLELVLPA----LRGKNTIICA-PTGSGKTRVAVYICRHHLEKRRSAgekgRVVVLVNKVPLVEQQLEKFFKYFRKG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 446 MSISSIYGLKELSDKVPD--ASTKIQIATVQGMIKRLfFSDDNSEKPSVGQYDFIIVDEAHRgyaEDKELSDNEYQF-YN 522
Cdd:cd18036 79 YKVTGLSGDSSHKVSFGQivKASDVIICTPQILINNL-LSGREEERVYLSDFSLLIFDECHH---TQKEHPYNKIMRmYL 154
|
170 180
....*....|....*....|....*...
gi 1993121499 523 QEEYVSQYRRvvdyfdATAIGMTATPAL 550
Cdd:cd18036 155 DKKLSSQGPL------PQILGLTASPGV 176
|
|
| HepA |
COG0553 |
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ... |
370-425 |
3.15e-03 |
|
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];
Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 41.36 E-value: 3.15e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1993121499 370 RPYQIDAINAMEDAIKNGKkRILLAMATGTGKTRTAISLMYRLLKHKRARRILYLV 425
Cdd:COG0553 243 RPYQLEGAAWLLFLRRLGL-GGLLADDMGLGKTIQALALLLELKERGLARPVLIVA 297
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
370-548 |
5.28e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 40.87 E-value: 5.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 370 RPYQID-AINAMedaikngKKRILLAMATGTGKTrtAISLM---YRLlkHKRARRILYLVDRNSLGRQTANAIKDN-KIG 444
Cdd:COG1111 5 RLYQLNlAASAL-------RKNTLVVLPTGLGKT--AVALLviaERL--HKKGGKVLFLAPTKPLVEQHAEFFKEAlNIP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1993121499 445 TMSISSIYGlKELSDKVPD--ASTKIQIATVQgmikrLFFSDDNSEKPSVGQYDFIIVDEAHRG---YAedkelsdneyq 519
Cdd:COG1111 74 EDEIVVFTG-EVSPEKRKElwEKARIIVATPQ-----VIENDLIAGRIDLDDVSLLIFDEAHRAvgnYA----------- 136
|
170 180 190
....*....|....*....|....*....|.
gi 1993121499 520 fYNQ--EEYVSQYRrvvdyfDATAIGMTATP 548
Cdd:COG1111 137 -YVYiaERYHEDAK------DPLILGMTASP 160
|
|
| |
