|
Name |
Accession |
Description |
Interval |
E-value |
| DEXXQc_UPF1 |
cd18039 |
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ... |
482-715 |
1.49e-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: 1.49e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 482 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 561
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 562 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 641
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1570527538 642 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 715
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
122-273 |
1.56e-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: 1.56e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 122 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 201
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 202 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 273
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
371-912 |
1.13e-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: 1.13e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 371 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 450
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 451 GyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 529
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 530 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 578
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 579 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 639
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 640 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 718
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 719 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 787
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 788 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 867
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 1570527538 868 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 912
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; ... |
123-243 |
8.24e-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: 8.24e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 123 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 202
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1570527538 203 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 243
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
716-905 |
4.84e-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: 4.84e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 716 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 795
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 796 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 874
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 1570527538 875 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 905
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 ... |
692-889 |
2.23e-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: 2.23e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 692 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 769
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 770 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 848
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1570527538 849 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 889
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
239-907 |
9.21e-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: 9.21e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 239 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 318
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 319 KKLKESQTQDNITVRWDLGLnKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 398
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 399 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQ 478
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 479 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 558
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 559 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 637
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 638 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 713
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 714 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 793
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 794 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 869
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 1570527538 870 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLNYYKEQ 907
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 ... |
486-683 |
4.97e-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: 4.97e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 486 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 551
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 552 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 589
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 590 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 668
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 1570527538 669 LILVGDHCQLGPVVM 683
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
439-893 |
8.45e-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: 8.45e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 439 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 517
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 518 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 597
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 598 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 667
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 668 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 746
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 747 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 792
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 793 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 849
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 1570527538 850 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 893
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
449-681 |
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 1570527538 449 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 517
Cdd:TIGR01447 100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 518 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 593
Cdd:TIGR01447 180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 594 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 671
Cdd:TIGR01447 244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290
|
250
....*....|
gi 1570527538 672 VGDHCQLGPV 681
Cdd:TIGR01447 291 LGDKNQLPSV 300
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
487-546 |
3.84e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.84e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 487 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 546
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 ... |
482-715 |
1.49e-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: 1.49e-175
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 482 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 561
Cdd:cd18039 1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 562 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 641
Cdd:cd18039 81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1570527538 642 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 715
Cdd:cd18039 161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
|
|
| UPF1_Zn_bind |
pfam09416 |
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ... |
122-273 |
1.56e-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: 1.56e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 122 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 201
Cdd:pfam09416 1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 202 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 273
Cdd:pfam09416 81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
|
|
| TIGR00376 |
TIGR00376 |
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ... |
371-912 |
1.13e-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: 1.13e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 371 GDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVS 450
Cdd:TIGR00376 61 GDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEALRALTENHSRLL 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 451 GyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPV 529
Cdd:TIGR00376 134 E----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELIRQLVKRGL-RV 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 530 LVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSPVSFLALHNQIR 578
Cdd:TIGR00376 205 LVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEERNKKTKPSPQKR 284
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 579 NmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccTCVGAGDPRLAK 639
Cdd:TIGR00376 285 R--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---TNSMAGSEILNG 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 640 MQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRLQVQYRMHP 718
Cdd:TIGR00376 360 QYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTLNVQYRMNQ 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 719 ALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNRTEAANVEK 787
Cdd:TIGR00376 437 KIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNPGEAELVSE 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 788 ITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRANEHQGIGFLND 867
Cdd:TIGR00376 516 IIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKD 588
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 1570527538 868 PRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 912
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; ... |
123-243 |
8.24e-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: 8.24e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 123 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 202
Cdd:cd21400 1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 1570527538 203 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 243
Cdd:cd21400 81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
|
|
| SF1_C_Upf1 |
cd18808 |
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ... |
716-905 |
4.84e-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: 4.84e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 716 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 795
Cdd:cd18808 1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 796 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 874
Cdd:cd18808 78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153
|
170 180 190
....*....|....*....|....*....|.
gi 1570527538 875 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 905
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 ... |
692-889 |
2.23e-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: 2.23e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 692 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 769
Cdd:pfam13087 1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 770 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 848
Cdd:pfam13087 80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 1570527538 849 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 889
Cdd:pfam13087 156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
|
|
| DNA2 |
COG1112 |
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]; |
239-907 |
9.21e-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: 9.21e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 239 FLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLLRYEDAYQYQNIFGPLVKLEADYD 318
Cdd:COG1112 154 ALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALLALALEDELALLLLLLLLALLLLLALLLLLDALLLLLA 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 319 KKLKESQTQDNITVRWDLGLnKKRIAYFTLPKTDSGNEDLVIIWLRDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDN 398
Cdd:COG1112 234 ALALLALALLLALLLLLLAL-LLLAALALLRAALRLDLLAALELLAALSLALLALLAALALALLLLAALALLLALALAAL 312
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 399 YGDEIAIELRSSVGAPVEVTHNFQVDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQ 478
Cdd:COG1112 313 LALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELALLRLLAALLLALALLLLLALEELLLLALLRLLAEGLA 392
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 479 GLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCA 558
Cdd:COG1112 393 LLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAALLALLLLLAAALAALLALLLLLLLALAALLLLLAAA 472
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 559 KSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRL 637
Cdd:COG1112 473 AALLALALLESLLEELIEEHPEELEKLIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPL 551
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 638 AKMQFRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQ 713
Cdd:COG1112 552 GEGSFDLVIIDEASQATLAEALGALAR-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREH 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 714 YRMHPALSAFPSNIFYEGSLQNGVTAADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLL 793
Cdd:COG1112 631 YRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELL 701
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 794 KAGAKPDQIGIITPYEGQRSYLVQYMQfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPR 869
Cdd:COG1112 702 EDGPDGESIGVITPYRAQVALIRELLR---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPR 778
|
650 660 670 680
....*....|....*....|....*....|....*....|.
gi 1570527538 870 RLNVALTRARYGVIIVGNPKALSKQP---LWNHLLNYYKEQ 907
Cdd:COG1112 779 RLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
|
|
| DEXXQc_SMUBP2 |
cd18044 |
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ... |
483-715 |
7.58e-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: 7.58e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLcaksr 561
Cdd:cd18044 2 LNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRI----- 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 562 eaidspvsflalHNQIRNMDSMpelqklqqlkdetgelssadekryraLKRTAERelLMNADVICCTCVGAGDPRLAK-M 640
Cdd:cd18044 76 ------------GHPARLLESV--------------------------LDHSLDA--LVAAQVVLATNTGAGSRQLLPnE 115
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1570527538 641 QFRSILIDESTQATEPECMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPI--RLQVQYR 715
Cdd:cd18044 116 LFDVVVIDEAAQALEASCWIPL-LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
|
|
| 1B_UPF1-like |
cd21407 |
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ... |
326-425 |
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 1570527538 326 TQDNITVRWDLGLNKKRIAYFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAI 405
Cdd:cd21407 1 TQENISVRWDVGLNKKRLAYFTLPKLDES----------ELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVAL 70
|
90 100
....*....|....*....|
gi 1570527538 406 ELRSSVGAPVEVTHNFQVDF 425
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 ... |
483-715 |
7.65e-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: 7.65e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA------------RQGNGPVLVCAPSNIAVDQLTEKIHQT- 549
Cdd:cd18040 2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAkqnreiqsvsgeGDGGPCVLYCGPSNKSVDVVAELLLKVp 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 550 GLKVVRLCAKSREAIDSPV---------------------SFLALHNQIRNmDSMPELQKLQQ----LKDETGELSSADE 604
Cdd:cd18040 82 GLKILRVYSEQIETTEYPIpneprhpnkksereskpnselSSITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 605 KRYRALKRTAERELLMNADVICCTCVGAGDPRL-AKMQFRSILIDESTQATEPECMVPVVLG--AKQLILVGDHCQLGPV 681
Cdd:cd18040 161 KTYKILIWEARFEELETVDVILCTCSEAASQKMrTHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRPV 240
|
250 260 270
....*....|....*....|....*....|....
gi 1570527538 682 VMCKKAAKAGLSQSLFERLVVlgiRPIRLQVQYR 715
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 ... |
486-683 |
4.97e-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: 4.97e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 486 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 551
Cdd:pfam13086 1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 552 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 589
Cdd:pfam13086 78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 590 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 668
Cdd:pfam13086 156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231
|
250
....*....|....*
gi 1570527538 669 LILVGDHCQLGPVVM 683
Cdd:pfam13086 232 VVLVGDPKQLPPTVI 246
|
|
| DEXXQc_Helz-like |
cd18038 |
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ... |
483-700 |
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 1570527538 483 LNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDQLTEKIHQTGLK---VV 554
Cdd:cd18038 2 LNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 555 RLCAKSREAIDSPvsflalhnqirnmdsmPELQKLQQLKDETGelssadekryralKRTAERELLMNADVICCTCVGAGd 634
Cdd:cd18038 82 RLNAPSRDRASVP----------------PELLPYCNSKAEGT-------------FRLPSLEELKKYRIVVCTLMTAG- 131
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1570527538 635 pRLAKMQ-----FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 700
Cdd:cd18038 132 -RLVQAGvpnghFTHIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
|
|
| UPF1_1B_dom |
pfam18141 |
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ... |
325-426 |
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 1570527538 325 QTQDNITVRWDLGLNKKRIAYFTLPKTDSGnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIA 404
Cdd:pfam18141 1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSG----------EMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVT 70
|
90 100
....*....|....*....|...
gi 1570527538 405 IELR-SSVGAPVEVTHNFQVDFV 426
Cdd:pfam18141 71 LELRsSSNNPPTDLTHGFTVEFV 93
|
|
| DEXXQc_SETX |
cd18042 |
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ... |
483-715 |
7.57e-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: 7.57e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSATIVYHL-----------------ARQGNGP-------VLVCAPSN 536
Cdd:cd18042 1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrKLQRNLNnkkkknrILVCAPSN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 537 IAVDQLTEKIHQTGL----------KVVRLcaksreaidspvsflalhnqirnmdsmpelqklqqlkdetGelssadekr 606
Cdd:cd18042 81 AAVDEIVLRLLSEGFldgdgrsykpNVVRV----------------------------------------G--------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 607 yralKRTAERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMC 684
Cdd:cd18042 112 ----RQELRASILNEADIVCTTLSSSGSDLLESLPrgFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFS 187
|
250 260 270
....*....|....*....|....*....|.
gi 1570527538 685 KKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 715
Cdd:cd18042 188 KVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
|
|
| DEXXQc_DNA2 |
cd18041 |
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ... |
483-715 |
2.80e-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: 145.07 E-value: 2.80e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 561
Cdd:cd18041 2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 562 eaIDSPVSFLALHNQIRNMDSMPELQklqqlkdetgelssadekryralkrtaerELLMNADVICCTCVGAGDPRLAKMQ 641
Cdd:cd18041 81 --IHPDVQEFTLEAILKSCKSVEELE-----------------------------SKYESVSVVATTCLGINHPIFRRRT 129
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1570527538 642 FRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYR 715
Cdd:cd18041 130 FDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVVqLTIQYR 203
|
|
| DEXXQc_Mov10L1 |
cd18078 |
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ... |
482-701 |
2.87e-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: 2.87e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 482 DLNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----TIVYHLARQgngPVLVCAPSNIAVDQLTEKIHQTGLKV 553
Cdd:cd18078 1 DLNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLPRS---RILVCAPSNSAADLVTSRLHESKVLK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 554 VRLCAKsreaidspvsfLALHNQIRNMDSmpelqklqqlkdetgelssadEKRYRALKRTAERELLMNADVICCTCVGAG 633
Cdd:cd18078 78 PGDMVR-----------LNAVNRFESTVI---------------------DARKLYCRLGEDLSKASRHRIVISTCSTAG 125
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1570527538 634 dpRLAKMQFRS-----ILIDESTQATEPECMVPVVL---GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLV 701
Cdd:cd18078 126 --LLYQMGLPVghfthVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLM 199
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
499-714 |
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 1570527538 499 LSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLtekihqtglkvvrlcaksreaidspvsflalhn 575
Cdd:cd17914 1 LSLIQGPPGTGKTRVLVKIVAALMQNkngEPGRILLVTPTNKAAAQL--------------------------------- 47
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 576 qirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprlakmqfRSILIDESTQATE 655
Cdd:cd17914 48 -------------------------------------------------------------------DNILVDEAAQILE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1570527538 656 PECM--VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 714
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 ... |
328-424 |
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 1570527538 328 DNITVRWDLGLNKKRIAYFTLPKTDSgnedlviiwlrDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIEL 407
Cdd:cd21344 1 LIITVRWRLALNDFRGAYFSLEKGKS-----------QCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALEL 69
|
90
....*....|....*..
gi 1570527538 408 RSSVGAPVEVTHNFQVD 424
Cdd:cd21344 70 KGSTTYPLTVTHIFVLT 86
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
499-715 |
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 1570527538 499 LSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDqltekihqtglkvvrlcaksreaidspvsflalhnqi 577
Cdd:cd17934 1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGKrVLVTAQSNVAVD------------------------------------- 43
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 578 rnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvgagdprlakmqfrsiLIDESTQATEPE 657
Cdd:cd17934 44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 658 CMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAG----LSQSLFERLVVLGIRPIRLQVQYR 715
Cdd:cd17934 61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
|
|
| EEXXEc_NFX1 |
cd17936 |
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ... |
483-714 |
6.21e-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: 6.21e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA----TIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGL-KVVRLc 557
Cdd:cd17936 2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRL- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 558 aksreaidspvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVICCTCVGAGDPR- 636
Cdd:cd17936 81 ---------------------------------------------------------------GARVIGMTTTGAAKYRe 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 637 -LAKMQFRSILIDESTQATEPE---CMVPVVlgaKQLILVGDHCQLGPVVMCKK--AAKAGLSQSLFERLVVLGIRPIRL 710
Cdd:cd17936 98 lLQALGPKVVIVEEAAEVLEAHilaALTPST---EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTL 174
|
....
gi 1570527538 711 QVQY 714
Cdd:cd17936 175 NVQR 178
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
801-886 |
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 1570527538 801 QIGIITPYEGQRSYLVQYMQFSgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHqgigflnDPRRLNVALTRARY 880
Cdd:cd18786 12 KGVVLTPYHRDRAYLNQYLQGL-SLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83
|
....*.
gi 1570527538 881 GVIIVG 886
Cdd:cd18786 84 RLVIYD 89
|
|
| EEXXQc_AQR |
cd17935 |
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ... |
484-722 |
7.35e-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: 7.35e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 484 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLarQGNGP---VLVCAPSNIAVDQLTEKIhqtglkvvrlcaks 560
Cdd:cd17935 7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNL--YHNFPnqrTLIVTHSNQALNQLFEKI-------------- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 561 rEAIDSPvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaERELL---MNADVICCTCVGAGDPR- 636
Cdd:cd17935 71 -MALDID-----------------------------------------------ERHLLrlgHGAKIIAMTCTHAALKRg 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 637 -LAKMQFR--SILIDESTQATEPECMVPVVL--------GAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLG 704
Cdd:cd17935 103 eLVELGFKydNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182
|
250
....*....|....*...
gi 1570527538 705 IRPIRLQVQYRMHPALSA 722
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 ... |
123-212 |
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 1570527538 123 ACSYCGIHDpacVVYCNTS--KKWFCNgrgntsgSHIVNHLVRAKCKEVTLHKdgplgetVLECYNCGCRNVFLLGFipa 200
Cdd:cd21343 1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60
|
90
....*....|..
gi 1570527538 201 kadSVVVLLCRQ 212
Cdd:cd21343 61 ---GGVSYRCVD 69
|
|
| DEXXQc_HELZ |
cd18077 |
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ... |
483-700 |
2.44e-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: 2.44e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 483 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHqtglkvvr 555
Cdd:cd18077 2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlYIKEYLH-------- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 556 lcaKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELssadekryralkRTAERELLMNADVICCT-----CV 630
Cdd:cd18077 73 ---PYVETGNPRARPLRVYYRNRWVKTVHPVVQKYCLIDEHGTF------------RMPTREDVMRHRVVVVTlstsqYL 137
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 631 GAGDprLAKMQFRSILIDESTQATEPECMVPVVLGAK--QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 700
Cdd:cd18077 138 CQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
439-893 |
8.45e-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: 8.45e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 439 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 517
Cdd:COG0507 83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 518 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 597
Cdd:COG0507 161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 598 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 667
Cdd:COG0507 208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 668 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 746
Cdd:COG0507 248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 747 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 792
Cdd:COG0507 304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 793 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 849
Cdd:COG0507 384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 1570527538 850 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 893
Cdd:COG0507 461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
|
|
| DEXXQc_SF1 |
cd18043 |
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ... |
484-683 |
6.53e-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: 6.53e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 484 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAvdqltekihqtgLKVVRLcaksrea 563
Cdd:cd18043 1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKR-VLFVSEKKAA------------LDVVRF------- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 564 idsPVSFLALHNQIRNMDsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprLAKMQFR 643
Cdd:cd18043 61 ---PCWIMSPLSVSQYLP-------------------------------------------------------LNRNLFD 82
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 1570527538 644 SILIDESTQAtEPECMVPVVLGAKQLILVGDHCQLGPVVM 683
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. ... |
487-546 |
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 1570527538 487 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLaRQGNGPVLVCAPSNIAVDQLTEKI 546
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 ... |
498-700 |
4.73e-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: 4.73e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 498 PLsLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHQtglkvvRLCAKSREAIdsPVSFLALHNQ 576
Cdd:cd18076 25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADiYIREYFHP------YVDKGHPEAR--PLRIKATDRP 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 577 IRNMDsmPELQKLQQLKDEtgelssadekryRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEP 656
Cdd:cd18076 96 NAITD--PDTITYCCLTKD------------RQCFRLPTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEAAQMLEC 161
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 1570527538 657 ECMVPVVLGA--KQLILVGDHCQLGPVVMCKKAAKAGlSQSLFERL 700
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 ... |
483-717 |
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 1570527538 483 LNHSQVYAVKTVL--QRPLSLIQGPPGTGKTVTSATIVYHLARQGnGPVLVCAPSNIAVDQLtekihqtglkvvrlcaks 560
Cdd:pfam13604 2 LNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTALKALREAWEAAG-YRVIGLAPTGRAAKVL------------------ 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 561 REAIDSPVSFLAlhnqirnmdsmpelqklqqlkdetgelssadekryRALKRTAERELLMNADVicctcvgagdprlakm 640
Cdd:pfam13604 63 GEELGIPADTIA-----------------------------------KLLHRLGGRAGLDPGTL---------------- 91
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 641 qfrsILIDESTQATEPEcMVPVV-----LGAKqLILVGDHCQLGPVvmckkaaKAGlsqSLFERLVVLGIRPIRLQVQYR 715
Cdd:pfam13604 92 ----LIVDEAGMVGTRQ-MARLLklaedAGAR-VILVGDPRQLPSV-------EAG---GAFRDLLAAGIGTAELTEIVR 155
|
..
gi 1570527538 716 MH 717
Cdd:pfam13604 156 QR 157
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
490-551 |
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 1570527538 490 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSNIAVDQLTEKihqTGL 551
Cdd:pfam13245 4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSER---TGL 64
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
449-681 |
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 1570527538 449 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 517
Cdd:TIGR01447 100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 518 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 593
Cdd:TIGR01447 180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 594 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 671
Cdd:TIGR01447 244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290
|
250
....*....|
gi 1570527538 672 VGDHCQLGPV 681
Cdd:TIGR01447 291 LGDKNQLPSV 300
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
483-557 |
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 1570527538 483 LNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSATIVYHLARQGNG-PVLVCAPSNIAVDQLTEKIHQTGLKVVRL 556
Cdd:pfam04851 4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIkKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83
|
.
gi 1570527538 557 C 557
Cdd:pfam04851 84 G 84
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
487-546 |
3.84e-06 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 49.03 E-value: 3.84e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 487 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 546
Cdd:smart00487 13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
501-548 |
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 1570527538 501 LIQGPPGTGKTVTSATIVYHLARQgnGPVLVCAPSNIAVDQLTEKIHQ 548
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 ... |
833-880 |
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 1570527538 833 VEIASVDAFQG---REKDFIILSCVRanehqgigflNDPRRLNVALTRARY 880
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 ... |
487-612 |
7.02e-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: 7.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 487 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN-GPVLVCAPSNIAVDQLTEKI----HQTGLKVVRLCAKSR 561
Cdd:cd18013 5 QKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDFtRRVLVIAPLRVARSTWPDEVekwnHLRNLTVSVAVGTER 84
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1570527538 562 E---AIDSPVSFLalhnqIRNMDSMPELQKLQQLK--------DETGELSSADEKRYRALKR 612
Cdd:cd18013 85 QrskAANTPADLY-----VINRENLKWLVNKSGDPwpfdmvviDELSSFKSPRSKRFKALRK 141
|
|
| gammaCoV_Nsp13-helicase |
cd21720 |
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ... |
833-885 |
1.68e-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: 1.68e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1570527538 833 VEIASVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 885
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 ... |
487-567 |
2.37e-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: 2.37e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1570527538 487 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLkVVRLCAKS 560
Cdd:pfam13191 8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86
|
....*..
gi 1570527538 561 REAIDSP 567
Cdd:pfam13191 87 ESSLLEA 93
|
|
| deltaCoV_Nsp13-helicase |
cd21721 |
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ... |
837-885 |
6.15e-03 |
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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: 6.15e-03
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gi 1570527538 837 SVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 885
Cdd:cd21721 283 TVDSSQGSEYDYVIF-CVTTDSAHALNM----SRLNVALTRAKIGILVV 326
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