|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
476-709 |
2.12e-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: 513.33 E-value: 2.12e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 476 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 555
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 556 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 635
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568955322 636 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 709
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
116-267 |
1.41e-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: 1.41e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 116 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 195
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 196 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 267
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
365-906 |
7.76e-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: 297.11 E-value: 7.76e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 365 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 444
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 445 GyiyhKLLGHEVEDVVIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 523
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 524 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 572
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 573 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 633
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 634 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 712
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 713 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 781
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 782 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 861
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 568955322 862 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLSYYKEQKALVE 906
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; ... |
117-237 |
7.81e-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: 7.81e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 117 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 196
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 568955322 197 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 237
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
710-899 |
8.12e-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: 261.78 E-value: 8.12e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 710 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 789
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 790 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 868
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 568955322 869 LTRARYGVIIVGNPKALSKQPLWNHLLSYYK 899
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 ... |
686-883 |
2.13e-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: 2.13e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 686 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 763
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 764 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 842
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 568955322 843 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 883
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
233-901 |
2.02e-71 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 255.44 E-value: 2.02e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 233 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 312
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 313 KKLKESQTQDNITVRWDLGLnKKRIAFFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 392
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 393 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVVIKCQLPKRFTAQ 472
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 473 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 552
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 553 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 631
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 632 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 707
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 708 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 787
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 788 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 863
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 568955322 864 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLSYYKEQ 901
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 ... |
480-677 |
5.76e-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: 5.76e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 480 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 545
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 546 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 583
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 584 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 662
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 568955322 663 LILVGDHCQLGPVVM 677
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
433-887 |
9.00e-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: 81.56 E-value: 9.00e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 433 LKTFAVDETSVSGYIyHKLLGHEVEDVVIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 511
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 512 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 591
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 592 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 661
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 662 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 740
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 741 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 786
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 787 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 843
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 568955322 844 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 887
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
481-675 |
1.43e-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: 55.54 E-value: 1.43e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 481 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSRE 556
Cdd:TIGR01447 149 RKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEAL 225
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 557 AIDSPVSFLALHnqirnmdsmpelqKLQQLKdetgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqf 636
Cdd:TIGR01447 226 IAALPSEAVTIH-------------RLLGIK--------PDTKRFRHHERNP-----LPLDV------------------ 261
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 568955322 637 rsILIDESTQATEP--ECMVPVVLGAKQLILVGDHCQLGPV 675
Cdd:TIGR01447 262 --LVVDEASMVDLPlmAKLLKALPPNTKLILLGDKNQLPSV 300
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
481-540 |
3.82e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.82e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 481 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 540
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 ... |
476-709 |
2.12e-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: 513.33 E-value: 2.12e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 476 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 555
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 556 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 635
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568955322 636 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 709
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
116-267 |
1.41e-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: 1.41e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 116 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 195
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 196 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 267
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
365-906 |
7.76e-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: 297.11 E-value: 7.76e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 365 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 444
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 445 GyiyhKLLGHEVEDVVIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 523
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 524 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 572
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 573 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 633
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 634 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 712
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 713 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 781
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 782 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 861
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 568955322 862 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLSYYKEQKALVE 906
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; ... |
117-237 |
7.81e-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: 7.81e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 117 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 196
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 568955322 197 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 237
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
710-899 |
8.12e-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: 261.78 E-value: 8.12e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 710 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 789
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 790 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 868
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 568955322 869 LTRARYGVIIVGNPKALSKQPLWNHLLSYYK 899
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 ... |
686-883 |
2.13e-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: 2.13e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 686 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 763
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 764 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 842
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 568955322 843 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 883
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
233-901 |
2.02e-71 |
|
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 255.44 E-value: 2.02e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 233 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 312
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 313 KKLKESQTQDNITVRWDLGLnKKRIAFFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 392
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 393 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVVIKCQLPKRFTAQ 472
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 473 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 552
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 553 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 631
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 632 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 707
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 708 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 787
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 788 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 863
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 568955322 864 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLSYYKEQ 901
Cdd:COG1112 779 RLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
|
|
| DEXXQc_SMUBP2 |
cd18044 |
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
477-709 |
9.87e-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: 182.81 E-value: 9.87e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLcaksr 555
Cdd:cd18044 2 LNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRI----- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 556 eaidspvsflalHNQIRNMDSMpelqklqqlkdetgelssadekryraLKRTAERelLMNADVICCTCVGAGDPRLAK-M 634
Cdd:cd18044 76 ------------GHPARLLESV--------------------------LDHSLDA--LVAAQVVLATNTGAGSRQLLPnE 115
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568955322 635 QFRSILIDESTQATEPECMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPI--RLQVQYR 709
Cdd:cd18044 116 LFDVVVIDEAAQALEASCWIPL-LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
|
|
| 1B_UPF1-like |
cd21407 |
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
320-419 |
3.43e-50 |
|
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: 171.56 E-value: 3.43e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 320 TQDNITVRWDLGLNKKRIAFFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAI 399
Cdd:cd21407 1 TQENISVRWDVGLNKKRLAYFTLPKLDES----------ELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVAL 70
|
90 100
....*....|....*....|
gi 568955322 400 ELRSSVGAPVEVTHNFQVDF 419
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 ... |
477-709 |
9.38e-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: 9.38e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA------------RQGNGPVLVCAPSNIAVDQLTEKIHQT- 543
Cdd:cd18040 2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAkqnreiqsvsgeGDGGPCVLYCGPSNKSVDVVAELLLKVp 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 544 GLKVVRLCAKSREAIDSPV---------------------SFLALHNQIRNmDSMPELQKLQQ----LKDETGELSSADE 598
Cdd:cd18040 82 GLKILRVYSEQIETTEYPIpneprhpnkksereskpnselSSITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 599 KRYRALKRTAERELLMNADVICCTCVGAGDPRL-AKMQFRSILIDESTQATEPECMVPVVLG--AKQLILVGDHCQLGPV 675
Cdd:cd18040 161 KTYKILIWEARFEELETVDVILCTCSEAASQKMrTHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRPV 240
|
250 260 270
....*....|....*....|....*....|....
gi 568955322 676 VMCKKAAKAGLSQSLFERLVVlgiRPIRLQVQYR 709
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 ... |
480-677 |
5.76e-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: 5.76e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 480 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 545
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 546 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 583
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 584 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 662
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 568955322 663 LILVGDHCQLGPVVM 677
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
477-694 |
1.42e-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: 1.42e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDQLTEKIHQTGLK---VV 548
Cdd:cd18038 2 LNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 549 RLCAKSREAIDSPvsflalhnqirnmdsmPELQKLQQLKDETGelssadekryralKRTAERELLMNADVICCTCVGAGd 628
Cdd:cd18038 82 RLNAPSRDRASVP----------------PELLPYCNSKAEGT-------------FRLPSLEELKKYRIVVCTLMTAG- 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 568955322 629 pRLAKMQ-----FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 694
Cdd:cd18038 132 -RLVQAGvpnghFTHIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
|
|
| UPF1_1B_dom |
pfam18141 |
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ... |
319-420 |
1.02e-43 |
|
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: 153.24 E-value: 1.02e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 319 QTQDNITVRWDLGLNKKRIAFFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIA 398
Cdd:pfam18141 1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSG----------EMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVT 70
|
90 100
....*....|....*....|...
gi 568955322 399 IELR-SSVGAPVEVTHNFQVDFV 420
Cdd:pfam18141 71 LELRsSSNNPPTDLTHGFTVEFV 93
|
|
| DEXXQc_SETX |
cd18042 |
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
477-709 |
7.60e-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: 155.83 E-value: 7.60e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSATIVYHL-----------------ARQGNGP-------VLVCAPSN 530
Cdd:cd18042 1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrKLQRNLNnkkkknrILVCAPSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 531 IAVDQLTEKIHQTGL----------KVVRLcaksreaidspvsflalhnqirnmdsmpelqklqqlkdetGelssadekr 600
Cdd:cd18042 81 AAVDEIVLRLLSEGFldgdgrsykpNVVRV----------------------------------------G--------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 601 yralKRTAERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMC 678
Cdd:cd18042 112 ----RQELRASILNEADIVCTTLSSSGSDLLESLPrgFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFS 187
|
250 260 270
....*....|....*....|....*....|.
gi 568955322 679 KKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 709
Cdd:cd18042 188 KVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
|
|
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
477-709 |
2.98e-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: 2.98e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 555
Cdd:cd18041 2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 556 eaIDSPVSFLALHNQIRNMDSMPELQklqqlkdetgelssadekryralkrtaerELLMNADVICCTCVGAGDPRLAKMQ 635
Cdd:cd18041 81 --IHPDVQEFTLEAILKSCKSVEELE-----------------------------SKYESVSVVATTCLGINHPIFRRRT 129
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 568955322 636 FRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYR 709
Cdd:cd18041 130 FDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVVqLTIQYR 203
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
476-695 |
2.85e-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: 2.85e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 476 DLNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----TIVYHLARQgngPVLVCAPSNIAVDQLTEKIHQTGLKV 547
Cdd:cd18078 1 DLNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLPRS---RILVCAPSNSAADLVTSRLHESKVLK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 548 VRLCAKsreaidspvsfLALHNQIRNMDSmpelqklqqlkdetgelssadEKRYRALKRTAERELLMNADVICCTCVGAG 627
Cdd:cd18078 78 PGDMVR-----------LNAVNRFESTVI---------------------DARKLYCRLGEDLSKASRHRIVISTCSTAG 125
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 568955322 628 dpRLAKMQFRS-----ILIDESTQATEPECMVPVVL---GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLV 695
Cdd:cd18078 126 --LLYQMGLPVghfthVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLM 199
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
493-708 |
1.70e-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: 1.70e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 493 LSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLtekihqtglkvvrlcaksreaidspvsflalhn 569
Cdd:cd17914 1 LSLIQGPPGTGKTRVLVKIVAALMQNkngEPGRILLVTPTNKAAAQL--------------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 570 qirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprlakmqfRSILIDESTQATE 649
Cdd:cd17914 48 -------------------------------------------------------------------DNILVDEAAQILE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568955322 650 PECM--VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 708
Cdd:cd17914 61 PETSrlIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
493-709 |
1.61e-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: 1.61e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 493 LSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDqltekihqtglkvvrlcaksreaidspvsflalhnqi 571
Cdd:cd17934 1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGKrVLVTAQSNVAVD------------------------------------- 43
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 572 rnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvgagdprlakmqfrsiLIDESTQATEPE 651
Cdd:cd17934 44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 652 CMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAG----LSQSLFERLVVLGIRPIRLQVQYR 709
Cdd:cd17934 61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
|
|
| 1B_UPF1_nv_SF1_Hel-like |
cd21344 |
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ... |
322-418 |
9.56e-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: 113.18 E-value: 9.56e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 322 DNITVRWDLGLNKKRIAFFTLPKTDSgnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIEL 401
Cdd:cd21344 1 LIITVRWRLALNDFRGAYFSLEKGKS-----------QCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALEL 69
|
90
....*....|....*..
gi 568955322 402 RSSVGAPVEVTHNFQVD 418
Cdd:cd21344 70 KGSTTYPLTVTHIFVLT 86
|
|
| EEXXEc_NFX1 |
cd17936 |
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
477-708 |
6.17e-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: 6.17e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA----TIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGL-KVVRLc 551
Cdd:cd17936 2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRL- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 552 aksreaidspvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVICCTCVGAGDPR- 630
Cdd:cd17936 81 ---------------------------------------------------------------GARVIGMTTTGAAKYRe 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 631 -LAKMQFRSILIDESTQATEPE---CMVPVVlgaKQLILVGDHCQLGPVVMCKK--AAKAGLSQSLFERLVVLGIRPIRL 704
Cdd:cd17936 98 lLQALGPKVVIVEEAAEVLEAHilaALTPST---EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTL 174
|
....
gi 568955322 705 QVQY 708
Cdd:cd17936 175 NVQR 178
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
795-880 |
4.56e-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: 4.56e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 795 QIGIITPYEGQRSYLVQYMQFSgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHqgigflnDPRRLNVALTRARY 874
Cdd:cd18786 12 KGVVLTPYHRDRAYLNQYLQGL-SLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83
|
....*.
gi 568955322 875 GVIIVG 880
Cdd:cd18786 84 RLVIYD 89
|
|
| EEXXQc_AQR |
cd17935 |
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
478-716 |
7.31e-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: 7.31e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 478 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLarQGNGP---VLVCAPSNIAVDQLTEKIhqtglkvvrlcaks 554
Cdd:cd17935 7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNL--YHNFPnqrTLIVTHSNQALNQLFEKI-------------- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 555 rEAIDSPvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaERELL---MNADVICCTCVGAGDPR- 630
Cdd:cd17935 71 -MALDID-----------------------------------------------ERHLLrlgHGAKIIAMTCTHAALKRg 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 631 -LAKMQFR--SILIDESTQATEPECMVPVVL--------GAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLG 698
Cdd:cd17935 103 eLVELGFKydNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182
|
250
....*....|....*...
gi 568955322 699 IRPIRLQVQYRMHPALSA 716
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 ... |
117-206 |
2.18e-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: 2.18e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 117 ACSYCGIHDpacVVYCNTS--KKWFCNgrgntsgSHIVNHLVRAKCKEVTLHKdgplgetVLECYNCGCRNVFLLGFipa 194
Cdd:cd21343 1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60
|
90
....*....|..
gi 568955322 195 kadSVVVLLCRQ 206
Cdd:cd21343 61 ---GGVSYRCVD 69
|
|
| DEXXQc_HELZ |
cd18077 |
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
477-694 |
2.85e-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: 79.07 E-value: 2.85e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHqtglkvvr 549
Cdd:cd18077 2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlYIKEYLH-------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 550 lcaKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELssadekryralkRTAERELLMNADVICCT-----CV 624
Cdd:cd18077 73 ---PYVETGNPRARPLRVYYRNRWVKTVHPVVQKYCLIDEHGTF------------RMPTREDVMRHRVVVVTlstsqYL 137
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 625 GAGDprLAKMQFRSILIDESTQATEPECMVPVVLGAK--QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 694
Cdd:cd18077 138 CQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
433-887 |
9.00e-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: 81.56 E-value: 9.00e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 433 LKTFAVDETSVSGYIyHKLLGHEVEDVVIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 511
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 512 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 591
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 592 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 661
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 662 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 740
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 741 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 786
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 787 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 843
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 568955322 844 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 887
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| DEXXQc_SF1 |
cd18043 |
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
478-677 |
6.62e-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: 6.62e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 478 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAvdqltekihqtgLKVVRLcaksrea 557
Cdd:cd18043 1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKR-VLFVSEKKAA------------LDVVRF------- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 558 idsPVSFLALHNQIRNMDsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprLAKMQFR 637
Cdd:cd18043 61 ---PCWIMSPLSVSQYLP-------------------------------------------------------LNRNLFD 82
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 568955322 638 SILIDESTQAtEPECMVPVVLGAKQLILVGDHCQLGPVVM 677
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. ... |
481-540 |
1.94e-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: 1.94e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 481 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLaRQGNGPVLVCAPSNIAVDQLTEKI 540
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 ... |
492-694 |
5.16e-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: 63.76 E-value: 5.16e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 492 PLsLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHQtglkvvRLCAKSREAIdsPVSFLALHNQ 570
Cdd:cd18076 25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADiYIREYFHP------YVDKGHPEAR--PLRIKATDRP 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 571 IRNMDsmPELQKLQQLKDEtgelssadekryRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEP 650
Cdd:cd18076 96 NAITD--PDTITYCCLTKD------------RQCFRLPTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEAAQMLEC 161
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 568955322 651 ECMVPVVLGA--KQLILVGDHCQLGPVVMCKKAAKAGlSQSLFERL 694
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 ... |
477-711 |
1.01e-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: 1.01e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVL--QRPLSLIQGPPGTGKTVTSATIVYHLARQGnGPVLVCAPSNIAVDQLtekihqtglkvvrlcaks 554
Cdd:pfam13604 2 LNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTALKALREAWEAAG-YRVIGLAPTGRAAKVL------------------ 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 555 REAIDSPVSFLAlhnqirnmdsmpelqklqqlkdetgelssadekryRALKRTAERELLMNADVicctcvgagdprlakm 634
Cdd:pfam13604 63 GEELGIPADTIA-----------------------------------KLLHRLGGRAGLDPGTL---------------- 91
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 635 qfrsILIDESTQATEPEcMVPVV-----LGAKqLILVGDHCQLGPVvmckkaaKAGlsqSLFERLVVLGIRPIRLQVQYR 709
Cdd:pfam13604 92 ----LIVDEAGMVGTRQ-MARLLklaedAGAR-VILVGDPRQLPSV-------EAG---GAFRDLLAAGIGTAELTEIVR 155
|
..
gi 568955322 710 MH 711
Cdd:pfam13604 156 QR 157
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
484-545 |
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 568955322 484 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSNIAVDQLTEKihqTGL 545
Cdd:pfam13245 4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSER---TGL 64
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
481-675 |
1.43e-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: 55.54 E-value: 1.43e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 481 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSRE 556
Cdd:TIGR01447 149 RKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEAL 225
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 557 AIDSPVSFLALHnqirnmdsmpelqKLQQLKdetgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqf 636
Cdd:TIGR01447 226 IAALPSEAVTIH-------------RLLGIK--------PDTKRFRHHERNP-----LPLDV------------------ 261
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 568955322 637 rsILIDESTQATEP--ECMVPVVLGAKQLILVGDHCQLGPV 675
Cdd:TIGR01447 262 --LVVDEASMVDLPlmAKLLKALPPNTKLILLGDKNQLPSV 300
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
477-551 |
2.88e-06 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 48.44 E-value: 2.88e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 477 LNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSATIVYHLARQGNG-PVLVCAPSNIAVDQLTEKIHQTGLKVVRL 550
Cdd:pfam04851 4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIkKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83
|
.
gi 568955322 551 C 551
Cdd:pfam04851 84 G 84
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
481-540 |
3.82e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.82e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 481 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 540
Cdd:smart00487 13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
495-542 |
1.63e-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: 1.63e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 568955322 495 LIQGPPGTGKTVTSATIVYHLARQgnGPVLVCAPSNIAVDQLTEKIHQ 542
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 ... |
827-874 |
2.75e-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: 2.75e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 568955322 827 VEIASVDAFQG---REKDFIILSCVRanehqgigflNDPRRLNVALTRARY 874
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 ... |
481-606 |
6.98e-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: 6.98e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 481 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN-GPVLVCAPSNIAVDQLTEKI----HQTGLKVVRLCAKSR 555
Cdd:cd18013 5 QKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDFtRRVLVIAPLRVARSTWPDEVekwnHLRNLTVSVAVGTER 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 568955322 556 E---AIDSPVSFLalhnqIRNMDSMPELQKLQQLK--------DETGELSSADEKRYRALKR 606
Cdd:cd18013 85 QrskAANTPADLY-----VINRENLKWLVNKSGDPwpfdmvviDELSSFKSPRSKRFKALRK 141
|
|
| gammaCoV_Nsp13-helicase |
cd21720 |
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ... |
827-879 |
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 568955322 827 VEIASVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 879
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 ... |
481-561 |
2.44e-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: 2.44e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568955322 481 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLkVVRLCAKS 554
Cdd:pfam13191 8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86
|
....*..
gi 568955322 555 REAIDSP 561
Cdd:pfam13191 87 ESSLLEA 93
|
|
| deltaCoV_Nsp13-helicase |
cd21721 |
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ... |
831-879 |
6.11e-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: 6.11e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 568955322 831 SVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 879
Cdd:cd21721 283 TVDSSQGSEYDYVIF-CVTTDSAHALNM----SRLNVALTRAKIGILVV 326
|
|
| |
