|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
481-714 |
1.52e-175 |
|
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350797 [Multi-domain] Cd Length: 234 Bit Score: 513.72 E-value: 1.52e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 481 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 560
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 561 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 640
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 662033888 641 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 714
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
121-272 |
1.54e-116 |
|
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD).
Pssm-ID: 401391 Cd Length: 152 Bit Score: 356.56 E-value: 1.54e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 121 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 200
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 201 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 272
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
370-911 |
1.11e-88 |
|
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 299.42 E-value: 1.11e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 370 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 449
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 450 GyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 528
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 529 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 577
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 578 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 638
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 639 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 717
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 718 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 786
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 787 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 866
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 662033888 867 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 911
Cdd:TIGR00376 589 LRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
|
|
| ZBD_UPF1-like |
cd21400 |
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ... |
122-242 |
8.17e-85 |
|
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core.
Pssm-ID: 439167 Cd Length: 120 Bit Score: 269.89 E-value: 8.17e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 122 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 201
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 662033888 202 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 242
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
715-904 |
4.81e-81 |
|
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 262.17 E-value: 4.81e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 715 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 794
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 795 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 873
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 662033888 874 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 904
Cdd:cd18808 154 LTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
691-888 |
2.21e-79 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 463780 [Multi-domain] Cd Length: 196 Bit Score: 258.25 E-value: 2.21e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 691 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 768
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 769 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 847
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 662033888 848 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 888
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
238-906 |
9.14e-72 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 256.21 E-value: 9.14e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 238 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 317
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 318 KKLKESQTQDNITVRWDLGLnKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 397
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 398 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQ 477
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 478 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 557
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 558 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 636
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 637 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 712
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 713 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 792
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 793 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 868
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 662033888 869 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLNYYKEQ 906
Cdd:COG1112 779 RLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
485-682 |
6.08e-49 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 174.45 E-value: 6.08e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 485 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 550
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 551 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 588
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 589 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 667
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 662033888 668 LILVGDHCQLGPVVM 682
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
438-892 |
8.44e-16 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 81.95 E-value: 8.44e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 438 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 516
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 517 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 596
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 597 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 666
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 667 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 745
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 746 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 791
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 792 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 848
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 662033888 849 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 892
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
448-680 |
1.03e-07 |
|
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 55.92 E-value: 1.03e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 448 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 516
Cdd:TIGR01447 100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 517 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 592
Cdd:TIGR01447 180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 593 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 670
Cdd:TIGR01447 244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290
|
250
....*....|
gi 662033888 671 VGDHCQLGPV 680
Cdd:TIGR01447 291 LGDKNQLPSV 300
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
486-545 |
3.83e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.83e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 486 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 545
Cdd:smart00487 13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
481-714 |
1.52e-175 |
|
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350797 [Multi-domain] Cd Length: 234 Bit Score: 513.72 E-value: 1.52e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 481 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 560
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 561 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 640
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 662033888 641 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 714
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
121-272 |
1.54e-116 |
|
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD).
Pssm-ID: 401391 Cd Length: 152 Bit Score: 356.56 E-value: 1.54e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 121 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 200
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 201 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 272
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
370-911 |
1.11e-88 |
|
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273041 [Multi-domain] Cd Length: 636 Bit Score: 299.42 E-value: 1.11e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 370 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 449
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 450 GyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 528
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 529 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 577
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 578 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 638
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 639 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 717
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 718 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 786
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 787 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 866
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 662033888 867 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 911
Cdd:TIGR00376 589 LRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
|
|
| ZBD_UPF1-like |
cd21400 |
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ... |
122-242 |
8.17e-85 |
|
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core.
Pssm-ID: 439167 Cd Length: 120 Bit Score: 269.89 E-value: 8.17e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 122 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 201
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 662033888 202 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 242
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
715-904 |
4.81e-81 |
|
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350195 [Multi-domain] Cd Length: 184 Bit Score: 262.17 E-value: 4.81e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 715 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 794
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 795 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 873
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 662033888 874 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 904
Cdd:cd18808 154 LTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
|
|
| AAA_12 |
pfam13087 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
691-888 |
2.21e-79 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 463780 [Multi-domain] Cd Length: 196 Bit Score: 258.25 E-value: 2.21e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 691 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 768
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 769 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 847
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 662033888 848 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 888
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
238-906 |
9.14e-72 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 256.21 E-value: 9.14e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 238 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 317
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 318 KKLKESQTQDNITVRWDLGLnKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 397
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 398 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQ 477
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 478 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 557
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 558 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 636
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 637 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 712
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 713 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 792
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 793 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 868
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 662033888 869 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLNYYKEQ 906
Cdd:COG1112 779 RLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
|
|
| DEXXQc_SMUBP2 |
cd18044 |
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
482-714 |
8.02e-53 |
|
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350802 [Multi-domain] Cd Length: 191 Bit Score: 183.19 E-value: 8.02e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLcaksr 560
Cdd:cd18044 2 LNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRI----- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 561 eaidspvsflalHNQIRNMDSMpelqklqqlkdetgelssadekryraLKRTAERelLMNADVICCTCVGAGDPRLAK-M 639
Cdd:cd18044 76 ------------GHPARLLESV--------------------------LDHSLDA--LVAAQVVLATNTGAGSRQLLPnE 115
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 662033888 640 QFRSILIDESTQATEPECMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPI--RLQVQYR 714
Cdd:cd18044 116 LFDVVVIDEAAQALEASCWIPL-LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
|
|
| 1B_UPF1-like |
cd21407 |
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
325-424 |
6.75e-51 |
|
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). It participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids.
Pssm-ID: 394815 Cd Length: 90 Bit Score: 173.87 E-value: 6.75e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 325 TQDNITVRWDLGLNKKRIAYFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAI 404
Cdd:cd21407 1 TQENISVRWDVGLNKKRLAYFTLPKLDES----------ELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVAL 70
|
90 100
....*....|....*....|
gi 662033888 405 ELRSSVGAPVEVTHNFQVDF 424
Cdd:cd21407 71 ELRSSKNAPTEITTGFSVEF 90
|
|
| DEXXc_HELZ2-C |
cd18040 |
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
482-714 |
8.17e-50 |
|
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350798 [Multi-domain] Cd Length: 271 Bit Score: 177.72 E-value: 8.17e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA------------RQGNGPVLVCAPSNIAVDQLTEKIHQT- 548
Cdd:cd18040 2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAkqnreiqsvsgeGDGGPCVLYCGPSNKSVDVVAELLLKVp 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 549 GLKVVRLCAKSREAIDSPV---------------------SFLALHNQIRNmDSMPELQKLQQ----LKDETGELSSADE 603
Cdd:cd18040 82 GLKILRVYSEQIETTEYPIpneprhpnkksereskpnselSSITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 604 KRYRALKRTAERELLMNADVICCTCVGAGDPRL-AKMQFRSILIDESTQATEPECMVPVVLG--AKQLILVGDHCQLGPV 680
Cdd:cd18040 161 KTYKILIWEARFEELETVDVILCTCSEAASQKMrTHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRPV 240
|
250 260 270
....*....|....*....|....*....|....
gi 662033888 681 VMCKKAAKAGLSQSLFERLVVlgiRPIRLQVQYR 714
Cdd:cd18040 241 VQNKEAQKLGLGRSLFERYAE---KACMLDTQYR 271
|
|
| AAA_11 |
pfam13086 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
485-682 |
6.08e-49 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.
Pssm-ID: 404072 [Multi-domain] Cd Length: 248 Bit Score: 174.45 E-value: 6.08e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 485 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 550
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 551 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 588
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 589 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 667
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 662033888 668 LILVGDHCQLGPVVM 682
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
482-699 |
1.43e-47 |
|
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350796 [Multi-domain] Cd Length: 229 Bit Score: 169.72 E-value: 1.43e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDQLTEKIHQTGLK---VV 553
Cdd:cd18038 2 LNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 554 RLCAKSREAIDSPvsflalhnqirnmdsmPELQKLQQLKDETGelssadekryralKRTAERELLMNADVICCTCVGAGd 633
Cdd:cd18038 82 RLNAPSRDRASVP----------------PELLPYCNSKAEGT-------------FRLPSLEELKKYRIVVCTLMTAG- 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 662033888 634 pRLAKMQ-----FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 699
Cdd:cd18038 132 -RLVQAGvpnghFTHIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
|
|
| UPF1_1B_dom |
pfam18141 |
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ... |
324-425 |
7.05e-44 |
|
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as a bridge between UPF1 and UPF3. UPF2 and UPF3 are non-enzymatic components of the complex that stimulate the activity of UPF1. UPF1 has a N-terminal cysteine/histidine-rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, followed by a helicase core that belongs to superfamily 1 (SF1). This entry represents 1B domain of UPF1 which has a regulatory role. It suffers conformational changes from an inhibitory state to a transition-state complex that modulate RNA binding.
Pssm-ID: 407973 Cd Length: 93 Bit Score: 154.01 E-value: 7.05e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 324 QTQDNITVRWDLGLNKKRIAYFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIA 403
Cdd:pfam18141 1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSG----------EMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVT 70
|
90 100
....*....|....*....|...
gi 662033888 404 IELR-SSVGAPVEVTHNFQVDFV 425
Cdd:pfam18141 71 LELRsSSNNPPTDLTHGFTVEFV 93
|
|
| DEXXQc_SETX |
cd18042 |
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
482-714 |
8.09e-43 |
|
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438712 [Multi-domain] Cd Length: 218 Bit Score: 155.45 E-value: 8.09e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSATIVYHL-----------------ARQGNGP-------VLVCAPSN 535
Cdd:cd18042 1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrKLQRNLNnkkkknrILVCAPSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 536 IAVDQLTEKIHQTGL----------KVVRLcaksreaidspvsflalhnqirnmdsmpelqklqqlkdetGelssadekr 605
Cdd:cd18042 81 AAVDEIVLRLLSEGFldgdgrsykpNVVRV----------------------------------------G--------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 606 yralKRTAERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMC 683
Cdd:cd18042 112 ----RQELRASILNEADIVCTTLSSSGSDLLESLPrgFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFS 187
|
250 260 270
....*....|....*....|....*....|.
gi 662033888 684 KKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 714
Cdd:cd18042 188 KVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
|
|
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
482-714 |
3.08e-39 |
|
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350799 [Multi-domain] Cd Length: 203 Bit Score: 144.69 E-value: 3.08e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 560
Cdd:cd18041 2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 561 eaIDSPVSFLALHNQIRNMDSMPELQklqqlkdetgelssadekryralkrtaerELLMNADVICCTCVGAGDPRLAKMQ 640
Cdd:cd18041 81 --IHPDVQEFTLEAILKSCKSVEELE-----------------------------SKYESVSVVATTCLGINHPIFRRRT 129
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 662033888 641 FRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYR 714
Cdd:cd18041 130 FDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVVqLTIQYR 203
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
481-700 |
2.86e-32 |
|
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350836 [Multi-domain] Cd Length: 230 Bit Score: 125.56 E-value: 2.86e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 481 DLNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----TIVYHLARQgngPVLVCAPSNIAVDQLTEKIHQTGLKV 552
Cdd:cd18078 1 DLNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLPRS---RILVCAPSNSAADLVTSRLHESKVLK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 553 VRLCAKsreaidspvsfLALHNQIRNMDSmpelqklqqlkdetgelssadEKRYRALKRTAERELLMNADVICCTCVGAG 632
Cdd:cd18078 78 PGDMVR-----------LNAVNRFESTVI---------------------DARKLYCRLGEDLSKASRHRIVISTCSTAG 125
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 662033888 633 dpRLAKMQFRS-----ILIDESTQATEPECMVPVVL---GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLV 700
Cdd:cd18078 126 --LLYQMGLPVghfthVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLM 199
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
498-713 |
1.71e-31 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438706 [Multi-domain] Cd Length: 121 Bit Score: 119.51 E-value: 1.71e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 498 LSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLtekihqtglkvvrlcaksreaidspvsflalhn 574
Cdd:cd17914 1 LSLIQGPPGTGKTRVLVKIVAALMQNkngEPGRILLVTPTNKAAAQL--------------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 575 qirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprlakmqfRSILIDESTQATE 654
Cdd:cd17914 48 -------------------------------------------------------------------DNILVDEAAQILE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 662033888 655 PECM--VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 713
Cdd:cd17914 61 PETSrlIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
|
|
| 1B_UPF1_nv_SF1_Hel-like |
cd21344 |
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ... |
327-423 |
1.52e-30 |
|
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), Equine arteritis virus (EAV) Nsp10, and eukaryotic UPF1 RNA helicase. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids.
Pssm-ID: 439170 Cd Length: 86 Bit Score: 115.49 E-value: 1.52e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 327 DNITVRWDLGLNKKRIAYFTLPKTDSgnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIEL 406
Cdd:cd21344 1 LIITVRWRLALNDFRGAYFSLEKGKS-----------QCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALEL 69
|
90
....*....|....*..
gi 662033888 407 RSSVGAPVEVTHNFQVD 423
Cdd:cd21344 70 KGSTTYPLTVTHIFVLT 86
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
498-714 |
1.62e-30 |
|
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 116.57 E-value: 1.62e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 498 LSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDqltekihqtglkvvrlcaksreaidspvsflalhnqi 576
Cdd:cd17934 1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGKrVLVTAQSNVAVD------------------------------------- 43
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 577 rnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvgagdprlakmqfrsiLIDESTQATEPE 656
Cdd:cd17934 44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 657 CMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAG----LSQSLFERLVVLGIRPIRLQVQYR 714
Cdd:cd17934 61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
|
|
| EEXXEc_NFX1 |
cd17936 |
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
482-713 |
6.20e-29 |
|
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350694 [Multi-domain] Cd Length: 178 Bit Score: 114.18 E-value: 6.20e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA----TIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGL-KVVRLc 556
Cdd:cd17936 2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRL- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 557 aksreaidspvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVICCTCVGAGDPR- 635
Cdd:cd17936 81 ---------------------------------------------------------------GARVIGMTTTGAAKYRe 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 636 -LAKMQFRSILIDESTQATEPE---CMVPVVlgaKQLILVGDHCQLGPVVMCKK--AAKAGLSQSLFERLVVLGIRPIRL 709
Cdd:cd17936 98 lLQALGPKVVIVEEAAEVLEAHilaALTPST---EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTL 174
|
....
gi 662033888 710 QVQY 713
Cdd:cd17936 175 NVQR 178
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
800-885 |
4.59e-26 |
|
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain] Cd Length: 89 Bit Score: 102.90 E-value: 4.59e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 800 QIGIITPYEGQRSYLVQYMQFSgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHqgigflnDPRRLNVALTRARY 879
Cdd:cd18786 12 KGVVLTPYHRDRAYLNQYLQGL-SLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83
|
....*.
gi 662033888 880 GVIIVG 885
Cdd:cd18786 84 RLVIYD 89
|
|
| EEXXQc_AQR |
cd17935 |
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
483-721 |
7.34e-21 |
|
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350693 [Multi-domain] Cd Length: 207 Bit Score: 92.10 E-value: 7.34e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 483 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLarQGNGP---VLVCAPSNIAVDQLTEKIhqtglkvvrlcaks 559
Cdd:cd17935 7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNL--YHNFPnqrTLIVTHSNQALNQLFEKI-------------- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 560 rEAIDSPvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaERELL---MNADVICCTCVGAGDPR- 635
Cdd:cd17935 71 -MALDID-----------------------------------------------ERHLLrlgHGAKIIAMTCTHAALKRg 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 636 -LAKMQFR--SILIDESTQATEPECMVPVVL--------GAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLG 703
Cdd:cd17935 103 eLVELGFKydNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182
|
250
....*....|....*...
gi 662033888 704 IRPIRLQVQYRMHPALSA 721
Cdd:cd17935 183 VPTVDLDAQGRARASISS 200
|
|
| ZBD_UPF1_nv_SF1_Hel-like |
cd21343 |
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ... |
122-211 |
2.19e-18 |
|
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands, and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10, as well as eukaryotic UPF1 helicase. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. UPF1, SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core.
Pssm-ID: 439166 Cd Length: 70 Bit Score: 80.23 E-value: 2.19e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 122 ACSYCGIHDpacVVYCNTS--KKWFCNgrgntsgSHIVNHLVRAKCKEVTLHKdgplgetVLECYNCGCRNVFLLGFipa 199
Cdd:cd21343 1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60
|
90
....*....|..
gi 662033888 200 kadSVVVLLCRQ 211
Cdd:cd21343 61 ---GGVSYRCVD 69
|
|
| DEXXQc_HELZ |
cd18077 |
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
482-699 |
2.71e-16 |
|
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350835 [Multi-domain] Cd Length: 226 Bit Score: 79.45 E-value: 2.71e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHqtglkvvr 554
Cdd:cd18077 2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlYIKEYLH-------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 555 lcaKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELssadekryralkRTAERELLMNADVICCT-----CV 629
Cdd:cd18077 73 ---PYVETGNPRARPLRVYYRNRWVKTVHPVVQKYCLIDEHGTF------------RMPTREDVMRHRVVVVTlstsqYL 137
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 630 GAGDprLAKMQFRSILIDESTQATEPECMVPVVLGAK--QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 699
Cdd:cd18077 138 CQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
438-892 |
8.44e-16 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 81.95 E-value: 8.44e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 438 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 516
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 517 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 596
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 597 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 666
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 667 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 745
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 746 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 791
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 792 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 848
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 662033888 849 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 892
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| DEXXQc_SF1 |
cd18043 |
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
483-682 |
6.65e-12 |
|
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350801 [Multi-domain] Cd Length: 127 Bit Score: 63.76 E-value: 6.65e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 483 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAvdqltekihqtgLKVVRLcaksrea 562
Cdd:cd18043 1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKR-VLFVSEKKAA------------LDVVRF------- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 563 idsPVSFLALHNQIRNMDsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprLAKMQFR 642
Cdd:cd18043 61 ---PCWIMSPLSVSQYLP-------------------------------------------------------LNRNLFD 82
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 662033888 643 SILIDESTQAtEPECMVPVVLGAKQLILVGDHCQLGPVVM 682
Cdd:cd18043 83 LVIFDEASQI-PIEEALPALFRGKQVVVVGDDKQLPPSIL 121
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
486-545 |
1.95e-11 |
|
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 63.34 E-value: 1.95e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 486 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLaRQGNGPVLVCAPSNIAVDQLTEKI 545
Cdd:cd17933 2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAAL-EAEGKRVVLAAPTGKAAKRLSEST 60
|
|
| DEXXQc_HELZ2-N |
cd18076 |
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ... |
497-699 |
4.72e-11 |
|
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350834 [Multi-domain] Cd Length: 230 Bit Score: 64.14 E-value: 4.72e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 497 PLsLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHQtglkvvRLCAKSREAIdsPVSFLALHNQ 575
Cdd:cd18076 25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADiYIREYFHP------YVDKGHPEAR--PLRIKATDRP 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 576 IRNMDsmPELQKLQQLKDEtgelssadekryRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEP 655
Cdd:cd18076 96 NAITD--PDTITYCCLTKD------------RQCFRLPTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEAAQMLEC 161
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 662033888 656 ECMVPVVLGA--KQLILVGDHCQLGPVVMCKKAAKAGlSQSLFERL 699
Cdd:cd18076 162 EALIPLSYAGpkTRVVLAGDHMQMTPKLFSVADYNRA-NHTLLNRL 206
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
482-716 |
1.02e-09 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 59.11 E-value: 1.02e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVL--QRPLSLIQGPPGTGKTVTSATIVYHLARQGnGPVLVCAPSNIAVDQLtekihqtglkvvrlcaks 559
Cdd:pfam13604 2 LNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTALKALREAWEAAG-YRVIGLAPTGRAAKVL------------------ 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 560 REAIDSPVSFLAlhnqirnmdsmpelqklqqlkdetgelssadekryRALKRTAERELLMNADVicctcvgagdprlakm 639
Cdd:pfam13604 63 GEELGIPADTIA-----------------------------------KLLHRLGGRAGLDPGTL---------------- 91
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 640 qfrsILIDESTQATEPEcMVPVV-----LGAKqLILVGDHCQLGPVvmckkaaKAGlsqSLFERLVVLGIRPIRLQVQYR 714
Cdd:pfam13604 92 ----LIVDEAGMVGTRQ-MARLLklaedAGAR-VILVGDPRQLPSV-------EAG---GAFRDLLAAGIGTAELTEIVR 155
|
..
gi 662033888 715 MH 716
Cdd:pfam13604 156 QR 157
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
489-550 |
1.13e-08 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 54.92 E-value: 1.13e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 662033888 489 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSNIAVDQLTEKihqTGL 550
Cdd:pfam13245 4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSER---TGL 64
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
448-680 |
1.03e-07 |
|
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 55.92 E-value: 1.03e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 448 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 516
Cdd:TIGR01447 100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 517 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 592
Cdd:TIGR01447 180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 593 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 670
Cdd:TIGR01447 244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290
|
250
....*....|
gi 662033888 671 VGDHCQLGPV 680
Cdd:TIGR01447 291 LGDKNQLPSV 300
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
482-556 |
2.89e-06 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 48.44 E-value: 2.89e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 482 LNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSATIVYHLARQGNG-PVLVCAPSNIAVDQLTEKIHQTGLKVVRL 555
Cdd:pfam04851 4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIkKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83
|
.
gi 662033888 556 C 556
Cdd:pfam04851 84 G 84
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
486-545 |
3.83e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.83e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 486 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 545
Cdd:smart00487 13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
500-547 |
1.64e-04 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 45.79 E-value: 1.64e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 662033888 500 LIQGPPGTGKTVTSATIVYHLARQgnGPVLVCAPSNIAVDQLTEKIHQ 547
Cdd:COG1061 104 LVVAPTGTGKTVLALALAAELLRG--KRVLVLVPRRELLEQWAEELRR 149
|
|
| DEAD-like_helicase_C |
cd09300 |
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ... |
832-879 |
2.77e-04 |
|
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved 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: 350171 [Multi-domain] Cd Length: 59 Bit Score: 39.84 E-value: 2.77e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 662033888 832 VEIASVDAFQG---REKDFIILSCVRanehqgigflNDPRRLNVALTRARY 879
Cdd:cd09300 8 VLIAVN*ALTGfdaPELNTIIVDKNL----------RSYRGLNQAFGRANR 48
|
|
| DEXQc_bact_SNF2 |
cd18013 |
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ... |
486-611 |
7.01e-04 |
|
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350771 [Multi-domain] Cd Length: 218 Bit Score: 42.34 E-value: 7.01e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 486 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN-GPVLVCAPSNIAVDQLTEKI----HQTGLKVVRLCAKSR 560
Cdd:cd18013 5 QKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDFtRRVLVIAPLRVARSTWPDEVekwnHLRNLTVSVAVGTER 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 662033888 561 E---AIDSPVSFLalhnqIRNMDSMPELQKLQQLK--------DETGELSSADEKRYRALKR 611
Cdd:cd18013 85 QrskAANTPADLY-----VINRENLKWLVNKSGDPwpfdmvviDELSSFKSPRSKRFKALRK 141
|
|
| gammaCoV_Nsp13-helicase |
cd21720 |
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ... |
832-884 |
1.67e-03 |
|
helicase domain of gammacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.
Pssm-ID: 409653 [Multi-domain] Cd Length: 343 Bit Score: 41.83 E-value: 1.67e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 662033888 832 VEIASVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 884
Cdd:cd21720 280 LNVQTVDSSQGSEYDYVIF-CVTADSQHALNI----NRFNVALTRAKRGILVV 327
|
|
| AAA_16 |
pfam13191 |
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ... |
486-566 |
2.36e-03 |
|
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.
Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 40.18 E-value: 2.36e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 662033888 486 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLkVVRLCAKS 559
Cdd:pfam13191 8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86
|
....*..
gi 662033888 560 REAIDSP 566
Cdd:pfam13191 87 ESSLLEA 93
|
|
| deltaCoV_Nsp13-helicase |
cd21721 |
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ... |
836-884 |
6.14e-03 |
|
helicase domain of deltacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from deltacoronavirus, including Bulbul coronavirus (CoV) HKU11 and Common moorhen CoV HKU21. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core.
Pssm-ID: 409654 [Multi-domain] Cd Length: 342 Bit Score: 40.29 E-value: 6.14e-03
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gi 662033888 836 SVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 884
Cdd:cd21721 283 TVDSSQGSEYDYVIF-CVTTDSAHALNM----SRLNVALTRAKIGILVV 326
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