|
Name |
Accession |
Description |
Interval |
E-value |
| recQ_fam |
TIGR00614 |
ATP-dependent DNA helicase, RecQ family; All proteins in this family for which functions are ... |
538-1010 |
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: 867.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 538 TCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPAC 617
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 618 FLGSAQSEN----VLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTA 693
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 694 LPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKtsshwEFEGPT-IIYCP 772
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK-----EFEGKSgIIYCP 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 773 SRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEI 852
Cdd:TIGR00614 235 SRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQES 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 853 GRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKaSLGIMGT 932
Cdd:TIGR00614 315 GRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMGT 393
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110735439 933 EKCCDNCRSRLDHCYsmDDSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLAD-QYRRHSLFGTGKDQ 1010
Cdd:TIGR00614 394 EKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDgGFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
540-1027 |
1.19e-177 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 537.42 E-value: 1.19e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 540 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFL 619
Cdd:COG0514 9 LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRAAGIRAAFL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQSEN----VLTDIKLGKYRIVYVTPEYCSgNMGLLQQLeADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALP 695
Cdd:COG0514 88 NSSLSAEerreVLRALRAGELKLLYVAPERLL-NPRFLELL-RRLKISLFAIDEAHCISQWGHDFRPDYRRLGELRERLP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 696 MVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTG-NILQDLQPFLVKTSshwefEGPTIIYCPSR 774
Cdd:COG0514 166 NVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP-----GGSGIVYCLSR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 775 KMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGR 854
Cdd:COG0514 241 KKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPKSIEAYYQEIGR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 855 AGRDGLQSSCHVLWAPADINLNRHLLTEIRN-EKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQvqkaslgimgTE 933
Cdd:COG0514 321 AGRDGLPAEALLLYGPEDVAIQRFFIEQSPPdEERKRVERAKLDAMLAYAETTGCRRQFLLRYFGEEL----------AE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 934 KC--CDNCRsrldhcysmddSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQ-YRRHSLFGTGKDQ 1010
Cdd:COG0514 391 PCgnCDNCL-----------GPPETFDGTEAAQKALSCVYRTGQRFGAGHVIDVLRGSKNEKIRQFgHDKLSTYGIGKDL 459
|
490
....*....|....*..
gi 110735439 1011 TESWWKAFSRQLITEGF 1027
Cdd:COG0514 460 SDKEWRSVIRQLLAQLF 476
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
535-1220 |
3.39e-123 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 397.16 E-value: 3.39e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 535 EQVtcLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNI 614
Cdd:PRK11057 14 KQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 615 PACFLGSAQSE----NVLTDIKLGKYRIVYVTPEYCSGNmGLLQQLeADIGITLIAVDEAHCISEWGHDFRDSFRKLGSL 690
Cdd:PRK11057 91 AAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPERLMMD-NFLEHL-AHWNPALLAVDEAHCISQWGHDFRPEYAALGQL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 691 KTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLylevrRKTgnILQDLQPflvkTSSHWEF----EGP 766
Cdd:PRK11057 169 RQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNI-----RYT--LVEKFKP----LDQLMRYvqeqRGK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 T-IIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDM 845
Cdd:PRK11057 238 SgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 846 ESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDkqvqka 925
Cdd:PRK11057 318 ESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAEAQTCRRLVLLNYFGE------ 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 926 slgimGTEKCCDNCRSRLDHCYSMDDSEDtswdfgpqAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLAD-QYRRHSLF 1004
Cdd:PRK11057 392 -----GRQEPCGNCDICLDPPKQYDGLED--------AQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDyGHDKLKVY 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1005 GTGKDQTESWWKAFSRQLITEGFLVE-VSRYNKfmkicaltkkgrnwlhkantesqsliLQANEELCPkklllpssktVS 1083
Cdd:PRK11057 459 GIGRDKSHEHWVSVIRQLIHLGLVTQnIAQHSA--------------------------LQLTEAARP----------VL 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1084 SGtkehcynQVPVELSTEKKSNLEKLYSYKpcdkiSSGSNISKKsimvqspekaysssqpvisaqeqetqivLYGKLVEA 1163
Cdd:PRK11057 503 RG-------EVSLQLAVPRIVALKPRAMQK-----SFGGNYDRK----------------------------LFAKLRKL 542
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 110735439 1164 RQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLA-PLLEVIK 1220
Cdd:PRK11057 543 RKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
537-731 |
1.04e-121 |
|
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: 377.19 E-value: 1.04e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 537 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPA 616
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 617 CFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEAdiGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPM 696
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 110735439 697 VPIVALTATASSSIREDIVRCLNLRNPQITCTGFD 731
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 |
2.06e-77 |
|
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: 252.82 E-value: 2.06e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 61 DCSFLSEDISMslsDGDVVGFDMEWPPLYNrgKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGI 140
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRR--YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 141 EGDQWKLLRDFDIKLKNFVELTDVANKKLKCtETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYAG 220
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 110735439 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 |
3.56e-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: 155.15 E-value: 3.56e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 57 YDASDCSFLSEDISMSLSDGDVVGFDMEWPPLYNRGKLGKVALIQLCVSEsKCYLF-HVSSMSVFPQGLKMLLENKAVKK 135
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGTGE-GAYIIdPLALGDDVLSALKRLLEDPNITK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 136 AGVGIEGDQWKLLRDFDIKLKNFVElTDVANKKLKCTETWSLNSLVKHLLGkqLLKDKSIRCSNWSKFPLTEDQKLYAAT 215
Cdd:pfam01612 80 VGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYAAL 156
|
170
....*....|...
gi 110735439 216 DAYAGFIIYRNLE 228
Cdd:pfam01612 157 DADYLLRLYDKLR 169
|
|
| DpdF |
NF041063 |
protein DpdF; |
568-887 |
1.52e-35 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 146.60 E-value: 1.52e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 568 VAVMATGYGKSLCFQYPPVYVGKIG---LVISPLISLMEDQVLQLK-MSNIPACFLG------SAQSEN----VLTDIKL 633
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRAReLLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 634 GKYRIVYVTPEycSGNMGLLQQLE--ADIG-ITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMV-----PI--VALT 703
Cdd:NF041063 242 GTQRILFTSPE--SLTGSLRPALFdaAEAGlLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLLRLapsgrPFrtLLLS 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 704 ATASSSIRE---------DIVRCLN---LRN-PQITCTGFDRPNLYLE-----VRRktgnilqdlqpfLVKtsshwefeg 765
Cdd:NF041063 320 ATLTESTLDtletlfgppGPFIVVSavqLRPePAYWVAKCDSEEERRErvleaLRH------------LPR--------- 378
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 766 PTIIYCPSRKMTQQVTGELRKLNLS-CGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKD 844
Cdd:NF041063 379 PLILYVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPET 458
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 110735439 845 MESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTE--IRNEK 887
Cdd:NF041063 459 LDRFYQEVGRGGRDGKASLSLLIYTPDDLDIAKSLNRPklISVEK 503
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
61-228 |
1.85e-31 |
|
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Pssm-ID: 214681 [Multi-domain] Cd Length: 172 Bit Score: 121.69 E-value: 1.85e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 61 DCSFLSEDISMSLSDGDVVGFDMEWPPLYNrgKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGI 140
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDS--YSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 141 EGDQWKLLRdFDIKLKNfVELTDVANK-KLKCTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAYlLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
....*....
gi 110735439 220 GFIIYRNLE 228
Cdd:smart00474 160 LLRLYEKLE 168
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
551-712 |
6.63e-27 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 108.48 E-value: 6.63e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 551 PVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYP------PVYVGKIGLVISPLISLMEDQVLQLK-----MSNIPACFL 619
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQSENVLTDIKlgKYRIVYVTPE---YCSGNMGLLQQLEadigitLIAVDEAHCISEWGhdFRDSFRKLgsLKTALPM 696
Cdd:pfam00270 81 GGDSRKEQLEKLK--GPDILVGTPGrllDLLQERKLLKNLK------LLVLDEAHRLLDMG--FGPDLEEI--LRRLPKK 148
|
170
....*....|....*.
gi 110735439 697 VPIVALTATASSSIRE 712
Cdd:pfam00270 149 RQILLLSATLPRNLED 164
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
958-1051 |
5.11e-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: 102.94 E-value: 5.11e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 958 DFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQ-YRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEvsrYNK 1036
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLRE---DGG 77
|
90
....*....|....*
gi 110735439 1037 FMKICALTKKGRNWL 1051
Cdd:smart00956 78 RYPYLKLTEKARPVL 92
|
|
| HTH_40 |
pfam14493 |
Helix-turn-helix domain; This presumed domain is found at the C-terminus of a large number of ... |
1258-1352 |
3.36e-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: 3.36e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1258 SMAITYSLFQEKkMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAgLTPEVQKIIADVIRNPPVNSdmskISLIRM 1337
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 110735439 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 ... |
1156-1229 |
1.92e-17 |
|
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: 78.11 E-value: 1.92e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 1156 LYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAP-LLEVIKHFCQTNSVQ 1229
Cdd:smart00341 7 LLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| HRDC |
pfam00570 |
HRDC domain; The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic ... |
1153-1219 |
1.45e-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: 61.01 E-value: 1.45e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110735439 1153 QIVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAP-LLEVI 1219
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
73-216 |
1.13e-09 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 61.81 E-value: 1.13e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 73 LSDGDVVGFDME-------WPplynrgklgKVALIQLCVSEsKCYLFHVSSMSVFPqGLKMLLENKAVKK----AGVGIE 141
Cdd:COG0349 15 LAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALIDPLAIGDLS-PLWELLADPAIVKvfhaAREDLE 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 142 GdqwkLLRDFDIKLKNFVElTDVANKKLKCTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATD 216
Cdd:COG0349 84 I----LYHLFGILPKPLFD-TQIAAALLGYGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEEQLEYAAAD 151
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
156-480 |
1.18e-05 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 50.17 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 156 KNFVELTDVANKKLKCTETW-----SLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYagfIIYRNLEIL 230
Cdd:PTZ00341 780 ANKEELANENNKLMNILKEYfgnneQINSITYNFENINLNEDNENGSKKILDLNHKDQKEIFEEIISY---IVDISLSDI 856
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 231 DDTVQRFAinkeeEILLSDMN---KQLTSISEEVMDLAKHL-PHAFSKLENPRRVSILLKDISENLYSlrrmiiGSTNIE 306
Cdd:PTZ00341 857 ENTAKNAA-----EQILSDEGldeKKLKKRAESLKKLANAIeKYAGGGKKDKKAKKKDAKDLSGNIAH------EINLIN 925
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 307 TELRPSNNLNLLSFEDSTTGGVQQ--KQIREHEVLIHVEDETWDPTLDHLAKHDGEDVLGNKVERKEDGFEDGVEDN--- 381
Cdd:PTZ00341 926 KELKNQNENVPEHLKEHAEANIEEdaEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENiee 1005
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 382 ----KLKENMERACLMSLDITEHELQILEQQSQEEYLSDIAYKSTEHLSPNDNENDTSYVIESDEDLEMEMLKHLSPNDN 457
Cdd:PTZ00341 1006 nveeNVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVE 1085
|
330 340
....*....|....*....|...
gi 110735439 458 ENDTSYVIESDEDLEMEMLKSLE 480
Cdd:PTZ00341 1086 ENVEENVEEIEENVEENVEENAE 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 ... |
538-1010 |
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: 867.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 538 TCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPAC 617
Cdd:TIGR00614 1 KILKKYFGLSSFRPVQLEVINAVLLGR-DCFVVMPTGGGKSLCYQLPALYSDGITLVISPLISLMEDQVLQLQALGIPAT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 618 FLGSAQSEN----VLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTA 693
Cdd:TIGR00614 80 FLNSAQTKEqqlnVLTDLKDGKIKLLYVTPEKISASNRLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 694 LPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKtsshwEFEGPT-IIYCP 772
Cdd:TIGR00614 160 FPNVPVMALTATASPSVREDILRQLNLLNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRK-----EFEGKSgIIYCP 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 773 SRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEI 852
Cdd:TIGR00614 235 SRKKVEQVAAELQKLGLAAGAYHAGLEDSARDDVQHKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQES 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 853 GRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKaSLGIMGT 932
Cdd:TIGR00614 315 GRAGRDGLPSECHLFYAPADMNRLRRLLMEEPDGNFRTYKLKLYEMMEYCLNSSTCRRLILLSYFGEKGFNK-SFCIMGT 393
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110735439 933 EKCCDNCRSRLDHCYsmDDSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLAD-QYRRHSLFGTGKDQ 1010
Cdd:TIGR00614 394 EKCCDNCCKRLDYKT--KDVTDKVYDFGPQAQKALSAVGRLNQKFGMGYPVDFLRGSNSQKIRDgGFRKHSLYGRGKDE 470
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
540-1027 |
1.19e-177 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 537.42 E-value: 1.19e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 540 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFL 619
Cdd:COG0514 9 LKRVFGYDSFRPGQEEIIEAVLA-GRDALVVMPTGGGKSLCYQLPALLLPGLTLVVSPLIALMKDQVDALRAAGIRAAFL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQSEN----VLTDIKLGKYRIVYVTPEYCSgNMGLLQQLeADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALP 695
Cdd:COG0514 88 NSSLSAEerreVLRALRAGELKLLYVAPERLL-NPRFLELL-RRLKISLFAIDEAHCISQWGHDFRPDYRRLGELRERLP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 696 MVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTG-NILQDLQPFLVKTSshwefEGPTIIYCPSR 774
Cdd:COG0514 166 NVPVLALTATATPRVRADIAEQLGLEDPRVFVGSFDRPNLRLEVVPKPPdDKLAQLLDFLKEHP-----GGSGIVYCLSR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 775 KMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGR 854
Cdd:COG0514 241 KKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPDVRFVIHYDLPKSIEAYYQEIGR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 855 AGRDGLQSSCHVLWAPADINLNRHLLTEIRN-EKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQvqkaslgimgTE 933
Cdd:COG0514 321 AGRDGLPAEALLLYGPEDVAIQRFFIEQSPPdEERKRVERAKLDAMLAYAETTGCRRQFLLRYFGEEL----------AE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 934 KC--CDNCRsrldhcysmddSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQ-YRRHSLFGTGKDQ 1010
Cdd:COG0514 391 PCgnCDNCL-----------GPPETFDGTEAAQKALSCVYRTGQRFGAGHVIDVLRGSKNEKIRQFgHDKLSTYGIGKDL 459
|
490
....*....|....*..
gi 110735439 1011 TESWWKAFSRQLITEGF 1027
Cdd:COG0514 460 SDKEWRSVIRQLLAQLF 476
|
|
| recQ |
TIGR01389 |
ATP-dependent DNA helicase RecQ; The ATP-dependent DNA helicase RecQ of E. coli is about 600 ... |
540-1220 |
1.98e-140 |
|
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: 442.97 E-value: 1.98e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 540 LKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFL 619
Cdd:TIGR01389 5 LKRTFGYDDFRPGQEEIISHVLDGR-DVLVVMPTGGGKSLCYQVPALLLKGLTVVISPLISLMKDQVDQLRAAGVAAAYL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQS----ENVLTDIKLGKYRIVYVTPEycsgnmGLLQ----QLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLK 691
Cdd:TIGR01389 84 NSTLSakeqQDIEKALVNGELKLLYVAPE------RLEQdyflNMLQRIPIALVAVDEAHCVSQWGHDFRPEYQRLGSLA 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 692 TALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTgNILQDLQPFLVKtssHWEFEGptIIYC 771
Cdd:TIGR01389 158 ERFPQVPRIALTATADAETRQDIRELLRLADANEFITSFDRPNLRFSVVKKN-NKQKFLLDYLKK---HRGQSG--IIYA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 772 PSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQE 851
Cdd:TIGR01389 232 SSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQE 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 852 IGRAGRDGLQSSCHVLWAPADINLNRHLLTEirNEKFRLYKLKMMAK---MEKYLHSSRCRRQIILSHFEDKQVqkaslg 928
Cdd:TIGR01389 312 AGRAGRDGLPAEAILLYSPADIALLKRRIEQ--SEADDDYKQIEREKlraMIAYCETQTCRRAYILRYFGENEV------ 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 929 imgtEKC--CDNCRsrldhcysmddSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLaDQYR--RHSLF 1004
Cdd:TIGR01389 384 ----EPCgnCDNCL-----------DPPKSYDATVEAQKALSCVYRMGQRFGVGYIIEVLRGSKNDKI-LQKGhdQLSTY 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1005 GTGKDQTESWWKAFSRQLITEGFLVEvsrynkfmkicaltkkgrnwlhkANTESQSLILQaneelcpkklllPSSKTVSS 1084
Cdd:TIGR01389 448 GIGKDYTQKEWRSLIDQLIAEGLLTE-----------------------NDEIYIGLQLT------------EAARKVLK 492
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1085 gtkehcyNQVPVELSTEKKSNLEKLYSYKpcdkissgsniskksIMVQSPEKAysssqpvisaqeqetqivLYGKLVEAR 1164
Cdd:TIGR01389 493 -------NEVEVLLRPFKVVAKEKTRVQK---------------NLSVGVDNA------------------LFEALRELR 532
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*..
gi 110735439 1165 QKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAP-LLEVIK 1220
Cdd:TIGR01389 533 KEQADEQNVPPYVIFSDSTLREMAEKRPATLNALLKIKGVGQNKLDRYGEaFLEVIR 589
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
535-1220 |
3.39e-123 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 397.16 E-value: 3.39e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 535 EQVtcLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNI 614
Cdd:PRK11057 14 KQV--LQETFGYQQFRPGQQEIIDAVLSGR-DCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLISLMKDQVDQLLANGV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 615 PACFLGSAQSE----NVLTDIKLGKYRIVYVTPEYCSGNmGLLQQLeADIGITLIAVDEAHCISEWGHDFRDSFRKLGSL 690
Cdd:PRK11057 91 AAACLNSTQTReqqlEVMAGCRTGQIKLLYIAPERLMMD-NFLEHL-AHWNPALLAVDEAHCISQWGHDFRPEYAALGQL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 691 KTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLylevrRKTgnILQDLQPflvkTSSHWEF----EGP 766
Cdd:PRK11057 169 RQRFPTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNI-----RYT--LVEKFKP----LDQLMRYvqeqRGK 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 T-IIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDM 845
Cdd:PRK11057 238 SgIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 846 ESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDkqvqka 925
Cdd:PRK11057 318 ESYYQETGRAGRDGLPAEAMLFYDPADMAWLRRCLEEKPAGQQQDIERHKLNAMGAFAEAQTCRRLVLLNYFGE------ 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 926 slgimGTEKCCDNCRSRLDHCYSMDDSEDtswdfgpqAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLAD-QYRRHSLF 1004
Cdd:PRK11057 392 -----GRQEPCGNCDICLDPPKQYDGLED--------AQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDyGHDKLKVY 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1005 GTGKDQTESWWKAFSRQLITEGFLVE-VSRYNKfmkicaltkkgrnwlhkantesqsliLQANEELCPkklllpssktVS 1083
Cdd:PRK11057 459 GIGRDKSHEHWVSVIRQLIHLGLVTQnIAQHSA--------------------------LQLTEAARP----------VL 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1084 SGtkehcynQVPVELSTEKKSNLEKLYSYKpcdkiSSGSNISKKsimvqspekaysssqpvisaqeqetqivLYGKLVEA 1163
Cdd:PRK11057 503 RG-------EVSLQLAVPRIVALKPRAMQK-----SFGGNYDRK----------------------------LFAKLRKL 542
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 110735439 1164 RQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLA-PLLEVIK 1220
Cdd:PRK11057 543 RKSIADEENIPPYVVFNDATLIEMAEQMPITASEMLSVNGVGQRKLERFGkPFMALIR 600
|
|
| DEXHc_RecQ3 |
cd18017 |
DEAH-box helicase domain of RecQ3; DEAD-like helicase RecQ3 (also called Werner syndrome ... |
537-731 |
1.04e-121 |
|
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: 377.19 E-value: 1.04e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 537 VTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPA 616
Cdd:cd18017 1 LNALNEYFGHSSFRPVQWKVIRSVLEERRDNLVVMATGYGKSLCYQYPSVLLNSLTLVISPLISLMEDQVLQLVMSNIPA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 617 CFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEAdiGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPM 696
Cdd:cd18017 81 CFLGSAQSQNVLDDIKMGKIRVIYVTPEFVSKGLELLQQLRN--GITLIAIDEAHCVSQWGHDFRSSYRHLGSIRNRLPN 158
|
170 180 190
....*....|....*....|....*....|....*
gi 110735439 697 VPIVALTATASSSIREDIVRCLNLRNPQITCTGFD 731
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 ... |
538-731 |
1.12e-86 |
|
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: 280.57 E-value: 1.12e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 538 TCLKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPAC 617
Cdd:cd17920 2 QILKEVFGYDEFRPGQLEAINAVLA-GRDVLVVMPTGGGKSLCYQLPALLLDGVTLVVSPLISLMQDQVDRLQQLGIRAA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 618 FLGSAQS----ENVLTDIKLGKYRIVYVTPEYC--SGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLK 691
Cdd:cd17920 81 ALNSTLSpeekREVLLRIKNGQYKLLYVTPERLlsPDFLELLQRLPERKRLALIVVDEAHCVSQWGHDFRPDYLRLGRLR 160
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 110735439 692 TALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFD 731
Cdd:cd17920 161 RALPGVPILALTATATPEVREDILKRLGLRNPVIFRASFD 200
|
|
| PLN03137 |
PLN03137 |
ATP-dependent DNA helicase; Q4-like; Provisional |
541-1107 |
1.01e-83 |
|
ATP-dependent DNA helicase; Q4-like; Provisional
Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 300.27 E-value: 1.01e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 541 KMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLG 620
Cdd:PLN03137 453 KKVFGNHSFRPNQREIINATMSGY-DVFVLMPTGGGKSLTYQLPALICPGITLVISPLVSLIQDQIMNLLQANIPAASLS 531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 621 S----AQSENVLTDI--KLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIA---VDEAHCISEWGHDFRDSFRKLGSLK 691
Cdd:PLN03137 532 AgmewAEQLEILQELssEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLArfvIDEAHCVSQWGHDFRPDYQGLGILK 611
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 692 TALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLvkTSSHweFEGPTIIYC 771
Cdd:PLN03137 612 QKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPKTKKCLEDIDKFI--KENH--FDECGIIYC 687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 772 PSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQE 851
Cdd:PLN03137 688 LSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQE 767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 852 IGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRL---YKLKM------------MAKMEKYLHSS-RCRRQIILS 915
Cdd:PLN03137 768 CGRAGRDGQRSSCVLYYSYSDYIRVKHMISQGGVEQSPMamgYNRMAssgriletntenLLRMVSYCENEvDCRRFLQLV 847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 916 HFEDKqvqkasLGIMGTEKCCDNCRSrldhCYSMDDSEDTSwdfgpQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLa 995
Cdd:PLN03137 848 HFGEK------FDSTNCKKTCDNCSS----SKSLIDKDVTE-----IARQLVELVKLTGERFSSAHILEVYRGSLNQYV- 911
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 996 dQYRRH---SLFGTGKDQTESWWKAFSRQLITEGFLVE-VSRYNKFMKICALTKKGRNWLHKANTESQSLILQaneelcp 1071
Cdd:PLN03137 912 -KKHRHetlSLHGAGKHLSKGEASRILHYLVTEDILAEdVKKSDLYGSVSSLLKVNESKAYKLFSGGQTIIMR------- 983
|
570 580 590
....*....|....*....|....*....|....*.
gi 110735439 1072 kkllLPSSKTVSSGTKEHCyNQVPVELSTEKKSNLE 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 |
2.06e-77 |
|
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: 252.82 E-value: 2.06e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 61 DCSFLSEDISMslsDGDVVGFDMEWPPLYNrgKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGI 140
Cdd:cd06129 1 ALSSLCEDLSM---DGDVIAFDMEWPPGRR--YYGEVALIQLCVSEEKCYLFDPLSLSVDWQGLKMLLENPSIVKALHGI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 141 EGDQWKLLRDFDIKLKNFVELTDVANKKLKCtETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYAG 220
Cdd:cd06129 76 EGDLWKLLRDFGEKLQRLFDTTIAANLKGLP-ERWSLASLVEHFLGKTL--DKSISCADWSYRPLTEDQKLYAAADVYAL 152
|
....*....
gi 110735439 221 FIIYRNLEI 229
Cdd:cd06129 153 LIIYTKLRN 161
|
|
| DEDDy_polA_RNaseD_like_exo |
cd09018 |
DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins; ... |
78-229 |
2.20e-72 |
|
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: 237.91 E-value: 2.20e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 78 VVGFDMEWPPLYNrgKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGIEGDQWKLLRDFDIKLKN 157
Cdd:cd09018 1 VFAFDTETDSLDN--ISANLVLIQLAIEPGVAALIPVAHDYLALELLKPLLEDEKALKVGQNLKYDRGILLNYFIELRGI 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110735439 158 FVELTDVANKKLKCTETWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYAGFIIYRNLEI 229
Cdd:cd09018 79 AFDTMLEAYILNSVAGRWDMDSLVERWLGHKLIKFESIAGKLWFNQPLTEEQGRYAAEDADVTLQIHLKLWP 150
|
|
| WRN_exo |
cd06141 |
DEDDy 3'-5' exonuclease domain of WRN and similar proteins; WRN is a unique RecQ DNA helicase ... |
61-228 |
1.23e-70 |
|
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: 233.62 E-value: 1.23e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 61 DCSFLSEDISMSLS-DGDVVGFDMEWPPLYNRGKLGKVALIQLCvSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVG 139
Cdd:cd06141 2 DSAQDAEEAVKELLgKEKVVGFDTEWRPSFRKGKRNKVALLQLA-TESRCLLFQLAHMDKLPPSLKQLLEDPSILKVGVG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 140 IEGDQWKLLRDFDIKLKNFVELTDVANKKLKCTETWSLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:cd06141 81 IKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEEVLGLPLSKPKKVRCSNWEARPLSKEQILYAATDAYA 160
|
....*....
gi 110735439 220 GFIIYRNLE 228
Cdd:cd06141 161 SLELYRKLL 169
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
732-868 |
6.24e-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: 227.48 E-value: 6.24e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 732 RPNLYLEVRRKTGNILQDLQPFLVKtssHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFV 811
Cdd:cd18794 1 RPNLFYSVRPKDKKDEKLDLLKRIK---VEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWL 77
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 110735439 812 RDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLW 868
Cdd:cd18794 78 RDKIQVIVATVAFGMGIDKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILFY 134
|
|
| DEXHc_RecQ1 |
cd18015 |
DEXH-box helicase domain of RecQ1; ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ ... |
540-723 |
1.03e-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: 178.33 E-value: 1.03e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 540 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFL 619
Cdd:cd18015 10 LKNVFKLEKFRPLQLETINATMA-GRDVFLVMPTGGGKSLCYQLPALCSDGFTLVVSPLISLMEDQLMALKKLGISATML 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQS-ENV------LTDIKlGKYRIVYVTPEYCSGNMGLLQQLEA--DIG-ITLIAVDEAHCISEWGHDFRDSFRKLGS 689
Cdd:cd18015 89 NASSSkEHVkwvhaaLTDKN-SELKLLYVTPEKIAKSKRFMSKLEKayNAGrLARIAIDEVHCCSQWGHDFRPDYKKLGI 167
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 110735439 690 LKTALPMVPIVALTATASSSIRED------IVRCLNLRNP 723
Cdd:cd18015 168 LKRQFPNVPILGLTATATSKVLKDvqkilcIQKCLTFTAS 207
|
|
| DEXHc_RecQ4-like |
cd18018 |
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
540-725 |
1.20e-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: 1.20e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 540 LKMYFGHSSFKPVQWKVIHSVLEeRRDNVAVMATGYGKSLCFQYP----PVYVGKIGLVISPLISLMEDQVLQLKMSNIP 615
Cdd:cd18018 4 LRRVFGHPSFRPGQEEAIARLLS-GRSTLVVLPTGAGKSLCYQLPalllRRRGPGLTLVVSPLIALMKDQVDALPRAIKA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 616 ACF---LGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMG--LLQQLEadiGITLIAVDEAHCISEWGHDFRDSFRKLGS- 689
Cdd:cd18018 83 AALnssLTREERRRILEKLRAGEVKILYVSPERLVNESFreLLRQTP---PISLLVVDEAHCISEWSHNFRPDYLRLCRv 159
|
170 180 190
....*....|....*....|....*....|....*.
gi 110735439 690 LKTALPMVPIVALTATASSSIREDIVRCLNLRNPQI 725
Cdd:cd18018 160 LRELLGAPPVLALTATATKRVVEDIASHLGIPESGV 195
|
|
| DEXHc_RecQ5 |
cd18014 |
DEAH-box helicase domain of RecQ5; ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ ... |
538-723 |
1.72e-45 |
|
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: 163.03 E-value: 1.72e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 538 TCLKMYFGHSSFK-PVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPA 616
Cdd:cd18014 2 STLKKVFGHSDFKsPLQEKATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVISPLIALIQDQVDHLKTLKIRV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 617 CFLGSAQS----ENVLTDIK--LGKYRIVYVTPEYCSGN--MGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLG 688
Cdd:cd18014 82 DSLNSKLSaqerKRIIADLEseKPQTKFLYITPEMAATSsfQPLLSSLVSRNLLSYLVVDEAHCVSQWGHDFRPDYLRLG 161
|
170 180 190
....*....|....*....|....*....|....*
gi 110735439 689 SLKTALPMVPIVALTATASSSIREDIVRCLNLRNP 723
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 |
3.56e-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: 155.15 E-value: 3.56e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 57 YDASDCSFLSEDISMSLSDGDVVGFDMEWPPLYNRGKLGKVALIQLCVSEsKCYLF-HVSSMSVFPQGLKMLLENKAVKK 135
Cdd:pfam01612 1 YRIVTTEDELEDLIEELLNAPYVAVDTETTSLDTYSYYLRGALIQIGTGE-GAYIIdPLALGDDVLSALKRLLEDPNITK 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 136 AGVGIEGDQWKLLRDFDIKLKNFVElTDVANKKLKCTETWSLNSLVKHLLGkqLLKDKSIRCSNWSKFPLTEDQKLYAAT 215
Cdd:pfam01612 80 VGHNAKFDLEVLARDFGIKLRNLFD-TMLAAYLLGYDRSHSLADLAEKYLG--VELDKEEQCSDWQARPLSEEQLRYAAL 156
|
170
....*....|...
gi 110735439 216 DAYAGFIIYRNLE 228
Cdd:pfam01612 157 DADYLLRLYDKLR 169
|
|
| DEXHc_RecQ2_BLM |
cd18016 |
DEAH-box helicase domain of RecQ2; ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom ... |
533-731 |
3.28e-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: 153.83 E-value: 3.28e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 533 NEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMS 612
Cdd:cd18016 2 SKEMMKIFHKKFGLHQFRTNQLEAINAALLGE-DCFVLMPTGGGKSLCYQLPACVSPGVTVVISPLRSLIVDQVQKLTSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 613 NIPACFLGSAQSENVLTDI--KLGK----YRIVYVTPEYCSGNMGLLQQLEADIGITLIA---VDEAHCISEWGHDFRDS 683
Cdd:cd18016 81 DIPATYLTGDKTDAEATKIylQLSKkdpiIKLLYVTPEKISASNRLISTLENLYERKLLArfvIDEAHCVSQWGHDFRPD 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 110735439 684 FRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFD 731
Cdd:cd18016 161 YKRLNMLRQKFPSVPMMALTATATPRVQKDILNQLKMLRPQVFTMSFN 208
|
|
| DpdF |
NF041063 |
protein DpdF; |
568-887 |
1.52e-35 |
|
protein DpdF;
Pssm-ID: 468990 [Multi-domain] Cd Length: 813 Bit Score: 146.60 E-value: 1.52e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 568 VAVMATGYGKSLCFQYPPVYVGKIG---LVISPLISLMEDQVLQLK-MSNIPACFLG------SAQSEN----VLTDIKL 633
Cdd:NF041063 162 IVNLPTGSGKSLVAQAPALLASRQGgltLVVVPTVALAIDQERRAReLLRRAGPDLGgplawhGGLSAEeraaIRQRIRD 241
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 634 GKYRIVYVTPEycSGNMGLLQQLE--ADIG-ITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMV-----PI--VALT 703
Cdd:NF041063 242 GTQRILFTSPE--SLTGSLRPALFdaAEAGlLRYLVVDEAHLVDQWGDGFRPEFQLLAGLRRSLLRLapsgrPFrtLLLS 319
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 704 ATASSSIRE---------DIVRCLN---LRN-PQITCTGFDRPNLYLE-----VRRktgnilqdlqpfLVKtsshwefeg 765
Cdd:NF041063 320 ATLTESTLDtletlfgppGPFIVVSavqLRPePAYWVAKCDSEEERRErvleaLRH------------LPR--------- 378
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 766 PTIIYCPSRKMTQQVTGELRKLNLS-CGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKD 844
Cdd:NF041063 379 PLILYVTKVEDAEAWLQRLRAAGFRrVALFHGDTPDAERERLIEQWRENELDIVVATSAFGLGMDKSDVRTVIHACVPET 458
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 110735439 845 MESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTE--IRNEK 887
Cdd:NF041063 459 LDRFYQEVGRGGRDGKASLSLLIYTPDDLDIAKSLNRPklISVEK 503
|
|
| 35EXOc |
smart00474 |
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner ... |
61-228 |
1.85e-31 |
|
3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Pssm-ID: 214681 [Multi-domain] Cd Length: 172 Bit Score: 121.69 E-value: 1.85e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 61 DCSFLSEDISMSLSDGDVVGFDMEWPPLYNrgKLGKVALIQLCVSESKCYLFHVSSMSVFPQGLKMLLENKAVKKAGVGI 140
Cdd:smart00474 6 DSETLEELLEKLRAAGGEVALDTETTGLDS--YSGKLVLIQISVTGEGAFIIDPLALGDDLEILKDLLEDETITKVGHNA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 141 EGDQWKLLRdFDIKLKNfVELTDVANK-KLKCTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATDAYA 219
Cdd:smart00474 84 KFDLHVLAR-FGIELEN-IFDTMLAAYlLLGGPSKHGLATLLLGYLGVEL--DKEEQKSDWGARPLSEEQLEYAAEDADA 159
|
....*....
gi 110735439 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 |
7.05e-29 |
|
DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins; The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Pssm-ID: 176655 Cd Length: 193 Bit Score: 115.08 E-value: 7.05e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 71 MSLSDGDVVGFDMEWPPLYNRGKLGKVALIQLCVsESKCYLFHVSSMS-----VFPQGLKMLLENKAVKKAGVGIEGDQW 145
Cdd:cd06146 17 LSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLAT-EDEVFLLDLLALEnleseDWDRLLKRLFEDPDVLKLGFGFKQDLK 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 146 KL------LRDFDIKLKNFVELTDVANKKLK----------CTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQ 209
Cdd:cd06146 96 ALsasypaLKCMFERVQNVLDLQNLAKELQKsdmgrlkgnlPSKTKGLADLVQEVLGKPL--DKSEQCSNWERRPLREEQ 173
|
170
....*....|....*....
gi 110735439 210 KLYAATDAYAGFIIYRNLE 228
Cdd:cd06146 174 ILYAALDAYCLLEVFDKLL 192
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
551-712 |
6.63e-27 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 108.48 E-value: 6.63e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 551 PVQWKVIHSVLEERrDNVAVMATGYGKSLCFQYP------PVYVGKIGLVISPLISLMEDQVLQLK-----MSNIPACFL 619
Cdd:pfam00270 2 PIQAEAIPAILEGR-DVLVQAPTGSGKTLAFLLPalealdKLDNGPQALVLAPTRELAEQIYEELKklgkgLGLKVASLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 620 GSAQSENVLTDIKlgKYRIVYVTPE---YCSGNMGLLQQLEadigitLIAVDEAHCISEWGhdFRDSFRKLgsLKTALPM 696
Cdd:pfam00270 81 GGDSRKEQLEKLK--GPDILVGTPGrllDLLQERKLLKNLK------LLVLDEAHRLLDMG--FGPDLEEI--LRRLPKK 148
|
170
....*....|....*.
gi 110735439 697 VPIVALTATASSSIRE 712
Cdd:pfam00270 149 RQILLLSATLPRNLED 164
|
|
| RQC |
smart00956 |
This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix ... |
958-1051 |
5.11e-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: 102.94 E-value: 5.11e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 958 DFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQ-YRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEvsrYNK 1036
Cdd:smart00956 1 DVTEEAQKLLSCVYRTGQRFGAGHVIDVLRGSKNKKIRQKgHDRLSTFGIGKDLSKKEWRRLIRQLIAEGYLRE---DGG 77
|
90
....*....|....*
gi 110735439 1037 FMKICALTKKGRNWL 1051
Cdd:smart00956 78 RYPYLKLTEKARPVL 92
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
543-740 |
2.16e-25 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 105.27 E-value: 2.16e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 543 YFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIG-----LVISPLISLMEDQVLQLK-----MS 612
Cdd:smart00487 3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGkggrvLVLVPTRELAEQWAEELKklgpsLG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 613 NIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYcsgnmgLLQQLEAD----IGITLIAVDEAHCISEWGhdFRDSFRKLg 688
Cdd:smart00487 83 LKVVGLYGGDSKREQLRKLESGKTDILVTTPGR------LLDLLENDklslSNVDLVILDEAHRLLDGG--FGDQLEKL- 153
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 110735439 689 sLKTALPMVPIVALTATASSSIREDIVRCLNLRnpqITCTGFDRPNLYLEVR 740
Cdd:smart00487 154 -LKLLPKNVQLLLLSATPPEEIENLLELFLNDP---VFIDVGFTPLEPIEQF 201
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
778-859 |
3.10e-23 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 94.97 E-value: 3.10e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 778 QQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGR 857
Cdd:smart00490 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80
|
..
gi 110735439 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 |
3.36e-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: 3.36e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 1258 SMAITYSLFQEKkMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAgLTPEVQKIIADVIRNPPVNSdmskISLIRM 1337
Cdd:pfam14493 1 SAEITLELYKEG-LSIEEIAEERGLKESTIEGHLAELIEAGEPVDIERL-VSEEEQKEILDAIEKLGSES----LKPIKE 74
|
90
....*....|....*
gi 110735439 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 |
1.91e-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: 84.95 E-value: 1.91e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 762 EFEGPTIIYCPSRKMTQqvTGEL-RKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYG 840
Cdd:pfam00271 13 ERGGKVLIFSQTKKTLE--AELLlEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYD 90
|
90
....*....|....*....
gi 110735439 841 APKDMESYYQEIGRAGRDG 859
Cdd:pfam00271 91 LPWNPASYIQRIGRAGRAG 109
|
|
| HRDC |
smart00341 |
Helicase and RNase D C-terminal; Hypothetical role in nucleic acid binding. Mutations in the ... |
1156-1229 |
1.92e-17 |
|
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: 78.11 E-value: 1.92e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 1156 LYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAP-LLEVIKHFCQTNSVQ 1229
Cdd:smart00341 7 LLRRLRQWRDEIARREDVPPYFVLPDETLIKMAAALPTNVSELLAIDGVGEEKARRYGKdLLAVIQEASDSPSEA 81
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
754-857 |
8.96e-16 |
|
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: 75.24 E-value: 8.96e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 754 LVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADI 833
Cdd:cd18787 17 LLLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRVLVATDVAARGLDIPGV 96
|
90 100
....*....|....*....|....
gi 110735439 834 RQVIHYGAPKDMESYYQEIGRAGR 857
Cdd:cd18787 97 DHVINYDLPRDAEDYVHRIGRTGR 120
|
|
| RQC |
pfam09382 |
RQC domain; This DNA-binding domain is found in the RecQ helicase among others and has a ... |
953-1051 |
3.12e-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: 72.96 E-value: 3.12e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 953 EDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLAdQYRRHSL--FGTGKDQTESWWKAFSRQLITEGFL-V 1029
Cdd:pfam09382 1 PPETVDVTEEAQKILSCVYRTGQRFGAGHLIDVLRGSKNKKIR-QLGHDKLstFGIGKDLSKKEWRRIIRQLIAEGYLeV 79
|
90 100
....*....|....*....|..
gi 110735439 1030 EVSRYNkfmkICALTKKGRNWL 1051
Cdd:pfam09382 80 DIEFYS----VLKLTPKAREVL 97
|
|
| RNaseD_exo |
cd06142 |
DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins; Ribonuclease (RNase) D ... |
73-216 |
5.63e-14 |
|
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: 71.41 E-value: 5.63e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 73 LSDGDVVGFDMEwpplYNRGK--LGKVALIQLCVSEsKCYLFHVSSMSVFPqGLKMLLENKAVKK----AGVGIEGdqwk 146
Cdd:cd06142 9 LASAGVIAVDTE----FMRLNtyYPRLCLIQISTGG-EVYLIDPLAIGDLS-PLKELLADPNIVKvfhaAREDLEL---- 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 147 LLRDFDIKLKNFVElTDVANKKLKCTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATD 216
Cdd:cd06142 79 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 |
6.45e-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: 70.36 E-value: 6.45e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 TIIYCPSRKMTQQVTGELR-------KLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHY 839
Cdd:cd18797 38 TIVFCRSRKLAELLLRYLKarlveegPLASKVASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLA 117
|
90 100
....*....|....*....|
gi 110735439 840 GAPKDMESYYQEIGRAGRDG 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 |
1.45e-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: 61.01 E-value: 1.45e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 110735439 1153 QIVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAP-LLEVI 1219
Cdd:pfam00570 1 QLALLKALREWRDELAREEDVPPYVIFPDKTLLEIAEKLPRTLEELLAIPGVGPRKVERYGEeILAAI 68
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
730-860 |
2.93e-11 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350182 [Multi-domain] Cd Length: 154 Bit Score: 62.96 E-value: 2.93e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 730 FDRPNLYLEVRRKTGNILQDLQPFLVKTSSHwEFEGPTIIYCPSRKMTQQVTgelrkLNLSC-GTYHAGMSFSTRKDIHH 808
Cdd:cd18795 10 LGFNGLGIKLRVDVMNKFDSDIIVLLKIETV-SEGKPVLVFCSSRKECEKTA-----KDLAGiAFHHAGLTREDRELVEE 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 110735439 809 RFVRDEIQCVIATIAFGMGIN-KAdiRQVI----HYGAPKDME-----SYYQEIGRAGRDGL 860
Cdd:cd18795 84 LFREGLIKVLVATSTLAAGVNlPA--RTVIikgtQRYDGKGYRelsplEYLQMIGRAGRPGF 143
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
562-855 |
1.68e-10 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 65.43 E-value: 1.68e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 562 EERRDNVAVMATGYGKSLCFQYPPVYVGKIG--LVISPLISLMEdQVLQlKMSNIPACFLGSAQSENVLTDIKLGKYRIV 639
Cdd:COG1061 98 RGGGRGLVVAPTGTGKTVLALALAAELLRGKrvLVLVPRRELLE-QWAE-ELRRFLGDPLAGGGKKDSDAPITVATYQSL 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 640 YvtpeycsgNMGLLQQLEADIGitLIAVDEAHcisewgHDFRDSFRKLGSlktALPMVPIVALTAT--ASSSIREDIVRC 717
Cdd:COG1061 176 A--------RRAHLDELGDRFG--LVIIDEAH------HAGAPSYRRILE---AFPAAYRLGLTATpfRSDGREILLFLF 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 718 LN---------------LRNP---QITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFE----GPTIIYCPSRK 775
Cdd:COG1061 237 DGivyeyslkeaiedgyLAPPeyyGIRVDLTDERAEYDALSERLREALAADAERKDKILRELLREhpddRKTLVFCSSVD 316
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 776 MTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRA 855
Cdd:COG1061 317 HAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRG 396
|
|
| Rnd |
COG0349 |
Ribonuclease D [Translation, ribosomal structure and biogenesis]; |
73-216 |
1.13e-09 |
|
Ribonuclease D [Translation, ribosomal structure and biogenesis];
Pssm-ID: 440118 [Multi-domain] Cd Length: 365 Bit Score: 61.81 E-value: 1.13e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 73 LSDGDVVGFDME-------WPplynrgklgKVALIQLCVSEsKCYLFHVSSMSVFPqGLKMLLENKAVKK----AGVGIE 141
Cdd:COG0349 15 LAQAPAVAVDTEfmrertyYP---------RLCLIQLADGE-EVALIDPLAIGDLS-PLWELLADPAIVKvfhaAREDLE 83
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 142 GdqwkLLRDFDIKLKNFVElTDVANKKLKCTETWSLNSLVKHLLGKQLlkDKSIRCSNWSKFPLTEDQKLYAATD 216
Cdd:COG0349 84 I----LYHLFGILPKPLFD-TQIAAALLGYGDSVGYAALVEELLGVEL--DKSEQRSDWLRRPLSEEQLEYAAAD 151
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
568-705 |
2.08e-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: 57.41 E-value: 2.08e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 568 VAVMATGYGKSLCFQYPPVYV----GKIGLVISPLISLMEDQ---VLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVY 640
Cdd:cd00046 5 LITAPTGSGKTLAALLAALLLllkkGKKVLVLVPTKALALQTaerLRELFGPGIRVAVLVGGSSAEEREKNKLGDADIII 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 641 VTPEYCSGNMGLLQQLEADiGITLIAVDEAHCISEWGHDFRDSfrKLGSLKTALPMVPIVALTAT 705
Cdd:cd00046 85 ATPDMLLNLLLREDRLFLK-DLKLIIVDEAHALLIDSRGALIL--DLAVRKAGLKNAQVILLSAT 146
|
|
| PLN00206 |
PLN00206 |
DEAD-box ATP-dependent RNA helicase; Provisional |
551-859 |
2.84e-09 |
|
DEAD-box ATP-dependent RNA helicase; Provisional
Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 61.34 E-value: 2.84e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 551 PVQWKVIHSVLEERrdNVAVMA-TGYGKSLCF-------------QYPPVYVGKIGLVISP---LISLMEDQVlQLKMSN 613
Cdd:PLN00206 146 PIQMQAIPAALSGR--SLLVSAdTGSGKTASFlvpiisrcctirsGHPSEQRNPLAMVLTPtreLCVQVEDQA-KVLGKG 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 614 IP---ACFLGSAQSENVLTDIKLGKYRIVYvTPeycsGNM-GLLQQLEADI-GITLIAVDEAHCISEWGhdFRDsfrKLG 688
Cdd:PLN00206 223 LPfktALVVGGDAMPQQLYRIQQGVELIVG-TP----GRLiDLLSKHDIELdNVSVLVLDEVDCMLERG--FRD---QVM 292
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 689 SLKTALPMVPIVALTATASSSIrEDIVRCLnLRNPQ-ITCTGFDRPN-------LYLEVRRKTGNILQdlqpfLVKTSSH 760
Cdd:PLN00206 293 QIFQALSQPQVLLFSATVSPEV-EKFASSL-AKDIIlISIGNPNRPNkavkqlaIWVETKQKKQKLFD-----ILKSKQH 365
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 761 weFEGPTIIYCPSRKMTQQVTGELRKLN-LSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHY 839
Cdd:PLN00206 366 --FKPPAVVFVSSRLGADLLANAITVVTgLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIF 443
|
330 340
....*....|....*....|
gi 110735439 840 GAPKDMESYYQEIGRAGRDG 859
Cdd:PLN00206 444 DMPNTIKEYIHQIGRASRMG 463
|
|
| Egl_like_exo |
cd06148 |
DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins; The ... |
77-217 |
2.87e-09 |
|
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: 58.45 E-value: 2.87e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 77 DVVGFDMEWpplYNRGKLGKVALIQLCVSESKCYLFHVSSM--SVFPQGLKMLLENKAVKKAGVGIEGDQWKLLRDFDIK 154
Cdd:cd06148 11 KVIGLDCEG---VNLGRKGKLCLVQIATRTGQIYLFDILKLgsIVFINGLKDILESKKILKVIHDCRRDSDALYHQYGIK 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 155 LKNFVElTDVANKKLKCTETW--------SLNSLVKHLLG----------KQLLKDksirCSNWSKFPLTEDQKLYAATD 216
Cdd:cd06148 88 LNNVFD-TQVADALLQEQETGgfnpdrviSLVQLLDKYLYisislkedvkKLMRED----PKFWALRPLTEDMIRYAALD 162
|
.
gi 110735439 217 A 217
Cdd:cd06148 163 V 163
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
767-859 |
6.67e-09 |
|
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: 60.62 E-value: 6.67e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 TIIYCPSRKMTQQVTGELRKLNLSCG------TYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYG 840
Cdd:COG1205 291 TLVFTRSRRGAELLARYARRALREPDladrvaAYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGGLDAVVLAG 370
|
90
....*....|....*....
gi 110735439 841 APKDMESYYQEIGRAGRDG 859
Cdd:COG1205 371 YPGTRASFWQQAGRAGRRG 389
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
767-860 |
3.21e-08 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 57.85 E-value: 3.21e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 TIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIAT-IAfGMGINKADIRQVIHYGAPKDM 845
Cdd:COG0513 244 AIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATdVA-ARGIDIDDVSHVINYDLPEDP 322
|
90
....*....|....*...
gi 110735439 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 |
3.21e-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: 51.52 E-value: 3.21e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 110735439 870 PADINLNRHLLT-EIRNEKFRLYKLKMMAKMEKY-LHSSRCRRQIILSHFEDKqvqkaslgiMGTEKC--CDNCR 940
Cdd:pfam16124 1 YQDVVRLRFLIEqSEADEERKEVELQKLQAMVAYcENTTDCRRKQLLRYFGEE---------FDSEPCgnCDNCL 66
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
800-859 |
8.90e-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: 50.78 E-value: 8.90e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 800 FSTRKDiHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDG 859
Cdd:cd18785 9 FTNSIE-HAEEIASSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGG 67
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
768-883 |
1.17e-07 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 55.99 E-value: 1.17e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 768 IIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMES 847
Cdd:PTZ00424 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPEN 350
|
90 100 110 120
....*....|....*....|....*....|....*....|
gi 110735439 848 YYQEIGRAGRDGLQSSCHVLWAPADI----NLNRHLLTEI 883
Cdd:PTZ00424 351 YIHRIGRSGRFGRKGVAINFVTPDDIeqlkEIERHYNTQI 390
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
767-857 |
2.16e-07 |
|
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: 51.88 E-value: 2.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 TIIYCPSRKMTQQVTGELRKL------NLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYG 840
Cdd:cd18796 41 TLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDVDLVIQIG 120
|
90
....*....|....*..
gi 110735439 841 APKDMESYYQEIGRAGR 857
Cdd:cd18796 121 SPKSVARLLQRLGRSGH 137
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
763-857 |
1.28e-06 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 52.97 E-value: 1.28e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 763 FEGPTIIYCPSRKMTQQVTgelRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGInkaDI--RQVIhyg 840
Cdd:COG1202 426 YRGQTIIFTNSRRRCHEIA---RALGYKAAPYHAGLDYGERKKVERRFADQELAAVVTTAALAAGV---DFpaSQVI--- 496
|
90 100
....*....|....*....|....*....
gi 110735439 841 apkdMES------------YYQEIGRAGR 857
Cdd:COG1202 497 ----FDSlamgiewlsvqeFHQMLGRAGR 521
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
156-480 |
1.18e-05 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 50.17 E-value: 1.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 156 KNFVELTDVANKKLKCTETW-----SLNSLVKHLLGKQLLKDKSIRCSNWSKFPLTEDQKLYAATDAYagfIIYRNLEIL 230
Cdd:PTZ00341 780 ANKEELANENNKLMNILKEYfgnneQINSITYNFENINLNEDNENGSKKILDLNHKDQKEIFEEIISY---IVDISLSDI 856
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 231 DDTVQRFAinkeeEILLSDMN---KQLTSISEEVMDLAKHL-PHAFSKLENPRRVSILLKDISENLYSlrrmiiGSTNIE 306
Cdd:PTZ00341 857 ENTAKNAA-----EQILSDEGldeKKLKKRAESLKKLANAIeKYAGGGKKDKKAKKKDAKDLSGNIAH------EINLIN 925
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 307 TELRPSNNLNLLSFEDSTTGGVQQ--KQIREHEVLIHVEDETWDPTLDHLAKHDGEDVLGNKVERKEDGFEDGVEDN--- 381
Cdd:PTZ00341 926 KELKNQNENVPEHLKEHAEANIEEdaEENVEEDAEENVEENVEENVEENVEENVEENVEENVEENVEENVEENVEENiee 1005
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 382 ----KLKENMERACLMSLDITEHELQILEQQSQEEYLSDIAYKSTEHLSPNDNENDTSYVIESDEDLEMEMLKHLSPNDN 457
Cdd:PTZ00341 1006 nveeNVEENIEENVEEYDEENVEEVEENVEEYDEENVEEIEENAEENVEENIEENIEEYDEENVEEIEENIEENIEENVE 1085
|
330 340
....*....|....*....|...
gi 110735439 458 ENDTSYVIESDEDLEMEMLKSLE 480
Cdd:PTZ00341 1086 ENVEENVEEIEENVEENVEENAE 1108
|
|
| SF2_C_SNF |
cd18793 |
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ... |
768-866 |
1.60e-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: 1.60e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 768 IIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCV--IATIAFGMGIN--KADIrqVIHYGAP- 842
Cdd:cd18793 31 LIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVflLSTKAGGVGLNltAANR--VILYDPWw 108
|
90 100
....*....|....*....|....*..
gi 110735439 843 ---KDMesyyQEIGRAGRDGLQSSCHV 866
Cdd:cd18793 109 npaVEE----QAIDRAHRIGQKKPVVV 131
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
548-707 |
5.54e-05 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 45.33 E-value: 5.54e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 548 SFKPVQWKVIHSVLEERrDNVAVMA-TGYGKSLCFQYPPV-----YVGKIgLVISPLISLMeDQV---LQLKMSNIP--- 615
Cdd:cd17921 1 LLNPIQREALRALYLSG-DSVLVSApTSSGKTLIAELAILralatSGGKA-VYIAPTRALV-NQKeadLRERFGPLGknv 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 616 ACFLGSAQSenvlTDIKLGKYRIVYVTPEYCSgnmGLLQQLEADIG--ITLIAVDEAHCISewghdfrDSFRK------L 687
Cdd:cd17921 78 GLLTGDPSV----NKLLLAEADILVATPEKLD---LLLRNGGERLIqdVRLVVVDEAHLIG-------DGERGvvlellL 143
|
170 180
....*....|....*....|
gi 110735439 688 GSLKTALPMVPIVALTATAS 707
Cdd:cd17921 144 SRLLRINKNARFVGLSATLP 163
|
|
| PTZ00110 |
PTZ00110 |
helicase; Provisional |
737-887 |
4.06e-04 |
|
helicase; Provisional
Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 44.76 E-value: 4.06e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 737 LEVRRKTGNILQDLQPFLVKTSShwefegpTIIYCPSRKMTQQVTGELRKLNLSCGTYHAgmsfsTRKDIHHRFVRDEIQ 816
Cdd:PTZ00110 357 VEEHEKRGKLKMLLQRIMRDGDK-------ILIFVETKKGADFLTKELRLDGWPALCIHG-----DKKQEERTWVLNEFK 424
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 110735439 817 C-----VIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEK 887
Cdd:PTZ00110 425 TgkspiMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAK 500
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
793-856 |
4.49e-04 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 44.92 E-value: 4.49e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 110735439 793 TYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAG 856
Cdd:PRK09751 306 SHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGRAG 369
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
551-705 |
1.54e-03 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 40.73 E-value: 1.54e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 551 PVQWKVIHSVLEERRDN----VAVMATGYGKS-----LCFQYPPVYVGKIGLVISPLISL---MEDQVLQLKMSNIPACF 618
Cdd:pfam04851 6 PYQIEAIENLLESIKNGqkrgLIVMATGSGKTltaakLIARLFKKGPIKKVLFLVPRKDLleqALEEFKKFLPNYVEIGE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 619 LGSAQSEnvltDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHcisewgHDFRDSFRKlgsLKTALPMVP 698
Cdd:pfam04851 86 IISGDKK----DESVDDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAH------RSGASSYRN---ILEYFKPAF 152
|
....*..
gi 110735439 699 IVALTAT 705
Cdd:pfam04851 153 LLGLTAT 159
|
|
| PRK11634 |
PRK11634 |
ATP-dependent RNA helicase DeaD; Provisional |
767-859 |
2.06e-03 |
|
ATP-dependent RNA helicase DeaD; Provisional
Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 42.53 E-value: 2.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 767 TIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDME 846
Cdd:PRK11634 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSE 327
|
90
....*....|...
gi 110735439 847 SYYQEIGRAGRDG 859
Cdd:PRK11634 328 SYVHRIGRTGRAG 340
|
|
| PTZ00341 |
PTZ00341 |
Ring-infected erythrocyte surface antigen; Provisional |
329-501 |
3.16e-03 |
|
Ring-infected erythrocyte surface antigen; Provisional
Pssm-ID: 173534 [Multi-domain] Cd Length: 1136 Bit Score: 42.08 E-value: 3.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 329 QQKQIREHEVLIHVEDETWDPTLDHLAKHDGEDVLGNKVERKEDGFEDGVEDNkLKENMERaclmslDITEHELQILEQQ 408
Cdd:PTZ00341 926 KELKNQNENVPEHLKEHAEANIEEDAEENVEEDAEENVEENVEENVEENVEEN-VEENVEE------NVEENVEENVEEN 998
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 409 SQEEYLSDIAYKSTEHLSPNDNENDTSYVIESDEDLE---MEMLKHLSPNDNENDTSYVIESDEDLEMEMLKSL-----E 480
Cdd:PTZ00341 999 VEENIEENVEENVEENIEENVEEYDEENVEEVEENVEeydEENVEEIEENAEENVEENIEENIEEYDEENVEEIeenieE 1078
|
170 180
....*....|....*....|.
gi 110735439 481 NLNSGTVEPTHSKCLKMERNL 501
Cdd:PTZ00341 1079 NIEENVEENVEENVEEIEENV 1099
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
548-707 |
4.16e-03 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 39.62 E-value: 4.16e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 548 SFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVY---VGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQS 624
Cdd:cd18028 1 ELYPPQAEAVRAGLLKGENLLISIPTASGKTLIAEMAMVNtllEGGKALYLVPLRALASEKYEEFKKLEEIGLKVGISTG 80
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110735439 625 ENVLTDIKLGKYRIVYVTPEYCSgnmGLLQQLEADIG-ITLIAVDEAHCISEWGHDFRDSFrKLGSLKTALPMVPIVALT 703
Cdd:cd18028 81 DYDEDDEWLGDYDIIVATYEKFD---SLLRHSPSWLRdVGVVVVDEIHLISDEERGPTLES-IVARLRRLNPNTQIIGLS 156
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....
gi 110735439 704 ATAS 707
Cdd:cd18028 157 ATIG 160
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