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Conserved domains on  [gi|1591540479|ref|XP_028259071|]
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regulator of nonsense transcripts 1 isoform X2 [Parambassis ranga]

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

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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 ...
 451-684 4.59e-174

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: 509.10  E-value: 4.59e-174
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  451 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSR 530
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  531 EAIESPVSFLALHNQISNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 610
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479  611 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 684
Cdd:cd18039    161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 102-253 6.60e-117

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: 356.94  E-value: 6.60e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  102 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 181
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  182 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKDN 253
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 329-881 9.13e-86

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: 290.95  E-value: 9.13e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  329 PKTDSDMRLMQGDEICLRYKGDLAPPWKGIghVIKVPDNYgdeIAIELRSSVgaPVEIPHNFQVDFVWKSTSFDRMQSAL 408
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  409 KTFAVDETSVSGyiyhKLLGHEVEDVTIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 487
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  488 YHLSRQGNgPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSReaIESPVSFLALHNQISNMDSMPELQKLQQLKDETGE 567
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPAR--LLKSNKQHSLDYLIENHPKYQIVADIREKIDELIE 271

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  568 LSSADEKRYRALKRT-AERELLMNA----------------------------DVIC------------------CTCVG 600
Cdd:TIGR00376  272 ERNKKTKPSPQKRRGlSDIKILRKAlkkreargieslkiasmaewietnksidRLLKllpeseerimneilaesdATNSM 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  601 AGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRL 679
Cdd:TIGR00376  352 AGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTL 428

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  680 QVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNR 748
Cdd:TIGR00376  429 NVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNP 507

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  749 TEAANVEKITTRLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqQVEIASVDAFQGREKDFIILSCVRANEH 828
Cdd:TIGR00376  508 GEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRK 580

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1591540479  829 QGIGFLNDPRRLNVALTRAKYGVIIVGNPKALSKQPLWNNLLNNYKEQKVLVE 881
Cdd:TIGR00376  581 GEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 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 ...
 451-684 4.59e-174

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: 509.10  E-value: 4.59e-174
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  451 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSR 530
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  531 EAIESPVSFLALHNQISNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 610
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479  611 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 684
Cdd:cd18039    161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 102-253 6.60e-117

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: 356.94  E-value: 6.60e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  102 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 181
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  182 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKDN 253
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 329-881 9.13e-86

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: 290.95  E-value: 9.13e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  329 PKTDSDMRLMQGDEICLRYKGDLAPPWKGIghVIKVPDNYgdeIAIELRSSVgaPVEIPHNFQVDFVWKSTSFDRMQSAL 408
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  409 KTFAVDETSVSGyiyhKLLGHEVEDVTIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 487
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  488 YHLSRQGNgPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSReaIESPVSFLALHNQISNMDSMPELQKLQQLKDETGE 567
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPAR--LLKSNKQHSLDYLIENHPKYQIVADIREKIDELIE 271

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  568 LSSADEKRYRALKRT-AERELLMNA----------------------------DVIC------------------CTCVG 600
Cdd:TIGR00376  272 ERNKKTKPSPQKRRGlSDIKILRKAlkkreargieslkiasmaewietnksidRLLKllpeseerimneilaesdATNSM 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  601 AGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRL 679
Cdd:TIGR00376  352 AGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTL 428

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  680 QVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNR 748
Cdd:TIGR00376  429 NVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNP 507

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  749 TEAANVEKITTRLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqQVEIASVDAFQGREKDFIILSCVRANEH 828
Cdd:TIGR00376  508 GEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRK 580

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1591540479  829 QGIGFLNDPRRLNVALTRAKYGVIIVGNPKALSKQPLWNNLLNNYKEQKVLVE 881
Cdd:TIGR00376  581 GEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 103-223 6.24e-85

Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core.


Pssm-ID: 439167  Cd Length: 120  Bit Score: 269.89  E-value: 6.24e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  103 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 182
Cdd:cd21400      1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  183 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 223
Cdd:cd21400     81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 685-874 2.84e-80

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: 259.86  E-value: 2.84e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  685 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTRLLKA 764
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  765 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQQVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 843
Cdd:cd18808     78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1591540479  844 LTRAKYGVIIVGNPKALSKQPLWNNLLNNYK 874
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 ...
 661-858 2.50e-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: 257.86  E-value: 2.50e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  661 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 738
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  739 ASSGTSYLNRTEAANVEKITTRLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLYqqVEIASVDAFQGREKDF 817
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKLE--IEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  818 IILSCVRANEHQGIGFLNDPRRLNVALTRAKYGVIIVGNPK 858
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
554-873 2.91e-70

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 251.59  E-value: 2.91e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  554 ELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVV 632
Cdd:COG1112    499 LIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALA 577

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  633 LgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 708
Cdd:COG1112    578 R-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSP 656

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  709 ADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTRLLKAGAKPDQIGIITPYEGQRSYLVQYM 788
Cdd:COG1112    657 KAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELL 727

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  789 QfsgSLHTKLYQQVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPRRLNVALTRAKYGVIIVGNPKALSKQP 864
Cdd:COG1112    728 R---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDP 804


                   ....*....
gi 1591540479  865 LwNNLLNNY 873
Cdd:COG1112    805 S-TPALKRL 812
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 455-652 2.32e-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: 175.61  E-value: 2.32e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  455 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLSRQGNGP---------VLVCAPSNIAVDQLTEKIDKTG----L 520
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  521 KVVRLCAKsrEAIESPVSFLALHNQISNMDSMPEL------------------------------------------QKL 558
Cdd:pfam13086   78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  559 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 637
Cdd:pfam13086  156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231

                          250
                   ....*....|....*
gi 1591540479  638 LILVGDHCQLGPVVM 652
Cdd:pfam13086  232 VVLVGDPKQLPPTVI 246
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 408-862 1.09e-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: 84.64  E-value: 1.09e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  408 LKTFAVDETSVSGYIyHKLLGHEVEDVTIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 486
Cdd:COG0507     83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  487 VYHLSRQGnGPVLVCAPSNIAVDQLTEKIDKTGlkvvrlcaksreaiespvsfLALHnqisnmdsmpelQKLQQLKDETG 566
Cdd:COG0507    161 LAALEALG-LRVALAAPTGKAAKRLSESTGIEA--------------------RTIH------------RLLGLRPDSGR 207

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  567 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 636
Cdd:COG0507    208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  637 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 715
Cdd:COG0507    248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  716 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTRL 761
Cdd:COG0507    304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  762 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSG----SLHTKLYQQVEIA---SVDAFQGREKD--FII 819
Cdd:COG0507    384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGreivTYDPSELDQLELAyaiTVHKSQGSTFDrvILV 461

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|...
gi 1591540479  820 LScvraNEHQGigfLNDPRRLNVALTRAKYGVIIVGNPKALSK 862
Cdd:COG0507    462 LP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 456-650 2.37e-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: 54.77  E-value: 2.37e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  456 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQ----GNGPVLVCAPSNIAVDQLTEKIDKtglKVVRLCAKSRE 531
Cdd:TIGR01447  149 RKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEAL 225

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  532 AIESPVSFLALHnqisnmdsmpelqKLQQLKdetgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqf 611
Cdd:TIGR01447  226 IAALPSEAVTIH-------------RLLGIK--------PDTKRFRHHERNP-----LPLDV------------------ 261

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  612 rsILIDESTQATEP--ECMVPVVLGAKQLILVGDHCQLGPV 650
Cdd:TIGR01447  262 --LVVDEASMVDLPlmAKLLKALPPNTKLILLGDKNQLPSV 300
DEXDc smart00487
DEAD-like helicases superfamily;
456-517 1.73e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 49.80  E-value: 1.73e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479   456 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDK 517
Cdd:smart00487   13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELKK 76
 
Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 451-684 4.59e-174

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: 509.10  E-value: 4.59e-174
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  451 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSR 530
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  531 EAIESPVSFLALHNQISNMDSMPELQKLQQLKDETGELSSADEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQ 610
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479  611 FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 684
Cdd:cd18039    161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 102-253 6.60e-117

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: 356.94  E-value: 6.60e-117
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  102 HACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAK 181
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  182 ADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKDN 253
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKDN 152
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 329-881 9.13e-86

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: 290.95  E-value: 9.13e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  329 PKTDSDMRLMQGDEICLRYKGDLAPPWKGIghVIKVPDNYgdeIAIELRSSVgaPVEIPHNFQVDFVWKSTSFDRMQSAL 408
Cdd:TIGR00376   50 RRKAIATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVALEESV--PQWSLKRVRIDLYANDVTFKRMKEAL 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  409 KTFAVDETSVSGyiyhKLLGHEVEDVTIKCQLPKRFTaqglPDLNHSQVYAVK-TVLQRPLSLIQGPPGTGKTVTSATIV 487
Cdd:TIGR00376  123 RALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTGKTRTVVELI 194

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  488 YHLSRQGNgPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSReaIESPVSFLALHNQISNMDSMPELQKLQQLKDETGE 567
Cdd:TIGR00376  195 RQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPAR--LLKSNKQHSLDYLIENHPKYQIVADIREKIDELIE 271

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  568 LSSADEKRYRALKRT-AERELLMNA----------------------------DVIC------------------CTCVG 600
Cdd:TIGR00376  272 ERNKKTKPSPQKRRGlSDIKILRKAlkkreargieslkiasmaewietnksidRLLKllpeseerimneilaesdATNSM 351

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  601 AGDPRLAKMQFRSILIDESTQATEPECMVPVVlGAKQLILVGDHCQLGPVVMCKKAAkaGLSQSLFERLVVL-GIRPIRL 679
Cdd:TIGR00376  352 AGSEILNGQYFDVAVIDEASQAMEPSCLIPLL-KARKLILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEyPERSRTL 428

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  680 QVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDK-------PMFFYVTQGQE----EIASSgTSYLNR 748
Cdd:TIGR00376  429 NVQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIDTSGCElfelKEADS-TSKYNP 507

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  749 TEAANVEKITTRLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSgslHTklyqQVEIASVDAFQGREKDFIILSCVRANEH 828
Cdd:TIGR00376  508 GEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLEHR---HI----DIEVSSVDGFQGREKEVIIISFVRSNRK 580

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1591540479  829 QGIGFLNDPRRLNVALTRAKYGVIIVGNPKALSKQPLWNNLLNNYKEQKVLVE 881
Cdd:TIGR00376  581 GEVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 103-223 6.24e-85

Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core.


Pssm-ID: 439167  Cd Length: 120  Bit Score: 269.89  E-value: 6.24e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  103 ACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDGPLGETVLECYNCGCRNVFLLGFIPAKA 182
Cdd:cd21400      1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  183 DSVVVLLCRQPCASQSSlKDINWDSSQWQPLIQDRCFLSWL 223
Cdd:cd21400     81 DSVVVLLCRQPCLSQSS-KDMNWDLSQWQPLIDDRQFLPWL 120
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 685-874 2.84e-80

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: 259.86  E-value: 2.84e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  685 MHPALSAFPSNIFYEGSLQNGVTAADRVkkgFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKITTRLLKA 764
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARL---NPPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  765 GAKPDQIGIITPYEGQRSYLVQYMQFSGSlhtkLYQQVEIASVDAFQGREKDFIILSCVRANEHQG-IGFLNDPRRLNVA 843
Cdd:cd18808     78 GVKPSSIGVITPYRAQVALIRELLRKRGG----LLEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1591540479  844 LTRAKYGVIIVGNPKALSKQPLWNNLLNNYK 874
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 ...
 661-858 2.50e-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: 257.86  E-value: 2.50e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  661 LSQSLFERLVVLG-IRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTAADRVKKGfDFQWPQPDKPMFFY-VTQGQEEI 738
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIdVDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  739 ASSGTSYLNRTEAANVEKITTRLLKAGAKPD-QIGIITPYEGQRSYLVQYmqFSGSLHTKLYqqVEIASVDAFQGREKDF 817
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPEEPsDIGVITPYRAQVRLIRKL--LKRKLGGKLE--IEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  818 IILSCVRANEHQGIGFLNDPRRLNVALTRAKYGVIIVGNPK 858
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
554-873 2.91e-70

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 251.59  E-value: 2.91e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  554 ELQKLQQLKDETGELSSADEKRyRALKRTAERELLMNADVICCTCVGAGD-PRLAKMQFRSILIDESTQATEPECMVPVV 632
Cdd:COG1112    499 LIAELREAARLRRALRRELKKR-RELRKLLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALA 577

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  633 LgAKQLILVGDHCQLGPVVMC---KKAAKAGLSQSLFERLV-VLGIRPIRLQVQYRMHPALSAFPSNIFYEGSLQNGVTA 708
Cdd:COG1112    578 R-AKRVVLVGDPKQLPPVVFGeeaEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSP 656

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  709 ADRvkkgfdfQWPQPDKPMFFYVTQGQEEiaSSGTSYLNRTEAANVEKITTRLLKAGAKPDQIGIITPYEGQRSYLVQYM 788
Cdd:COG1112    657 KAR-------RLADPDSPLVFIDVDGVYE--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELL 727

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  789 QfsgSLHTKLYQQVEIASVDAFQGREKDFIILSCVRANEH---QGIGFLN-DPRRLNVALTRAKYGVIIVGNPKALSKQP 864
Cdd:COG1112    728 R---EALGDGLEPVFVGTVDRFQGDERDVIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDP 804


                   ....*....
gi 1591540479  865 LwNNLLNNY 873
Cdd:COG1112    805 S-TPALKRL 812
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 306-394 3.00e-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: 177.72  E-value: 3.00e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  306 TQDNITVRWDLGLNKKRIAYFTLPKTD-SDMRLMQGDEICLRYKGDLAPPWKGIGHVIKVPDNYGDEIAIELRSSVGAPV 384
Cdd:cd21407      1 TQENISVRWDVGLNKKRLAYFTLPKLDeSELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKNAPT 80

                           90
                   ....*....|
gi 1591540479  385 EIPHNFQVDF 394
Cdd:cd21407     81 EITTGFSVEF 90
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 452-684 7.31e-52

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: 180.50  E-value: 7.31e-52
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATIVYHLSRQGNgPVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSR 530
Cdd:cd18044      2 LNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRIGHPAR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  531 EaiespvsflalhnqisnmdsmpeLQKLQQlkdetgelSSADEkryralkrtaerelLMNADVICCTCVGAGDPRLAK-M 609
Cdd:cd18044     81 L-----------------------LESVLD--------HSLDA--------------LVAAQVVLATNTGAGSRQLLPnE 115

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1591540479  610 QFRSILIDESTQATEPECMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPI--RLQVQYR 684
Cdd:cd18044    116 LFDVVVIDEAAQALEASCWIPL-LKARRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 455-652 2.32e-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: 175.61  E-value: 2.32e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  455 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTsatIVYHLSRQGNGP---------VLVCAPSNIAVDQLTEKIDKTG----L 520
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTT---IVELIRQLLSYPatsaaagprILVCAPSNAAVDNILERLLRKGqkygP 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  521 KVVRLCAKsrEAIESPVSFLALHNQISNMDSMPEL------------------------------------------QKL 558
Cdd:pfam13086   78 KIVRIGHP--AAISEAVLPVSLDYLVESKLNNEEDaqivkdiskeleklakalrafekeiivekllksrnkdkskleQER 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  559 QQLKDETGELSsadeKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKM-QFRSILIDESTQATEPECMVPVVLGAKQ 637
Cdd:pfam13086  156 RKLRSERKELR----KELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKK 231

                          250
                   ....*....|....*
gi 1591540479  638 LILVGDHCQLGPVVM 652
Cdd:pfam13086  232 VVLVGDPKQLPPTVI 246
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 452-684 1.91e-48

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: 173.86  E-value: 1.91e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHL------------SRQGNGPVLVCAPSNIAVDQLTEKIDKT- 518
Cdd:cd18040      2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFakqnreiqsvsgEGDGGPCVLYCGPSNKSVDVVAELLLKVp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  519 GLKVVRLCAKSREAIESPV---------------------SFLALHNQISNmDSMPELQKLQQ----LKDETGELSSADE 573
Cdd:cd18040     82 GLKILRVYSEQIETTEYPIpneprhpnkksereskpnselSSITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  574 KRYRALKRTAERELLMNADVICCTCVGAGDPRL-AKMQFRSILIDESTQATEPECMVPVVLG--AKQLILVGDHCQLGPV 650
Cdd:cd18040    161 KTYKILIWEARFEELETVDVILCTCSEAASQKMrTHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRPV 240

                          250       260       270
                   ....*....|....*....|....*....|....
gi 1591540479  651 VMCKKAAKAGLSQSLFERLVVlgiRPIRLQVQYR 684
Cdd:cd18040    241 VQNKEAQKLGLGRSLFERYAE---KACMLDTQYR 271
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 452-669 3.05e-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: 168.57  E-value: 3.05e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSATIVYHLSRQGNGP-VLVCAPSNIAVDQLTEKIDKTGLK---VV 523
Cdd:cd18038      2 LNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPPEArILVCAPSNSAADLLAERLLNALVTkreIL 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  524 RLCAKSREAIESPVSFLALHNQISN-MDSMPELQKLqqlkdetgelssadeKRYRalkrtaerellmnadVICCTCVGAG 602
Cdd:cd18038     82 RLNAPSRDRASVPPELLPYCNSKAEgTFRLPSLEEL---------------KKYR---------------IVVCTLMTAG 131

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1591540479  603 dpRLAKMQ-----FRSILIDESTQATEPECMVPVVLGAK---QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 669
Cdd:cd18038    132 --RLVQAGvpnghFTHIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERL 204
UPF1_1B_dom pfam18141
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ...
 305-395 1.37e-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: 155.93  E-value: 1.37e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  305 QTQDNITVRWDLGLNKKRIAYFTLPKTDS-DMRLMQGDEICLRYKGDLAPPWKGIGHVIKVPDNYGDEIAIELR-SSVGA 382
Cdd:pfam18141    1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSgEMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVTLELRsSSNNP 80

                           90
                   ....*....|...
gi 1591540479  383 PVEIPHNFQVDFV 395
Cdd:pfam18141   81 PTDLTHGFTVEFV 93
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 452-684 8.56e-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: 8.56e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSATIVYHL------------------------SRQGNGPVLVCAPSN 505
Cdd:cd18042      1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrklqrnlnNKKKKNRILVCAPSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  506 IAVDQLTEKIDKTGL----------KVVRLcaksreaiespvsflalhnqisnmdsmpelqklqqlkdetGelssadekr 575
Cdd:cd18042     81 AAVDEIVLRLLSEGFldgdgrsykpNVVRV----------------------------------------G--------- 111

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  576 yralKRTAERELLMNADVICCTCVGAGDPRLAKMQ--FRSILIDESTQATEPECMVPVVLGAKQLILVGDHCQLGPVVMC 653
Cdd:cd18042    112 ----RQELRASILNEADIVCTTLSSSGSDLLESLPrgFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFS 187

                          250       260       270
                   ....*....|....*....|....*....|.
gi 1591540479  654 KKAAKAGLSQSLFERLVVLGIRPIRLQVQYR 684
Cdd:cd18042    188 KVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 452-684 4.15e-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: 144.30  E-value: 4.15e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSATIVYHLSRQGNGpVLVCAPSNIAVDQLTEKIDKTGLKVVRLCAKSR 530
Cdd:cd18041      2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  531 eaIESPVSFLALHNQISNMDSMPELQklqqlkdetgelssadekryralkrtaerELLMNADVICCTCVGAGDPRLAKMQ 610
Cdd:cd18041     81 --IHPDVQEFTLEAILKSCKSVEELE-----------------------------SKYESVSVVATTCLGINHPIFRRRT 129

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1591540479  611 FRSILIDESTQATEPECMVPVVLgAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIR-LQVQYR 684
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 ...
 308-393 2.07e-31

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: 118.18  E-value: 2.07e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  308 DNITVRWDLGLNKKRIAYFTLPKTDSDMRLMQGDEICLRYKGDLAPPWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEIP 387
Cdd:cd21344      1 LIITVRWRLALNDFRGAYFSLEKGKSQCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALELKGSTTYPLTVT 80


                   ....*.
gi 1591540479  388 HNFQVD 393
Cdd:cd21344     81 HIFVLT 86
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 451-670 3.61e-31

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: 122.48  E-value: 3.61e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  451 DLNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----TIVYHL--SRqgngpVLVCAPSNIAVDQLTEKIDKTGL 520
Cdd:cd18078      1 DLNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLprSR-----ILVCAPSNSAADLVTSRLHESKV 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  521 KVVRLCAKsreaiespvsfLALHNQISNMDSmpelqklqqlkdetgelssadEKRYRALKRTAERELLMNADVICCTCVG 600
Cdd:cd18078     76 LKPGDMVR-----------LNAVNRFESTVI---------------------DARKLYCRLGEDLSKASRHRIVISTCST 123

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1591540479  601 AGdpRLAKMQFRS-----ILIDESTQATEPECMVPVVL---GAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLV 670
Cdd:cd18078    124 AG--LLYQMGLPVghfthVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLM 199
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 468-683 4.93e-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: 118.36  E-value: 4.93e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  468 LSLIQGPPGTGKTVTSATIVYHLSRQ---GNGPVLVCAPSNIAVDQLtekidktglkvvrlcaksreaiespvsflalhn 544
Cdd:cd17914      1 LSLIQGPPGTGKTRVLVKIVAALMQNkngEPGRILLVTPTNKAAAQL--------------------------------- 47

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  545 qisnmdsmpelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprlakmqfRSILIDESTQATE 624
Cdd:cd17914     48 -------------------------------------------------------------------DNILVDEAAQILE 60

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1591540479  625 PECM--VPVVLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQY 683
Cdd:cd17914     61 PETSrlIDLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 468-684 3.11e-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: 115.80  E-value: 3.11e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  468 LSLIQGPPGTGKTVTSATIVYHLSRQGNGP-VLVCAPSNIAVDqltekidktglkvvrlcaksreaiespvsflalhnqi 546
Cdd:cd17934      1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGKrVLVTAQSNVAVD------------------------------------- 43

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  547 snmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvgagdprlakmqfrsiLIDESTQATEPE 626
Cdd:cd17934     44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  627 CMVPVvLGAKQLILVGDHCQLGPVVMCKKAAKAG----LSQSLFERLVVLGIRPIRLQVQYR 684
Cdd:cd17934     61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGlsfiLSLLLLFRLLLPGSPKVMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 452-683 1.40e-28

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: 113.41  E-value: 1.40e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA----TIVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDKTGL-KVVRLc 526
Cdd:cd17936      2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRL- 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  527 aksreaiespvsflalhnqisnmdsmpelqklqqlkdetgelssadekryralkrtaerellmNADVICCTCVGAGDPR- 605
Cdd:cd17936     81 ---------------------------------------------------------------GARVIGMTTTGAAKYRe 97

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  606 -LAKMQFRSILIDESTQATEPE---CMVPVVlgaKQLILVGDHCQLGPVVMCKK--AAKAGLSQSLFERLVVLGIRPIRL 679
Cdd:cd17936     98 lLQALGPKVVIVEEAAEVLEAHilaALTPST---EHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTL 174


                   ....
gi 1591540479  680 QVQY 683
Cdd:cd17936    175 NVQR 178
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 770-855 1.26e-25

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: 101.75  E-value: 1.26e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  770 QIGIITPYEGQRSYLVQYMQFSgSLHTKLYQQVEIASVDAFQGREKDFIILSCVRANEHqgigflnDPRRLNVALTRAKY 849
Cdd:cd18786     12 KGVVLTPYHRDRAYLNQYLQGL-SLDEFDLQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83


                   ....*.
gi 1591540479  850 GVIIVG 855
Cdd:cd18786     84 RLVIYD 89
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 453-691 6.11e-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: 6.11e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  453 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLsrQGNGP---VLVCAPSNIAVDQLTEKIDKtglkvvrlcaks 529
Cdd:cd17935      7 TPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNL--YHNFPnqrTLIVTHSNQALNQLFEKIMA------------ 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  530 reaiespvsflalhnqisnmdsmpelqklqqlkdetgelssadekryralKRTAERELL---MNADVICCTCVGAGDPR- 605
Cdd:cd17935     73 --------------------------------------------------LDIDERHLLrlgHGAKIIAMTCTHAALKRg 102

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  606 -LAKMQFR--SILIDESTQATEPECMVPVVL--------GAKQLILVGDHCQLGPVVMCKKAAK-AGLSQSLFERLVVLG 673
Cdd:cd17935    103 eLVELGFKydNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182

                          250
                   ....*....|....*...
gi 1591540479  674 IRPIRLQVQYRMHPALSA 691
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 ...
 103-192 2.13e-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: 2.13e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  103 ACSYCGIHDpacVVYCNTS--KKWFCNgrgntsgSHIVNHLVRAKCKEVTLHKdgplgetVLECYNCGCRNVFLLGFipa 180
Cdd:cd21343      1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60

                           90
                   ....*....|..
gi 1591540479  181 kadSVVVLLCRQ 192
Cdd:cd21343     61 ---GGVSYRCVD 69
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 408-862 1.09e-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: 84.64  E-value: 1.09e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  408 LKTFAVDETSVSGYIyHKLLGHEVEDVTIKCQLPKRFTAQGLpDLNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSATI 486
Cdd:COG0507     83 LTRLLEAEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRAL 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  487 VYHLSRQGnGPVLVCAPSNIAVDQLTEKIDKTGlkvvrlcaksreaiespvsfLALHnqisnmdsmpelQKLQQLKDETG 566
Cdd:COG0507    161 LAALEALG-LRVALAAPTGKAAKRLSESTGIEA--------------------RTIH------------RLLGLRPDSGR 207

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  567 elssadekryralKRTAERELLMNADVicctcvgagdprlakmqfrsILIDESTqatepecMVPVVLGAK---------- 636
Cdd:COG0507    208 -------------FRHNRDNPLTPADL--------------------LVVDEAS-------MVDTRLMAAllealpraga 247

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  637 QLILVGDHCQLGPVVmckkaakAGlsqSLFERLVVLGIRP-IRLQVQYRMhpalsAFPSNIfyegslqngVTAADRVKKG 715
Cdd:COG0507    248 RLILVGDPDQLPSVG-------AG---AVLRDLIESGTVPvVELTEVYRQ-----ADDSRI---------IELAHAIREG 303

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  716 -FDFQWPQPDKPMFFYVTQGQEEIASS-----------------------GTSYLNR----------TEAANVEKITTRL 761
Cdd:COG0507    304 dAPEALNARYADVVFVEAEDAEEAAEAivelyadrpaggediqvlaptnaGVDALNQairealnpagELERELAEDGELE 383

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  762 LKAGAK-------PD------QIGIITPYEGQRSYLVqyMQFSG----SLHTKLYQQVEIA---SVDAFQGREKD--FII 819
Cdd:COG0507    384 LYVGDRvmftrndYDlgvfngDIGTVLSIDEDEGRLT--VRFDGreivTYDPSELDQLELAyaiTVHKSQGSTFDrvILV 461

                          490       500       510       520
                   ....*....|....*....|....*....|....*....|...
gi 1591540479  820 LScvraNEHQGigfLNDPRRLNVALTRAKYGVIIVGNPKALSK 862
Cdd:COG0507    462 LP----SEHSP---LLSRELLYTALTRARELLTLVGDRDALAR 497
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 452-669 2.82e-15

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: 76.37  E-value: 2.82e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVD----QLTEKIDKTG-- 519
Cdd:cd18077      2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlyikEYLHPYVETGnp 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  520 -LKVVRLCAKSReaiespvSFLALHnqisnmdsmPELQKlQQLKDETGELssadekryralkRTAERELLMNADVICCT- 597
Cdd:cd18077     81 rARPLRVYYRNR-------WVKTVH---------PVVQK-YCLIDEHGTF------------RMPTREDVMRHRVVVVTl 131

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1591540479  598 ----CVGAGDprLAKMQFRSILIDESTQATEPECMVPVVLGAK--QLILVGDHCQLGPVVMCKKAAKAGLSQSLFERL 669
Cdd:cd18077    132 stsqYLCQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 467-669 7.63e-12

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: 66.45  E-value: 7.63e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  467 PLsLIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVDQLTekidktglkvvrlcaksREAiespvsflaLHNQI 546
Cdd:cd18076     25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADIYI-----------------REY---------FHPYV 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  547 SNMDsmPELQKLQQLKDETG-ELSSADEKRYRALK------RTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDES 619
Cdd:cd18076     78 DKGH--PEARPLRIKATDRPnAITDPDTITYCCLTkdrqcfRLPTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEA 155

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  620 TQATEPECMVPVVLGA--KQLILVGDHCQLGPVVMCKKAAKAGlSQSLFERL 669
Cdd:cd18076    156 AQMLECEALIPLSYAGpkTRVVLAGDHMQMTPKLFSVADYNRA-NHTLLNRL 206
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 456-515 1.89e-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: 1.89e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  456 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLsRQGNGPVLVCAPSNIAVDQLTEKI 515
Cdd:cd17933      2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAAL-EAEGKRVVLAAPTGKAAKRLSEST 60
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 453-652 2.42e-11

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: 62.21  E-value: 2.42e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  453 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQGNGpVLVCAPSNIAvdqltekidktgLKVVRLcaksrea 532
Cdd:cd18043      1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALARGKR-VLFVSEKKAA------------LDVVRF------- 60

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  533 iesPVSFLALHnqiSNMDSMPelqklqqlkdetgelssadekryralkrtaerellmnadvicctcvgagdprLAKMQFR 612
Cdd:cd18043     61 ---PCWIMSPL---SVSQYLP----------------------------------------------------LNRNLFD 82

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1591540479  613 SILIDESTQAtEPECMVPVVLGAKQLILVGDHCQLGPVVM 652
Cdd:cd18043     83 LVIFDEASQI-PIEEALPALFRGKQVVVVGDDKQLPPSIL 121
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 452-686 3.98e-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: 57.57  E-value: 3.98e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVL--QRPLSLIQGPPGTGKTVTSATIVYHLSRQGnGPVLVCAPSNIAVDQLtekidktglkvvrlcaks 529
Cdd:pfam13604    2 LNAEQAAAVRALLtsGDRVAVLVGPAGTGKTTALKALREAWEAAG-YRVIGLAPTGRAAKVL------------------ 62

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  530 REAIESPVSFLAlhnqisnmdsmpelqklqqlkdetgelssadekryRALKRTAERELLMNADVicctcvgagdprlakm 609
Cdd:pfam13604   63 GEELGIPADTIA-----------------------------------KLLHRLGGRAGLDPGTL---------------- 91

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  610 qfrsILIDESTQATEPEcMVPVV-----LGAKqLILVGDHCQLGPVvmckkaaKAGlsqSLFERLVVLGIRPIRLQVQYR 684
Cdd:pfam13604   92 ----LIVDEAGMVGTRQ-MARLLklaedAGAR-VILVGDPRQLPSV-------EAG---GAFRDLLAAGIGTAELTEIVR 155


                   ..
gi 1591540479  685 MH 686
Cdd:pfam13604  156 QR 157
AAA_19 pfam13245
AAA domain;
459-517 8.47e-09

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 54.92  E-value: 8.47e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1591540479  459 AVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQG--NGPVLVCAPSNIAVDQLTEKIDK 517
Cdd:pfam13245    4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSERTGL 64
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 456-650 2.37e-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: 54.77  E-value: 2.37e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  456 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQ----GNGPVLVCAPSNIAVDQLTEKIDKtglKVVRLCAKSRE 531
Cdd:TIGR01447  149 RKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQspkqGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEAL 225

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  532 AIESPVSFLALHnqisnmdsmpelqKLQQLKdetgelssADEKRYRALKRTAerellMNADVicctcvgagdprlakmqf 611
Cdd:TIGR01447  226 IAALPSEAVTIH-------------RLLGIK--------PDTKRFRHHERNP-----LPLDV------------------ 261

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1591540479  612 rsILIDESTQATEP--ECMVPVVLGAKQLILVGDHCQLGPV 650
Cdd:TIGR01447  262 --LVVDEASMVDLPlmAKLLKALPPNTKLILLGDKNQLPSV 300
ResIII pfam04851
Type III restriction enzyme, res subunit;
452-526 8.55e-07

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 49.98  E-value: 8.55e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  452 LNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSATIVYHLSRQGNG-PVLVCAPSNIAVDQLTEKIDKTGLKVVRL 525
Cdd:pfam04851    4 LRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIkKVLFLVPRKDLLEQALEEFKKFLPNYVEI 83


                   .
gi 1591540479  526 C 526
Cdd:pfam04851   84 G 84
DEXDc smart00487
DEAD-like helicases superfamily;
456-517 1.73e-06

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 49.80  E-value: 1.73e-06
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479   456 QVYAVKTVLQRPLS-LIQGPPGTGKTVTSAT-IVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDK 517
Cdd:smart00487   13 QKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELKK 76
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 449-854 8.03e-05

helicase domain of coronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. 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: 409652 [Multi-domain]  Cd Length: 341  Bit Score: 45.98  E-value: 8.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  449 LPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSrqgNGPVLVCAPSNIAVDQLTEKIDKTgLKVvRLCAK 528
Cdd:cd21718      8 IPHDFSNHVPSYQKIGKQKYTTVQGPPGTGKSHFAIGLALYYP---GARIVYTACSHAAVDALCEKASKW-LPN-DKCSR 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  529 ---SREAIESPVSFLALHNQ----ISNMDSMPELqklqqlkdetgelssadekryralkrtaerellmNADVIcctcvga 601
Cdd:cd21718     83 ivpQRARVECFDGFKVNNTNaqyiFSTINALPEC----------------------------------SADIV------- 121

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  602 gdprlakmqfrsiLIDESTQATEPE-CMVPVVLGAKQLILVGDHCQL-GPVVMCKKAAKAGLSQSLFERLVVlGIRP-IR 678
Cdd:cd21718    122 -------------VVDEVSMCTNYDlSVVNARLKYKHIVYVGDPAQLpAPRTLLTEGSLEPKDYNVVTRLMV-GSGPdVF 187

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  679 LQVQYRMHPALSAFPSNIFYEGSLQngvtaadrvkkgfdfqwPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVEKIT 758
Cdd:cd21718    188 LSKCYRCPKEIVDTVSKLVYDNKLK-----------------AIKPKSRQCFKTFGKGDVRHDNGSAINRPQLEFVKRFL 250

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  759 TRllkaGAKPDQIGIITPYEGQRSYLVQYMQFSgslhtklyqqveIASVDAFQGREKDFIILsCVRANEHQGIGFlndpR 838
Cdd:cd21718    251 DR----NPRWRKAVFISPYNAMNNRASRLLGLS------------TQTVDSSQGSEYDYVIF-CQTTDTAHALNI----N 309

                          410
                   ....*....|....*.
gi 1591540479  839 RLNVALTRAKYGVIIV 854
Cdd:cd21718    310 RFNVAITRAKHGILVI 325
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 802-849 8.95e-05

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: 41.38  E-value: 8.95e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1591540479  802 VEIASVDAFQG---REKDFIILSCVRanehqgigflNDPRRLNVALTRAKY 849
Cdd:cd09300      8 VLIAVN*ALTGfdaPELNTIIVDKNL----------RSYRGLNQAFGRANR 48
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
470-517 1.56e-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: 1.56e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1591540479  470 LIQGPPGTGKTVTSATIVYHLSRQgnGPVLVCAPSNIAVDQLTEKIDK 517
Cdd:COG1061    104 LVVAPTGTGKTVLALALAAELLRG--KRVLVLVPRRELLEQWAEELRR 149
DEXQc_bact_SNF2 cd18013
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
 456-581 2.33e-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: 43.88  E-value: 2.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  456 QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLSRQGN-GPVLVCAPSNIAVDQLTEKIDK----TGLKVVRLCAKSR 530
Cdd:cd18013      5 QKVAINFIIEHPYCGLFLDMGLGKTVTTLTALSDLQLDDFtRRVLVIAPLRVARSTWPDEVEKwnhlRNLTVSVAVGTER 84

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1591540479  531 E---AIESPVSFLalhnqISNMDSMPELQKLQQLK--------DETGELSSADEKRYRALKR 581
Cdd:cd18013     85 QrskAANTPADLY-----VINRENLKWLVNKSGDPwpfdmvviDELSSFKSPRSKRFKALRK 141
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 793-854 4.59e-04

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: 43.75  E-value: 4.59e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1591540479  793 SLHTKLYQQV--EIASVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRAKYGVIIV 854
Cdd:cd21720    269 AMNQRAYRMLglNVQTVDSSQGSEYDYVIF-CVTADSQHALNI----NRFNVALTRAKRGILVV 327
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 456-536 1.44e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 40.56  E-value: 1.44e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1591540479  456 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSATIVYHLSRQGNGPVLVCAPSNIAVDQLTEKIDKTGLkVVRLCAKS 529
Cdd:pfam13191    8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86


                   ....*..
gi 1591540479  530 REAIESP 536
Cdd:pfam13191   87 ESSLLEA 93
deltaCoV_Nsp13-helicase cd21721
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ...
 806-854 2.01e-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: 41.83  E-value: 2.01e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1591540479  806 SVDAFQGREKDFIILsCVRANEHQGIGFlndpRRLNVALTRAKYGVIIV 854
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.
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