|
Name |
Accession |
Description |
Interval |
E-value |
| recQ_fam |
TIGR00614 |
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
537-1010 |
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: 854.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 537 TCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTC 616
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 617 FLGSAQSEN----VLTDIKLGKYRIVYITPEYCSGNIGLLQQLEADIGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTA 692
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 693 LPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTGNILQDLQPFLVKttsshwEFEGPT-IIYC 771
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK------EFEGKSgIIYC 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 772 PSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQE 851
Cdd:TIGR00614 234 PSRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 852 IGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKaSLGITG 931
Cdd:TIGR00614 314 SGRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMG 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 932 TEKCCDNCRSRLGHCYsmDDSEDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLAD-QYRKHSLFGTGKDQ 1010
Cdd:TIGR00614 393 TEKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDgGFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
539-1027 |
1.53e-176 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 534.34 E-value: 1.53e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 539 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTCFL 618
Cdd:COG0514 9 LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRAAGIRAAFL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQSEN----VLTDIKLGKYRIVYITPEYCS--GNIGLLQQleadIGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTA 692
Cdd:COG0514 88 NSSLSAEerreVLRALRAGELKLLYVAPERLLnpRFLELLRR----LKISLFAIDEAHCISQWGHDFRPDYRRLGELRER 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 693 LPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTG-NILQDLQPFLVKTTsshwefEGPTIIYC 771
Cdd:COG0514 164 LPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP------GGSGIVYC 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 772 PSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQE 851
Cdd:COG0514 238 LSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPKSIEAYYQE 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 852 IGRAGRDGLQSSCHILWAPADINLNRHLLTEIRN-EKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQvqkaslgiT 930
Cdd:COG0514 318 IGRAGRDGLPAEALLLYGPEDVAIQRFFIEQSPPdEERKRVERAKLDAMLAYAETTGCRRQFLLRYFGEEL--------A 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 931 GTEKCCDNCRsrlghcysmddSEDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLADQ-YRKHSLFGTGKD 1009
Cdd:COG0514 390 EPCGNCDNCL-----------GPPETFDGTEAAQKALSCVYRTGQRFGAGHVIDVLRGSKNEKIRQFgHDKLSTYGIGKD 458
|
490
....*....|....*...
gi 1622959916 1010 QTESWWKAFSRQLIIEGF 1027
Cdd:COG0514 459 LSDKEWRSVIRQLLAQLF 476
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
534-1220 |
4.69e-122 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 394.08 E-value: 4.69e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 534 EQVtcLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNI 613
Cdd:PRK11057 14 KQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 614 PTCFLGSAQSE----NVLTDIKLGKYRIVYITPEYCSGNiGLLQQLeADIGITLIAVDEAHCISEWGHDFRNSFRKLGSL 689
Cdd:PRK11057 91 AAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPERLMMD-NFLEHL-AHWNPALLAVDEAHCISQWGHDFRPEYAALGQL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 690 KTALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKtgnilqdlqpflVKTTSSHWEF----EG 765
Cdd:PRK11057 169 RQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEK------------FKPLDQLMRYvqeqRG 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 766 PT-IIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKE 844
Cdd:PRK11057 237 KSgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRN 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 845 MESYYQEIGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDkqvqk 924
Cdd:PRK11057 317 IESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAEAQTCRRLVLLNYFGE----- 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 925 aslgitGTEKCCDNCRSRLGHCYSMDDSEDtswdfgpqAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLAD-QYRKHSL 1003
Cdd:PRK11057 392 ------GRQEPCGNCDICLDPPKQYDGLED--------AQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDyGHDKLKV 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1004 FGTGKDQTESWWKAFSRQLIIEGFLVEvsgsnkfiKIctltekgrnwlhkanreSQSLILQANEElcpkkfllpsSRTVS 1083
Cdd:PRK11057 458 YGIGRDKSHEHWVSVIRQLIHLGLVTQ--------NI-----------------AQHSALQLTEA----------ARPVL 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1084 SGtkehsynQVPVELTAEKKSNLEKLYSYKpcdkvSSGSNISKKsimvqapeksysssepvisaqeqetqtvLYGKLVEA 1163
Cdd:PRK11057 503 RG-------EVSLQLAVPRIVALKPRAMQK-----SFGGNYDRK----------------------------LFAKLRKL 542
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 1164 RQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLA-PLLEVIK 1220
Cdd:PRK11057 543 RKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
536-730 |
3.66e-120 |
|
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: 372.96 E-value: 3.66e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 536 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPT 615
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 616 CFLGSAQSENVLTDIKLGKYRIVYITPEYCSGNIGLLQQLEAdiGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTALPM 695
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 1622959916 696 VPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
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 ... |
61-229 |
1.36e-76 |
|
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: 250.51 E-value: 1.36e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 61 DCSFLSEDICMslsDGDVVGFDMEWPPLYNKGklGKVALIQLCVSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVGI 140
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRRYY--GEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 141 EGDQWKLLRDFDIKLKNFVELTDVANKKLKCtETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYAG 220
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 1622959916 221 FIIYRNLEI 229
Cdd:cd06129 153 LIIYTKLRN 161
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
57-228 |
1.35e-43 |
|
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: 156.31 E-value: 1.35e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 57 YDASDCSFLSEDICMSLSDGDVVGFDMEWPPLYNKGKLGKVALIQLCVsesKCYLFHISSMSVFP---QGLKMLLENKAI 133
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGT---GEGAYIIDPLALGDdvlSALKRLLEDPNI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 134 KKAGVGIEGDQWKLLRDFDIKLKNFVElTDVANKKLKCTETWSLSGLVKHLLGkqLLKDKSIRCSNWSKFPLTEDQKLYA 213
Cdd:pfam01612 78 TKVGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYA 154
|
170
....*....|....*
gi 1622959916 214 ATDAYAGFIIYRNLE 228
Cdd:pfam01612 155 ALDADYLLRLYDKLR 169
|
|
| DpdF |
NF041063 |
protein DpdF; |
567-887 |
5.42e-36 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 148.14 E-value: 5.42e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 567 VAVMATGYGKSLCFQYPPVYVGKIG---LVISPLISLMEDQVLQLK-MSNIPTCFLG------SAQSEN----VLTDIKL 632
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRAReLLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 633 GKYRIVYITPE-YCSGnigLLQQLE--ADIG-ITLIAVDEAHCISEWGHDFRNSFRKLGSLKTALPMV-----PI--VAL 701
Cdd:NF041063 242 GTQRILFTSPEsLTGS---LRPALFdaAEAGlLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLLRLapsgrPFrtLLL 318
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 702 TATATSSIREDIVRclnL----RNPQIICTGFDRP----NLY----LEVRRKTgnILQDLQpFLVKttsshwefegPTII 769
Cdd:NF041063 319 SATLTESTLDTLET---LfgppGPFIVVSAVQLRPepayWVAkcdsEEERRER--VLEALR-HLPR----------PLIL 382
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 770 YCPSRKMTEQVTAELRKLNLS-CETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESY 848
Cdd:NF041063 383 YVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRF 462
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 1622959916 849 YQEIGRAGRDGLQSSCHILWAPADINLNRHLLTE--IRNEK 887
Cdd:NF041063 463 YQEVGRGGRDGKASLSLLIYTPDDLDIAKSLNRPklISVEK 503
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
61-228 |
1.07e-30 |
|
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: 119.38 E-value: 1.07e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 61 DCSFLSEDICMSLSDGDVVGFDMEWPPLYNKGklGKVALIQLCVSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVGI 140
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDSYS--GKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 141 EGDQWKLLRdFDIKLKNfVELTDVANK-KLKCTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAYlLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
....*....
gi 1622959916 220 GFIIYRNLE 228
Cdd:smart00474 160 LLRLYEKLE 168
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
958-1051 |
7.50e-26 |
|
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: 102.55 E-value: 7.50e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 958 DFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLADQ-YRKHSLFGTGKDQTESWWKAFSRQLIIEGFLVEVSGSNk 1036
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLREDGGRY- 79
|
90
....*....|....*
gi 1622959916 1037 fiKICTLTEKGRNWL 1051
Cdd:smart00956 80 --PYLKLTEKARPVL 92
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
550-711 |
1.09e-25 |
|
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: 105.02 E-value: 1.09e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 550 PVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYP------PVYVGKIGLVISPLISLMEDQVLQLK-----MSNIPTCFL 618
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQSENVLTDIKlgKYRIVYITPEYCSGNIGLLQQLEadiGITLIAVDEAHCISEWGhdFRNSFRKLgsLKTALPMVPI 698
Cdd:pfam00270 81 GGDSRKEQLEKLK--GPDILVGTPGRLLDLLQERKLLK---NLKLLVLDEAHRLLDMG--FGPDLEEI--LRRLPKKRQI 151
|
170
....*....|...
gi 1622959916 699 VALTATATSSIRE 711
Cdd:pfam00270 152 LLLSATLPRNLED 164
|
|
| HTH_40 |
pfam14493 |
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of ... |
1258-1352 |
3.34e-20 |
|
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: 86.41 E-value: 3.34e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1258 SMAITYSLFQEKkMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAgLTPEVQKIIADVIRNPPINSdmskINLIRM 1337
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 1622959916 1338 LVPENIDTYLIHMAI 1352
Cdd:pfam14493 75 ALPEEISYFEIRLVL 89
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
1151-1229 |
2.83e-18 |
|
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: 80.80 E-value: 2.83e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1151 ETQTVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLAP-LLEVIKHFCQTNSVQ 1229
Cdd:smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
1153-1219 |
1.24e-11 |
|
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: 61.40 E-value: 1.24e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 1153 QTVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLAP-LLEVI 1219
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
67-216 |
2.37e-11 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 67.20 E-value: 2.37e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 67 EDICMSLSDGDVVGFDME-------WPplynkgklgKVALIQLCVSEsKCYL---FHISSMSVFPQglkmLLENKAIKK- 135
Cdd:COG0349 9 AALCARLAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALidpLAIGDLSPLWE----LLADPAIVKv 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 136 ---AGVGIEGdqwkLLRDFDIKLKNFVElTDVANKKLKCTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLY 212
Cdd:COG0349 75 fhaAREDLEI----LYHLFGILPKPLFD-TQIAAALLGYGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEEQLEY 147
|
....
gi 1622959916 213 AATD 216
Cdd:COG0349 148 AAAD 151
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
335-480 |
3.05e-04 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 45.55 E-value: 3.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 335 EHKIFINVEDETWDPTLDHLAKHGGEDVLGNKVERKEDGFEEGVEDNkLKENMERACLMSLDITEHELQILEQQAQEKYL 414
Cdd:PTZ00341 964 EENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEEN-VEENIEENVEEYDEENVEEVEENVEEYDEENV 1042
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622959916 415 SDIAYKSTEHLSPTNNENDTSYVIESDEDLEMEMLKHLSPTNNENDTSYVIESDEDLEMEMLKSLE 480
Cdd:PTZ00341 1043 EEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAE 1108
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| recQ_fam |
TIGR00614 |
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
537-1010 |
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: 854.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 537 TCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTC 616
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 617 FLGSAQSEN----VLTDIKLGKYRIVYITPEYCSGNIGLLQQLEADIGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTA 692
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 693 LPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTGNILQDLQPFLVKttsshwEFEGPT-IIYC 771
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK------EFEGKSgIIYC 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 772 PSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQE 851
Cdd:TIGR00614 234 PSRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQE 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 852 IGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKaSLGITG 931
Cdd:TIGR00614 314 SGRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMG 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 932 TEKCCDNCRSRLGHCYsmDDSEDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLAD-QYRKHSLFGTGKDQ 1010
Cdd:TIGR00614 393 TEKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDgGFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
539-1027 |
1.53e-176 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 534.34 E-value: 1.53e-176
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 539 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTCFL 618
Cdd:COG0514 9 LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRAAGIRAAFL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQSEN----VLTDIKLGKYRIVYITPEYCS--GNIGLLQQleadIGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTA 692
Cdd:COG0514 88 NSSLSAEerreVLRALRAGELKLLYVAPERLLnpRFLELLRR----LKISLFAIDEAHCISQWGHDFRPDYRRLGELRER 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 693 LPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTG-NILQDLQPFLVKTTsshwefEGPTIIYC 771
Cdd:COG0514 164 LPNVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP------GGSGIVYC 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 772 PSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQE 851
Cdd:COG0514 238 LSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPKSIEAYYQE 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 852 IGRAGRDGLQSSCHILWAPADINLNRHLLTEIRN-EKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQvqkaslgiT 930
Cdd:COG0514 318 IGRAGRDGLPAEALLLYGPEDVAIQRFFIEQSPPdEERKRVERAKLDAMLAYAETTGCRRQFLLRYFGEEL--------A 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 931 GTEKCCDNCRsrlghcysmddSEDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLADQ-YRKHSLFGTGKD 1009
Cdd:COG0514 390 EPCGNCDNCL-----------GPPETFDGTEAAQKALSCVYRTGQRFGAGHVIDVLRGSKNEKIRQFgHDKLSTYGIGKD 458
|
490
....*....|....*...
gi 1622959916 1010 QTESWWKAFSRQLIIEGF 1027
Cdd:COG0514 459 LSDKEWRSVIRQLLAQLF 476
|
|
| recQ |
TIGR01389 |
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ... |
539-1220 |
2.38e-141 |
|
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: 445.29 E-value: 2.38e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 539 LKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTCFL 618
Cdd:TIGR01389 5 LKRTFGYDDFRPGQEEIISHVLDGR-DVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKDQVDQLRAAGVAAAYL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQS----ENVLTDIKLGKYRIVYITPEycsgniGLLQ----QLEADIGITLIAVDEAHCISEWGHDFRNSFRKLGSLK 690
Cdd:TIGR01389 84 NSTLSakeqQDIEKALVNGELKLLYVAPE------RLEQdyflNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLA 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 691 TALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTgNILQDLQPFLVKttssHWEFEGptIIY 770
Cdd:TIGR01389 158 ERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKN-NKQKFLLDYLKK----HRGQSG--IIY 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 771 CPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQ 850
Cdd:TIGR01389 231 ASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQ 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 851 EIGRAGRDGLQSSCHILWAPADINLNRHLLTEirNEKFRLYKLKMMAK---MEKYLHSSRCRRQIILSHFedkqvqkasl 927
Cdd:TIGR01389 311 EAGRAGRDGLPAEAILLYSPADIALLKRRIEQ--SEADDDYKQIEREKlraMIAYCETQTCRRAYILRYF---------- 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 928 GITGTEKC--CDNCRsrlghcysmddSEDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLaDQYR--KHSL 1003
Cdd:TIGR01389 379 GENEVEPCgnCDNCL-----------DPPKSYDATVEAQKALSCVYRMGQRFGVGYIIEVLRGSKNDKI-LQKGhdQLST 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1004 FGTGKDQTESWWKAFSRQLIIEGFLVEvsgsnkfikictltekgrnwlhkanresqslilqaNEELCPKKFLLPSSRTVS 1083
Cdd:TIGR01389 447 YGIGKDYTQKEWRSLIDQLIAEGLLTE-----------------------------------NDEIYIGLQLTEAARKVL 491
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1084 SgtkehsyNQVPVELTAEKksnleklysykpcdkvssgsniskksimVQAPEKSYSSSEPVISAQEqetqtVLYGKLVEA 1163
Cdd:TIGR01389 492 K-------NEVEVLLRPFK----------------------------VVAKEKTRVQKNLSVGVDN-----ALFEALREL 531
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 1164 RQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLAP-LLEVIK 1220
Cdd:TIGR01389 532 RKEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEaFLEVIR 589
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
534-1220 |
4.69e-122 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 394.08 E-value: 4.69e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 534 EQVtcLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNI 613
Cdd:PRK11057 14 KQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 614 PTCFLGSAQSE----NVLTDIKLGKYRIVYITPEYCSGNiGLLQQLeADIGITLIAVDEAHCISEWGHDFRNSFRKLGSL 689
Cdd:PRK11057 91 AAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPERLMMD-NFLEHL-AHWNPALLAVDEAHCISQWGHDFRPEYAALGQL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 690 KTALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKtgnilqdlqpflVKTTSSHWEF----EG 765
Cdd:PRK11057 169 RQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYTLVEK------------FKPLDQLMRYvqeqRG 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 766 PT-IIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKE 844
Cdd:PRK11057 237 KSgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRN 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 845 MESYYQEIGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDkqvqk 924
Cdd:PRK11057 317 IESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAEAQTCRRLVLLNYFGE----- 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 925 aslgitGTEKCCDNCRSRLGHCYSMDDSEDtswdfgpqAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLAD-QYRKHSL 1003
Cdd:PRK11057 392 ------GRQEPCGNCDICLDPPKQYDGLED--------AQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDyGHDKLKV 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1004 FGTGKDQTESWWKAFSRQLIIEGFLVEvsgsnkfiKIctltekgrnwlhkanreSQSLILQANEElcpkkfllpsSRTVS 1083
Cdd:PRK11057 458 YGIGRDKSHEHWVSVIRQLIHLGLVTQ--------NI-----------------AQHSALQLTEA----------ARPVL 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1084 SGtkehsynQVPVELTAEKKSNLEKLYSYKpcdkvSSGSNISKKsimvqapeksysssepvisaqeqetqtvLYGKLVEA 1163
Cdd:PRK11057 503 RG-------EVSLQLAVPRIVALKPRAMQK-----SFGGNYDRK----------------------------LFAKLRKL 542
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 1164 RQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLA-PLLEVIK 1220
Cdd:PRK11057 543 RKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
536-730 |
3.66e-120 |
|
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: 372.96 E-value: 3.66e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 536 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPT 615
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 616 CFLGSAQSENVLTDIKLGKYRIVYITPEYCSGNIGLLQQLEAdiGITLIAVDEAHCISEWGHDFRNSFRKLGSLKTALPM 695
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 1622959916 696 VPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
Cdd:cd18017 159 VPIVALTATATPSVRDDIIKNLNLRNPQITCTSFD 193
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
537-730 |
1.03e-85 |
|
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: 277.88 E-value: 1.03e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 537 TCLKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTC 616
Cdd:cd17920 2 QILKEVFGYDEFRPGQLEAINAVLA-GRDVLVVMPTGGGKSLCYQLPALLLDGVTLVVSPLISLMQDQVDRLQQLGIRAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 617 FLGSAQS----ENVLTDIKLGKYRIVYITPEYC--SGNIGLLQQLEADIGITLIAVDEAHCISEWGHDFRNSFRKLGSLK 690
Cdd:cd17920 81 ALNSTLSpeekREVLLRIKNGQYKLLYVTPERLlsPDFLELLQRLPERKRLALIVVDEAHCVSQWGHDFRPDYLRLGRLR 160
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1622959916 691 TALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
Cdd:cd17920 161 RALPGVPILALTATATPEVREDILKRLGLRNPVIFRASFD 200
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
540-1107 |
3.81e-85 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 304.51 E-value: 3.81e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 540 KMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTCFLG 619
Cdd:PLN03137 453 KKVFGNHSFRPNQREIINATMSGY-DVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQANIPAASLS 531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 620 S----AQSENVLTDI--KLGKYRIVYITPEYCSGNIGLLQQLEADIGITLIA---VDEAHCISEWGHDFRNSFRKLGSLK 690
Cdd:PLN03137 532 AgmewAEQLEILQELssEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLArfvIDEAHCVSQWGHDFRPDYQGLGILK 611
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 691 TALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFDRPNLYLEVRRKTGNILQDLQPFLvktTSSHweFEGPTIIY 770
Cdd:PLN03137 612 QKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFI---KENH--FDECGIIY 686
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 771 CPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQ 850
Cdd:PLN03137 687 CLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQ 766
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 851 EIGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEKFRL---YKLKM------------MAKMEKYLHSS-RCRRQIIL 914
Cdd:PLN03137 767 ECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMamgYNRMAssgriletntenLLRMVSYCENEvDCRRFLQL 846
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 915 SHFEDKqvqkasLGITGTEKCCDNCRSrlghCYSMDDSEDTSwdfgpQAFQLLSAVDILGGKFGIGLPILFLRGSNSQrL 994
Cdd:PLN03137 847 VHFGEK------FDSTNCKKTCDNCSS----SKSLIDKDVTE-----IARQLVELVKLTGERFSSAHILEVYRGSLNQ-Y 910
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 995 ADQYRKH--SLFGTGKDQTESWWKAFSRQLIIEGFLVE-VSGSNKFIKICTLTEKGRNWLHKANRESQSLILQaneelcp 1071
Cdd:PLN03137 911 VKKHRHEtlSLHGAGKHLSKGEASRILHYLVTEDILAEdVKKSDLYGSVSSLLKVNESKAYKLFSGGQTIIMR------- 983
|
570 580 590
....*....|....*....|....*....|....*.
gi 1622959916 1072 kkflLPSSRTVSSGTKEHSyNQVPVELTAEKKSNLE 1107
Cdd:PLN03137 984 ----FPSSVKASKPSKFEA-TPAKGPLTSGKQSTLP 1014
|
|
| RNaseD_like |
cd06129 |
DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins; The RNase D-like group ... |
61-229 |
1.36e-76 |
|
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: 250.51 E-value: 1.36e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 61 DCSFLSEDICMslsDGDVVGFDMEWPPLYNKGklGKVALIQLCVSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVGI 140
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRRYY--GEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 141 EGDQWKLLRDFDIKLKNFVELTDVANKKLKCtETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYAG 220
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 1622959916 221 FIIYRNLEI 229
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 ... |
61-228 |
1.42e-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: 239.40 E-value: 1.42e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 61 DCSFLSEDICMSLS-DGDVVGFDMEWPPLYNKGKLGKVALIQLCvSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVG 139
Cdd:cd06141 2 DSAQDAEEAVKELLgKEKVVGFDTEWRPSFRKGKRNKVALLQLA-TESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 140 IEGDQWKLLRDFDIKLKNFVELTDVANKKLKCTETWSLSGLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:cd06141 81 IKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYA 160
|
....*....
gi 1622959916 220 GFIIYRNLE 228
Cdd:cd06141 161 SLELYRKLL 169
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
78-229 |
1.24e-70 |
|
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: 232.90 E-value: 1.24e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 78 VVGFDMEWPPLYNKgkLGKVALIQLCVSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVGIEGDQWKLLRDFDIKLKN 157
Cdd:cd09018 1 VFAFDTETDSLDNI--SANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622959916 158 FVELTDVANKKLKCTETWSLSGLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYAGFIIYRNLEI 229
Cdd:cd09018 79 AFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
731-868 |
3.64e-69 |
|
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: 227.86 E-value: 3.64e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 731 RPNLYLEVRRKTGNILQDLQPFLVKttssHWEFEGPTIIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKF 810
Cdd:cd18794 1 RPNLFYSVRPKDKKDEKLDLLKRIK----VEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKW 76
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 811 VRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAGRDGLQSSCHILW 868
Cdd:cd18794 77 LRDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILFY 134
|
|
| DEXHc_RecQ1 |
cd18015 |
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
539-730 |
6.65e-50 |
|
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: 176.02 E-value: 6.65e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 539 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPTCFL 618
Cdd:cd18015 10 LKNVFKLEKFRPLQLETINATMA-GRDVFLVMPTGGGKSLCYQLPALCSDGFTLVVSPLISLMEDQLMALKKLGISATML 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQS-ENV------LTDIKlGKYRIVYITPEYCSGNIGLLQQLEA--DIG-ITLIAVDEAHCISEWGHDFRNSFRKLGS 688
Cdd:cd18015 89 NASSSkEHVkwvhaaLTDKN-SELKLLYVTPEKIAKSKRFMSKLEKayNAGrLARIAIDEVHCCSQWGHDFRPDYKKLGI 167
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1622959916 689 LKTALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
Cdd:cd18015 168 LKRQFPNVPILGLTATATSKVLKDVQKILCIQKCLTFTASFN 209
|
|
| DEXHc_RecQ4-like |
cd18018 |
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
539-730 |
1.44e-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: 1.44e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 539 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYP----PVYVGKIGLVISPLISLMEDQVLQLKMSNIP 614
Cdd:cd18018 4 LRRVFGHPSFRPGQEEAIARLLS-GRSTLVVLPTGAGKSLCYQLPalllRRRGPGLTLVVSPLIALMKDQVDALPRAIKA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 615 TCF---LGSAQSENVLTDIKLGKYRIVYITPE-YCSGNIGLLQQLEADIGitLIAVDEAHCISEWGHDFRNSFRKLGS-L 689
Cdd:cd18018 83 AALnssLTREERRRILEKLRAGEVKILYVSPErLVNESFRELLRQTPPIS--LLVVDEAHCISEWSHNFRPDYLRLCRvL 160
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1622959916 690 KTALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
Cdd:cd18018 161 RELLGAPPVLALTATATKRVVEDIASHLGIPESGVVRGPLY 201
|
|
| DEXHc_RecQ5 |
cd18014 |
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ... |
537-722 |
2.05e-46 |
|
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: 165.72 E-value: 2.05e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 537 TCLKMYFGHSSFK-PVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPT 615
Cdd:cd18014 2 STLKKVFGHSDFKsPLQEKATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVISPLIALIQDQVDHLKTLKIRV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 616 CFLGSAQS----ENVLTDIK--LGKYRIVYITPEYCSGNI--GLLQQLEADIGITLIAVDEAHCISEWGHDFRNSFRKLG 687
Cdd:cd18014 82 DSLNSKLSaqerKRIIADLEseKPQTKFLYITPEMAATSSfqPLLSSLVSRNLLSYLVVDEAHCVSQWGHDFRPDYLRLG 161
|
170 180 190
....*....|....*....|....*....|....*
gi 1622959916 688 SLKTALPMVPIVALTATATSSIREDIVRCLNLRNP 722
Cdd:cd18014 162 ALRSRYGHVPWVALTATATPQVQEDIFAQLRLKKP 196
|
|
| DNA_pol_A_exo1 |
pfam01612 |
3'-5' exonuclease; This domain is responsible for the 3'-5' exonuclease proofreading activity ... |
57-228 |
1.35e-43 |
|
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: 156.31 E-value: 1.35e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 57 YDASDCSFLSEDICMSLSDGDVVGFDMEWPPLYNKGKLGKVALIQLCVsesKCYLFHISSMSVFP---QGLKMLLENKAI 133
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGT---GEGAYIIDPLALGDdvlSALKRLLEDPNI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 134 KKAGVGIEGDQWKLLRDFDIKLKNFVElTDVANKKLKCTETWSLSGLVKHLLGkqLLKDKSIRCSNWSKFPLTEDQKLYA 213
Cdd:pfam01612 78 TKVGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYA 154
|
170
....*....|....*
gi 1622959916 214 ATDAYAGFIIYRNLE 228
Cdd:pfam01612 155 ALDADYLLRLYDKLR 169
|
|
| DEXHc_RecQ2_BLM |
cd18016 |
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
532-730 |
9.25e-42 |
|
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: 152.67 E-value: 9.25e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 532 NEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMS 611
Cdd:cd18016 2 SKEMMKIFHKKFGLHQFRTNQLEAINAALLGE-DCFVLMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 612 NIPTCFLGSAQSENVLTDI--KLGK----YRIVYITPEYCSGNIGLLQQLEADIGITLIA---VDEAHCISEWGHDFRNS 682
Cdd:cd18016 81 DIPATYLTGDKTDAEATKIylQLSKkdpiIKLLYVTPEKISASNRLISTLENLYERKLLArfvIDEAHCVSQWGHDFRPD 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 1622959916 683 FRKLGSLKTALPMVPIVALTATATSSIREDIVRCLNLRNPQIICTGFD 730
Cdd:cd18016 161 YKRLNMLRQKFPSVPMMALTATATPRVQKDILNQLKMLRPQVFTMSFN 208
|
|
| DpdF |
NF041063 |
protein DpdF; |
567-887 |
5.42e-36 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 148.14 E-value: 5.42e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 567 VAVMATGYGKSLCFQYPPVYVGKIG---LVISPLISLMEDQVLQLK-MSNIPTCFLG------SAQSEN----VLTDIKL 632
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRAReLLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 633 GKYRIVYITPE-YCSGnigLLQQLE--ADIG-ITLIAVDEAHCISEWGHDFRNSFRKLGSLKTALPMV-----PI--VAL 701
Cdd:NF041063 242 GTQRILFTSPEsLTGS---LRPALFdaAEAGlLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLLRLapsgrPFrtLLL 318
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 702 TATATSSIREDIVRclnL----RNPQIICTGFDRP----NLY----LEVRRKTgnILQDLQpFLVKttsshwefegPTII 769
Cdd:NF041063 319 SATLTESTLDTLET---LfgppGPFIVVSAVQLRPepayWVAkcdsEEERRER--VLEALR-HLPR----------PLIL 382
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 770 YCPSRKMTEQVTAELRKLNLS-CETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESY 848
Cdd:NF041063 383 YVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPETLDRF 462
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 1622959916 849 YQEIGRAGRDGLQSSCHILWAPADINLNRHLLTE--IRNEK 887
Cdd:NF041063 463 YQEVGRGGRDGKASLSLLIYTPDDLDIAKSLNRPklISVEK 503
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
61-228 |
1.07e-30 |
|
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: 119.38 E-value: 1.07e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 61 DCSFLSEDICMSLSDGDVVGFDMEWPPLYNKGklGKVALIQLCVSESKCYLFHISSMSVFPQGLKMLLENKAIKKAGVGI 140
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDSYS--GKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 141 EGDQWKLLRdFDIKLKNfVELTDVANK-KLKCTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAYlLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
....*....
gi 1622959916 220 GFIIYRNLE 228
Cdd:smart00474 160 LLRLYEKLE 168
|
|
| mut-7_like_exo |
cd06146 |
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 ... |
71-228 |
8.17e-30 |
|
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: 117.78 E-value: 8.17e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 71 MSLSDGDVVGFDMEWPPLYNKGKLGKVALIQLCVsESKCYLF-----HISSMSVFPQGLKMLLENKAIKKAGVGIEGDQW 145
Cdd:cd06146 17 LSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT-EDEVFLLdllalENLESEDWDRLLKRLFEDPDVLKLGFGFKQDLK 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 146 KL------LRDFDIKLKNFVELTDVANKKLK----------CTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQ 209
Cdd:cd06146 96 ALsasypaLKCMFERVQNVLDLQNLAKELQKsdmgrlkgnlPSKTKGLADLVQEVLGKPL--DKSEQCSNWERRPLREEQ 173
|
170
....*....|....*....
gi 1622959916 210 KLYAATDAYAGFIIYRNLE 228
Cdd:cd06146 174 ILYAALDAYCLLEVFDKLL 192
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
958-1051 |
7.50e-26 |
|
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: 102.55 E-value: 7.50e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 958 DFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLADQ-YRKHSLFGTGKDQTESWWKAFSRQLIIEGFLVEVSGSNk 1036
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLREDGGRY- 79
|
90
....*....|....*
gi 1622959916 1037 fiKICTLTEKGRNWL 1051
Cdd:smart00956 80 --PYLKLTEKARPVL 92
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
550-711 |
1.09e-25 |
|
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: 105.02 E-value: 1.09e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 550 PVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYP------PVYVGKIGLVISPLISLMEDQVLQLK-----MSNIPTCFL 618
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 619 GSAQSENVLTDIKlgKYRIVYITPEYCSGNIGLLQQLEadiGITLIAVDEAHCISEWGhdFRNSFRKLgsLKTALPMVPI 698
Cdd:pfam00270 81 GGDSRKEQLEKLK--GPDILVGTPGRLLDLLQERKLLK---NLKLLVLDEAHRLLDMG--FGPDLEEI--LRRLPKKRQI 151
|
170
....*....|...
gi 1622959916 699 VALTATATSSIRE 711
Cdd:pfam00270 152 LLLSATLPRNLED 164
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
542-739 |
3.17e-24 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 101.80 E-value: 3.17e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 542 YFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIG-----LVISPLISLMEDQVLQLK-----MS 611
Cdd:smart00487 3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGkggrvLVLVPTRELAEQWAEELKklgpsLG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 612 NIPTCFLGSAQSENVLTDIKLGKYRIVYITPEYcsgnigLLQQLEAD----IGITLIAVDEAHCISEWGhdFRNSFRKLg 687
Cdd:smart00487 83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGR------LLDLLENDklslSNVDLVILDEAHRLLDGG--FGDQLEKL- 153
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1622959916 688 sLKTALPMVPIVALTATATSSIREDIVRCLNLRnpqIICTGFDRPNLYLEVR 739
Cdd:smart00487 154 -LKLLPKNVQLLLLSATPPEEIENLLELFLNDP---VFIDVGFTPLEPIEQF 201
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
778-859 |
2.50e-22 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 92.27 E-value: 2.50e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 778 EQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAGR 857
Cdd:smart00490 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
|
..
gi 1622959916 858 DG 859
Cdd:smart00490 81 AG 82
|
|
| HTH_40 |
pfam14493 |
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of ... |
1258-1352 |
3.34e-20 |
|
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: 86.41 E-value: 3.34e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1258 SMAITYSLFQEKkMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAgLTPEVQKIIADVIRNPPINSdmskINLIRM 1337
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 1622959916 1338 LVPENIDTYLIHMAI 1352
Cdd:pfam14493 75 ALPEEISYFEIRLVL 89
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
762-859 |
5.02e-19 |
|
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: 83.80 E-value: 5.02e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 762 EFEGPTIIYCPSRKMTEqVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGA 841
Cdd:pfam00271 13 ERGGKVLIFSQTKKTLE-AELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDL 91
|
90
....*....|....*...
gi 1622959916 842 PKEMESYYQEIGRAGRDG 859
Cdd:pfam00271 92 PWNPASYIQRIGRAGRAG 109
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
1151-1229 |
2.83e-18 |
|
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: 80.80 E-value: 2.83e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 1151 ETQTVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLAP-LLEVIKHFCQTNSVQ 1229
Cdd:smart00341 2 ERQLRLLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
762-857 |
1.79e-15 |
|
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: 74.47 E-value: 1.79e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 762 EFEGPTIIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGA 841
Cdd:cd18787 25 LKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGVDHVINYDL 104
|
90
....*....|....*.
gi 1622959916 842 PKEMESYYQEIGRAGR 857
Cdd:cd18787 105 PRDAEDYVHRIGRTGR 120
|
|
| RQC |
pfam09382 |
RQC domain; This DNA-binding domain is found in the RecQ helicase among others and has a ... |
953-1051 |
6.25e-15 |
|
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: 72.19 E-value: 6.25e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 953 EDTSWDFGPQAFQLLSAVDILGGKFGIGLPILFLRGSNSQRLADQ-YRKHSLFGTGKDQTESWWKAFSRQLIIEGFLVEV 1031
Cdd:pfam09382 1 PPETVDVTEEAQKILSCVYRTGQRFGAGHLIDVLRGSKNKKIRQLgHDKLSTFGIGKDLSKKEWRRIIRQLIAEGYLEVD 80
|
90 100
....*....|....*....|
gi 1622959916 1032 SGSNKFIKictLTEKGRNWL 1051
Cdd:pfam09382 81 IEFYSVLK---LTPKAREVL 97
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
67-216 |
7.20e-15 |
|
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: 74.11 E-value: 7.20e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 67 EDICMSLSDGDVVGFDME---WPPLYnkgklGKVALIQLCVSEsKCYLFHISSMSVFPqGLKMLLENKAIKK----AGVG 139
Cdd:cd06142 3 EDLCERLASAGVIAVDTEfmrLNTYY-----PRLCLIQISTGG-EVYLIDPLAIGDLS-PLKELLADPNIVKvfhaARED 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1622959916 140 IEGdqwkLLRDFDIKLKNFVElTDVANKKLKCTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATD 216
Cdd:cd06142 76 LEL----LKRDFGILPQNLFD-TQIAARLLGLGDSVGLAALVEELLGVEL--DKGEQRSDWSKRPLTDEQLEYAALD 145
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
767-859 |
3.78e-14 |
|
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: 71.13 E-value: 3.78e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELR-------KLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHY 839
Cdd:cd18797 38 TIVFCRSRKLAELLLRYLKarlveegPLASKVASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLA 117
|
90 100
....*....|....*....|
gi 1622959916 840 GAPKEMESYYQEIGRAGRDG 859
Cdd:cd18797 118 GYPGSLASLWQQAGRAGRRG 137
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
1153-1219 |
1.24e-11 |
|
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: 61.40 E-value: 1.24e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1622959916 1153 QTVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENIKRIDGVSEGKAAMLAP-LLEVI 1219
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
67-216 |
2.37e-11 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 67.20 E-value: 2.37e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 67 EDICMSLSDGDVVGFDME-------WPplynkgklgKVALIQLCVSEsKCYL---FHISSMSVFPQglkmLLENKAIKK- 135
Cdd:COG0349 9 AALCARLAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALidpLAIGDLSPLWE----LLADPAIVKv 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 136 ---AGVGIEGdqwkLLRDFDIKLKNFVElTDVANKKLKCTETWSLSGLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLY 212
Cdd:COG0349 75 fhaAREDLEI----LYHLFGILPKPLFD-TQIAAALLGYGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEEQLEY 147
|
....
gi 1622959916 213 AATD 216
Cdd:COG0349 148 AAAD 151
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
767-859 |
7.10e-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: 66.78 E-value: 7.10e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELRK------LNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYG 840
Cdd:COG1205 291 TLVFTRSRRGAELLARYARRalrepdLADRVAAYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAG 370
|
90
....*....|....*....
gi 1622959916 841 APKEMESYYQEIGRAGRDG 859
Cdd:COG1205 371 YPGTRASFWQQAGRAGRRG 389
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
561-855 |
1.13e-10 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 66.20 E-value: 1.13e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 561 EERRDNVAVMATGYGKSLCFQYPPVYVGKIG--LVISPLISLMEdQVLQlKMSNIPTCFLGSAQSENVLTDIKLGKYRIV 638
Cdd:COG1061 98 RGGGRGLVVAPTGTGKTVLALALAAELLRGKrvLVLVPRRELLE-QWAE-ELRRFLGDPLAGGGKKDSDAPITVATYQSL 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 639 YITPEycsgniglLQQLEADIGitLIAVDEAHcisewgHDFRNSFRKLGSlktALPMVPIVALTAT--ATSSIREDIVRC 716
Cdd:COG1061 176 ARRAH--------LDELGDRFG--LVIIDEAH------HAGAPSYRRILE---AFPAAYRLGLTATpfRSDGREILLFLF 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 717 LN---------------LRNP---QIICTGFDRPNLYLEVRRKTGNILQDLQPFLVKTTSSHWEFEG---PTIIYCPSRK 775
Cdd:COG1061 237 DGivyeyslkeaiedgyLAPPeyyGIRVDLTDERAEYDALSERLREALAADAERKDKILRELLREHPddrKTLVFCSSVD 316
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 776 MTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRA 855
Cdd:COG1061 317 HAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRG 396
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
764-860 |
2.28e-10 |
|
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: 60.64 E-value: 2.28e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 764 EGPTIIYCPSRKMTEQvTAelrkLNLSC-ETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGIN-KAdiRQVI---- 837
Cdd:cd18795 43 GKPVLVFCSSRKECEK-TA----KDLAGiAFHHAGLTREDRELVEELFREGLIKVLVATSTLAAGVNlPA--RTVIikgt 115
|
90 100
....*....|....*....|....*...
gi 1622959916 838 HYGAPKEME-----SYYQEIGRAGRDGL 860
Cdd:cd18795 116 QRYDGKGYRelsplEYLQMIGRAGRPGF 143
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
767-857 |
4.42e-10 |
|
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: 59.59 E-value: 4.42e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELRKL------NLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYG 840
Cdd:cd18796 41 TLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIG 120
|
90
....*....|....*..
gi 1622959916 841 APKEMESYYQEIGRAGR 857
Cdd:cd18796 121 SPKSVARLLQRLGRSGH 137
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
567-704 |
3.84e-09 |
|
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: 56.64 E-value: 3.84e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 567 VAVMATGYGKSLCFQYPPVYV----GKIGLVISPLISLMEDQ---VLQLKMSNIPTCFLGSAQSENVLTDIKLGKYRIVY 639
Cdd:cd00046 5 LITAPTGSGKTLAALLAALLLllkkGKKVLVLVPTKALALQTaerLRELFGPGIRVAVLVGGSSAEEREKNKLGDADIII 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622959916 640 ITPEYCSGNIGLLQQLEADiGITLIAVDEAHCISEWGHDFRNSfrKLGSLKTALPMVPIVALTAT 704
Cdd:cd00046 85 ATPDMLLNLLLREDRLFLK-DLKLIIVDEAHALLIDSRGALIL--DLAVRKAGLKNAQVILLSAT 146
|
|
| PLN00206 |
PLN00206 |
DEAD-box ATP-dependent RNA helicase; Provisional |
550-859 |
4.09e-09 |
|
DEAD-box ATP-dependent RNA helicase; Provisional
Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 60.96 E-value: 4.09e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 550 PVQWKVIHSVLEERrdNVAVMA-TGYGKSLCF-------------QYPPVYVGKIGLVISP---LISLMEDQVLQL-KMS 611
Cdd:PLN00206 146 PIQMQAIPAALSGR--SLLVSAdTGSGKTASFlvpiisrcctirsGHPSEQRNPLAMVLTPtreLCVQVEDQAKVLgKGL 223
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 612 NIPTCFL--GSAQSENVLTdIKLGKYRIVYiTPeycsGN-IGLLQQLEADI-GITLIAVDEAHCISEWGhdFRNsfrKLG 687
Cdd:PLN00206 224 PFKTALVvgGDAMPQQLYR-IQQGVELIVG-TP----GRlIDLLSKHDIELdNVSVLVLDEVDCMLERG--FRD---QVM 292
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 688 SLKTALPMVPIVALTATATSSIrEDIVRCLnLRNPQIICTGF-DRPN-------LYLEVRRKTGNIlqdlqpFLVKTTSS 759
Cdd:PLN00206 293 QIFQALSQPQVLLFSATVSPEV-EKFASSL-AKDIILISIGNpNRPNkavkqlaIWVETKQKKQKL------FDILKSKQ 364
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 760 HweFEGPTIIYCPSRKMTEQVTAELRKLN-LSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIH 838
Cdd:PLN00206 365 H--FKPPAVVFVSSRLGADLLANAITVVTgLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVII 442
|
330 340
....*....|....*....|.
gi 1622959916 839 YGAPKEMESYYQEIGRAGRDG 859
Cdd:PLN00206 443 FDMPNTIKEYIHQIGRASRMG 463
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
77-217 |
1.30e-08 |
|
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: 56.52 E-value: 1.30e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 77 DVVGFDMEWpplYNKGKLGKVALIQLCVSESKCYLFHISSM--SVFPQGLKMLLENKAIKKAGVGIEGDQWKLLRDFDIK 154
Cdd:cd06148 11 KVIGLDCEG---VNLGRKGKLCLVQIATRTGQIYLFDILKLgsIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 155 LKNFVElTDVANKKLKCTETW--------SLSGLVKHLLG----------KQLLKDksirCSNWSKFPLTEDQKLYAATD 216
Cdd:cd06148 88 LNNVFD-TQVADALLQEQETGgfnpdrviSLVQLLDKYLYisislkedvkKLMRED----PKFWALRPLTEDMIRYAALD 162
|
.
gi 1622959916 217 A 217
Cdd:cd06148 163 V 163
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
767-860 |
1.53e-08 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 58.62 E-value: 1.53e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIAT-IAfGMGINKADIRQVIHYGAPKEM 845
Cdd:COG0513 244 AIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATdVA-ARGIDIDDVSHVINYDLPEDP 322
|
90
....*....|....*...
gi 1622959916 846 ESYYQEIG---RAGRDGL 860
Cdd:COG0513 323 EDYVHRIGrtgRAGAEGT 340
|
|
| RecQ_Zn_bind |
pfam16124 |
RecQ zinc-binding; This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ. |
870-940 |
1.63e-08 |
|
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: 52.29 E-value: 1.63e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1622959916 870 PADINLNRHLLT-EIRNEKFRLYKLKMMAKMEKY-LHSSRCRRQIILSHFEDKqvqkaslgiTGTEKC--CDNCR 940
Cdd:pfam16124 1 YQDVVRLRFLIEqSEADEERKEVELQKLQAMVAYcENTTDCRRKQLLRYFGEE---------FDSEPCgnCDNCL 66
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
755-857 |
4.08e-08 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 57.98 E-value: 4.08e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 755 KTTSSHwEFEGPTIIYCPSRKMTEQVTaelRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGInkaDI- 833
Cdd:COG1202 419 DTKSSK-GYRGQTIIFTNSRRRCHEIA---RALGYKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGV---DFp 491
|
90 100 110
....*....|....*....|....*....|....*..
gi 1622959916 834 -RQVIhygapkeMES------------YYQEIGRAGR 857
Cdd:COG1202 492 aSQVI-------FDSlamgiewlsvqeFHQMLGRAGR 521
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
746-883 |
4.67e-08 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 57.14 E-value: 4.67e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 746 LQDLQPFLVKTTSSHWEFEG-----------PTIIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDE 814
Cdd:PTZ00424 238 LEGIRQFYVAVEKEEWKFDTlcdlyetltitQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGS 317
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1622959916 815 IQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAGRDGLQSSCHILWAPADI----NLNRHLLTEI 883
Cdd:PTZ00424 318 TRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIeqlkEIERHYNTQI 390
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
800-859 |
4.69e-08 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 51.55 E-value: 4.69e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 800 FSRRKDvHHKFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAGRDG 859
Cdd:cd18785 9 FTNSIE-HAEEIASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGG 67
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
768-866 |
1.46e-05 |
|
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: 45.93 E-value: 1.46e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 768 IIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEIQCV--IATIAFGMGIN--KADIrqVIHYGAP- 842
Cdd:cd18793 31 LIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVflLSTKAGGVGLNltAANR--VILYDPWw 108
|
90 100
....*....|....*....|....*..
gi 1622959916 843 ---KEMesyyQEIGRAGRDGLQSSCHI 866
Cdd:cd18793 109 npaVEE----QAIDRAHRIGQKKPVVV 131
|
|
| PTZ00110 |
PTZ00110 |
helicase; Provisional |
736-887 |
5.02e-05 |
|
helicase; Provisional
Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 47.85 E-value: 5.02e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 736 LEVRRKTGNILQDLQPFLVKTtsshwefeGPTIIYCPSRKMTEQVTAELRKLNLSCETYHAGMSFSRRKDVHHKFVRDEI 815
Cdd:PTZ00110 357 VEEHEKRGKLKMLLQRIMRDG--------DKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKS 428
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1622959916 816 QCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAGRDGLQSSCHILWAPADINLNRHLLTEIRNEK 887
Cdd:PTZ00110 429 PIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAK 500
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
767-856 |
9.63e-05 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 47.23 E-value: 9.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELRKL---------------------------------NLSCETYHAGMSFSRRKDVHHKFVRD 813
Cdd:PRK09751 247 TIVFTNSRGLAEKLTARLNELyaarlqrspsiavdaahfestsgatsnrvqssdVFIARSHHGSVSKEQRAITEQALKSG 326
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1622959916 814 EIQCVIATIAFGMGINKADIRQVIHYGAPKEMESYYQEIGRAG 856
Cdd:PRK09751 327 ELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAG 369
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
335-480 |
3.05e-04 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 45.55 E-value: 3.05e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 335 EHKIFINVEDETWDPTLDHLAKHGGEDVLGNKVERKEDGFEEGVEDNkLKENMERACLMSLDITEHELQILEQQAQEKYL 414
Cdd:PTZ00341 964 EENVEENVEENVEENVEENVEENVEENVEENVEENVEENIEENVEEN-VEENIEENVEEYDEENVEEVEENVEEYDEENV 1042
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1622959916 415 SDIAYKSTEHLSPTNNENDTSYVIESDEDLEMEMLKHLSPTNNENDTSYVIESDEDLEMEMLKSLE 480
Cdd:PTZ00341 1043 EEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVEENVEENVEEIEENVEENVEENAE 1108
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
547-705 |
3.18e-04 |
|
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: 43.02 E-value: 3.18e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 547 SFKPVQWKVIHSVLEERrDNVAVMA-TGYGKSLCFQYPPV-----YVGKIgLVISPLISLMeDQVLQ-----LKMSNIPT 615
Cdd:cd17921 1 LLNPIQREALRALYLSG-DSVLVSApTSSGKTLIAELAILralatSGGKA-VYIAPTRALV-NQKEAdlrerFGPLGKNV 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 616 CFLGSAQSENvltDIKLGKYRIVYITPE-----YCSGNIGLLQQleadigITLIAVDEAHCIS--------EWGhdfrns 682
Cdd:cd17921 78 GLLTGDPSVN---KLLLAEADILVATPEkldllLRNGGERLIQD------VRLVVVDEAHLIGdgergvvlELL------ 142
|
170 180
....*....|....*....|...
gi 1622959916 683 frkLGSLKTALPMVPIVALTATA 705
Cdd:cd17921 143 ---LSRLLRINKNARFVGLSATL 162
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
301-501 |
3.49e-04 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 45.16 E-value: 3.49e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 301 GSTNIETELRPSNNLNLLSFEDSTTGGVqqkqigEHKIFINVEDETWDPTLDHLAKHGGEDVLGNKVERKEDGFEEGVED 380
Cdd:PTZ00341 920 EINLINKELKNQNENVPEHLKEHAEANI------EEDAEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEE 993
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 381 NkLKENMERaclmslDITEHELQILEQQAQEKyLSDIAYKSTEHLSPTNNENDTSYVIESDEDLEMEMLKHLSPTNNEND 460
Cdd:PTZ00341 994 N-VEENVEE------NIEENVEENVEENIEEN-VEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYD 1065
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1622959916 461 TSYVIESDEDLEmemlkslENLNSGTVEPTHSKCLDMERNL 501
Cdd:PTZ00341 1066 EENVEEIEENIE-------ENIEENVEENVEENVEEIEENV 1099
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
550-704 |
1.33e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 41.12 E-value: 1.33e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 550 PVQWKVIHSVLEERRDN----VAVMATGYGKS-----LCFQYPPVYVGKIGLVISPLISL---MEDQVLQLKMSNIPTCF 617
Cdd:pfam04851 6 PYQIEAIENLLESIKNGqkrgLIVMATGSGKTltaakLIARLFKKGPIKKVLFLVPRKDLleqALEEFKKFLPNYVEIGE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 618 LGSAQSEnvltDIKLGKYRIVYITPEYCSGNIGLLQQLEADIGITLIAVDEAHcisewgHDFRNSFRKlgsLKTALPMVP 697
Cdd:pfam04851 86 IISGDKK----DESVDDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAH------RSGASSYRN---ILEYFKPAF 152
|
....*..
gi 1622959916 698 IVALTAT 704
Cdd:pfam04851 153 LLGLTAT 159
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
792-859 |
2.18e-03 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 39.88 E-value: 2.18e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1622959916 792 ETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGInkaDIRQ---VIHYGAPKEMESYYQEIGRAGRDG 859
Cdd:cd18802 68 QRKRSLMTQRKQKETLDKFRDGELNLLIATSVLEEGI---DVPAcnlVIRFDLPKTLRSYIQSRGRARAPN 135
|
|
| PRK13767 |
PRK13767 |
ATP-dependent helicase; Provisional |
767-856 |
3.89e-03 |
|
ATP-dependent helicase; Provisional
Pssm-ID: 237497 [Multi-domain] Cd Length: 876 Bit Score: 41.80 E-value: 3.89e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1622959916 767 TIIYCPSRKMTEQVTAELRKL-------NLScETYHAGMSFSRRKDVHHKFVRDEIQCVIATIAFGMGINKADIRQVIHY 839
Cdd:PRK13767 287 TLIFTNTRSGAERVLYNLRKRfpeeydeDNI-GAHHSSLSREVRLEVEEKLKRGELKVVVSSTSLELGIDIGYIDLVVLL 365
|
90
....*....|....*..
gi 1622959916 840 GAPKEMESYYQEIGRAG 856
Cdd:PRK13767 366 GSPKSVSRLLQRIGRAG 382
|
|
| |
