NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|18375673|ref|NP_002902|]
View 

regulator of nonsense transcripts 1 isoform 2 [Homo sapiens]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 13761155)

DEAD/DEAH box containing ATP-dependent helicase catalyzes the unwinding of DNA or RNA; similar to regulator of nonsense transcripts 1, an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons

CATH:  3.40.50.300
EC:  3.6.4.-
Gene Ontology:  GO:0016887|GO:0003676|GO:0004386|GO:0005524
PubMed:  20206133|20225155

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 470-703 1.60e-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: 1.60e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  470 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 549
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  550 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 629
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18375673  630 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 703
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 121-272 1.27e-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: 1.27e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    121 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 200
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673    201 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 272
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 348-900 4.63e-89

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]


The actual alignment was detected with superfamily member TIGR00376:

Pssm-ID: 273041 [Multi-domain]  Cd Length: 636  Bit Score: 300.19  E-value: 4.63e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    348 PKTDSDMRLMQGDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSAL 427
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    428 KTFAVDETSVSGyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 506
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    507 YHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSP 555
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEER 273

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    556 VSFLALHNQIRNmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccT 616
Cdd:TIGR00376  274 NKKTKPSPQKRR--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---T 348

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    617 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRP 695
Cdd:TIGR00376  349 NSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERS 425

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    696 IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSY 764
Cdd:TIGR00376  426 RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSK 504

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    765 LNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRA 844
Cdd:TIGR00376  505 YNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRS 577

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 18375673    845 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 900
Cdd:TIGR00376  578 NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
 
Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 470-703 1.60e-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: 1.60e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  470 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 549
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  550 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 629
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18375673  630 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 703
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 121-272 1.27e-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: 1.27e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    121 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 200
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673    201 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 272
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 348-900 4.63e-89

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: 300.19  E-value: 4.63e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    348 PKTDSDMRLMQGDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSAL 427
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    428 KTFAVDETSVSGyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 506
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    507 YHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSP 555
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEER 273

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    556 VSFLALHNQIRNmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccT 616
Cdd:TIGR00376  274 NKKTKPSPQKRR--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---T 348

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    617 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRP 695
Cdd:TIGR00376  349 NSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERS 425

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    696 IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSY 764
Cdd:TIGR00376  426 RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSK 504

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    765 LNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRA 844
Cdd:TIGR00376  505 YNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRS 577

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 18375673    845 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 900
Cdd:TIGR00376  578 NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 122-242 7.40e-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: 7.40e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  122 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 201
Cdd:cd21400    1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 18375673  202 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 242
Cdd:cd21400   81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 704-893 4.39e-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: 4.39e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  704 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 783
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  784 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 862
Cdd:cd18808   78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 18375673  863 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 893
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 ...
 680-877 2.03e-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: 2.03e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    680 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 757
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    758 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 836
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 18375673    837 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 877
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
573-895 3.40e-71

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 254.67  E-value: 3.40e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  573 ELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVV 651
Cdd:COG1112  499 LIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALA 577

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  652 LgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 727
Cdd:COG1112  578 R-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSP 656

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  728 ADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYM 807
Cdd:COG1112  657 KAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELL 727

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  808 QfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPRRLNVALTRARYGVIIVGNPKALSKQP 883
Cdd:COG1112  728 R---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDP 804

                        330
                 ....*....|....*
gi 18375673  884 ---LWNHLLNYYKEQ 895
Cdd:COG1112  805 stpALKRLLEYLERA 819
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 474-671 6.00e-49

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 174.45  E-value: 6.00e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    474 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 539
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    540 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 577
Cdd:pfam13086   78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    578 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 656
Cdd:pfam13086  156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231

                          250
                   ....*....|....*
gi 18375673    657 LILVGDHCQLGPVVM 671
Cdd:pfam13086  232 VVLVGDPKQLPPTVI 246
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 427-881 8.33e-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: 8.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  427 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 505
Cdd:COG0507   83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  506 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 585
Cdd:COG0507  161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  586 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 655
Cdd:COG0507  208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  656 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 734
Cdd:COG0507  248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  735 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 780
Cdd:COG0507  304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  781 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 837
Cdd:COG0507  384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....
gi 18375673  838 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 881
Cdd:COG0507  461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 437-669 1.02e-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: 1.02e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    437 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 505
Cdd:TIGR01447  100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    506 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 581
Cdd:TIGR01447  180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    582 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 659
Cdd:TIGR01447  244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290

                          250
                   ....*....|
gi 18375673    660 VGDHCQLGPV 669
Cdd:TIGR01447  291 LGDKNQLPSV 300
DEXDc smart00487
DEAD-like helicases superfamily;
475-534 3.79e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 49.03  E-value: 3.79e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673     475 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 534
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 ...
 470-703 1.60e-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: 1.60e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  470 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 549
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  550 EAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 629
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18375673  630 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 703
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 121-272 1.27e-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: 1.27e-116
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    121 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 200
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673    201 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN 272
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 348-900 4.63e-89

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: 300.19  E-value: 4.63e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    348 PKTDSDMRLMQGDEICLRYKGDLAPLWKGIghVIKVPDNYgdeIAIELRSSVgaPVEVTHNFQVDFVWKSTSFDRMQSAL 427
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    428 KTFAVDETSVSGyiyhKLLGHEVEDVIIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 506
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    507 YHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR-------------------------------EAIDSP 555
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARllksnkqhsldylienhpkyqivadirekidELIEER 273

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    556 VSFLALHNQIRNmdSMPELQKLQQLKDETG----------------ELSSADEKRYRALKRTAER---ELLMNADViccT 616
Cdd:TIGR00376  274 NKKTKPSPQKRR--GLSDIKILRKALKKREargieslkiasmaewiETNKSIDRLLKLLPESEERimnEILAESDA---T 348

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    617 CVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRP 695
Cdd:TIGR00376  349 NSMAGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERS 425

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    696 IRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSY 764
Cdd:TIGR00376  426 RTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSK 504

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    765 LNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqEVEIASVDAFQGREKDFIILSCVRA 844
Cdd:TIGR00376  505 YNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRS 577

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 18375673    845 NEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKEQKVLVE 900
Cdd:TIGR00376  578 NRKGEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 122-242 7.40e-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: 7.40e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  122 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 201
Cdd:cd21400    1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 18375673  202 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 242
Cdd:cd21400   81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 704-893 4.39e-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: 4.39e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  704 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTKLLKA 783
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  784 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQEVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 862
Cdd:cd18808   78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 18375673  863 LTRARYGVIIVGNPKALSKQPLWNHLLNYYK 893
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 ...
 680-877 2.03e-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: 2.03e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    680 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 757
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    758 ASSGTSYLNRTEAANVEKITTKLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLyqEVEIASVDAFQGREKDF 836
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKL--EIEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 18375673    837 IILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPK 877
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
573-895 3.40e-71

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 254.67  E-value: 3.40e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  573 ELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVV 651
Cdd:COG1112  499 LIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALA 577

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  652 LgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 727
Cdd:COG1112  578 R-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSP 656

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  728 ADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYM 807
Cdd:COG1112  657 KAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELL 727

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  808 QfsgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPRRLNVALTRARYGVIIVGNPKALSKQP 883
Cdd:COG1112  728 R---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDP 804

                        330
                 ....*....|....*
gi 18375673  884 ---LWNHLLNYYKEQ 895
Cdd:COG1112  805 stpALKRLLEYLERA 819
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 471-703 7.46e-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: 7.46e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATIVYHLARQGNgPVLVCAPSNIAVDQLTEKIHQTGLKVVRLcaksr 549
Cdd:cd18044    2 LNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRI----- 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  550 eaidspvsflalHNQIRNMDSMpelqklqqlkdetgelssadekryraLKRTAERelLMNADVICCTCVGAGDPRLAK-M 628
Cdd:cd18044   76 ------------GHPARLLESV--------------------------LDHSLDA--LVAAQVVLATNTGAGSRQLLPnE 115

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18375673  629 QFRSILIDESTQATEPECMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPI--RLQVQYR 703
Cdd:cd18044  116 LFDVVVIDEAAQALEASCWIPL-LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 325-413 7.43e-52

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: 176.56  E-value: 7.43e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  325 TQDNITVRWDLGLNKKRIAYFTLPKTD-SDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPV 403
Cdd:cd21407    1 TQENISVRWDVGLNKKRLAYFTLPKLDeSELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKNAPT 80

                         90
                 ....*....|
gi 18375673  404 EVTHNFQVDF 413
Cdd:cd21407   81 EITTGFSVEF 90
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 471-703 1.01e-49

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: 177.33  E-value: 1.01e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLA------------RQGNGPVLVCAPSNIAVDQLTEKIHQT- 537
Cdd:cd18040    2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAkqnreiqsvsgeGDGGPCVLYCGPSNKSVDVVAELLLKVp 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  538 GLKVVRLCAKSREAIDSPV---------------------SFLALHNQIRNmDSMPELQKLQQ----LKDETGELSSADE 592
Cdd:cd18040   82 GLKILRVYSEQIETTEYPIpneprhpnkksereskpnselSSITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  593 KRYRALKRTAERELLMNADVICCTCVGAGDPRL-AKMQFRSILIDESTQATEPECMVPVVLG--AKQLILVGDHCQLGPV 669
Cdd:cd18040  161 KTYKILIWEARFEELETVDVILCTCSEAASQKMrTHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRPV 240

                        250       260       270
                 ....*....|....*....|....*....|....
gi 18375673  670 VMCKKAAKAGLSQSLFERLVVlgiRPIRLQVQYR 703
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 ...
 474-671 6.00e-49

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.


Pssm-ID: 404072 [Multi-domain]  Cd Length: 248  Bit Score: 174.45  E-value: 6.00e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    474 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLARQGNGP---------VLVCAPSNIAVDQLTEKIHQTG----L 539
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    540 KVVRLCAKsrEAIDSPVSFLALHNQIRNMDSMPEL------------------------------------------QKL 577
Cdd:pfam13086   78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    578 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 656
Cdd:pfam13086  156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231

                          250
                   ....*....|....*
gi 18375673    657 LILVGDHCQLGPVVM 671
Cdd:pfam13086  232 VVLVGDPKQLPPTVI 246
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 471-688 1.41e-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: 1.41e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDQLTEKIHQTGLK---VV 542
Cdd:cd18038    2 LNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  543 RLCAKSREAIDSPvsflalhnqirnmdsmPELQKLQQLKDETGelssadekryralKRTAERELLMNADVICCTCVGAGd 622
Cdd:cd18038   82 RLNAPSRDRASVP----------------PELLPYCNSKAEGT-------------FRLPSLEELKKYRIVVCTLMTAG- 131

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18375673  623 pRLAKMQ-----FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 688
Cdd:cd18038  132 -RLVQAGvpnghFTHIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
UPF1_1B_dom pfam18141
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ...
 324-414 1.90e-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: 155.55  E-value: 1.90e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    324 QTQDNITVRWDLGLNKKRIAYFTLPKTDS-DMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELR-SSVGA 401
Cdd:pfam18141    1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSgEMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVTLELRsSSNNP 80

                           90
                   ....*....|...
gi 18375673    402 PVEVTHNFQVDFV 414
Cdd:pfam18141   81 PTDLTHGFTVEFV 93
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 471-703 8.32e-43

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 155.45  E-value: 8.32e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSATIVYHL-----------------ARQGNGP-------VLVCAPSN 524
Cdd:cd18042    1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrKLQRNLNnkkkknrILVCAPSN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  525 IAVDQLTEKIHQTGL----------KVVRLcaksreaidspvsflalhnqirnmdsmpelqklqqlkdetGelssadekr 594
Cdd:cd18042   81 AAVDEIVLRLLSEGFldgdgrsykpNVVRV----------------------------------------G--------- 111

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  595 yralKRTAERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMC 672
Cdd:cd18042  112 ----RQELRASILNEADIVCTTLSSSGSDLLESLPrgFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFS 187

                        250       260       270
                 ....*....|....*....|....*....|.
gi 18375673  673 KKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 703
Cdd:cd18042  188 KVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 471-703 3.29e-39

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 144.69  E-value: 3.29e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAVDQLTEKIHQTGLKVVRLCAKSR 549
Cdd:cd18041    2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  550 eaIDSPVSFLALHNQIRNMDSMPELQklqqlkdetgelssadekryralkrtaerELLMNADVICCTCVGAGDPRLAKMQ 629
Cdd:cd18041   81 --IHPDVQEFTLEAILKSCKSVEELE-----------------------------SKYESVSVVATTCLGINHPIFRRRT 129

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18375673  630 FRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYR 703
Cdd:cd18041  130 FDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVVqLTIQYR 203
1B_UPF1_nv_SF1_Hel-like cd21344
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ...
 327-412 1.61e-33

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: 123.96  E-value: 1.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  327 DNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVT 406
Cdd:cd21344    1 LIITVRWRLALNDFRGAYFSLEKGKSQCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALELKGSTTYPLTVT 80


                 ....*.
gi 18375673  407 HNFQVD 412
Cdd:cd21344   81 HIFVLT 86
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 470-689 2.83e-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: 2.83e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  470 DLNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----TIVYHLARQgngPVLVCAPSNIAVDQLTEKIHQTGLKV 541
Cdd:cd18078    1 DLNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLPRS---RILVCAPSNSAADLVTSRLHESKVLK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  542 VRLCAKsreaidspvsfLALHNQIRNMDSmpelqklqqlkdetgelssadEKRYRALKRTAERELLMNADVICCTCVGAG 621
Cdd:cd18078   78 PGDMVR-----------LNAVNRFESTVI---------------------DARKLYCRLGEDLSKASRHRIVISTCSTAG 125

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18375673  622 dpRLAKMQFRS-----ILIDESTQATEPECMVPVVL---GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLV 689
Cdd:cd18078  126 --LLYQMGLPVghfthVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLM 199
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 487-702 1.69e-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: 1.69e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  487 LSLIQGPPGTGKTVTSATIVYHLARQ---GNGPVLVCAPSNIAVDQLtekihqtglkvvrlcaksreaidspvsflalhn 563
Cdd:cd17914    1 LSLIQGPPGTGKTRVLVKIVAALMQNkngEPGRILLVTPTNKAAAQL--------------------------------- 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  564 qirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprlakmqfRSILIDESTQATE 643
Cdd:cd17914   48 -------------------------------------------------------------------DNILVDEAAQILE 60

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18375673  644 PECM--VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 702
Cdd:cd17914   61 PETSrlIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 487-703 1.60e-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: 1.60e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  487 LSLIQGPPGTGKTVTSATIVYHLARQGNGP-VLVCAPSNIAVDqltekihqtglkvvrlcaksreaidspvsflalhnqi 565
Cdd:cd17934    1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGKrVLVTAQSNVAVD------------------------------------- 43

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  566 rnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvgagdprlakmqfrsiLIDESTQATEPE 645
Cdd:cd17934   44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673  646 CMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAG----LSQSLFERLVVLGIRPIRLQVQYR 703
Cdd:cd17934   61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 471-702 6.14e-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: 6.14e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA----TIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGL-KVVRLc 545
Cdd:cd17936    2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRL- 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  546 aksreaidspvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVICCTCVGAGDPR- 624
Cdd:cd17936   81 ---------------------------------------------------------------GARVIGMTTTGAAKYRe 97

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  625 -LAKMQFRSILIDESTQATEPE---CMVPVVlgaKQLILVGDHCQLGPVVMCKK--AAKAGLSQSLFERLVVLGIRPIRL 698
Cdd:cd17936   98 lLQALGPKVVIVEEAAEVLEAHilaALTPST---EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTL 174


                 ....
gi 18375673  699 QVQY 702
Cdd:cd17936  175 NVQR 178
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 789-874 4.54e-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: 4.54e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  789 QIGIITPYEGQRSYLVQYMQFSgSLHTKLYQEVEIASVDAFQGREKDFIILSCVRANEHqgigflnDPRRLNVALTRARY 868
Cdd:cd18786   12 KGVVLTPYHRDRAYLNQYLQGL-SLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83


                 ....*.
gi 18375673  869 GVIIVG 874
Cdd:cd18786   84 RLVIYD 89
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 472-710 7.26e-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: 7.26e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  472 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLarQGNGP---VLVCAPSNIAVDQLTEKIhqtglkvvrlcaks 548
Cdd:cd17935    7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNL--YHNFPnqrTLIVTHSNQALNQLFEKI-------------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  549 rEAIDSPvsflalhnqirnmdsmpelqklqqlkdetgelssadekryralkrtaERELL---MNADVICCTCVGAGDPR- 624
Cdd:cd17935   71 -MALDID-----------------------------------------------ERHLLrlgHGAKIIAMTCTHAALKRg 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  625 -LAKMQFR--SILIDESTQATEPECMVPVVL--------GAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLG 692
Cdd:cd17935  103 eLVELGFKydNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182

                        250
                 ....*....|....*...
gi 18375673  693 IRPIRLQVQYRMHPALSA 710
Cdd:cd17935  183 VPTVDLDAQGRARASISS 200
ZBD_UPF1_nv_SF1_Hel-like cd21343
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ...
 122-211 2.16e-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: 2.16e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  122 ACSYCGIHDpacVVYCNTS--KKWFCNgrgntsgSHIVNHLVRAKCKEVTLHKdgplgetVLECYNCGCRNVFLLGFipa 199
Cdd:cd21343    1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60

                         90
                 ....*....|..
gi 18375673  200 kadSVVVLLCRQ 211
Cdd:cd21343   61 ---GGVSYRCVD 69
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 471-688 2.89e-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: 2.89e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  471 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHqtglkvvr 543
Cdd:cd18077    2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlYIKEYLH-------- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  544 lcaKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELssadekryralkRTAERELLMNADVICCT-----CV 618
Cdd:cd18077   73 ---PYVETGNPRARPLRVYYRNRWVKTVHPVVQKYCLIDEHGTF------------RMPTREDVMRHRVVVVTlstsqYL 137

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673  619 GAGDprLAKMQFRSILIDESTQATEPECMVPVVLGAK--QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 688
Cdd:cd18077  138 CQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 427-881 8.33e-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: 8.33e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  427 LKTFAVDETSVSGYIyHKLLGHEVEDVIIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 505
Cdd:COG0507   83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  506 VYHLARQGnGPVLVCAPSNIAVDQLTEKIhqtglkvvrlcakSREAidspvsfLALHnqirnmdsmpelQKLQQLKDETG 585
Cdd:COG0507  161 LAALEALG-LRVALAAPTGKAAKRLSEST-------------GIEA-------RTIH------------RLLGLRPDSGR 207

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  586 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 655
Cdd:COG0507  208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  656 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 734
Cdd:COG0507  248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  735 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTKL 780
Cdd:COG0507  304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  781 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSGSLHTKlYQEVEIASVD-AF-------QGREKD--FI 837
Cdd:COG0507  384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGREIVT-YDPSELDQLElAYaitvhksQGSTFDrvIL 460

                        490       500       510       520
                 ....*....|....*....|....*....|....*....|....
gi 18375673  838 ILScvraNEHQGigfLNDPRRLNVALTRARYGVIIVGNPKALSK 881
Cdd:COG0507  461 VLP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 472-671 6.52e-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: 6.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  472 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGpVLVCAPSNIAvdqltekihqtgLKVVRLcaksrea 551
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKR-VLFVSEKKAA------------LDVVRF------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  552 idsPVSFLALHNQIRNMDsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprLAKMQFR 631
Cdd:cd18043   61 ---PCWIMSPLSVSQYLP-------------------------------------------------------LNRNLFD 82

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 18375673  632 SILIDESTQAtEPECMVPVVLGAKQLILVGDHCQLGPVVM 671
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. ...
 475-534 1.93e-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: 1.93e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  475 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLaRQGNGPVLVCAPSNIAVDQLTEKI 534
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 ...
 486-688 5.13e-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: 5.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  486 PLsLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVD-QLTEKIHQtglkvvRLCAKSREAIdsPVSFLALHNQ 564
Cdd:cd18076   25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADiYIREYFHP------YVDKGHPEAR--PLRIKATDRP 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  565 IRNMDsmPELQKLQQLKDEtgelssadekryRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEP 644
Cdd:cd18076   96 NAITD--PDTITYCCLTKD------------RQCFRLPTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEAAQMLEC 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 18375673  645 ECMVPVVLGA--KQLILVGDHCQLGPVVMCKKAAKAGlSQSLFERL 688
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 ...
 471-705 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 18375673    471 LNHSQVYAVKTVL--QRPLSLIQGPPGTGKTVTSATIVYHLARQGnGPVLVCAPSNIAVDQLtekihqtglkvvrlcaks 548
Cdd:pfam13604    2 LNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTALKALREAWEAAG-YRVIGLAPTGRAAKVL------------------ 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    549 REAIDSPVSFLAlhnqirnmdsmpelqklqqlkdetgelssadekryRALKRTAERELLMNADVicctcvgagdprlakm 628
Cdd:pfam13604   63 GEELGIPADTIA-----------------------------------KLLHRLGGRAGLDPGTL---------------- 91

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    629 qfrsILIDESTQATEPEcMVPVV-----LGAKqLILVGDHCQLGPVvmckkaaKAGlsqSLFERLVVLGIRPIRLQVQYR 703
Cdd:pfam13604   92 ----LIVDEAGMVGTRQ-MARLLklaedAGAR-VILVGDPRQLPSV-------EAG---GAFRDLLAAGIGTAELTEIVR 155


                   ..
gi 18375673    704 MH 705
Cdd:pfam13604  156 QR 157
AAA_19 pfam13245
AAA domain;
478-539 1.12e-08

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 54.92  E-value: 1.12e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18375673    478 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQG--NGPVLVCAPSNIAVDQLTEKihqTGL 539
Cdd:pfam13245    4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSER---TGL 64
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 437-669 1.02e-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: 1.02e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    437 VSGYIYHKLLGHEVEDVIIKCQ--LPKRFTAQGLPDLNHS---------QVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 505
Cdd:TIGR01447  100 CDGRLYLRRYWREEEKLAAKLRtlLEARKRTAPSAILENLfpllneqnwRKTAVALALKSNFSLITGGPGTGKTTTVARL 179

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    506 VYHLARQ----GNGPVLVCAPSNIAVDQLTEKIHQtglKVVRLCAKSREAIDSPVSFLALHnqirnmdsmpelqKLQQLK 581
Cdd:TIGR01447  180 LLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH-------------RLLGIK 243

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    582 detgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqfrsILIDESTQATEP--ECMVPVVLGAKQLIL 659
Cdd:TIGR01447  244 --------PDTKRFRHHERNP-----LPLDV--------------------LVVDEASMVDLPlmAKLLKALPPNTKLIL 290

                          250
                   ....*....|
gi 18375673    660 VGDHCQLGPV 669
Cdd:TIGR01447  291 LGDKNQLPSV 300
ResIII pfam04851
Type III restriction enzyme, res subunit;
471-545 2.86e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 48.44  E-value: 2.86e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    471 LNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSATIVYHLARQGNG-PVLVCAPSNIAVDQLTEKIHQTGLKVVRL 544
Cdd:pfam04851    4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIkKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83


                   .
gi 18375673    545 C 545
Cdd:pfam04851   84 G 84
DEXDc smart00487
DEAD-like helicases superfamily;
475-534 3.79e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 49.03  E-value: 3.79e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673     475 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLARQGNGPVLVCAPSNIAVDQLTEKI 534
Cdd:smart00487   13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
489-536 1.62e-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: 1.62e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 18375673  489 LIQGPPGTGKTVTSATIVYHLARQgnGPVLVCAPSNIAVDQLTEKIHQ 536
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 ...
 821-868 2.74e-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: 2.74e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 18375673  821 VEIASVDAFQG---REKDFIILSCVRanehqgigflNDPRRLNVALTRARY 868
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 ...
 475-600 6.93e-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: 6.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673  475 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGN-GPVLVCAPSNIAVDQLTEKI----HQTGLKVVRLCAKSR 549
Cdd:cd18013    5 QKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDFtRRVLVIAPLRVARSTWPDEVekwnHLRNLTVSVAVGTER 84

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18375673  550 E---AIDSPVSFLalhnqIRNMDSMPELQKLQQLK--------DETGELSSADEKRYRALKR 600
Cdd:cd18013   85 QrskAANTPADLY-----VINRENLKWLVNKSGDPwpfdmvviDELSSFKSPRSKRFKALRK 141
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 821-873 1.64e-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: 42.21  E-value: 1.64e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 18375673  821 VEIASVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 873
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 ...
 475-555 2.34e-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: 2.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18375673    475 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKIHQTGLkVVRLCAKS 548
Cdd:pfam13191    8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86


                   ....*..
gi 18375673    549 REAIDSP 555
Cdd:pfam13191   87 ESSLLEA 93
deltaCoV_Nsp13-helicase cd21721
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ...
 825-873 6.08e-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: 6.08e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 18375673  825 SVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRARYGVIIV 873
Cdd:cd21721  283 TVDSSQGSEYDYVIF-CVTTDSAHALNM----SRLNVALTRAKIGILVV 326
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH