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Conserved domains on  [gi|28922775|gb|EAA31997|]
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ATP-dependent helicase NAM7 [Neurospora crassa OR74A]

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 ...
 455-688 1.01e-161

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: 477.12  E-value: 1.01e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKSR 534
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  535 EDVESSVSFLALHEQVRMNTTNKELDGLVKLKTETGELSSQDEKRFKQLTRQAEREILQNADVVCCTCVGAGDPRLSKMK 614
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28922775  615 FRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPIRLKVQYR 688
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 101-251 1.58e-103

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: 321.12  E-value: 1.58e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    101 HACAYCGIHSPSSVVKCLTCNKWFCSAKGSAFSSHIVNHLVRARHKEVQLHPESSLGDTVLECYNCGTKNVFILGFIPAK 180
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775    181 SDTVVVLLCRQPCGASTSTKDMSWDISRWQPLIEDRAFLNWLVTPPTDAEQLRARHLTPPMIAKLEEMWKE 251
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKD 151
TIGR00376 super family cl36628
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 335-885 1.00e-92

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: 309.82  E-value: 1.00e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    335 DVKLAVGDEMRLKYKGELRPPWEGVgyVIKIPNNQsdeVEVELrksanDKSVPTECTHNFSADYVWKATSYDRMQLAMKT 414
Cdd:TIGR00376   55 ATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVAL-----EESVPQWSLKRVRIDLYANDVTFKRMKEALRA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    415 FAVDEMSVSGyifhKLLGHEvqvAPTKITMPKKFHvPGLPELNASQIAAIKQVLSNP-LSLIQGPPGTGKTVTSATIIYH 493
Cdd:TIGR00376  125 LTENHSRLLE----FLLGRE---APSKASEIHDFQ-FFDPNLNESQKEAVLFALSSKdLFLIHGPPGTGKTRTVVELIRQ 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    494 LAKmSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRL---TAKSREDVESSVSFLAL-HEQ-------------------- 549
Cdd:TIGR00376  197 LVK-RGLRVLVTAPSNIAVDNLLERLALCDQKIVRLghpARLLKSNKQHSLDYLIEnHPKyqivadirekidelieernk 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    550 -----------------VRMNTTNKELDGLVKLK-------TETGELSSQDEKRFKQLTRQAEREILQNADVVCCTcvgA 605
Cdd:TIGR00376  276 ktkpspqkrrglsdikiLRKALKKREARGIESLKiasmaewIETNKSIDRLLKLLPESEERIMNEILAESDATNSM---A 352

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    606 GDPRLSKMKFRNVLIDESTQSAEPECMIPLVLGCKqVVLVGDHKQLGPVIMNKKAAkaGLNQSLFERLVKLQFTPIR-LK 684
Cdd:TIGR00376  353 GSEILNGQYFDVAVIDEASQAMEPSCLIPLLKARK-LILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSRtLN 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    685 VQYRMHPCLSEFPSNMFYEGSLQNGVTAAERLRKDVDFPWPVPET-------PMMFW--SNLGNEEIS-ASGTSYLNRTE 754
Cdd:TIGR00376  430 VQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIdtSGCELFELKeADSTSKYNPGE 509

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    755 AANVEKIVTRFFKAGVKPADIGVITPYEGQRSYIVNTMQntgtfkkESYREVEVASVDAFQGREKDFIVLSCVRSNENQG 834
Cdd:TIGR00376  510 AELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLE-------HRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGE 582

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|.
gi 28922775    835 IGFLSDPRRLNVALTRAKYGLVIIGNPKVLCKHELWHHLLVHFKDKKCLVE 885
Cdd:TIGR00376  583 VGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 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 ...
 455-688 1.01e-161

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: 477.12  E-value: 1.01e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKSR 534
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  535 EDVESSVSFLALHEQVRMNTTNKELDGLVKLKTETGELSSQDEKRFKQLTRQAEREILQNADVVCCTCVGAGDPRLSKMK 614
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28922775  615 FRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPIRLKVQYR 688
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 101-251 1.58e-103

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: 321.12  E-value: 1.58e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    101 HACAYCGIHSPSSVVKCLTCNKWFCSAKGSAFSSHIVNHLVRARHKEVQLHPESSLGDTVLECYNCGTKNVFILGFIPAK 180
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775    181 SDTVVVLLCRQPCGASTSTKDMSWDISRWQPLIEDRAFLNWLVTPPTDAEQLRARHLTPPMIAKLEEMWKE 251
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKD 151
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 335-885 1.00e-92

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: 309.82  E-value: 1.00e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    335 DVKLAVGDEMRLKYKGELRPPWEGVgyVIKIPNNQsdeVEVELrksanDKSVPTECTHNFSADYVWKATSYDRMQLAMKT 414
Cdd:TIGR00376   55 ATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVAL-----EESVPQWSLKRVRIDLYANDVTFKRMKEALRA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    415 FAVDEMSVSGyifhKLLGHEvqvAPTKITMPKKFHvPGLPELNASQIAAIKQVLSNP-LSLIQGPPGTGKTVTSATIIYH 493
Cdd:TIGR00376  125 LTENHSRLLE----FLLGRE---APSKASEIHDFQ-FFDPNLNESQKEAVLFALSSKdLFLIHGPPGTGKTRTVVELIRQ 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    494 LAKmSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRL---TAKSREDVESSVSFLAL-HEQ-------------------- 549
Cdd:TIGR00376  197 LVK-RGLRVLVTAPSNIAVDNLLERLALCDQKIVRLghpARLLKSNKQHSLDYLIEnHPKyqivadirekidelieernk 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    550 -----------------VRMNTTNKELDGLVKLK-------TETGELSSQDEKRFKQLTRQAEREILQNADVVCCTcvgA 605
Cdd:TIGR00376  276 ktkpspqkrrglsdikiLRKALKKREARGIESLKiasmaewIETNKSIDRLLKLLPESEERIMNEILAESDATNSM---A 352

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    606 GDPRLSKMKFRNVLIDESTQSAEPECMIPLVLGCKqVVLVGDHKQLGPVIMNKKAAkaGLNQSLFERLVKLQFTPIR-LK 684
Cdd:TIGR00376  353 GSEILNGQYFDVAVIDEASQAMEPSCLIPLLKARK-LILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSRtLN 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    685 VQYRMHPCLSEFPSNMFYEGSLQNGVTAAERLRKDVDFPWPVPET-------PMMFW--SNLGNEEIS-ASGTSYLNRTE 754
Cdd:TIGR00376  430 VQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIdtSGCELFELKeADSTSKYNPGE 509

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    755 AANVEKIVTRFFKAGVKPADIGVITPYEGQRSYIVNTMQntgtfkkESYREVEVASVDAFQGREKDFIVLSCVRSNENQG 834
Cdd:TIGR00376  510 AELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLE-------HRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGE 582

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|.
gi 28922775    835 IGFLSDPRRLNVALTRAKYGLVIIGNPKVLCKHELWHHLLVHFKDKKCLVE 885
Cdd:TIGR00376  583 VGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 665-862 3.30e-81

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: 262.87  E-value: 3.30e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    665 LNQSLFERLVKLQFTPIR-LKVQYRMHPCLSEFPSNMFYEGSLQNGVTAAERlRKDVDFPWPVPETPMMFWS-NLGNEEI 742
Cdd:pfam13087    1 LDRSLFERLQELGPSAVVmLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAER-PLPDDFHLPDPLGPLVFIDvDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    743 SASGTSYLNRTEAANVEKIVTRFFKAGV-KPADIGVITPYEGQRSYIVNTMQNTGTFKkesyREVEVASVDAFQGREKDF 821
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGK----LEIEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 28922775    822 IVLSCVRSNENQGIGFLSDPRRLNVALTRAKYGLVIIGNPK 862
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 689-878 3.18e-79

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: 256.78  E-value: 3.18e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  689 MHPCLSEFPSNMFYEGSLQNGVTAAERLRkdvDFPWPVPETPMMFWSNLGNEEISASGTSYLNRTEAANVEKIVTRFFKA 768
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARLN---PPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  769 GVKPADIGVITPYEGQRSYIVNTMQNTGTFkkesYREVEVASVDAFQGREKDFIVLSCVRSNENQG-IGFLSDPRRLNVA 847
Cdd:cd18808   78 GVKPSSIGVITPYRAQVALIRELLRKRGGL----LEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 28922775  848 LTRAKYGLVIIGNPKVLCKHELWHHLLVHFK 878
Cdd:cd18808  154 LTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 102-222 2.40e-78

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: 251.78  E-value: 2.40e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  102 ACAYCGIHSPSSVVKCLTCNKWFCSAKGSAFSSHIVNHLVRARHKEVQLHPESSLGDTVLECYNCGTKNVFILGFIPAKS 181
Cdd:cd21400    1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 28922775  182 DTVVVLLCRQPCgASTSTKDMSWDISRWQPLIEDRAFLNWL 222
Cdd:cd21400   81 DSVVVLLCRQPC-LSQSSKDMNWDLSQWQPLIDDRQFLPWL 120
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
506-880 1.37e-66

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 240.80  E-value: 1.37e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  506 APSNVAVDQLCERIHRTGLKVVRLTAKSREDVESSVSFLALHEQVRMNTTNKELDGLVKLKtetgELSSQDEKRFKQLTR 585
Cdd:COG1112  450 ALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLR----RALRRELKKRRELRK 525

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  586 QAEREILQNADVVCCTCVGAGD-PRLSKMKFRNVLIDESTQSAEPECMIPLVLGcKQVVLVGDHKQLGPVIMN---KKAA 661
Cdd:COG1112  526 LLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALARA-KRVVLVGDPKQLPPVVFGeeaEEVA 604

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  662 KAGLNQSLFERLVK-LQFTPIRLKVQYRMHPCLSEFPSNMFYEGSLQNGVTAAERlrkdvdfPWPVPETPMMFWSNLGNE 740
Cdd:COG1112  605 EEGLDESLLDRLLArLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVY 677

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  741 EisASGTSYLNRTEAANVEKIVTRFFKAGVKPADIGVITPYEGQRSYIVNTMQNTGTFKKEsyrEVEVASVDAFQGREKD 820
Cdd:COG1112  678 E--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALGDGLE---PVFVGTVDRFQGDERD 752

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28922775  821 FIVLSCVRSNEN---QGIGFLS-DPRRLNVALTRAKYGLVIIGNPKVL---CKHELWHHLLVHFKDK 880
Cdd:COG1112  753 VIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYLERA 819
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 459-658 2.00e-55

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: 192.94  E-value: 2.00e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    459 SQIAAIKQVLSNP-LSLIQGPPGTGKTVTSATIIYHLAKMSN------SQVLVCAPSNVAVDQLCERIHRTG----LKVV 527
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTTIVELIRQLLSYPAtsaaagPRILVCAPSNAAVDNILERLLRKGqkygPKIV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    528 RLTAKSRedVESSVSFLALHEQVR-----------MNTTNKELDGLVKLKTETGELSSQDE------------------- 577
Cdd:pfam13086   81 RIGHPAA--ISEAVLPVSLDYLVEsklnneedaqiVKDISKELEKLAKALRAFEKEIIVEKllksrnkdkskleqerrkl 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    578 --------KRFKQLTRQAEREILQNADVVCCTCVGAGDPRLSKM-KFRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDH 648
Cdd:pfam13086  159 rserkelrKELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDP 238

                          250
                   ....*....|
gi 28922775    649 KQLGPVIMNK 658
Cdd:pfam13086  239 KQLPPTVISK 248
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 455-864 2.87e-15

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: 80.02  E-value: 2.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVL-SNPLSLIQGPPGTGKTVTSATIIYHLAKMsNSQVLVCAPSNVAVDQLCER-------IHRtglkv 526
Cdd:COG0507  124 TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEAL-GLRVALAAPTGKAAKRLSEStgieartIHR----- 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  527 vrltaksredvessvsFLALheqvrmnttnkeldglvklktetgelsSQDEKRFkqltRQAEREILQNADVvcctcvgag 606
Cdd:COG0507  198 ----------------LLGL---------------------------RPDSGRF----RHNRDNPLTPADL--------- 221

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  607 dprlskmkfrnVLIDESTqsaepecMIPLVL-----------GCkQVVLVGDHKQLGPVimnkkaaKAGlnqSLFERLVK 675
Cdd:COG0507  222 -----------LVVDEAS-------MVDTRLmaallealpraGA-RLILVGDPDQLPSV-------GAG---AVLRDLIE 272

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  676 LQFTP-IRLKVQYR------------------MHPCLSEFPSNmFYEGSLQNGVTAAERLRKDV-DFPWPVPETPMMFWS 735
Cdd:COG0507  273 SGTVPvVELTEVYRqaddsriielahairegdAPEALNARYAD-VVFVEAEDAEEAAEAIVELYaDRPAGGEDIQVLAPT 351

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  736 NLGNEEISASGTSYLNRTEAANVEKIV--TRFFKAG-------------VKPADIGVITPYEGQRSYIVNTMQNTG--TF 798
Cdd:COG0507  352 NAGVDALNQAIREALNPAGELERELAEdgELELYVGdrvmftrndydlgVFNGDIGTVLSIDEDEGRLTVRFDGREivTY 431

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775  799 KKESYREVEVA---SVDAFQGREKD--FIVLSCVRSNenqgigfLSDPRRLNVALTRAKYGLVIIGNPKVL 864
Cdd:COG0507  432 DPSELDQLELAyaiTVHKSQGSTFDrvILVLPSEHSP-------LLSRELLYTALTRARELLTLVGDRDAL 495
DEXDc smart00487
DEAD-like helicases superfamily;
448-541 4.07e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 57.50  E-value: 4.07e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775     448 FHVPGLPELNASQIAAIKQVLSNPLS-LIQGPPGTGKTVTSAT-IIYHLAKMSNSQVLVCAPSNVAVDQLCERI-----H 520
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100
                    ....*....|....*....|.
gi 28922775     521 RTGLKVVRLTAKSREDVESSV 541
Cdd:smart00487   81 LGLKVVGLYGGDSKREQLRKL 101
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 426-654 1.60e-05

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: 48.99  E-value: 1.60e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    426 IFHKLLgheVQVAPTKITMPKKF--HVPGLPELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSQ-- 501
Cdd:TIGR01447  116 LAAKLR---TLLEARKRTAPSAIleNLFPLLNEQNWRKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQgk 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    502 --VLVCAPSNVAVDQLCERIhRTGLKVVRLTAKSREDVESSVsflalheqvrmnTTNKELDGLVKlktetgelssqDEKR 579
Cdd:TIGR01447  193 lrIALAAPTGKAAARLAESL-RKAVKNLAAAEALIAALPSEA------------VTIHRLLGIKP-----------DTKR 248

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    580 FkqltRQAEREILqNADVvcctcvgagdprlskmkfrnVLIDESTqsaepecMIPLVLGCK---------QVVLVGDHKQ 650
Cdd:TIGR01447  249 F----RHHERNPL-PLDV--------------------LVVDEAS-------MVDLPLMAKllkalppntKLILLGDKNQ 296


                   ....
gi 28922775    651 LGPV 654
Cdd:TIGR01447  297 LPSV 300
 
Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 455-688 1.01e-161

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: 477.12  E-value: 1.01e-161
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKSR 534
Cdd:cd18039    1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  535 EDVESSVSFLALHEQVRMNTTNKELDGLVKLKTETGELSSQDEKRFKQLTRQAEREILQNADVVCCTCVGAGDPRLSKMK 614
Cdd:cd18039   81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRNADVICCTCVGAGDPRLSKMK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28922775  615 FRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPIRLKVQYR 688
Cdd:cd18039  161 FRTVLIDEATQATEPECLIPLVHGAKQVILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 101-251 1.58e-103

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: 321.12  E-value: 1.58e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    101 HACAYCGIHSPSSVVKCLTCNKWFCSAKGSAFSSHIVNHLVRARHKEVQLHPESSLGDTVLECYNCGTKNVFILGFIPAK 180
Cdd:pfam09416    1 HACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAK 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775    181 SDTVVVLLCRQPCGASTSTKDMSWDISRWQPLIEDRAFLNWLVTPPTDAEQLRARHLTPPMIAKLEEMWKE 251
Cdd:pfam09416   81 SDSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQITPAQINKLEELWKD 151
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 335-885 1.00e-92

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: 309.82  E-value: 1.00e-92
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    335 DVKLAVGDEMRLKYKGELRPPWEGVgyVIKIPNNQsdeVEVELrksanDKSVPTECTHNFSADYVWKATSYDRMQLAMKT 414
Cdd:TIGR00376   55 ATEISVGDIVLVSRGNPLQSDLTGV--VTRVGKRF---ITVAL-----EESVPQWSLKRVRIDLYANDVTFKRMKEALRA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    415 FAVDEMSVSGyifhKLLGHEvqvAPTKITMPKKFHvPGLPELNASQIAAIKQVLSNP-LSLIQGPPGTGKTVTSATIIYH 493
Cdd:TIGR00376  125 LTENHSRLLE----FLLGRE---APSKASEIHDFQ-FFDPNLNESQKEAVLFALSSKdLFLIHGPPGTGKTRTVVELIRQ 196

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    494 LAKmSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRL---TAKSREDVESSVSFLAL-HEQ-------------------- 549
Cdd:TIGR00376  197 LVK-RGLRVLVTAPSNIAVDNLLERLALCDQKIVRLghpARLLKSNKQHSLDYLIEnHPKyqivadirekidelieernk 275

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    550 -----------------VRMNTTNKELDGLVKLK-------TETGELSSQDEKRFKQLTRQAEREILQNADVVCCTcvgA 605
Cdd:TIGR00376  276 ktkpspqkrrglsdikiLRKALKKREARGIESLKiasmaewIETNKSIDRLLKLLPESEERIMNEILAESDATNSM---A 352

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    606 GDPRLSKMKFRNVLIDESTQSAEPECMIPLVLGCKqVVLVGDHKQLGPVIMNKKAAkaGLNQSLFERLVKLQFTPIR-LK 684
Cdd:TIGR00376  353 GSEILNGQYFDVAVIDEASQAMEPSCLIPLLKARK-LILAGDHKQLPPTILSHDAE--ELSLTLFERLIKEYPERSRtLN 429

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    685 VQYRMHPCLSEFPSNMFYEGSLQNGVTAAERLRKDVDFPWPVPET-------PMMFW--SNLGNEEIS-ASGTSYLNRTE 754
Cdd:TIGR00376  430 VQYRMNQKIMEFPSREFYNGKLTAHESVANILLRDLPKVEATESEddletgiPLLFIdtSGCELFELKeADSTSKYNPGE 509

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    755 AANVEKIVTRFFKAGVKPADIGVITPYEGQRSYIVNTMQntgtfkkESYREVEVASVDAFQGREKDFIVLSCVRSNENQG 834
Cdd:TIGR00376  510 AELVSEIIQALVKMGVPANDIGVITPYDAQVDLLRQLLE-------HRHIDIEVSSVDGFQGREKEVIIISFVRSNRKGE 582

                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|.
gi 28922775    835 IGFLSDPRRLNVALTRAKYGLVIIGNPKVLCKHELWHHLLVHFKDKKCLVE 885
Cdd:TIGR00376  583 VGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 665-862 3.30e-81

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: 262.87  E-value: 3.30e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    665 LNQSLFERLVKLQFTPIR-LKVQYRMHPCLSEFPSNMFYEGSLQNGVTAAERlRKDVDFPWPVPETPMMFWS-NLGNEEI 742
Cdd:pfam13087    1 LDRSLFERLQELGPSAVVmLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAER-PLPDDFHLPDPLGPLVFIDvDGSEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    743 SASGTSYLNRTEAANVEKIVTRFFKAGV-KPADIGVITPYEGQRSYIVNTMQNTGTFKkesyREVEVASVDAFQGREKDF 821
Cdd:pfam13087   80 SDGGTSYSNEAEAELVVQLVEKLIKSGPeEPSDIGVITPYRAQVRLIRKLLKRKLGGK----LEIEVNTVDGFQGREKDV 155

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 28922775    822 IVLSCVRSNENQGIGFLSDPRRLNVALTRAKYGLVIIGNPK 862
Cdd:pfam13087  156 IIFSCVRSNEKGGIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 689-878 3.18e-79

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: 256.78  E-value: 3.18e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  689 MHPCLSEFPSNMFYEGSLQNGVTAAERLRkdvDFPWPVPETPMMFWSNLGNEEISASGTSYLNRTEAANVEKIVTRFFKA 768
Cdd:cd18808    1 MHPEISEFPSKLFYEGKLKAGVSVAARLN---PPPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEAELVVELVKYLLKS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  769 GVKPADIGVITPYEGQRSYIVNTMQNTGTFkkesYREVEVASVDAFQGREKDFIVLSCVRSNENQG-IGFLSDPRRLNVA 847
Cdd:cd18808   78 GVKPSSIGVITPYRAQVALIRELLRKRGGL----LEDVEVGTVDNFQGREKDVIILSLVRSNESGGsIGFLSDPRRLNVA 153

                        170       180       190
                 ....*....|....*....|....*....|.
gi 28922775  848 LTRAKYGLVIIGNPKVLCKHELWHHLLVHFK 878
Cdd:cd18808  154 LTRAKRGLIIVGNPDTLSKDPLWKKLLEYLE 184
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 102-222 2.40e-78

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: 251.78  E-value: 2.40e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  102 ACAYCGIHSPSSVVKCLTCNKWFCSAKGSAFSSHIVNHLVRARHKEVQLHPESSLGDTVLECYNCGTKNVFILGFIPAKS 181
Cdd:cd21400    1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 28922775  182 DTVVVLLCRQPCgASTSTKDMSWDISRWQPLIEDRAFLNWL 222
Cdd:cd21400   81 DSVVVLLCRQPC-LSQSSKDMNWDLSQWQPLIDDRQFLPWL 120
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
506-880 1.37e-66

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 240.80  E-value: 1.37e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  506 APSNVAVDQLCERIHRTGLKVVRLTAKSREDVESSVSFLALHEQVRMNTTNKELDGLVKLKtetgELSSQDEKRFKQLTR 585
Cdd:COG1112  450 ALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEELEKLIAELREAARLR----RALRRELKKRRELRK 525

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  586 QAEREILQNADVVCCTCVGAGD-PRLSKMKFRNVLIDESTQSAEPECMIPLVLGcKQVVLVGDHKQLGPVIMN---KKAA 661
Cdd:COG1112  526 LLWDALLELAPVVGMTPASVARlLPLGEGSFDLVIIDEASQATLAEALGALARA-KRVVLVGDPKQLPPVVFGeeaEEVA 604

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  662 KAGLNQSLFERLVK-LQFTPIRLKVQYRMHPCLSEFPSNMFYEGSLQNGVTAAERlrkdvdfPWPVPETPMMFWSNLGNE 740
Cdd:COG1112  605 EEGLDESLLDRLLArLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFIDVDGVY 677

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  741 EisASGTSYLNRTEAANVEKIVTRFFKAGVKPADIGVITPYEGQRSYIVNTMQNTGTFKKEsyrEVEVASVDAFQGREKD 820
Cdd:COG1112  678 E--RRGGSRTNPEEAEAVVELVRELLEDGPDGESIGVITPYRAQVALIRELLREALGDGLE---PVFVGTVDRFQGDERD 752

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28922775  821 FIVLSCVRSNEN---QGIGFLS-DPRRLNVALTRAKYGLVIIGNPKVL---CKHELWHHLLVHFKDK 880
Cdd:COG1112  753 VIIFSLVYSNDEdvpRNFGFLNgGPRRLNVAVSRARRKLIVVGSRELLdsdPSTPALKRLLEYLERA 819
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 455-688 9.51e-56

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: 191.67  E-value: 9.51e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLS-NPLSLIQGPPGTGKTVTSATIIYHLAKmSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKS 533
Cdd:cd18044    1 NLNDSQKEAVKFALSqKDVALIHGPPGTGKTTTVVEIILQAVK-RGEKVLACAPSNIAVDNLVERLVALKVKVVRIGHPA 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  534 RedVESSVsflalheqvrmntTNKELDGLVKlktetgelssqdekrfkqltrqaereilqnADVVCCTCVGAGDPRL-SK 612
Cdd:cd18044   80 R--LLESV-------------LDHSLDALVA------------------------------AQVVLATNTGAGSRQLlPN 114

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28922775  613 MKFRNVLIDESTQSAEPECMIPLVLGcKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPI--RLKVQYR 688
Cdd:cd18044  115 ELFDVVVIDEAAQALEASCWIPLLKA-RRCILAGDHKQLPPTILSDKAARGGLGVTLFERLVNLYGESVvrMLTVQYR 191
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 459-658 2.00e-55

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: 192.94  E-value: 2.00e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    459 SQIAAIKQVLSNP-LSLIQGPPGTGKTVTSATIIYHLAKMSN------SQVLVCAPSNVAVDQLCERIHRTG----LKVV 527
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTTIVELIRQLLSYPAtsaaagPRILVCAPSNAAVDNILERLLRKGqkygPKIV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    528 RLTAKSRedVESSVSFLALHEQVR-----------MNTTNKELDGLVKLKTETGELSSQDE------------------- 577
Cdd:pfam13086   81 RIGHPAA--ISEAVLPVSLDYLVEsklnneedaqiVKDISKELEKLAKALRAFEKEIIVEKllksrnkdkskleqerrkl 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    578 --------KRFKQLTRQAEREILQNADVVCCTCVGAGDPRLSKM-KFRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDH 648
Cdd:pfam13086  159 rserkelrKELRRREQSLEREILDEAQIVCSTLSGAGSRLLSSLaNFDVVIIDEAAQALEPSTLIPLLRGPKKVVLVGDP 238

                          250
                   ....*....|
gi 28922775    649 KQLGPVIMNK 658
Cdd:pfam13086  239 KQLPPTVISK 248
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 456-688 5.94e-53

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: 184.72  E-value: 5.94e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQIAAIKQVLSN--PLSLIQGPPGTGKTVTSATIIYHL------------------------AKMSNSQVLVCAPSN 509
Cdd:cd18042    1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLlagkyrkyyekvkkklrklqrnlnNKKKKNRILVCAPSN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  510 VAVDQLCERIHRTGLKvvrltaksreDVESSVSFLALheqVRMnttnkeldglvklktetGelssqdekrfkqlTRQAER 589
Cdd:cd18042   81 AAVDEIVLRLLSEGFL----------DGDGRSYKPNV---VRV-----------------G-------------RQELRA 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  590 EILQNADVVCCTCVGAGDPRLSKM--KFRNVLIDESTQSAEPECMIPLVLGCKQVVLVGDHKQLGPVIMNKKAAKAGLNQ 667
Cdd:cd18042  118 SILNEADIVCTTLSSSGSDLLESLprGFDTVIIDEAAQAVELSTLIPLRLGCKRLILVGDPKQLPATVFSKVAQKLGYDR 197

                        250       260
                 ....*....|....*....|.
gi 28922775  668 SLFERLVKLQFTPIRLKVQYR 688
Cdd:cd18042  198 SLFERLQLAGYPVLMLTTQYR 218
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 456-688 2.47e-52

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: 185.04  E-value: 2.47e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKM------------SNSQVLVCAPSNVAVDQLCERI-HRT 522
Cdd:cd18040    2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAKQnreiqsvsgegdGGPCVLYCGPSNKSVDVVAELLlKVP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  523 GLKVVRLTAKSREDVE---------------------SSVSFLALHEQVRMNTTN-----KELDGLVKLKTETgeLSSQD 576
Cdd:cd18040   82 GLKILRVYSEQIETTEypipneprhpnkksereskpnSELSSITLHHRIRQPSNPhsqqiKAFEARFERTQEK--ITEED 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  577 EKRFKQLTRQAEREILQNADVVCCTCVGAGDPRLS-KMKFRNVLIDESTQSAEPECMIPLVLG--CKQVVLVGDHKQLGP 653
Cdd:cd18040  160 IKTYKILIWEARFEELETVDVILCTCSEAASQKMRtHANVKQCIVDECGMCTEPESLIPIVSAprAEQVVLIGDHKQLRP 239

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 28922775  654 VIMNKKAAKAGLNQSLFERLVKLQFTpirLKVQYR 688
Cdd:cd18040  240 VVQNKEAQKLGLGRSLFERYAEKACM---LDTQYR 271
UPF1_1B_dom pfam18141
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ...
 305-399 2.64e-46

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: 160.56  E-value: 2.64e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    305 QSEDGLQVRWHLGLNSKHVASFILPKIESGDVKLAVGDEMRLKYKGELRPPWEGVGYVIKIPNNQSDEVEVELRKSanDK 384
Cdd:pfam18141    1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSGEMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVTLELRSS--SN 78

                           90
                   ....*....|....*
gi 28922775    385 SVPTECTHNFSADYV 399
Cdd:pfam18141   79 NPPTDLTHGFTVEFV 93
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 455-676 2.78e-46

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: 165.87  E-value: 2.78e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLS----NPLSLIQGPPGTGKTVTSATIIYHLAKM-SNSQVLVCAPSNVAVDQLCERIHRTGLK---V 526
Cdd:cd18038    1 ELNDEQKLAVRNIVTgtsrPPPYIIFGPPGTGKTVTLVEAILQVLRQpPEARILVCAPSNSAADLLAERLLNALVTkreI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  527 VRLTAKSReDVESsvsflaLHEQVRMNTTNKeldglvklktetgelssqDEKRFkqltRQAEREILQNADVVCCTCVGAG 606
Cdd:cd18038   81 LRLNAPSR-DRAS------VPPELLPYCNSK------------------AEGTF----RLPSLEELKKYRIVVCTLMTAG 131

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28922775  607 dpRLSKMKFRN-----VLIDESTQSAEPECMIPLVLGCK---QVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKL 676
Cdd:cd18038  132 --RLVQAGVPNghfthIFIDEAGQATEPEALIPLSELASkntQIVLAGDPKQLGPVVRSPLARKYGLGKSLLERLMER 207
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 306-398 4.54e-46

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: 160.00  E-value: 4.54e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  306 SEDGLQVRWHLGLNSKHVASFILPKIESGDVKLAVGDEMRLKYKGELRPPWEGVGYVIKIPNNQSDEVEVELRKSANdks 385
Cdd:cd21407    1 TQENISVRWDVGLNKKRLAYFTLPKLDESELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKN--- 77

                         90
                 ....*....|...
gi 28922775  386 VPTECTHNFSADY 398
Cdd:cd21407   78 APTEITTGFSVEF 90
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 456-688 1.52e-43

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: 157.01  E-value: 1.52e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQIAAIKQVL-SNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSqVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKSR 534
Cdd:cd18041    2 LNKDQRQAIKKVLnAKDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  535 EdvessvsflalHEQVRMNTTNKELdglvklktetgelssQDEKRFKQLtrqaeREILQNADVVCCTCVGAGDPRLSKMK 614
Cdd:cd18041   81 I-----------HPDVQEFTLEAIL---------------KSCKSVEEL-----ESKYESVSVVATTCLGINHPIFRRRT 129

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28922775  615 FRNVLIDESTQSAEPECMIPLVLgCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPIR-LKVQYR 688
Cdd:cd18041  130 FDYCIVDEASQITLPICLGPLRL-AKKFVLVGDHYQLPPLVKSREARELGMDESLFKRLSEAHPDAVVqLTIQYR 203
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 456-697 3.46e-33

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: 128.26  E-value: 3.46e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQIAAIKQVL---SNPLS-LIQGPPGTGKTVT-SATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLkvvrlt 530
Cdd:cd18078    2 LNELQKEAVKRILggeCRPLPyILFGPPGTGKTVTiIEAILQVVYNLPRSRILVCAPSNSAADLVTSRLHESKV------ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  531 aksredvessvsfLALHEQVRMNTTNKeldglvklkteTGELSSQDEKRFKQLTRQAEREIlqNADVVCCTCVGAGdpRL 610
Cdd:cd18078   76 -------------LKPGDMVRLNAVNR-----------FESTVIDARKLYCRLGEDLSKAS--RHRIVISTCSTAG--LL 127

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  611 SKMKFR-----NVLIDESTQSAEPECMIPLVL---GCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKlqfTPIR 682
Cdd:cd18078  128 YQMGLPvghftHVFVDEAGQATEPESLIPLGLissRDGQIILAGDPMQLGPVIKSRLASAYGLGVSFLERLMN---RPLY 204

                        250
                 ....*....|....*
gi 28922775  683 LKVQYRMHPCLSEFP 697
Cdd:cd18078  205 LRDPNRFGESGGYNP 219
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 472-688 1.18e-29

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: 114.25  E-value: 1.18e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  472 LSLIQGPPGTGKTVTSATIIYHLAKMS-NSQVLVCAPSNVAVDqlcerihrtglkvvrltaksredvessvsflalheqv 550
Cdd:cd17934    1 ISLIQGPPGTGKTTTIAAIVLQLLKGLrGKRVLVTAQSNVAVD------------------------------------- 43

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  551 rmnttnkeldglvklktetgelssqdekrfkqltrqaereilqNADVVcctcvgagdprlskmkfrnvLIDESTQSAEPE 630
Cdd:cd17934   44 -------------------------------------------NVDVV--------------------IIDEASQITEPE 60

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 28922775  631 CMIPLvLGCKQVVLVGDHKQLGPVIMNKKAAKAGLN----QSLFERLVKLQFTPIRLKVQYR 688
Cdd:cd17934   61 LLIAL-IRAKKVVLVGDPKQLPPVVQEDHAALLGLSfilsLLLLFRLLLPGSPKVMLDTQYR 121
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 456-687 2.87e-29

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 115.33  E-value: 2.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSA----TIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGL-KVVRLT 530
Cdd:cd17936    2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVklvrALLQNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  531 AksreDVessvsflalheqVRMNTTnkeldGLVKLktetgelssqdekrfkqltrqaeREILQnadvvcctcvgagdprl 610
Cdd:cd17936   82 A----RV------------IGMTTT-----GAAKY-----------------------RELLQ----------------- 100

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  611 sKMKFRNVLIDESTQSAEPE---CMIPlvlGCKQVVLVGDHKQLGPVIMNKK--AAKAGLNQSLFERLVKLQFTPIRLKV 685
Cdd:cd17936  101 -ALGPKVVIVEEAAEVLEAHilaALTP---STEHLILIGDHKQLRPKVNVYEltAKKYNLDVSLFERLVKNGLPFVTLNV 176


                 ..
gi 28922775  686 QY 687
Cdd:cd17936  177 QR 178
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 472-687 1.89e-25

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: 102.18  E-value: 1.89e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  472 LSLIQGPPGTGKTVTSATIIYHLAKMSNSQ---VLVCAPSNVAVDQLcerihrtglkvvrltaksredvessvsflalhe 548
Cdd:cd17914    1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGEpgrILLVTPTNKAAAQL--------------------------------- 47

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  549 qvrmnttnkeldglvklktetgelssqdekrfkqltrqaereilqnadvvcctcvgagdprlskmkfRNVLIDESTQSAE 628
Cdd:cd17914   48 -------------------------------------------------------------------DNILVDEAAQILE 60

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775  629 PECMIP--LVLGCKQVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERLVKLQFTPIRLKVQY 687
Cdd:cd17914   61 PETSRLidLALDQGRVILVGDHDQLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 455-695 1.32e-22

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: 97.11  E-value: 1.32e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMS-NSQVLVCAPSNVAVDQLCERIhrtglkvvrltakS 533
Cdd:cd17935    5 KFTPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVQIISNLYHNFpNQRTLIVTHSNQALNQLFEKI-------------M 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  534 REDVEssvsflalheqvrmnttnkeldglvklktetgelssqdekrfkqltrqaEREIL---QNADVVCCTCVGAGDPR- 609
Cdd:cd17935   72 ALDID-------------------------------------------------ERHLLrlgHGAKIIAMTCTHAALKRg 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  610 -LSKM--KFRNVLIDESTQSAEPECMIPLVL--------GCKQVVLVGDHKQLGPVIMNKKAAK-AGLNQSLFERLVKLQ 677
Cdd:cd17935  103 eLVELgfKYDNILMEEAAQILEIETFIPLLLqnpedgpnRLKRLIMIGDHHQLPPVIKNMAFQKySNMEQSLFTRLVRLG 182

                        250
                 ....*....|....*...
gi 28922775  678 FTPIRLKVQYRMHPCLSE 695
Cdd:cd17935  183 VPTVDLDAQGRARASISS 200
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 774-859 1.31e-20

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: 87.11  E-value: 1.31e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  774 DIGVITPYEGQRSYIVNTMQNTGTFKKEsYREVEVASVDAFQGREKDFIVLSCVRSNENqgigflsDPRRLNVALTRAKY 853
Cdd:cd18786   12 KGVVLTPYHRDRAYLNQYLQGLSLDEFD-LQLVGAITIDSSQGLTFDVVTLYLPTANSL-------TPRRLYVALTRARK 83


                 ....*.
gi 28922775  854 GLVIIG 859
Cdd:cd18786   84 RLVIYD 89
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 457-656 4.74e-17

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: 78.39  E-value: 4.74e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  457 NASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKmSNSQVLVCAPSNVAvdqlcerihrtgLKVVRLtaksred 536
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALA-RGKRVLFVSEKKAA------------LDVVRF------- 60

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  537 vessvsflalheQVRMNTTNKELDGLvklktetgelssqdekrfkqltrqaereilqnadvvcctcvgagdpRLSKMKFR 616
Cdd:cd18043   61 ------------PCWIMSPLSVSQYL----------------------------------------------PLNRNLFD 82

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 28922775  617 NVLIDESTQSaEPECMIPLVLGCKQVVLVGDHKQLGPVIM 656
Cdd:cd18043   83 LVIFDEASQI-PIEEALPALFRGKQVVVVGDDKQLPPSIL 121
1B_UPF1_nv_SF1_Hel-like cd21344
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ...
 312-397 9.17e-17

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: 76.20  E-value: 9.17e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  312 VRWHLGLNSKHVASFILPKIESgDVKLAVGDEMRLKYKGELRPPWEGVGYVIKIPNNQSDEVEVELRKSandKSVPTECT 391
Cdd:cd21344    5 VRWRLALNDFRGAYFSLEKGKS-QCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALELKGS---TTYPLTVT 80


                 ....*.
gi 28922775  392 HNFSAD 397
Cdd:cd21344   81 HIFVLT 86
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 456-673 3.34e-16

DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350835 [Multi-domain]  Cd Length: 226  Bit Score: 79.07  E-value: 3.34e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  456 LNASQ---IAAIKQVLSNPLS--LIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVD-QLCERIH---RTG--- 523
Cdd:cd18077    2 LNAKQkeaVLAITTPLSIQLPpvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAADlYIKEYLHpyvETGnpr 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  524 LKVVRLTAKSRedvessvsflalheqvRMNTTNkeldGLVKLKTETGELSsqdekRFkqltRQAEREILQNADVVCCT-- 601
Cdd:cd18077   82 ARPLRVYYRNR----------------WVKTVH----PVVQKYCLIDEHG-----TF----RMPTREDVMRHRVVVVTls 132

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28922775  602 ---CVGAGDprLSKMKFRNVLIDESTQSAEPECMIPLVLGCK--QVVLVGDHKQLGPVIMNKKAAKAGLNQSLFERL 673
Cdd:cd18077  133 tsqYLCQLD--LEPGFFTHILLDEAAQAMECEAIMPLALATKstRIVLAGDHMQLSPEVYSEFARERNLHISLLERL 207
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 455-864 2.87e-15

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: 80.02  E-value: 2.87e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  455 ELNASQIAAIKQVL-SNPLSLIQGPPGTGKTVTSATIIYHLAKMsNSQVLVCAPSNVAVDQLCER-------IHRtglkv 526
Cdd:COG0507  124 TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEAL-GLRVALAAPTGKAAKRLSEStgieartIHR----- 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  527 vrltaksredvessvsFLALheqvrmnttnkeldglvklktetgelsSQDEKRFkqltRQAEREILQNADVvcctcvgag 606
Cdd:COG0507  198 ----------------LLGL---------------------------RPDSGRF----RHNRDNPLTPADL--------- 221

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  607 dprlskmkfrnVLIDESTqsaepecMIPLVL-----------GCkQVVLVGDHKQLGPVimnkkaaKAGlnqSLFERLVK 675
Cdd:COG0507  222 -----------LVVDEAS-------MVDTRLmaallealpraGA-RLILVGDPDQLPSV-------GAG---AVLRDLIE 272

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  676 LQFTP-IRLKVQYR------------------MHPCLSEFPSNmFYEGSLQNGVTAAERLRKDV-DFPWPVPETPMMFWS 735
Cdd:COG0507  273 SGTVPvVELTEVYRqaddsriielahairegdAPEALNARYAD-VVFVEAEDAEEAAEAIVELYaDRPAGGEDIQVLAPT 351

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  736 NLGNEEISASGTSYLNRTEAANVEKIV--TRFFKAG-------------VKPADIGVITPYEGQRSYIVNTMQNTG--TF 798
Cdd:COG0507  352 NAGVDALNQAIREALNPAGELERELAEdgELELYVGdrvmftrndydlgVFNGDIGTVLSIDEDEGRLTVRFDGREivTY 431

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775  799 KKESYREVEVA---SVDAFQGREKD--FIVLSCVRSNenqgigfLSDPRRLNVALTRAKYGLVIIGNPKVL 864
Cdd:COG0507  432 DPSELDQLELAyaiTVHKSQGSTFDrvILVLPSEHSP-------LLSRELLYTALTRARELLTLVGDRDAL 495
ZBD_UPF1_nv_SF1_Hel-like cd21343
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ...
 102-191 1.03e-12

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: 64.05  E-value: 1.03e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  102 ACAYCGIHSpssVVKCLTCN--KWFCSakgsafsSHIVNHLVRARHKEVQLHpesslgdTVLECYNCGTKNVFILGFipa 179
Cdd:cd21343    1 ACYVCGSHT---VVRCGTCIrrPWFCN-------SCIYDHLIRTKHKEVLLA-------SPYVCAGCGESDITLLYF--- 60

                         90
                 ....*....|..
gi 28922775  180 ksdTVVVLLCRQ 191
Cdd:cd21343   61 ---GGVSYRCVD 69
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 460-521 4.23e-12

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: 65.27  E-value: 4.23e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28922775  460 QIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLaKMSNSQVLVCAPSNVAVDQLCER-------IHR 521
Cdd:cd17933    2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAAL-EAEGKRVVLAAPTGKAAKRLSEStgieastIHR 69
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 471-673 1.27e-11

N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350834 [Multi-domain]  Cd Length: 230  Bit Score: 65.68  E-value: 1.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  471 PLsLIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCerihrtglkvvrltaksREDVESSVSflalheqv 550
Cdd:cd18076   25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADIYI-----------------REYFHPYVD-------- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  551 rmnTTNKELDGLVKLKTETG-ELSSQDEKRFKQLT--RQA----EREILQNADVVCCTCVGAGDPRLSKMKFRNVLIDES 623
Cdd:cd18076   79 ---KGHPEARPLRIKATDRPnAITDPDTITYCCLTkdRQCfrlpTRDELDFHNIVITTTAMAFNLHVLSGFFTHIFIDEA 155

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 28922775  624 TQSAEPECMIPLVLGC--KQVVLVGDHKQLGPVIMNKKAAKAGlNQSLFERL 673
Cdd:cd18076  156 AQMLECEALIPLSYAGpkTRVVLAGDHMQMTPKLFSVADYNRA-NHTLLNRL 206
DEXDc smart00487
DEAD-like helicases superfamily;
448-541 4.07e-09

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 57.50  E-value: 4.07e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775     448 FHVPGLPELNASQIAAIKQVLSNPLS-LIQGPPGTGKTVTSAT-IIYHLAKMSNSQVLVCAPSNVAVDQLCERI-----H 520
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLRDvILAAPTGSGKTLAALLpALEALKRGKGGRVLVLVPTRELAEQWAEELkklgpS 80

                            90       100
                    ....*....|....*....|.
gi 28922775     521 RTGLKVVRLTAKSREDVESSV 541
Cdd:smart00487   81 LGLKVVGLYGGDSKREQLRKL 101
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 455-515 4.73e-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: 57.19  E-value: 4.73e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28922775    455 ELNASQIAAIKQVLSNP--LSLIQGPPGTGKTvTSATIIYHLAKMSNSQVLVCAPSNVAVDQL 515
Cdd:pfam13604    1 TLNAEQAAAVRALLTSGdrVAVLVGPAGTGKT-TALKALREAWEAAGYRVIGLAPTGRAAKVL 62
AAA_19 pfam13245
AAA domain;
460-521 2.15e-08

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 53.76  E-value: 2.15e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775    460 QIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKM--SNSQVLVCAPSNVAVDQLCER-------IHR 521
Cdd:pfam13245    1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALggVSFPILLAAPTGRAAKRLSERtglpastIHR 71
gammaCoV_Nsp13-helicase cd21720
helicase domain of gammacoronavirus non-structural protein 13; This model represents the ...
 453-858 8.22e-07

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: 52.61  E-value: 8.22e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  453 LPELNASQIAAIKQVLSNPLSLIQGPPGTGKtvtSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERihrtglkvvrltak 532
Cdd:cd21720    8 VPECFVNNIPLYHLVGKQKRTTVQGPPGSGK---SHFAIGLAAYFSNARVVFTACSHAAVDALCEK-------------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  533 sredvesSVSFLALHEQVRMNTTNKELDGLVKLK-TETGelssqdeKRFKQLTRQAEREIlqNADVVcctcvgagdprls 611
Cdd:cd21720   71 -------AFKFLKVDDCTRIVPQRTTVDCFSKFKaNDTG-------KKYIFSTINALPEV--SCDIL------------- 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  612 kmkfrnvLIDESTQSAEPE-CMIPLVLGCKQVVLVGDHKQLgpvimnkKAAKAGLNQSLFER-------LVKLQFTPIRL 683
Cdd:cd21720  122 -------LVDEVSMLTNYElSFINGKINYQYVVYVGDPAQL-------PAPRTLLNGSLSPKdynvvtnLMVCVKPDIFL 187

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  684 KVQYRMHPCLSEFPSNMFYEGslqngvtaaerlrkdvDFPWPVPETPMMF--WSNLGNEEISASGTSYLNRTEAanveKI 761
Cdd:cd21720  188 AKCYRCPKEIVDTVSTLVYDG----------------KFIANNPESRQCFkvIVNNGNSDVGHESGSAYNTTQL----EF 247

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  762 VTRFFKAGVKPADIGVITPYegqrsyivNTMQntgtfkKESYREV--EVASVDAFQGREKDFIVLsCVRSNENQGIGFls 839
Cdd:cd21720  248 VKDFVCRNKEWREATFISPY--------NAMN------QRAYRMLglNVQTVDSSQGSEYDYVIF-CVTADSQHALNI-- 310

                        410
                 ....*....|....*....
gi 28922775  840 dpRRLNVALTRAKYGLVII 858
Cdd:cd21720  311 --NRFNVALTRAKRGILVV 327
CoV_Nsp13-helicase cd21718
helicase domain of coronavirus non-structural protein 13; This model represents the helicase ...
 453-858 3.89e-06

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: 50.22  E-value: 3.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  453 LPELNASQIAAIKQVLSNPLSLIQGPPGTGKTvtsaTIIYHLAK-MSNSQVLVCAPSNVAVDQLCERihrtglkvvrlta 531
Cdd:cd21718    8 IPHDFSNHVPSYQKIGKQKYTTVQGPPGTGKS----HFAIGLALyYPGARIVYTACSHAAVDALCEK------------- 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  532 ksredvesSVSFLALHEQVRMNTTNKELDGLVKLKtetgelSSQDEKRFKQLTRQAEREIlqNADVvcctcvgagdprls 611
Cdd:cd21718   71 --------ASKWLPNDKCSRIVPQRARVECFDGFK------VNNTNAQYIFSTINALPEC--SADI-------------- 120

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  612 kmkfrnVLIDESTQSAEPE-CMIPLVLGCKQVVLVGDHKQL-GPVIMNKKAAKAGLNQSLFERLVKLQFTPIRLKVQYRM 689
Cdd:cd21718  121 ------VVVDEVSMCTNYDlSVVNARLKYKHIVYVGDPAQLpAPRTLLTEGSLEPKDYNVVTRLMVGSGPDVFLSKCYRC 194

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  690 HPCLSEFPSNMFYEGSLQngvtAAErlrkdvdfpwpvPETPMMFWSNlGNEEISASGTSYLNRTEAanveKIVTRFFKAG 769
Cdd:cd21718  195 PKEIVDTVSKLVYDNKLK----AIK------------PKSRQCFKTF-GKGDVRHDNGSAINRPQL----EFVKRFLDRN 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  770 VKPADIGVITPYegqrsyivNTMQNtgtfKKESYREVEVASVDAFQGREKDFIVLsCVRSNENQGigflSDPRRLNVALT 849
Cdd:cd21718  254 PRWRKAVFISPY--------NAMNN----RASRLLGLSTQTVDSSQGSEYDYVIF-CQTTDTAHA----LNINRFNVAIT 316


                 ....*....
gi 28922775  850 RAKYGLVII 858
Cdd:cd21718  317 RAKHGILVI 325
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
454-521 1.45e-05

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 48.87  E-value: 1.45e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28922775  454 PELNASQIAAIKQVLSNPLS-----LIQGPPGTGKTVTSATIIYHLAKmsNSQVLVCAPSNVAVDQLCERIHR 521
Cdd:COG1061   79 FELRPYQQEALEALLAALERgggrgLVVAPTGTGKTVLALALAAELLR--GKRVLVLVPRRELLEQWAEELRR 149
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 426-654 1.60e-05

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: 48.99  E-value: 1.60e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    426 IFHKLLgheVQVAPTKITMPKKF--HVPGLPELNASQIAAIKQVLSNPLSLIQGPPGTGKTVTSATIIYHLAKMSNSQ-- 501
Cdd:TIGR01447  116 LAAKLR---TLLEARKRTAPSAIleNLFPLLNEQNWRKTAVALALKSNFSLITGGPGTGKTTTVARLLLALVKQSPKQgk 192

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    502 --VLVCAPSNVAVDQLCERIhRTGLKVVRLTAKSREDVESSVsflalheqvrmnTTNKELDGLVKlktetgelssqDEKR 579
Cdd:TIGR01447  193 lrIALAAPTGKAAARLAESL-RKAVKNLAAAEALIAALPSEA------------VTIHRLLGIKP-----------DTKR 248

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    580 FkqltRQAEREILqNADVvcctcvgagdprlskmkfrnVLIDESTqsaepecMIPLVLGCK---------QVVLVGDHKQ 650
Cdd:TIGR01447  249 F----RHHERNPL-PLDV--------------------LVVDEAS-------MVDLPLMAKllkalppntKLILLGDKNQ 296


                   ....
gi 28922775    651 LGPV 654
Cdd:TIGR01447  297 LPSV 300
ResIII pfam04851
Type III restriction enzyme, res subunit;
455-519 1.62e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 46.13  E-value: 1.62e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28922775    455 ELNASQIAAIKQVLSNPLS-----LIQGPPGTGKTVTSATIIYHLAKMSNSQ-VLVCAPSNVAVDQLCERI 519
Cdd:pfam04851    3 ELRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIKkVLFLVPRKDLLEQALEEF 73
DEAD-like_helicase_C cd09300
C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases ...
 806-853 3.29e-04

C-terminal helicase domain of the DEAD-like helicases; This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350171 [Multi-domain]  Cd Length: 59  Bit Score: 39.84  E-value: 3.29e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 28922775  806 VEVASVDAFQG---REKDFIVLSCVRSnenqgigflsDPRRLNVALTRAKY 853
Cdd:cd09300    8 VLIAVN*ALTGfdaPELNTIIVDKNLR----------SYRGLNQAFGRANR 48
deltaCoV_Nsp13-helicase cd21721
helicase domain of deltacoronavirus non-structural protein 13; This model represents the ...
 736-858 6.58e-04

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: 43.37  E-value: 6.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  736 NLGNEEISASGTSYLNRTEaanvekivTRF---FKAGVKPADIGVITPYegqrsyivNTMqNTgtfkKESYREVEVASVD 812
Cdd:cd21721  227 NNGNNDIAHEGQSAYNEPQ--------LRFalaFRQYKRWDNVTFISPY--------NAM-NV----KAAMAGFSTQTVD 285

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 28922775  813 AFQGREKDFIVLsCVRSNENQGIGFlsdpRRLNVALTRAKYGLVII 858
Cdd:cd21721  286 SSQGSEYDYVIF-CVTTDSAHALNM----SRLNVALTRAKIGILVV 326
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 457-535 1.17e-03

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 40.59  E-value: 1.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  457 NASQIAAIKQVLSNPLS---LIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLKVVRLTAKS 533
Cdd:cd00009    3 QEEAIEALREALELPPPknlLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEK 82


                 ..
gi 28922775  534 RE 535
Cdd:cd00009   83 AK 84
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 460-541 1.82e-03

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part 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: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 39.98  E-value: 1.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  460 QIAAIKQVL---SNPLSLIQGPPGTGKTVTSATIIYHLAKMSnsqVLVCAPSNVAVDQLCERIHRTGLKVV--RLTAKSR 534
Cdd:cd17926    5 QEEALEAWLahkNNRRGILVLPTGSGKTLTALALIAYLKELR---TLIVVPTDALLDQWKERFEDFLGDSSigLIGGGKK 81


                 ....*..
gi 28922775  535 EDVESSV 541
Cdd:cd17926   82 KDFDDAN 88
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 474-525 3.57e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 39.28  E-value: 3.57e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 28922775     474 LIQGPPGTGKTVTSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTGLK 525
Cdd:smart00382    6 LIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGK 57
DEXSMc_CoV_Nsp13 cd22649
DEXSM-box helicase domain of coronavirus Nsp13 helicase; Helicases catalyze the NTP-dependent ...
 453-536 4.02e-03

DEXSM-box helicase domain of coronavirus Nsp13 helicase; Helicases catalyze the NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified into six superfamilies based on the arrangement of conserved motifs. This family contains coronavirus (CoV) non-structural protein 13 (Nsp13) helicase, including those from highly pathogenic human betaCoVs such as Severe Acute Respiratory Syndrome coronavirus (SARS) and SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus). Nsp13 helicase is a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is strongly inhibited by natural flavonoids, myricetin and scutellarein, and is emerging as a target for development of anti-SARS medications. It contains an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B regulatory domain, and an SF1 helicase core that carries a DEAD-box helicase domain. Nsp13 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: 438713 [Multi-domain]  Cd Length: 202  Bit Score: 39.69  E-value: 4.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775  453 LPELNASQIAAIKQVLSNPLSLIQGPPGTGKtvtSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHRTgLKVVRLT-- 530
Cdd:cd22649   17 VPEEFSNNVPNYQKIGMQKYTTVQGPPGTGK---SHFAIGLALYYPSARVVYTACSHAAVDALCEKAFKF-LNIDKCTri 92


                 ....*...
gi 28922775  531 --AKSRED 536
Cdd:cd22649   93 ipARARVE 100
betaCoV_Nsp13-helicase cd21722
helicase domain of betacoronavirus non-structural protein 13; This model represents the ...
 453-521 4.82e-03

helicase domain of betacoronavirus non-structural protein 13; This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, 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: 409655 [Multi-domain]  Cd Length: 340  Bit Score: 40.55  E-value: 4.82e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 28922775  453 LPELNASQIAAIKQVLSNPLSLIQGPPGTGKtvtSATIIYHLAKMSNSQVLVCAPSNVAVDQLCERIHR 521
Cdd:cd21722    8 VPEEFQNNVVNYQKIGMKRYCTVQGPPGTGK---SHLAIGLAVYYPTARVVYTACSHAAVDALCEKAFK 73
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 460-537 9.81e-03

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 37.99  E-value: 9.81e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28922775    460 QIAAIKQVLSNPLSLIQGPPGTGKTVTSA-TIIYHLAKMSN-SQVLVCAPS-----NVaVDQLCERIHRTGLKVVR-LTA 531
Cdd:pfam00270    4 QAEAIPAILEGRDVLVQAPTGSGKTLAFLlPALEALDKLDNgPQALVLAPTrelaeQI-YEELKKLGKGLGLKVASlLGG 82


                   ....*.
gi 28922775    532 KSREDV 537
Cdd:pfam00270   83 DSRKEQ 88
 
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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