|
Name |
Accession |
Description |
Interval |
E-value |
| recQ_fam |
TIGR00614 |
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
502-975 |
0e+00 |
|
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 129701 [Multi-domain] Cd Length: 470 Bit Score: 857.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 502 NCLKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPAC 581
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 582 LLGSAQSKN----ILGDVKLGKYRVIYITPEFCSGNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTA 657
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 658 LPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTGNILQDLKPFLVRkassawEFEGPT-IIYC 736
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK------EFEGKSgIIYC 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 737 PSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQE 816
Cdd:TIGR00614 234 PSRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 817 IGRAGRDGLQSSCHLLWAPADFNTSRNLLIEIHDEKFRLYKLKMMVKMEKYLHSSQCRRRIILSHFEDKCLQKaSLDIMG 896
Cdd:TIGR00614 314 SGRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMG 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 897 TEKCCDNCRPRLNHCLtaNNSEDASQDFGPQAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLPDK-YRGHRLFGAGKEQ 975
Cdd:TIGR00614 393 TEKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDGgFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
496-992 |
4.01e-170 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 517.00 E-value: 4.01e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 496 PNAKQIncLKTYFGHSSFKPVQWKVIHSVLEeRRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLEL 575
Cdd:COG0514 3 DDALEV--LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 576 SNVPACLLGSAQSKN----ILGDVKLGKYRVIYITPEFCS--GNLDLLQQldssIGITLIAVDEAHCISEWGHDFRSSFR 649
Cdd:COG0514 80 AGIRAAFLNSSLSAEerreVLRALRAGELKLLYVAPERLLnpRFLELLRR----LKISLFAIDEAHCISQWGHDFRPDYR 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 650 MLGSLKTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTG-NILQDLKPFLVRKAssawef 728
Cdd:COG0514 156 RLGELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP------ 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 729 EGPTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPK 808
Cdd:COG0514 230 GGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPK 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 809 EMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLieihDEKF--------RLYKLKMMVkmeKYLHSSQCRRRIILS 880
Cdd:COG0514 310 SIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQRFFI----EQSPpdeerkrvERAKLDAML---AYAETTGCRRQFLLR 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 881 HFEDKClqkasldimgTEKC--CDNcrprlnhCLTANNSEDASQDfgpqAFQLLSAVDILQEKFGIGIPILFLRGSNSQR 958
Cdd:COG0514 383 YFGEEL----------AEPCgnCDN-------CLGPPETFDGTEA----AQKALSCVYRTGQRFGAGHVIDVLRGSKNEK 441
|
490 500 510
....*....|....*....|....*....|....*.
gi 170763504 959 LPDkYRGHRL--FGAGKEQAESWWKTLSHHLIAEGF 992
Cdd:COG0514 442 IRQ-FGHDKLstYGIGKDLSDKEWRSVIRQLLAQLF 476
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
494-1185 |
8.57e-122 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 392.92 E-value: 8.57e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 494 PEPNAKQIncLKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQL 573
Cdd:PRK11057 9 LESLAKQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 574 ELSNVPACLLGSAQSK----NILGDVKLGKYRVIYITPE--FCSGNLDLLQQLDSSigitLIAVDEAHCISEWGHDFRSS 647
Cdd:PRK11057 86 LANGVAAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPErlMMDNFLEHLAHWNPA----LLAVDEAHCISQWGHDFRPE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 648 FRMLGSLKTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLylevgRKTgnILQDLKPFlvrkaSSAWE 727
Cdd:PRK11057 162 YAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNI-----RYT--LVEKFKPL-----DQLMR 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 728 F----EGPT-IIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVI 802
Cdd:PRK11057 230 YvqeqRGKSgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 803 HYGAPKEMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLieihDEK-------FRLYKLKmmvKMEKYLHSSQCRR 875
Cdd:PRK11057 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL----EEKpagqqqdIERHKLN---AMGAFAEAQTCRR 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 876 RIILSHFEDkclqkasldimGTEKCCDNCrprlNHCLTANNSEDASQDfgpqAFQLLSAVDILQEKFGIGIPILFLRGSN 955
Cdd:PRK11057 383 LVLLNYFGE-----------GRQEPCGNC----DICLDPPKQYDGLED----AQKALSCIYRVNQRFGMGYVVEVLRGAN 443
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 956 SQRLPDkyRGH---RLFGAGKEQAESWWKTLSHHLIAEGFLVEVPKENkyiKTCSLTKKGRKWL-GEAssqsppSLLLQA 1031
Cdd:PRK11057 444 NQRIRD--YGHdklKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQH---SALQLTEAARPVLrGEV------SLQLAV 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1032 neemfPRKVllpssnpvspettqhssnqnpaglttkqsNLERTHSYKvpekvSSGTNIPKKsavmpspgtsssplepais 1111
Cdd:PRK11057 513 -----PRIV-----------------------------ALKPRAMQK-----SFGGNYDRK------------------- 534
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170763504 1112 aqeldartgLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLA-PLLEVIK 1185
Cdd:PRK11057 535 ---------LFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
501-695 |
2.48e-114 |
|
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ATP-dependent helicase or WRN) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Werner's syndrome.
Pssm-ID: 350775 [Multi-domain] Cd Length: 193 Bit Score: 356.78 E-value: 2.48e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 501 INCLKTYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPA 580
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 581 CLLGSAQSKNILGDVKLGKYRVIYITPEFCSGNLDLLQQLDSsiGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTALPL 660
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 170763504 661 VPVIALSATASSSIREDIISCLNLKDPQITCTGFD 695
Cdd:cd18017 159 VPIVALTATATPSVRDDIIKNLNLRNPQITCTSFD 193
|
|
| RNaseD_like |
cd06129 |
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ... |
55-223 |
3.13e-78 |
|
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.
Pssm-ID: 176650 [Multi-domain] Cd Length: 161 Bit Score: 255.13 E-value: 3.13e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 55 DCSFLSEDISMrlsDGDVVGFDMEWPPIYKpgKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGI 134
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRR--YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 135 EGDQWKLLRDFDVKLESFVELTDVANEKLKCaETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYAG 214
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 170763504 215 LIIYQKLGN 223
Cdd:cd06129 153 LIIYTKLRN 161
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
51-226 |
7.25e-46 |
|
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
Pssm-ID: 396266 [Multi-domain] Cd Length: 173 Bit Score: 162.86 E-value: 7.25e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 51 YEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVsesKCYLFHISSMSVFP---QGLKMLLENKSI 127
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGT---GEGAYIIDPLALGDdvlSALKRLLEDPNI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 128 KKAGVGIEGDQWKLLRDFDVKLESFVElTDVANEKLKCAETWSLNGLVKHVLGkqLLKDKSIRCSNWSNFPLTEDQKLYA 207
Cdd:pfam01612 78 TKVGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYA 154
|
170
....*....|....*....
gi 170763504 208 ATDAYAGLIIYQKLGNLGD 226
Cdd:pfam01612 155 ALDADYLLRLYDKLRKELE 173
|
|
| DpdF |
NF041063 |
protein DpdF; |
532-844 |
5.49e-39 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 157.38 E-value: 5.49e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 532 VVVMATGYGKSLCFQYPPVYTGKIG---IVISPLISLMEDQVLQL-ELSNVPACLLG------SAQSKN----ILGDVKL 597
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRArELLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 598 GKYRVIYITPE-FCSGNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTAL--------PLVpVIALSA 668
Cdd:NF041063 242 GTQRILFTSPEsLTGSLRPALFDAAEAGLLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLlrlapsgrPFR-TLLLSA 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 669 TASSSirediisCLN-LKD-------PQITCTGFDRP----NLYLEVGR--KTGNILQdlkpfLVRKASSawefegPTII 734
Cdd:NF041063 321 TLTES-------TLDtLETlfgppgpFIVVSAVQLRPepayWVAKCDSEeeRRERVLE-----ALRHLPR------PLIL 382
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 735 YCPSRKMTEQVTAELGKLNLA-CRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESY 813
Cdd:NF041063 383 YVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRF 462
|
330 340 350
....*....|....*....|....*....|.
gi 170763504 814 YQEIGRAGRDGLQSSCHLLWAPADFNTSRNL 844
Cdd:NF041063 463 YQEVGRGGRDGKASLSLLIYTPDDLDIAKSL 493
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
55-226 |
6.27e-31 |
|
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Pssm-ID: 214681 [Multi-domain] Cd Length: 172 Bit Score: 120.15 E-value: 6.27e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 55 DCSFLSEDISMRLSDGDVVGFDMEWPPIYKpgKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGI 134
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDS--YSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 135 EGDQWKLLRdFDVKLESfVELTDVAN-EKLKCAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYA 213
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAyLLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
170
....*....|...
gi 170763504 214 GLIIYQKLGNLGD 226
Cdd:smart00474 160 LLRLYEKLEKELE 172
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
515-676 |
7.20e-27 |
|
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: 108.10 E-value: 7.20e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 515 PVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYP------PVYTGKIGIVISPLISLMEDQVLQLE-----LSNVPACLL 583
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 584 GSAQSKNILGdvKLGKYRVIYITPEFCSGNLDLLQQLDSsigITLIAVDEAHCISEWGhdFRSSFRMLgsLKTALPLVPV 663
Cdd:pfam00270 81 GGDSRKEQLE--KLKGPDILVGTPGRLLDLLQERKLLKN---LKLLVLDEAHRLLDMG--FGPDLEEI--LRRLPKKRQI 151
|
170
....*....|...
gi 170763504 664 IALSATASSSIRE 676
Cdd:pfam00270 152 LLLSATLPRNLED 164
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
923-1016 |
1.51e-24 |
|
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain.
Pssm-ID: 214936 [Multi-domain] Cd Length: 92 Bit Score: 98.70 E-value: 1.51e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 923 DFGPQAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLPDK-YRGHRLFGAGKEQAESWWKTLSHHLIAEGFLVEVPKENK 1001
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLREDGGRYP 80
|
90
....*....|....*
gi 170763504 1002 YIKtcsLTKKGRKWL 1016
Cdd:smart00956 81 YLK---LTEKARPVL 92
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
1116-1194 |
7.28e-20 |
|
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Pssm-ID: 128635 [Multi-domain] Cd Length: 81 Bit Score: 85.04 E-value: 7.28e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1116 DARTGLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVIKHFCQVTSVQ 1194
Cdd:smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| HTH_40 |
pfam14493 |
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of ... |
1223-1317 |
4.16e-17 |
|
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of helicase proteins.
Pssm-ID: 464189 Cd Length: 89 Bit Score: 77.55 E-value: 4.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1223 SVAVTYTLFQEKkMPLHSIAENRLLPLTAAGMHLAQAVKAGYPLDMERAgLTPETWKIIMDVIRNPPINSdmykVKLIRM 1302
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 170763504 1303 LVPENLDTYLIHMAI 1317
Cdd:pfam14493 75 ALPEEISYFEIRLVL 89
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
1120-1184 |
4.80e-13 |
|
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Pssm-ID: 425755 [Multi-domain] Cd Length: 68 Bit Score: 65.25 E-value: 4.80e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 170763504 1120 GLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVI 1184
Cdd:pfam00570 3 ALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
66-275 |
3.11e-07 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 54.11 E-value: 3.11e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 66 RLSDGDVVGFDME-------WPpiykpgkrsRVAVIQLCVSEsKCYL---FHISSMSVFPQglkmLLENKSIKK---AGv 132
Cdd:COG0349 14 RLAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALidpLAIGDLSPLWE----LLADPAIVKvfhAA- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 133 giegdqwkllrDFDvkLESFVELTDVANEKLKC----------AETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTED 202
Cdd:COG0349 79 -----------RED--LEILYHLFGILPKPLFDtqiaaallgyGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEE 143
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 170763504 203 QKLYAATDAYAGLIIYQKLgnlgdTAQVFALNK----AEENLPLEMKKQLNSISEEM-RDLANRFPVTCRNLETLQRV 275
Cdd:COG0349 144 QLEYAAADVRYLLPLYEKL-----LEELEREGRlewaEEECARLLDPATYREDPEEAwLRLKGAWKLNPRQLAVLREL 216
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
1094-1185 |
5.15e-04 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 44.09 E-value: 5.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1094 AVMPSPGTSSSPLEPAI----SAQELDART-GLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDG 1168
Cdd:COG0349 180 ARLLDPATYREDPEEAWlrlkGAWKLNPRQlAVLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEELARLRG 259
|
90
....*....|....*...
gi 170763504 1169 VSEGKAALLAP-LLEVIK 1185
Cdd:COG0349 260 LSPGEIRRHGEeLLAAVA 277
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
156-344 |
6.63e-04 |
|
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]
Pssm-ID: 130455 [Multi-domain] Cd Length: 367 Bit Score: 43.60 E-value: 6.63e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 156 TDVANEKLKCAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLgnlgdTAQVFALNK 235
Cdd:TIGR01388 99 TQIAAAFCGFGMSMGYAKLVQEVLGVEL--DKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKL-----MERLEESGR 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 236 A----EENLPLEMKKQLNSISEEM-RDLANRFPVTCRNLETLQRvpviLKSISENLCSLRKVICGPTNTETRLKPGSSFN 310
Cdd:TIGR01388 172 LawleEECTLLTDRRTYVVNPEDAwRDIKNAWQLRPQQLAVLQA----LAAWREREARERDLPRNFVLKEEALWELARQA 247
|
170 180 190
....*....|....*....|....*....|....*.
gi 170763504 311 LLSSEDSAAAGEKEKQIGKHSTF--AKIKEEPWDPE 344
Cdd:TIGR01388 248 PGNLTELASLGPKGSEIRKHGDTllALVKTALALPE 283
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| recQ_fam |
TIGR00614 |
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
502-975 |
0e+00 |
|
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 129701 [Multi-domain] Cd Length: 470 Bit Score: 857.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 502 NCLKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPAC 581
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 582 LLGSAQSKN----ILGDVKLGKYRVIYITPEFCSGNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTA 657
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 658 LPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTGNILQDLKPFLVRkassawEFEGPT-IIYC 736
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK------EFEGKSgIIYC 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 737 PSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQE 816
Cdd:TIGR00614 234 PSRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 817 IGRAGRDGLQSSCHLLWAPADFNTSRNLLIEIHDEKFRLYKLKMMVKMEKYLHSSQCRRRIILSHFEDKCLQKaSLDIMG 896
Cdd:TIGR00614 314 SGRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMG 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 897 TEKCCDNCRPRLNHCLtaNNSEDASQDFGPQAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLPDK-YRGHRLFGAGKEQ 975
Cdd:TIGR00614 393 TEKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDGgFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
496-992 |
4.01e-170 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 517.00 E-value: 4.01e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 496 PNAKQIncLKTYFGHSSFKPVQWKVIHSVLEeRRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLEL 575
Cdd:COG0514 3 DDALEV--LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 576 SNVPACLLGSAQSKN----ILGDVKLGKYRVIYITPEFCS--GNLDLLQQldssIGITLIAVDEAHCISEWGHDFRSSFR 649
Cdd:COG0514 80 AGIRAAFLNSSLSAEerreVLRALRAGELKLLYVAPERLLnpRFLELLRR----LKISLFAIDEAHCISQWGHDFRPDYR 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 650 MLGSLKTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTG-NILQDLKPFLVRKAssawef 728
Cdd:COG0514 156 RLGELRERLPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP------ 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 729 EGPTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPK 808
Cdd:COG0514 230 GGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPK 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 809 EMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLieihDEKF--------RLYKLKMMVkmeKYLHSSQCRRRIILS 880
Cdd:COG0514 310 SIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQRFFI----EQSPpdeerkrvERAKLDAML---AYAETTGCRRQFLLR 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 881 HFEDKClqkasldimgTEKC--CDNcrprlnhCLTANNSEDASQDfgpqAFQLLSAVDILQEKFGIGIPILFLRGSNSQR 958
Cdd:COG0514 383 YFGEEL----------AEPCgnCDN-------CLGPPETFDGTEA----AQKALSCVYRTGQRFGAGHVIDVLRGSKNEK 441
|
490 500 510
....*....|....*....|....*....|....*.
gi 170763504 959 LPDkYRGHRL--FGAGKEQAESWWKTLSHHLIAEGF 992
Cdd:COG0514 442 IRQ-FGHDKLstYGIGKDLSDKEWRSVIRQLLAQLF 476
|
|
| recQ |
TIGR01389 |
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ... |
498-1185 |
6.03e-134 |
|
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273594 [Multi-domain] Cd Length: 591 Bit Score: 425.26 E-value: 6.03e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 498 AKQIncLKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSN 577
Cdd:TIGR01389 1 AQQV--LKRTFGYDDFRPGQEEIISHVLDGR-DVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKDQVDQLRAAG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 578 VPACLLGSAQS----KNILGDVKLGKYRVIYITPE-FCSGN-LDLLQQLDssigITLIAVDEAHCISEWGHDFRSSFRML 651
Cdd:TIGR01389 78 VAAAYLNSTLSakeqQDIEKALVNGELKLLYVAPErLEQDYfLNMLQRIP----IALVAVDEAHCVSQWGHDFRPEYQRL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 652 GSLKTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTgNILQDLKPFLVRkassawEFEGP 731
Cdd:TIGR01389 154 GSLAERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKN-NKQKFLLDYLKK------HRGQS 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEME 811
Cdd:TIGR01389 227 GIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLE 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 812 SYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLIE-IHDEKfrlYKLKMMVK---MEKYLHSSQCRRRIILSHFEDKcl 887
Cdd:TIGR01389 307 SYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQsEADDD---YKQIEREKlraMIAYCETQTCRRAYILRYFGEN-- 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 888 qkasldimGTEKC--CDNcrprlnhCLTANNSEDASQDfgpqAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLPDKyrG 965
Cdd:TIGR01389 382 --------EVEPCgnCDN-------CLDPPKSYDATVE----AQKALSCVYRMGQRFGVGYIIEVLRGSKNDKILQK--G 440
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 966 H-RL--FGAGKEQAESWWKTLSHHLIAEGFLVEVPkeNKYIktcsltkkgrkwlgeASSQSPPSLLLQANEemfpRKVLL 1042
Cdd:TIGR01389 441 HdQLstYGIGKDYTQKEWRSLIDQLIAEGLLTEND--EIYI---------------GLQLTEAARKVLKNE----VEVLL 499
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1043 PSSNPVSPETTQhssnqnpaglttKQSNLerthsykvpekvssgtnipkksavmpspgtsssplepAISAQELdartgLY 1122
Cdd:TIGR01389 500 RPFKVVAKEKTR------------VQKNL-------------------------------------SVGVDNA-----LF 525
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 170763504 1123 ARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVIK 1185
Cdd:TIGR01389 526 EALRELRKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEaFLEVIR 589
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
494-1185 |
8.57e-122 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 392.92 E-value: 8.57e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 494 PEPNAKQIncLKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQL 573
Cdd:PRK11057 9 LESLAKQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQL 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 574 ELSNVPACLLGSAQSK----NILGDVKLGKYRVIYITPE--FCSGNLDLLQQLDSSigitLIAVDEAHCISEWGHDFRSS 647
Cdd:PRK11057 86 LANGVAAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPErlMMDNFLEHLAHWNPA----LLAVDEAHCISQWGHDFRPE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 648 FRMLGSLKTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLylevgRKTgnILQDLKPFlvrkaSSAWE 727
Cdd:PRK11057 162 YAALGQLRQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNI-----RYT--LVEKFKPL-----DQLMR 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 728 F----EGPT-IIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVI 802
Cdd:PRK11057 230 YvqeqRGKSgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVV 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 803 HYGAPKEMESYYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLLieihDEK-------FRLYKLKmmvKMEKYLHSSQCRR 875
Cdd:PRK11057 310 HFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCL----EEKpagqqqdIERHKLN---AMGAFAEAQTCRR 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 876 RIILSHFEDkclqkasldimGTEKCCDNCrprlNHCLTANNSEDASQDfgpqAFQLLSAVDILQEKFGIGIPILFLRGSN 955
Cdd:PRK11057 383 LVLLNYFGE-----------GRQEPCGNC----DICLDPPKQYDGLED----AQKALSCIYRVNQRFGMGYVVEVLRGAN 443
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 956 SQRLPDkyRGH---RLFGAGKEQAESWWKTLSHHLIAEGFLVEVPKENkyiKTCSLTKKGRKWL-GEAssqsppSLLLQA 1031
Cdd:PRK11057 444 NQRIRD--YGHdklKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQH---SALQLTEAARPVLrGEV------SLQLAV 512
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1032 neemfPRKVllpssnpvspettqhssnqnpaglttkqsNLERTHSYKvpekvSSGTNIPKKsavmpspgtsssplepais 1111
Cdd:PRK11057 513 -----PRIV-----------------------------ALKPRAMQK-----SFGGNYDRK------------------- 534
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170763504 1112 aqeldartgLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLA-PLLEVIK 1185
Cdd:PRK11057 535 ---------LFAKLRKLRKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
501-695 |
2.48e-114 |
|
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ATP-dependent helicase or WRN) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Werner's syndrome.
Pssm-ID: 350775 [Multi-domain] Cd Length: 193 Bit Score: 356.78 E-value: 2.48e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 501 INCLKTYFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPA 580
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 581 CLLGSAQSKNILGDVKLGKYRVIYITPEFCSGNLDLLQQLDSsiGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTALPL 660
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 170763504 661 VPVIALSATASSSIREDIISCLNLKDPQITCTGFD 695
Cdd:cd18017 159 VPIVALTATATPSVRDDIIKNLNLRNPQITCTSFD 193
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
505-1184 |
7.33e-84 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 300.27 E-value: 7.33e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 505 KTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPACLLG 584
Cdd:PLN03137 453 KKVFGNHSFRPNQREIINATMSGY-DVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQANIPAASLS 531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 585 S----AQSKNILGDV--KLGKYRVIYITPEFCSGNLDLLQQLDSSIGITLIA---VDEAHCISEWGHDFRSSFRMLGSLK 655
Cdd:PLN03137 532 AgmewAEQLEILQELssEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLArfvIDEAHCVSQWGHDFRPDYQGLGILK 611
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 656 TALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFDRPNLYLEVGRKTGNILQDLKPFLVRKassawEFEGPTIIY 735
Cdd:PLN03137 612 QKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFIKEN-----HFDECGIIY 686
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 736 CPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQ 815
Cdd:PLN03137 687 CLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQ 766
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 816 EIGRAGRDGLQSSCHLLWAPADF-----------------------NTSRNLLIEIHDEKFrlykLKMMVKMEkylHSSQ 872
Cdd:PLN03137 767 ECGRAGRDGQRSSCVLYYSYSDYirvkhmisqggveqspmamgynrMASSGRILETNTENL----LRMVSYCE---NEVD 839
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 873 CRRRIILSHFEDKclqkasLDIMGTEKCCDNCrprlnhcltANNSEDASQDFGPQAFQLLSAVDILQEKFGIGIPILFLR 952
Cdd:PLN03137 840 CRRFLQLVHFGEK------FDSTNCKKTCDNC---------SSSKSLIDKDVTEIARQLVELVKLTGERFSSAHILEVYR 904
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 953 GSNSQRLpDKYRGH--RLFGAGKEQAESWWKTLSHHLIAEGFLVE-VPKENKYIKTCSLTKKGRkwlgeassqSPPSLLL 1029
Cdd:PLN03137 905 GSLNQYV-KKHRHEtlSLHGAGKHLSKGEASRILHYLVTEDILAEdVKKSDLYGSVSSLLKVNE---------SKAYKLF 974
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1030 QANEEMFPRkvlLPSSNPVSpettqhssnqnpaglttKQSNLERThsykvPEKVSSGTNipkKSAVMPSPGTSSSPLEPA 1109
Cdd:PLN03137 975 SGGQTIIMR---FPSSVKAS-----------------KPSKFEAT-----PAKGPLTSG---KQSTLPMATPAQPPVDLN 1026
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1110 ISAQELDARTGLYARLVEarqkhankmDVPPAILA----TNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVI 1184
Cdd:PLN03137 1027 LSAILYTALRKLRTALVK---------EAGDGVMAyhifGNATLQQISKRIPRTKEELLEINGLGKAKVSKYGDrLLETI 1097
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
503-695 |
1.81e-80 |
|
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.
Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 262.86 E-value: 1.81e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 503 CLKTYFGHSSFKPVQWKVIHSVLEeRRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPACL 582
Cdd:cd17920 3 ILKEVFGYDEFRPGQLEAINAVLA-GRDVLVVMPTGGGKSLCYQLPALLLDGVTLVVSPLISLMQDQVDRLQQLGIRAAA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 583 LGSAQS----KNILGDVKLGKYRVIYITPEFC--SGNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKT 656
Cdd:cd17920 82 LNSTLSpeekREVLLRIKNGQYKLLYVTPERLlsPDFLELLQRLPERKRLALIVVDEAHCVSQWGHDFRPDYLRLGRLRR 161
|
170 180 190
....*....|....*....|....*....|....*....
gi 170763504 657 ALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFD 695
Cdd:cd17920 162 ALPGVPILALTATATPEVREDILKRLGLRNPVIFRASFD 200
|
|
| RNaseD_like |
cd06129 |
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ... |
55-223 |
3.13e-78 |
|
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif.
Pssm-ID: 176650 [Multi-domain] Cd Length: 161 Bit Score: 255.13 E-value: 3.13e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 55 DCSFLSEDISMrlsDGDVVGFDMEWPPIYKpgKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGI 134
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRR--YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 135 EGDQWKLLRDFDVKLESFVELTDVANEKLKCaETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYAG 214
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 170763504 215 LIIYQKLGN 223
Cdd:cd06129 153 LIIYTKLRN 161
|
|
| WRN_exo |
cd06141 |
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ... |
55-221 |
2.67e-72 |
|
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Pssm-ID: 176653 [Multi-domain] Cd Length: 170 Bit Score: 238.63 E-value: 2.67e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 55 DCSFLSEDISMRLS-DGDVVGFDMEWPPIYKPGKRSRVAVIQLCvSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVG 133
Cdd:cd06141 2 DSAQDAEEAVKELLgKEKVVGFDTEWRPSFRKGKRNKVALLQLA-TESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 134 IEGDQWKLLRDFDVKLESFVELTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYA 213
Cdd:cd06141 81 IKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYA 160
|
....*...
gi 170763504 214 GLIIYQKL 221
Cdd:cd06141 161 SLELYRKL 168
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
696-833 |
1.38e-68 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 226.32 E-value: 1.38e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 696 RPNLYLEVGRKTGNILQDLKPFLVRKassaWEFEGPTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRF 775
Cdd:cd18794 1 RPNLFYSVRPKDKKDEKLDLLKRIKV----EHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKW 76
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 170763504 776 LRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQEIGRAGRDGLQSSCHLLW 833
Cdd:cd18794 77 LRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILFY 134
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
72-221 |
7.56e-64 |
|
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.
Pssm-ID: 176656 [Multi-domain] Cd Length: 150 Bit Score: 213.64 E-value: 7.56e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 72 VVGFDMEWPPIYKpgKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDVKLES 151
Cdd:cd09018 1 VFAFDTETDSLDN--ISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 152 FVELTDVANEKLKCAETWSLNGLVKHVLGKQLLKDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKL 221
Cdd:cd09018 79 AFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKL 148
|
|
| DEXHc_RecQ4-like |
cd18018 |
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
508-689 |
1.41e-49 |
|
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.
Pssm-ID: 350776 [Multi-domain] Cd Length: 201 Bit Score: 174.75 E-value: 1.41e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 508 FGHSSFKPVQWKVIHSVLEeRRDNVVVMATGYGKSLCFQYP----PVYTGKIGIVISPLISLMEDQVLQLELSNVPACL- 582
Cdd:cd18018 8 FGHPSFRPGQEEAIARLLS-GRSTLVVLPTGAGKSLCYQLPalllRRRGPGLTLVVSPLIALMKDQVDALPRAIKAAALn 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 583 --LGSAQSKNILGDVKLGKYRVIYITPE-FCsgNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGS-LKTAL 658
Cdd:cd18018 87 ssLTREERRRILEKLRAGEVKILYVSPErLV--NESFRELLRQTPPISLLVVDEAHCISEWSHNFRPDYLRLCRvLRELL 164
|
170 180 190
....*....|....*....|....*....|.
gi 170763504 659 PLVPVIALSATASSSIREDIISCLNLKDPQI 689
Cdd:cd18018 165 GAPPVLALTATATKRVVEDIASHLGIPESGV 195
|
|
| DEXHc_RecQ5 |
cd18014 |
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ... |
502-687 |
3.44e-48 |
|
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350772 [Multi-domain] Cd Length: 205 Bit Score: 170.73 E-value: 3.44e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 502 NCLKTYFGHSSFK-PVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPA 580
Cdd:cd18014 2 STLKKVFGHSDFKsPLQEKATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVISPLIALIQDQVDHLKTLKIRV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 581 CLLGSAQS----KNILGDVK--LGKYRVIYITPEFCSGNL--DLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLG 652
Cdd:cd18014 82 DSLNSKLSaqerKRIIADLEseKPQTKFLYITPEMAATSSfqPLLSSLVSRNLLSYLVVDEAHCVSQWGHDFRPDYLRLG 161
|
170 180 190
....*....|....*....|....*....|....*
gi 170763504 653 SLKTALPLVPVIALSATASSSIREDIISCLNLKDP 687
Cdd:cd18014 162 ALRSRYGHVPWVALTATATPQVQEDIFAQLRLKKP 196
|
|
| DEXHc_RecQ1 |
cd18015 |
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
504-695 |
1.96e-46 |
|
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350773 [Multi-domain] Cd Length: 209 Bit Score: 166.00 E-value: 1.96e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 504 LKTYFGHSSFKPVQWKVIHSVLEeRRDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPACLL 583
Cdd:cd18015 10 LKNVFKLEKFRPLQLETINATMA-GRDVFLVMPTGGGKSLCYQLPALCSDGFTLVVSPLISLMEDQLMALKKLGISATML 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 584 GSAQSKNILGDV------KLGKYRVIYITPEFCSGNLDLLQQLDS--SIG-ITLIAVDEAHCISEWGHDFRSSFRMLGSL 654
Cdd:cd18015 89 NASSSKEHVKWVhaaltdKNSELKLLYVTPEKIAKSKRFMSKLEKayNAGrLARIAIDEVHCCSQWGHDFRPDYKKLGIL 168
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 170763504 655 KTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFD 695
Cdd:cd18015 169 KRQFPNVPILGLTATATSKVLKDVQKILCIQKCLTFTASFN 209
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
51-226 |
7.25e-46 |
|
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.
Pssm-ID: 396266 [Multi-domain] Cd Length: 173 Bit Score: 162.86 E-value: 7.25e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 51 YEASDCSFLSEDISMRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVsesKCYLFHISSMSVFP---QGLKMLLENKSI 127
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGT---GEGAYIIDPLALGDdvlSALKRLLEDPNI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 128 KKAGVGIEGDQWKLLRDFDVKLESFVElTDVANEKLKCAETWSLNGLVKHVLGkqLLKDKSIRCSNWSNFPLTEDQKLYA 207
Cdd:pfam01612 78 TKVGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYA 154
|
170
....*....|....*....
gi 170763504 208 ATDAYAGLIIYQKLGNLGD 226
Cdd:pfam01612 155 ALDADYLLRLYDKLRKELE 173
|
|
| DEXHc_RecQ2_BLM |
cd18016 |
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
504-695 |
8.22e-40 |
|
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom syndrome protein homolog or BLM) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations in RecQ2 cause Bloom syndrome.
Pssm-ID: 350774 [Multi-domain] Cd Length: 208 Bit Score: 146.90 E-value: 8.22e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 504 LKTYFGHSSFKPVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYPPVYTGKIGIVISPLISLMEDQVLQLELSNVPACLL 583
Cdd:cd18016 9 FHKKFGLHQFRTNQLEAINAALLGE-DCFVLMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSLDIPATYL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 584 ----GSAQSKNILGDVKLGK--YRVIYITPE-FCSGN--LDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSL 654
Cdd:cd18016 88 tgdkTDAEATKIYLQLSKKDpiIKLLYVTPEkISASNrlISTLENLYERKLLARFVIDEAHCVSQWGHDFRPDYKRLNML 167
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 170763504 655 KTALPLVPVIALSATASSSIREDIISCLNLKDPQITCTGFD 695
Cdd:cd18016 168 RQKFPSVPMMALTATATPRVQKDILNQLKMLRPQVFTMSFN 208
|
|
| DpdF |
NF041063 |
protein DpdF; |
532-844 |
5.49e-39 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 157.38 E-value: 5.49e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 532 VVVMATGYGKSLCFQYPPVYTGKIG---IVISPLISLMEDQVLQL-ELSNVPACLLG------SAQSKN----ILGDVKL 597
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRArELLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 598 GKYRVIYITPE-FCSGNLDLLQQLDSSIGITLIAVDEAHCISEWGHDFRSSFRMLGSLKTAL--------PLVpVIALSA 668
Cdd:NF041063 242 GTQRILFTSPEsLTGSLRPALFDAAEAGLLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLlrlapsgrPFR-TLLLSA 320
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 669 TASSSirediisCLN-LKD-------PQITCTGFDRP----NLYLEVGR--KTGNILQdlkpfLVRKASSawefegPTII 734
Cdd:NF041063 321 TLTES-------TLDtLETlfgppgpFIVVSAVQLRPepayWVAKCDSEeeRRERVLE-----ALRHLPR------PLIL 382
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 735 YCPSRKMTEQVTAELGKLNLA-CRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESY 813
Cdd:NF041063 383 YVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRF 462
|
330 340 350
....*....|....*....|....*....|.
gi 170763504 814 YQEIGRAGRDGLQSSCHLLWAPADFNTSRNL 844
Cdd:NF041063 463 YQEVGRGGRDGKASLSLLIYTPDDLDIAKSL 493
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
55-226 |
6.27e-31 |
|
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Pssm-ID: 214681 [Multi-domain] Cd Length: 172 Bit Score: 120.15 E-value: 6.27e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 55 DCSFLSEDISMRLSDGDVVGFDMEWPPIYKpgKRSRVAVIQLCVSESKCYLFHISSMSVFPQGLKMLLENKSIKKAGVGI 134
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDS--YSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 135 EGDQWKLLRdFDVKLESfVELTDVAN-EKLKCAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYA 213
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAyLLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
170
....*....|...
gi 170763504 214 GLIIYQKLGNLGD 226
Cdd:smart00474 160 LLRLYEKLEKELE 172
|
|
| mut-7_like_exo |
cd06146 |
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ... |
65-221 |
4.73e-29 |
|
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Pssm-ID: 176655 Cd Length: 193 Bit Score: 115.47 E-value: 4.73e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 65 MRLSDGDVVGFDMEWPPIYKPGKRSRVAVIQLCVsESKCYLF-----HISSMSVFPQGLKMLLENKSIKKAGVGIEGDQW 139
Cdd:cd06146 17 LSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT-EDEVFLLdllalENLESEDWDRLLKRLFEDPDVLKLGFGFKQDLK 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 140 KL------LRDFDVKLESFVELTDVANEKLK----------CAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQ 203
Cdd:cd06146 96 ALsasypaLKCMFERVQNVLDLQNLAKELQKsdmgrlkgnlPSKTKGLADLVQEVLGKPL--DKSEQCSNWERRPLREEQ 173
|
170
....*....|....*...
gi 170763504 204 KLYAATDAYAGLIIYQKL 221
Cdd:cd06146 174 ILYAALDAYCLLEVFDKL 191
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
515-676 |
7.20e-27 |
|
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: 108.10 E-value: 7.20e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 515 PVQWKVIHSVLEERrDNVVVMATGYGKSLCFQYP------PVYTGKIGIVISPLISLMEDQVLQLE-----LSNVPACLL 583
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 584 GSAQSKNILGdvKLGKYRVIYITPEFCSGNLDLLQQLDSsigITLIAVDEAHCISEWGhdFRSSFRMLgsLKTALPLVPV 663
Cdd:pfam00270 81 GGDSRKEQLE--KLKGPDILVGTPGRLLDLLQERKLLKN---LKLLVLDEAHRLLDMG--FGPDLEEI--LRRLPKKRQI 151
|
170
....*....|...
gi 170763504 664 IALSATASSSIRE 676
Cdd:pfam00270 152 LLLSATLPRNLED 164
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
923-1016 |
1.51e-24 |
|
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure; The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain.
Pssm-ID: 214936 [Multi-domain] Cd Length: 92 Bit Score: 98.70 E-value: 1.51e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 923 DFGPQAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLPDK-YRGHRLFGAGKEQAESWWKTLSHHLIAEGFLVEVPKENK 1001
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLREDGGRYP 80
|
90
....*....|....*
gi 170763504 1002 YIKtcsLTKKGRKWL 1016
Cdd:smart00956 81 YLK---LTEKARPVL 92
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
507-703 |
1.07e-23 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 100.26 E-value: 1.07e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 507 YFGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYTGKIG-----IVISPLISLMEDQVLQLE-----LS 576
Cdd:smart00487 3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGkggrvLVLVPTRELAEQWAEELKklgpsLG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 577 NVPACLLGSAQSKNILGDVKLGKYRVIYITPEFCsgNLDLLQQLDSSIGITLIAVDEAHCISEWGhdFRSSFRMLgsLKT 656
Cdd:smart00487 83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL--LDLLENDKLSLSNVDLVILDEAHRLLDGG--FGDQLEKL--LKL 156
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 170763504 657 ALPLVPVIALSATASSSIREDIISCLNLKdpqITCTGFDRPNLYLEV 703
Cdd:smart00487 157 LPKNVQLLLLSATPPEEIENLLELFLNDP---VFIDVGFTPLEPIEQ 200
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
743-824 |
3.41e-22 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 91.89 E-value: 3.41e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 743 EQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQEIGRAGR 822
Cdd:smart00490 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
|
..
gi 170763504 823 DG 824
Cdd:smart00490 81 AG 82
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
727-824 |
4.93e-20 |
|
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: 86.50 E-value: 4.93e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 727 EFEGPTIIYCPSRKMTEqVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGA 806
Cdd:pfam00271 13 ERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDL 91
|
90
....*....|....*...
gi 170763504 807 PKEMESYYQEIGRAGRDG 824
Cdd:pfam00271 92 PWNPASYIQRIGRAGRAG 109
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
1116-1194 |
7.28e-20 |
|
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Pssm-ID: 128635 [Multi-domain] Cd Length: 81 Bit Score: 85.04 E-value: 7.28e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1116 DARTGLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVIKHFCQVTSVQ 1194
Cdd:smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| HTH_40 |
pfam14493 |
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of ... |
1223-1317 |
4.16e-17 |
|
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of helicase proteins.
Pssm-ID: 464189 Cd Length: 89 Bit Score: 77.55 E-value: 4.16e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1223 SVAVTYTLFQEKkMPLHSIAENRLLPLTAAGMHLAQAVKAGYPLDMERAgLTPETWKIIMDVIRNPPINSdmykVKLIRM 1302
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 170763504 1303 LVPENLDTYLIHMAI 1317
Cdd:pfam14493 75 ALPEEISYFEIRLVL 89
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
732-824 |
1.57e-15 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 74.99 E-value: 1.57e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAEL-------GKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHY 804
Cdd:cd18797 38 TIVFCRSRKLAELLLRYLkarlveeGPLASKVASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLA 117
|
90 100
....*....|....*....|
gi 170763504 805 GAPKEMESYYQEIGRAGRDG 824
Cdd:cd18797 118 GYPGSLASLWQQAGRAGRRG 137
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
727-822 |
2.23e-14 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 71.38 E-value: 2.23e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 727 EFEGPTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVAT-VAfGMGINKADIRKVIHYG 805
Cdd:cd18787 25 LKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATdVA-ARGLDIPGVDHVINYD 103
|
90
....*....|....*..
gi 170763504 806 APKEMESYYQEIGRAGR 822
Cdd:cd18787 104 LPRDAEDYVHRIGRTGR 120
|
|
| RQC |
pfam09382 |
RQC domain; This DNA-binding domain is found in the RecQ helicase among others and has a ... |
922-1016 |
3.33e-14 |
|
RQC domain; This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain.
Pssm-ID: 462780 [Multi-domain] Cd Length: 108 Bit Score: 69.87 E-value: 3.33e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 922 QDFGPQAFQLLSAVDILQEKFGIGIPILFLRGSNSQRLpDKYRGHRL--FGAGKEQAESWWKTLSHHLIAEGFLVEVPKE 999
Cdd:pfam09382 5 VDVTEEAQKILSCVYRTGQRFGAGHLIDVLRGSKNKKI-RQLGHDKLstFGIGKDLSKKEWRRIIRQLIAEGYLEVDIEF 83
|
90
....*....|....*..
gi 170763504 1000 NKYIKtcsLTKKGRKWL 1016
Cdd:pfam09382 84 YSVLK---LTPKAREVL 97
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
1120-1184 |
4.80e-13 |
|
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Pssm-ID: 425755 [Multi-domain] Cd Length: 68 Bit Score: 65.25 E-value: 4.80e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 170763504 1120 GLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDGVSEGKAALLAP-LLEVI 1184
Cdd:pfam00570 3 ALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| PLN00206 |
PLN00206 |
DEAD-box ATP-dependent RNA helicase; Provisional |
515-824 |
9.28e-13 |
|
DEAD-box ATP-dependent RNA helicase; Provisional
Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 72.51 E-value: 9.28e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 515 PVQWKVIHSVLEERrdNVVVMA-TGYGKSLCF-------------QYPPVYTGKIGIVISP---LISLMEDQ--VLQLEL 575
Cdd:PLN00206 146 PIQMQAIPAALSGR--SLLVSAdTGSGKTASFlvpiisrcctirsGHPSEQRNPLAMVLTPtreLCVQVEDQakVLGKGL 223
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 576 SNVPACLLGsaqsknilGDVKLGK-YRV------IYITPefcsGNL-DLLQQLDSSI-GITLIAVDEAHCISEWGhdFRS 646
Cdd:PLN00206 224 PFKTALVVG--------GDAMPQQlYRIqqgvelIVGTP----GRLiDLLSKHDIELdNVSVLVLDEVDCMLERG--FRD 289
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 647 SfrmLGSLKTALPLVPVIALSATASSSIrEDIISCLnLKDPQ-ITCTGFDRPN-------LYLEVGRKTGNILQDLKpfl 718
Cdd:PLN00206 290 Q---VMQIFQALSQPQVLLFSATVSPEV-EKFASSL-AKDIIlISIGNPNRPNkavkqlaIWVETKQKKQKLFDILK--- 361
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 719 vrkasSAWEFEGPTIIYCPSRK----MTEQVTAELGklnLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGIN 794
Cdd:PLN00206 362 -----SKQHFKPPAVVFVSSRLgadlLANAITVVTG---LKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVD 433
|
330 340 350
....*....|....*....|....*....|
gi 170763504 795 KADIRKVIHYGAPKEMESYYQEIGRAGRDG 824
Cdd:PLN00206 434 LLRVRQVIIFDMPNTIKEYIHQIGRASRMG 463
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
508-825 |
8.04e-12 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 69.54 E-value: 8.04e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 508 FGHSSFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYT---GKIGIVISPLISLMeDQVLQlELSNvpacLLG 584
Cdd:COG1204 18 RGIEELYPPQAEALEAGLLEGKNLVVSAPTASGKTLIAELAILKAllnGGKALYIVPLRALA-SEKYR-EFKR----DFE 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 585 SAQSK-------NILGDVKLGKYRVIYITPEfcsgNLDLLQQLDSSIG--ITLIAVDEAHCIsewgHDFRSSFRM---LG 652
Cdd:COG1204 92 ELGIKvgvstgdYDSDDEWLGRYDILVATPE----KLDSLLRNGPSWLrdVDLVVVDEAHLI----DDESRGPTLevlLA 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 653 SLKTALPLVPVIALSATASSSirEDIISCLNLKD--------PQITCTGFDRPNLYLEVGRKTGNILQDlkpfLVRKASs 724
Cdd:COG1204 164 RLRRLNPEAQIVALSATIGNA--EEIAEWLDAELvksdwrpvPLNEGVLYDGVLRFDDGSRRSKDPTLA----LALDLL- 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 725 awEFEGPTIIYCPSRKMTEQV----------------TAELGKLNLACRTY---------------------HAGMKISE 767
Cdd:COG1204 237 --EEGGQVLVFVSSRRDAESLakkladelkrrltpeeREELEELAEELLEVseethtnekladclekgvafhHAGLPSEL 314
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 170763504 768 RKDVHHRFLRDEIQCVVATVAFGMGINKAdIRKVI----HYGAPKEMES--YYQEIGRAGRDGL 825
Cdd:COG1204 315 RRLVEDAFREGLIKVLVATPTLAAGVNLP-ARRVIirdtKRGGMVPIPVleFKQMAGRAGRPGY 377
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
421-820 |
1.08e-11 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 69.28 E-value: 1.08e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 421 NDDENDSSYIIESDEDLEMEMLKSLENLNSDVVEPTHSTWLEMGTNGRLPPEEEDGHGNEAIKEEQEEEDHLLP---EPN 497
Cdd:COG1061 3 LRGIAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAEALEAGDEASGtsfELR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 498 AKQINCLKTYFGHSSfkpvqwkvihsvlEERRDNVVVMATGYGKSLCFQYPPVYTGKIG--IVISPLISLMEdQVLQlEL 575
Cdd:COG1061 83 PYQQEALEALLAALE-------------RGGGRGLVVAPTGTGKTVLALALAAELLRGKrvLVLVPRRELLE-QWAE-EL 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 576 SNVPACLLGSAQSKNILGDVKLGKYRVIYitpefcsgNLDLLQQLDSSIGitLIAVDEAHcisewgHDFRSSFRMLGSlk 655
Cdd:COG1061 148 RRFLGDPLAGGGKKDSDAPITVATYQSLA--------RRAHLDELGDRFG--LVIIDEAH------HAGAPSYRRILE-- 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 656 tALPLVPVIALSATAsssIRED-----------IISCLNLKD--------P----QITCTGFDRPNLYLEVGRKTGNILQ 712
Cdd:COG1061 210 -AFPAAYRLGLTATP---FRSDgreillflfdgIVYEYSLKEaiedgylaPpeyyGIRVDLTDERAEYDALSERLREALA 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 713 DLKPFLVRKASSAWEFEG---PTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAF 789
Cdd:COG1061 286 ADAERKDKILRELLREHPddrKTLVFCSSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVL 365
|
410 420 430
....*....|....*....|....*....|.
gi 170763504 790 GMGINKADIRKVIHYGAPKEMESYYQEIGRA 820
Cdd:COG1061 366 NEGVDVPRLDVAILLRPTGSPREFIQRLGRG 396
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
729-825 |
2.00e-11 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases 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: 350182 [Multi-domain] Cd Length: 154 Bit Score: 63.34 E-value: 2.00e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 729 EGPTIIYCPSRKMTEQvTAelgkLNLACRTY-HAGMKISERKDVHHRFLRDEIQCVVATVAFGMGIN---KADIRKVIHY 804
Cdd:cd18795 43 GKPVLVFCSSRKECEK-TA----KDLAGIAFhHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNlpaRTVIIKGTQR 117
|
90 100
....*....|....*....|....*.
gi 170763504 805 GAPKEME-----SYYQEIGRAGRDGL 825
Cdd:cd18795 118 YDGKGYRelsplEYLQMIGRAGRPGF 143
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
66-221 |
4.64e-11 |
|
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Pssm-ID: 176654 [Multi-domain] Cd Length: 178 Bit Score: 62.94 E-value: 4.64e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 66 RLSDGDVVGFDME--WPPIYKPgkrsRVAVIQLCVSEsKCYLFHISSMSVFPqGLKMLLENKSIKK----AGVGIEGdqw 139
Cdd:cd06142 8 RLASAGVIAVDTEfmRLNTYYP----RLCLIQISTGG-EVYLIDPLAIGDLS-PLKELLADPNIVKvfhaAREDLEL--- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 140 kLLRDFDVKLESFVElTDVANEKLKCAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQ 219
Cdd:cd06142 79 -LKRDFGILPQNLFD-TQIAARLLGLGDSVGLAALVEELLGVEL--DKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYE 154
|
..
gi 170763504 220 KL 221
Cdd:cd06142 155 KL 156
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
732-824 |
4.66e-11 |
|
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];
Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 67.55 E-value: 4.66e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGK------LNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYG 805
Cdd:COG1205 291 TLVFTRSRRGAELLARYARRalrepdLADRVAAYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAG 370
|
90
....*....|....*....
gi 170763504 806 APKEMESYYQEIGRAGRDG 824
Cdd:COG1205 371 YPGTRASFWQQAGRAGRRG 389
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
532-669 |
7.33e-11 |
|
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: 61.65 E-value: 7.33e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 532 VVVMATGYGKSLCFQYPPVY----TGKIGIVISPLISLMEDQ---VLQLELSNVPACLLGSAQSKNILGDVKLGKYRVIY 604
Cdd:cd00046 5 LITAPTGSGKTLAALLAALLlllkKGKKVLVLVPTKALALQTaerLRELFGPGIRVAVLVGGSSAEEREKNKLGDADIII 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170763504 605 ITPEFCSGNLDLLQQLDSSiGITLIAVDEAHCISEWGHDFRSSfrMLGSLKTALPLVPVIALSAT 669
Cdd:cd00046 85 ATPDMLLNLLLREDRLFLK-DLKLIIVDEAHALLIDSRGALIL--DLAVRKAGLKNAQVILLSAT 146
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
731-824 |
9.45e-09 |
|
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: 53.48 E-value: 9.45e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 731 PTIIYCPSRKMTEQVTAELgklnlacrtyhagmkiserkdvhhrflrdeiQCVVATVAFGMGINKADIRKVIHYGAPKEM 810
Cdd:cd18785 5 KIIVFTNSIEHAEEIASSL-------------------------------EILVATNVLGEGIDVPSLDTVIFFDPPSSA 53
|
90
....*....|....
gi 170763504 811 ESYYQEIGRAGRDG 824
Cdd:cd18785 54 ASYIQRVGRAGRGG 67
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
732-822 |
6.36e-08 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 53.42 E-value: 6.36e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGKL------NLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYG 805
Cdd:cd18796 41 TLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIG 120
|
90
....*....|....*..
gi 170763504 806 APKEMESYYQEIGRAGR 822
Cdd:cd18796 121 SPKSVARLLQRLGRSGH 137
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
732-825 |
6.91e-08 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 56.69 E-value: 6.91e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVAT-VAfGMGINKADIRKVIHYGAPKEM 810
Cdd:COG0513 244 AIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATdVA-ARGIDIDDVSHVINYDLPEDP 322
|
90
....*....|....*...
gi 170763504 811 ESYYQEIG---RAGRDGL 825
Cdd:COG0513 323 EDYVHRIGrtgRAGAEGT 340
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
66-275 |
3.11e-07 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 54.11 E-value: 3.11e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 66 RLSDGDVVGFDME-------WPpiykpgkrsRVAVIQLCVSEsKCYL---FHISSMSVFPQglkmLLENKSIKK---AGv 132
Cdd:COG0349 14 RLAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALidpLAIGDLSPLWE----LLADPAIVKvfhAA- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 133 giegdqwkllrDFDvkLESFVELTDVANEKLKC----------AETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTED 202
Cdd:COG0349 79 -----------RED--LEILYHLFGILPKPLFDtqiaaallgyGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEE 143
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 170763504 203 QKLYAATDAYAGLIIYQKLgnlgdTAQVFALNK----AEENLPLEMKKQLNSISEEM-RDLANRFPVTCRNLETLQRV 275
Cdd:COG0349 144 QLEYAAADVRYLLPLYEKL-----LEELEREGRlewaEEECARLLDPATYREDPEEAwLRLKGAWKLNPRQLAVLREL 216
|
|
| RecQ_Zn_bind |
pfam16124 |
RecQ zinc-binding; This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ. |
835-905 |
4.65e-07 |
|
RecQ zinc-binding; This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ.
Pssm-ID: 465031 [Multi-domain] Cd Length: 66 Bit Score: 48.44 E-value: 4.65e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 170763504 835 PADFNTSRNLL-IEIHDEKFRLYKLKMMVKMEKY-LHSSQCRRRIILSHFEDKclqkasldiMGTEKC--CDNCR 905
Cdd:pfam16124 1 YQDVVRLRFLIeQSEADEERKEVELQKLQAMVAYcENTTDCRRKQLLRYFGEE---------FDSEPCgnCDNCL 66
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
711-824 |
5.11e-07 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 53.68 E-value: 5.11e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 711 LQDLKPFLVRKASSAWEFEG-----------PTIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDE 779
Cdd:PTZ00424 238 LEGIRQFYVAVEKEEWKFDTlcdlyetltitQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGS 317
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 170763504 780 IQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQEIGRAGRDG 824
Cdd:PTZ00424 318 TRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
728-822 |
5.86e-07 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 54.13 E-value: 5.86e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 728 FEGPTIIYCPSRKMTEQVTAELGklnLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFG----------------M 791
Cdd:COG1202 426 YRGQTIIFTNSRRRCHEIARALG---YKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAagvdfpasqvifdslaM 502
|
90 100 110
....*....|....*....|....*....|.
gi 170763504 792 GINkadirkvihYGAPKEmesYYQEIGRAGR 822
Cdd:COG1202 503 GIE---------WLSVQE---FHQMLGRAGR 521
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
71-224 |
1.01e-06 |
|
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Pssm-ID: 99851 Cd Length: 197 Bit Score: 50.75 E-value: 1.01e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 71 DVVGFDMEWppiYKPGKRSRVAVIQLCVSESKCYLFHISSM--SVFPQGLKMLLENKSIKKAGVGIEGDQWKLLRDFDVK 148
Cdd:cd06148 11 KVIGLDCEG---VNLGRKGKLCLVQIATRTGQIYLFDILKLgsIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 149 LESFVElTDVANEKLKCAETW--------SLNGLVKHVLG----------KQLLKDksirCSNWSNFPLTEDQKLYAATD 210
Cdd:cd06148 88 LNNVFD-TQVADALLQEQETGgfnpdrviSLVQLLDKYLYisislkedvkKLMRED----PKFWALRPLTEDMIRYAALD 162
|
170
....*....|....*
gi 170763504 211 A-YAGLIIYQKLGNL 224
Cdd:cd06148 163 VlCLLPLYYAMLDAL 177
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
733-830 |
8.21e-06 |
|
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They 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: 350180 [Multi-domain] Cd Length: 135 Bit Score: 46.70 E-value: 8.21e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 733 IIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCV--VATVAFGMGIN--KADirKVIHYGAP- 807
Cdd:cd18793 31 LIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVflLSTKAGGVGLNltAAN--RVILYDPWw 108
|
90 100
....*....|....*....|....*.
gi 170763504 808 ---KEMesyyQEIGRAGRDGLQSSCH 830
Cdd:cd18793 109 npaVEE----QAIDRAHRIGQKKPVV 130
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
512-671 |
9.33e-06 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 47.71 E-value: 9.33e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 512 SFKPVQWKVIHSVLEERRDNVVVMATGYGKSLCFQYPPVYT---GKIGIVISPLISLMEDQVLQLELSNVPACLLGSAQS 588
Cdd:cd18028 1 ELYPPQAEAVRAGLLKGENLLISIPTASGKTLIAEMAMVNTlleGGKALYLVPLRALASEKYEEFKKLEEIGLKVGISTG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 589 KNILGDVKLGKYRVIYITPEfcsgNLDLLQQLDSSI--GITLIAVDEAHCISEWGHDFRSSFrMLGSLKTALPLVPVIAL 666
Cdd:cd18028 81 DYDEDDEWLGDYDIIVATYE----KFDSLLRHSPSWlrDVGVVVVDEIHLISDEERGPTLES-IVARLRRLNPNTQIIGL 155
|
....*
gi 170763504 667 SATAS 671
Cdd:cd18028 156 SATIG 160
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
732-821 |
1.38e-05 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 49.92 E-value: 1.38e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGKLNLA---------------------------------CRTYHAGMKISERKDVHHRFLRD 778
Cdd:PRK09751 247 TIVFTNSRGLAEKLTARLNELYAArlqrspsiavdaahfestsgatsnrvqssdvfiARSHHGSVSKEQRAITEQALKSG 326
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 170763504 779 EIQCVVATVAFGMGINKADIRKVIHYGAPKEMESYYQEIGRAG 821
Cdd:PRK09751 327 ELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAG 369
|
|
| PTZ00110 |
PTZ00110 |
helicase; Provisional |
733-845 |
2.30e-05 |
|
helicase; Provisional
Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 48.62 E-value: 2.30e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 733 IIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVATVAFGMGINKADIRKVIHYGAPKEMES 812
Cdd:PTZ00110 381 LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIED 460
|
90 100 110
....*....|....*....|....*....|...
gi 170763504 813 YYQEIGRAGRDGLQSSCHLLWAPADFNTSRNLL 845
Cdd:PTZ00110 461 YVHRIGRTGRAGAKGASYTFLTPDKYRLARDLV 493
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
512-686 |
4.40e-05 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 45.72 E-value: 4.40e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 512 SFKPVQWKVIHSVLEERrDNVVVMA-TGYGKSLCFQYPPV-----YTGKIgIVISPLISLMeDQVLQ-----LELSNVPA 580
Cdd:cd17921 1 LLNPIQREALRALYLSG-DSVLVSApTSSGKTLIAELAILralatSGGKA-VYIAPTRALV-NQKEAdlrerFGPLGKNV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 581 CLLGSAQSKNILgdvKLGKYRVIYITPEfcsgNLDLL-----QQLDSSIGitLIAVDEAHCIS--------EWGhdfrss 647
Cdd:cd17921 78 GLLTGDPSVNKL---LLAEADILVATPE----KLDLLlrnggERLIQDVR--LVVVDEAHLIGdgergvvlELL------ 142
|
170 180 190
....*....|....*....|....*....|....*....
gi 170763504 648 frmLGSLKTALPLVPVIALSATASSSirEDIISCLNLKD 686
Cdd:cd17921 143 ---LSRLLRINKNARFVGLSATLPNA--EDLAEWLGVED 176
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
515-669 |
1.51e-04 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 43.81 E-value: 1.51e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 515 PVQWKVIHSVLEERRDN----VVVMATGYGKS-----LCFQYPPVYTGKIGIVISPLISL---MEDQVLQLELSNVPACL 582
Cdd:pfam04851 6 PYQIEAIENLLESIKNGqkrgLIVMATGSGKTltaakLIARLFKKGPIKKVLFLVPRKDLleqALEEFKKFLPNYVEIGE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 583 LGSAQSKNIlgdvKLGKYRVIYITPEFCSGNLDLLQQLDSSIGITLIAVDEAHcisewgHDFRSSFRmlgSLKTALPLVP 662
Cdd:pfam04851 86 IISGDKKDE----SVDDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAH------RSGASSYR---NILEYFKPAF 152
|
....*..
gi 170763504 663 VIALSAT 669
Cdd:pfam04851 153 LLGLTAT 159
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
1094-1185 |
5.15e-04 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 44.09 E-value: 5.15e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 1094 AVMPSPGTSSSPLEPAI----SAQELDART-GLYARLVEARQKHANKMDVPPAILATNKVLLDMAKMRPTTVENMKQIDG 1168
Cdd:COG0349 180 ARLLDPATYREDPEEAWlrlkGAWKLNPRQlAVLRELAAWREREARKRDVPRNRVLKDEALLELARRQPKSLEELARLRG 259
|
90
....*....|....*...
gi 170763504 1169 VSEGKAALLAP-LLEVIK 1185
Cdd:COG0349 260 LSPGEIRRHGEeLLAAVA 277
|
|
| rnd |
TIGR01388 |
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA ... |
156-344 |
6.63e-04 |
|
ribonuclease D; This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing]
Pssm-ID: 130455 [Multi-domain] Cd Length: 367 Bit Score: 43.60 E-value: 6.63e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 156 TDVANEKLKCAETWSLNGLVKHVLGKQLlkDKSIRCSNWSNFPLTEDQKLYAATDAYAGLIIYQKLgnlgdTAQVFALNK 235
Cdd:TIGR01388 99 TQIAAAFCGFGMSMGYAKLVQEVLGVEL--DKSESRTDWLARPLTDAQLEYAAADVTYLLPLYAKL-----MERLEESGR 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 236 A----EENLPLEMKKQLNSISEEM-RDLANRFPVTCRNLETLQRvpviLKSISENLCSLRKVICGPTNTETRLKPGSSFN 310
Cdd:TIGR01388 172 LawleEECTLLTDRRTYVVNPEDAwRDIKNAWQLRPQQLAVLQA----LAAWREREARERDLPRNFVLKEEALWELARQA 247
|
170 180 190
....*....|....*....|....*....|....*.
gi 170763504 311 LLSSEDSAAAGEKEKQIGKHSTF--AKIKEEPWDPE 344
Cdd:TIGR01388 248 PGNLTELASLGPKGSEIRKHGDTllALVKTALALPE 283
|
|
| PRK11192 |
PRK11192 |
ATP-dependent RNA helicase SrmB; Provisional |
732-878 |
8.40e-03 |
|
ATP-dependent RNA helicase SrmB; Provisional
Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 40.31 E-value: 8.40e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 170763504 732 TIIYCPSRKMTEQVTAELGKLNLACRTYHAGMKISERKDVHHRFLRDEIQCVVAT-VAfGMGINKADIRKVIHYGAPKEM 810
Cdd:PRK11192 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATdVA-ARGIDIDDVSHVINFDMPRSA 326
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 170763504 811 ESYYQEIG---RAGRDGLQSSchllwapadfntsrnlLIEIHDekfrlykLKMMVKMEKYLhSSQCRRRII 878
Cdd:PRK11192 327 DTYLHRIGrtgRAGRKGTAIS----------------LVEAHD-------HLLLGKIERYI-EEPLKARVI 373
|
|
| |
