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Conserved domains on  [gi|1005460229|ref|XP_015767194|]
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PREDICTED: LOW QUALITY PROTEIN: regulator of nonsense transcripts 1-like [Acropora digitifera]

Protein Classification

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 ...
 403-633 4.91e-108

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: 338.07  E-value: 4.91e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR 482
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  483 EAIDSPVAFLALHNQVRNMDSVPELQKLQQLKDEQGELSAADEKRYRSLKRNCERELLQ----VWNCCV*A--------- 549
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRnadvICCTCVGAgdprlskmk 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  550 -TFALIAYSIFVIECHlpylss*fqnwk*dyFIITIEH--H*DIFFGE--QLSVKIFVKKAANAGLSQSLFERLVVLGIR 624
Cdd:cd18039    161 fRTVLIDEATQATEPE---------------CLIPLVHgaKQVILVGDhcQLGPVVMCKKAAKAGLSQSLFERLVQLGIR 225


                   ....*....
gi 1005460229  625 PIRLQVQYR 633
Cdd:cd18039    226 PIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 117-253 4.70e-96

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: 302.63  E-value: 4.70e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDPASVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTLHKDGPLGETVLECYNCACRNVFLLGFIPAKA 196
Cdd:pfam09416    2 ACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAKS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1005460229  197 DSVVVLLCRQPCATQSNAKDMNWDQSQWNPLINDRCFLSWLVKVPPDEDQLRARQAS 253
Cdd:pfam09416   82 DSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQIT 138
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 258-346 8.61e-54

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: 181.96  E-value: 8.61e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  258 TQDNIVVRWDIGLNKKRIAYFSFPKTND-DMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELRSNLGAPV 336
Cdd:cd21407      1 TQENISVRWDVGLNKKRLAYFTLPKLDEsELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKNAPT 80

                           90
                   ....*....|
gi 1005460229  337 ECTHNFVVDF 346
Cdd:cd21407     81 EITTGFSVEF 90
AAA_12 super family cl38387
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 610-754 5.33e-38

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.


The actual alignment was detected with superfamily member pfam13087:

Pssm-ID: 463780 [Multi-domain]  Cd Length: 196  Bit Score: 141.15  E-value: 5.33e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  610 LSQSLFERLVVLG-IRPIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERQQPGiDFPWPVPDKPMFFYSTMG-QEEI 687
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIDVDGsEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  688 ASSGTSYLNRCQ-------LTLFVIIITIIIII-------ISMARFLFKIL------------------QG--------- 726
Cdd:pfam13087   80 SDGGTSYSNEAEaelvvqlVEKLIKSGPEEPSDigvitpyRAQVRLIRKLLkrklggkleievntvdgfQGrekdviifs 159

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1005460229  727 ---------IGFLNDPRRLNVALTRAKYGIIVIGNPK 754
Cdd:pfam13087  160 cvrsnekggIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1019-1128 1.27e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 49.77  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1019 TIPPAAAARIPVPVGMFIPPVPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHPHQPMTYAPHM-PASQAS-QDASQ 1096
Cdd:pfam03154  189 PGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPpPPSQVSpQPLPQ 268

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1005460229 1097 PLSQGPMTQGGMS-------MSQPMASQPLSQPDLSQDS 1128
Cdd:pfam03154  269 PSLHGQMPPMPHSlqtgpshMQHPVPPQPFPLTPQSSQS 307
 
Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 403-633 4.91e-108

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: 338.07  E-value: 4.91e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR 482
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  483 EAIDSPVAFLALHNQVRNMDSVPELQKLQQLKDEQGELSAADEKRYRSLKRNCERELLQ----VWNCCV*A--------- 549
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRnadvICCTCVGAgdprlskmk 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  550 -TFALIAYSIFVIECHlpylss*fqnwk*dyFIITIEH--H*DIFFGE--QLSVKIFVKKAANAGLSQSLFERLVVLGIR 624
Cdd:cd18039    161 fRTVLIDEATQATEPE---------------CLIPLVHgaKQVILVGDhcQLGPVVMCKKAAKAGLSQSLFERLVQLGIR 225


                   ....*....
gi 1005460229  625 PIRLQVQYR 633
Cdd:cd18039    226 PIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 117-253 4.70e-96

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: 302.63  E-value: 4.70e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDPASVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTLHKDGPLGETVLECYNCACRNVFLLGFIPAKA 196
Cdd:pfam09416    2 ACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAKS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1005460229  197 DSVVVLLCRQPCATQSNAKDMNWDQSQWNPLINDRCFLSWLVKVPPDEDQLRARQAS 253
Cdd:pfam09416   82 DSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQIT 138
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 117-237 3.49e-82

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: 263.34  E-value: 3.49e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDPASVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTLHKDGPLGETVLECYNCACRNVFLLGFIPAKA 196
Cdd:cd21400      1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1005460229  197 DSVVVLLCRQPCAtQSNAKDMNWDQSQWNPLINDRCFLSWL 237
Cdd:cd21400     81 DSVVVLLCRQPCL-SQSSKDMNWDLSQWQPLIDDRQFLPWL 120
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 258-346 8.61e-54

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: 181.96  E-value: 8.61e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  258 TQDNIVVRWDIGLNKKRIAYFSFPKTND-DMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELRSNLGAPV 336
Cdd:cd21407      1 TQENISVRWDVGLNKKRLAYFTLPKLDEsELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKNAPT 80

                           90
                   ....*....|
gi 1005460229  337 ECTHNFVVDF 346
Cdd:cd21407     81 EITTGFSVEF 90
UPF1_1B_dom pfam18141
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ...
 257-347 5.12e-47

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: 162.87  E-value: 5.12e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  257 QTQDNIVVRWDIGLNKKRIAYFSFPKTND-DMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELR-SNLGA 334
Cdd:pfam18141    1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSgEMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVTLELRsSSNNP 80

                           90
                   ....*....|...
gi 1005460229  335 PVECTHNFVVDFV 347
Cdd:pfam18141   81 PTDLTHGFTVEFV 93
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 610-754 5.33e-38

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: 141.15  E-value: 5.33e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  610 LSQSLFERLVVLG-IRPIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERQQPGiDFPWPVPDKPMFFYSTMG-QEEI 687
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIDVDGsEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  688 ASSGTSYLNRCQ-------LTLFVIIITIIIII-------ISMARFLFKIL------------------QG--------- 726
Cdd:pfam13087   80 SDGGTSYSNEAEaelvvqlVEKLIKSGPEEPSDigvitpyRAQVRLIRKLLkrklggkleievntvdgfQGrekdviifs 159

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1005460229  727 ---------IGFLNDPRRLNVALTRAKYGIIVIGNPK 754
Cdd:pfam13087  160 cvrsnekggIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 352-777 2.18e-37

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: 150.35  E-value: 2.18e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  352 SFDRMQTGMKTFAVDETSVSGyiyhKLLGHEVEEQVVKCQLPKRFSaqglPELNHSQVYAVK-TVLQRPLSLIQGPPGTG 430
Cdd:TIGR00376  114 TFKRMKEALRALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTG 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  431 KTVTSASVVYHLAKQNNgQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR---EAIDSPVAFLALHN----------- 496
Cdd:TIGR00376  186 KTRTVVELIRQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARllkSNKQHSLDYLIENHpkyqivadire 264

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  497 ------QVRNMDSVPELQKLQQLKDEQGELSAADEKRYRSLKRNCERELLQVWN---------CCV*ATFALIAYSIFV- 560
Cdd:TIGR00376  265 kideliEERNKKTKPSPQKRRGLSDIKILRKALKKREARGIESLKIASMAEWIEtnksidrllKLLPESEERIMNEILAe 344

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  561 IECHLPYLSS*FQN-WK*DYFII--------------TIEHH*DIFFGEQLSVKIFVKKAANAGLSQSLFERLVVL-GIR 624
Cdd:TIGR00376  345 SDATNSMAGSEILNgQYFDVAVIdeasqamepsclipLLKARKLILAGDHKQLPPTILSHDAEELSLTLFERLIKEyPER 424

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  625 PIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERQQpgIDFPWPVPDK---------PMFFYSTMGQE----EIASSg 691
Cdd:TIGR00376  425 SRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILL--RDLPKVEATEseddletgiPLLFIDTSGCElfelKEADS- 501

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  692 TSYLNRCQLTLFVIIITIIIIII----------------SMARFLFKI------------LQG----------------- 726
Cdd:TIGR00376  502 TSKYNPGEAELVSEIIQALVKMGvpandigvitpydaqvDLLRQLLEHrhidievssvdgFQGrekeviiisfvrsnrkg 581

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1005460229  727 -IGFLNDPRRLNVALTRAKYGIIVIGNPKILSRQPLWNHLLNYYKENKALME 777
Cdd:TIGR00376  582 eVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 634-770 1.30e-32

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: 125.04  E-value: 1.30e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  634 MHPSLSEFPSNLFYDGTLQNGVTIAERQQPgidFPWPVPDKPMFFYSTMGQEEIASSGTSYLNRCQ----LTLFVIIITI 709
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARLNP---PPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEaelvVELVKYLLKS 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  710 IIIIISMA--------RFLFKIL-------------------QG-------------------IGFLNDPRRLNVALTRA 743
Cdd:cd18808     78 GVKPSSIGvitpyraqVALIRELlrkrgglledvevgtvdnfQGrekdviilslvrsnesggsIGFLSDPRRLNVALTRA 157

                          170       180
                   ....*....|....*....|....*..
gi 1005460229  744 KYGIIVIGNPKILSRQPLWNHLLNYYK 770
Cdd:cd18808    158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 407-523 1.44e-19

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: 89.33  E-value: 1.44e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  407 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTSASVVYHLAKQNN------GQVLVCAPSNIAVDQLTEKI----HKTGLKVV 475
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTTIVELIRQLLSYPAtsaaagPRILVCAPSNAAVDNILERLlrkgQKYGPKIV 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1005460229  476 RLCAKsrEAIDSPVAFLALHNQVRN-MDSVPELQKLQQLKDEQGELSAA 523
Cdd:pfam13086   81 RIGHP--AAISEAVLPVSLDYLVESkLNNEEDAQIVKDISKELEKLAKA 127
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
602-772 2.56e-19

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 94.04  E-value: 2.56e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  602 VKKAANAGLSQSLFERLV-VLGIRPIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERqqpgidfPWPVPDKPMFFYS 680
Cdd:COG1112    600 AEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFID 672

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  681 TMGQEEiaSSGTSYLNRCQ--------LTLFVIIITII-------------------IIIISMARFLFKI-----LQG-- 726
Cdd:COG1112    673 VDGVYE--RRGGSRTNPEEaeavvelvRELLEDGPDGEsigvitpyraqvalirellREALGDGLEPVFVgtvdrFQGde 750

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1005460229  727 -------------------IGFLN-DPRRLNVALTRAKYGIIVIGNPKILSRQP---LWNHLLNYYKEN 772
Cdd:COG1112    751 rdviifslvysndedvprnFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 366-471 4.22e-11

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: 66.92  E-value: 4.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  366 DETSVSGYIyHKLLGHEVEEQVVKCQLPKRFSAQGLpELNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSASVVYHLAK 444
Cdd:COG0507     89 AEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEA 166

                           90       100
                   ....*....|....*....|....*..
gi 1005460229  445 QnNGQVLVCAPSNIAVDQLTEKIHKTG 471
Cdd:COG0507    167 L-GLRVALAAPTGKAAKRLSESTGIEA 192
DEXDc smart00487
DEAD-like helicases superfamily;
396-469 4.80e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 51.72  E-value: 4.80e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1005460229   396 FSAQGLPELNHSQVYAVKTVLQRPLS-LIQGPPGTGKTVT-SASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHK 469
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLRDvILAAPTGSGKTLAaLLPALEALKRGKGGRVLVLVPTRELAEQWAEELKK 76
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1019-1128 1.27e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 49.77  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1019 TIPPAAAARIPVPVGMFIPPVPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHPHQPMTYAPHM-PASQAS-QDASQ 1096
Cdd:pfam03154  189 PGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPpPPSQVSpQPLPQ 268

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1005460229 1097 PLSQGPMTQGGMS-------MSQPMASQPLSQPDLSQDS 1128
Cdd:pfam03154  269 PSLHGQMPPMPHSlqtgpshMQHPVPPQPFPLTPQSSQS 307
KLF1_2_4_N-like cd22056
N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of ...
 1037-1120 7.34e-04

N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of Kruppel-like factor (KLF)1, KLF2, and KLF4; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domains of an unknown subfamily of KLFs, predominantly found in fish, related to the N-terminal domains of KLF1, KLF2, and KLF4.


Pssm-ID: 409231 [Multi-domain]  Cd Length: 339  Bit Score: 43.11  E-value: 7.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1037 PPVPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHPHQPMTYAPHMPASQASQDASQPLSQ-----------GPMTQ 1105
Cdd:cd22056    215 SVHPQAFTHHQAAGPGALQGRGGRGGPDCHLLHSSHHHHHHHHLQYQYMNAPYPPHYAHQGAPQfhgqysvfrepMRVHH 294

                           90
                   ....*....|....*..
gi 1005460229 1106 GGMSMSQ--PMASQPLS 1120
Cdd:cd22056    295 QGHPGSMltPPSSPPLL 311
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 1016-1132 2.92e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 41.62  E-value: 2.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1016 AERTIPPAAAARIPVPVGMFIPPVPPPhhnffgqplAGRMPPhgrPVQQPRQRNQRNHHPHQPMtyAPHMPASQASQDAS 1095
Cdd:PRK14951   392 APVAQAAAAPAPAAAPAAAASAPAAPP---------AAAPPA---PVAAPAAAAPAAAPAAAPA--AVALAPAPPAQAAP 457

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1005460229 1096 QPLSQGPMTQGGMSM-SQPMASQPLSQPDLSQDSYLGD 1132
Cdd:PRK14951   458 ETVAIPVRVAPEPAVaSAAPAPAAAPAAARLTPTEEGD 495
 
Name Accession Description Interval E-value
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 403-633 4.91e-108

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: 338.07  E-value: 4.91e-108
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR 482
Cdd:cd18039      1 ELNHSQVDAVKTALQRPLSLIQGPPGTGKTVTSATIVYHLVKQGNGPVLVCAPSNVAVDQLTEKIHQTGLKVVRLCAKSR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  483 EAIDSPVAFLALHNQVRNMDSVPELQKLQQLKDEQGELSAADEKRYRSLKRNCERELLQ----VWNCCV*A--------- 549
Cdd:cd18039     81 EAVESPVSFLALHNQVRNLDSAEKLELLKLLKLETGELSSADEKRYRKLKRKAERELLRnadvICCTCVGAgdprlskmk 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  550 -TFALIAYSIFVIECHlpylss*fqnwk*dyFIITIEH--H*DIFFGE--QLSVKIFVKKAANAGLSQSLFERLVVLGIR 624
Cdd:cd18039    161 fRTVLIDEATQATEPE---------------CLIPLVHgaKQVILVGDhcQLGPVVMCKKAAKAGLSQSLFERLVQLGIR 225


                   ....*....
gi 1005460229  625 PIRLQVQYR 633
Cdd:cd18039    226 PIRLQVQYR 234
UPF1_Zn_bind pfam09416
RNA helicase (UPF2 interacting domain); UPF1 is an essential RNA helicase that detects mRNAs ...
 117-253 4.70e-96

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: 302.63  E-value: 4.70e-96
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDPASVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTLHKDGPLGETVLECYNCACRNVFLLGFIPAKA 196
Cdd:pfam09416    2 ACAYCGIHDPACVVKCLTCGKWFCNGRGNTSGSHIINHLVRSKHKEVSLHPDSPLGDTVLECYNCGSKNVFLLGFIPAKS 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1005460229  197 DSVVVLLCRQPCATQSNAKDMNWDQSQWNPLINDRCFLSWLVKVPPDEDQLRARQAS 253
Cdd:pfam09416   82 DSVVVLLCRQPCAQAKSLKDMNWDTSQWQPLIEDRQFLPWLVKVPSEEEQLRARQIT 138
ZBD_UPF1-like cd21400
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins; ...
 117-237 3.49e-82

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: 263.34  E-value: 3.49e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDPASVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTLHKDGPLGETVLECYNCACRNVFLLGFIPAKA 196
Cdd:cd21400      1 ACAYCGIHDPACLVKCLTCGKWFCNGRGNTSGSHIVQHLVRSKHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKA 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1005460229  197 DSVVVLLCRQPCAtQSNAKDMNWDQSQWNPLINDRCFLSWL 237
Cdd:cd21400     81 DSVVVLLCRQPCL-SQSSKDMNWDLSQWQPLIDDRQFLPWL 120
1B_UPF1-like cd21407
1B domain of eukaryotic UPF1 RNA helicase and related proteins; Helicases catalyze ...
 258-346 8.61e-54

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: 181.96  E-value: 8.61e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  258 TQDNIVVRWDIGLNKKRIAYFSFPKTND-DMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELRSNLGAPV 336
Cdd:cd21407      1 TQENISVRWDVGLNKKRLAYFTLPKLDEsELRLMVGDELRLRYKGDLREPWEGVGHVIKIPDNYSEEVALELRSSKNAPT 80

                           90
                   ....*....|
gi 1005460229  337 ECTHNFVVDF 346
Cdd:cd21407     81 EITTGFSVEF 90
UPF1_1B_dom pfam18141
RNA helicase UPF1, 1B domain; UPF1 (or regulator of nonsense transcripts 1 homolog) is an ...
 257-347 5.12e-47

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: 162.87  E-value: 5.12e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  257 QTQDNIVVRWDIGLNKKRIAYFSFPKTND-DMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELR-SNLGA 334
Cdd:pfam18141    1 QTQDDISVRWDVGLNKKHLAWFSLPKLDSgEMKLAVGDELRLRYTGSLAEPWEGVGHVVKIPDNSSEEVTLELRsSSNNP 80

                           90
                   ....*....|...
gi 1005460229  335 PVECTHNFVVDFV 347
Cdd:pfam18141   81 PTDLTHGFTVEFV 93
AAA_12 pfam13087
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 610-754 5.33e-38

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: 141.15  E-value: 5.33e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  610 LSQSLFERLVVLG-IRPIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERQQPGiDFPWPVPDKPMFFYSTMG-QEEI 687
Cdd:pfam13087    1 LDRSLFERLQELGpSAVVMLDTQYRMHPEIMEFPSKLFYGGKLKDGPSVAERPLPD-DFHLPDPLGPLVFIDVDGsEEEE 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  688 ASSGTSYLNRCQ-------LTLFVIIITIIIII-------ISMARFLFKIL------------------QG--------- 726
Cdd:pfam13087   80 SDGGTSYSNEAEaelvvqlVEKLIKSGPEEPSDigvitpyRAQVRLIRKLLkrklggkleievntvdgfQGrekdviifs 159

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 1005460229  727 ---------IGFLNDPRRLNVALTRAKYGIIVIGNPK 754
Cdd:pfam13087  160 cvrsnekggIGFLSDPRRLNVALTRAKRGLIIVGNAK 196
TIGR00376 TIGR00376
DNA helicase, putative; The gene product may represent a DNA helicase. Eukaryotic members of ...
 352-777 2.18e-37

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: 150.35  E-value: 2.18e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  352 SFDRMQTGMKTFAVDETSVSGyiyhKLLGHEVEEQVVKCQLPKRFSaqglPELNHSQVYAVK-TVLQRPLSLIQGPPGTG 430
Cdd:TIGR00376  114 TFKRMKEALRALTENHSRLLE----FLLGREAPSKASEIHDFQFFD----PNLNESQKEAVLfALSSKDLFLIHGPPGTG 185

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  431 KTVTSASVVYHLAKQNNgQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR---EAIDSPVAFLALHN----------- 496
Cdd:TIGR00376  186 KTRTVVELIRQLVKRGL-RVLVTAPSNIAVDNLLERLALCDQKIVRLGHPARllkSNKQHSLDYLIENHpkyqivadire 264

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  497 ------QVRNMDSVPELQKLQQLKDEQGELSAADEKRYRSLKRNCERELLQVWN---------CCV*ATFALIAYSIFV- 560
Cdd:TIGR00376  265 kideliEERNKKTKPSPQKRRGLSDIKILRKALKKREARGIESLKIASMAEWIEtnksidrllKLLPESEERIMNEILAe 344

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  561 IECHLPYLSS*FQN-WK*DYFII--------------TIEHH*DIFFGEQLSVKIFVKKAANAGLSQSLFERLVVL-GIR 624
Cdd:TIGR00376  345 SDATNSMAGSEILNgQYFDVAVIdeasqamepsclipLLKARKLILAGDHKQLPPTILSHDAEELSLTLFERLIKEyPER 424

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  625 PIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERQQpgIDFPWPVPDK---------PMFFYSTMGQE----EIASSg 691
Cdd:TIGR00376  425 SRTLNVQYRMNQKIMEFPSREFYNGKLTAHESVANILL--RDLPKVEATEseddletgiPLLFIDTSGCElfelKEADS- 501

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  692 TSYLNRCQLTLFVIIITIIIIII----------------SMARFLFKI------------LQG----------------- 726
Cdd:TIGR00376  502 TSKYNPGEAELVSEIIQALVKMGvpandigvitpydaqvDLLRQLLEHrhidievssvdgFQGrekeviiisfvrsnrkg 581

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1005460229  727 -IGFLNDPRRLNVALTRAKYGIIVIGNPKILSRQPLWNHLLNYYKENKALME 777
Cdd:TIGR00376  582 eVGFLKDLRRLNVALTRARRKLIVIGDSRTLSNHKFYKRLIEWCKQHGEVRE 633
SF1_C_Upf1 cd18808
C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family ...
 634-770 1.30e-32

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: 125.04  E-value: 1.30e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  634 MHPSLSEFPSNLFYDGTLQNGVTIAERQQPgidFPWPVPDKPMFFYSTMGQEEIASSGTSYLNRCQ----LTLFVIIITI 709
Cdd:cd18808      1 MHPEISEFPSKLFYEGKLKAGVSVAARLNP---PPLPGPSKPLVFVDVSGGEEREESGTSKSNEAEaelvVELVKYLLKS 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  710 IIIIISMA--------RFLFKIL-------------------QG-------------------IGFLNDPRRLNVALTRA 743
Cdd:cd18808     78 GVKPSSIGvitpyraqVALIRELlrkrgglledvevgtvdnfQGrekdviilslvrsnesggsIGFLSDPRRLNVALTRA 157

                          170       180
                   ....*....|....*....|....*..
gi 1005460229  744 KYGIIVIGNPKILSRQPLWNHLLNYYK 770
Cdd:cd18808    158 KRGLIIVGNPDTLSKDPLWKKLLEYLE 184
1B_UPF1_nv_SF1_Hel-like cd21344
1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and ...
 260-345 3.10e-24

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: 97.77  E-value: 3.10e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  260 DNIVVRWDIGLNKKRIAYFSFPKTNDDMRLMPGDELRLRYVGELHKPWQGVGHVIKVPNNFGEEVGIELRSNLGAPVECT 339
Cdd:cd21344      1 LIITVRWRLALNDFRGAYFSLEKGKSQCKPPLGDEIVLTYYGDTVPLWEGIGEVIDLPNTGNDDDALELKGSTTYPLTVT 80


                   ....*.
gi 1005460229  340 HNFVVD 345
Cdd:cd21344     81 HIFVLT 86
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 403-477 1.87e-23

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: 99.22  E-value: 1.87e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1005460229  403 ELNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSASVVYHLAKQNNgQVLVCAPSNIAVDQLTEKIHKTGLKVVRL 477
Cdd:cd18044      1 NLNDSQKEAVKFALsQKDVALIHGPPGTGKTTTVVEIILQAVKRGE-KVLACAPSNIAVDNLVERLVALKVKVVRI 75
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 404-633 4.45e-23

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: 100.29  E-value: 4.45e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  404 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKQNN------------GQVLVCAPSNIAVDQLTEKIHKT- 470
Cdd:cd18040      2 LNPSQNHAVRTALTKPFTLIQGPPGTGKTVTGVHIAYWFAKQNReiqsvsgegdggPCVLYCGPSNKSVDVVAELLLKVp 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  471 GLKVVRLCAKSREAIDSPVAF---------------------LALHNQVRNmDSVPELQKLQQ----LKDEQGELSAADE 525
Cdd:cd18040     82 GLKILRVYSEQIETTEYPIPNeprhpnkksereskpnselssITLHHRIRQ-PSNPHSQQIKAfearFERTQEKITEEDI 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  526 KRYRSL--KRNCERE-----LLQVWNCCV*ATFALIA--YSIFVIECH-------LPYLSS*FQNWK*dyFIITIEHh*d 589
Cdd:cd18040    161 KTYKILiwEARFEELetvdvILCTCSEAASQKMRTHAnvKQCIVDECGmctepesLIPIVSAPRAEQ---VVLIGDH--- 234

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....
gi 1005460229  590 iffgEQLSVKIFVKKAANAGLSQSLFERLVVlgiRPIRLQVQYR 633
Cdd:cd18040    235 ----KQLRPVVQNKEAQKLGLGRSLFERYAE---KACMLDTQYR 271
AAA_11 pfam13086
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 407-523 1.44e-19

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: 89.33  E-value: 1.44e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  407 SQVYAVKTVLQRP-LSLIQGPPGTGKTVTSASVVYHLAKQNN------GQVLVCAPSNIAVDQLTEKI----HKTGLKVV 475
Cdd:pfam13086    1 SQREAIRSALSSShFTLIQGPPGTGKTTTIVELIRQLLSYPAtsaaagPRILVCAPSNAAVDNILERLlrkgQKYGPKIV 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1005460229  476 RLCAKsrEAIDSPVAFLALHNQVRN-MDSVPELQKLQQLKDEQGELSAA 523
Cdd:pfam13086   81 RIGHP--AAISEAVLPVSLDYLVESkLNNEEDAQIVKDISKELEKLAKA 127
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
602-772 2.56e-19

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


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 94.04  E-value: 2.56e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  602 VKKAANAGLSQSLFERLV-VLGIRPIRLQVQYRMHPSLSEFPSNLFYDGTLQNGVTIAERqqpgidfPWPVPDKPMFFYS 680
Cdd:COG1112    600 AEEVAEEGLDESLLDRLLaRLPERGVMLREHYRMHPEIIAFSNRLFYDGKLVPLPSPKAR-------RLADPDSPLVFID 672

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  681 TMGQEEiaSSGTSYLNRCQ--------LTLFVIIITII-------------------IIIISMARFLFKI-----LQG-- 726
Cdd:COG1112    673 VDGVYE--RRGGSRTNPEEaeavvelvRELLEDGPDGEsigvitpyraqvalirellREALGDGLEPVFVgtvdrFQGde 750

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1005460229  727 -------------------IGFLN-DPRRLNVALTRAKYGIIVIGNPKILSRQP---LWNHLLNYYKEN 772
Cdd:COG1112    751 rdviifslvysndedvprnFGFLNgGPRRLNVAVSRARRKLIVVGSRELLDSDPstpALKRLLEYLERA 819
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 403-512 2.58e-18

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: 85.36  E-value: 2.58e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQR----PLSLIQGPPGTGKTVTSASVVYHLAKQN-NGQVLVCAPSNIAVDQLTEKIHKTGLK---V 474
Cdd:cd18038      1 ELNDEQKLAVRNIVTGtsrpPPYIIFGPPGTGKTVTLVEAILQVLRQPpEARILVCAPSNSAADLLAERLLNALVTkreI 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1005460229  475 VRLCAKSREAIDSPVAFLALHNQVRN-MDSVPELQKLQQ 512
Cdd:cd18038     81 LRLNAPSRDRASVPPELLPYCNSKAEgTFRLPSLEELKK 119
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 404-632 5.39e-18

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: 82.98  E-value: 5.39e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  404 LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVY----HLAKQNNGQVLVCAPSNIAVDQLTEKIHKTGL-KVVRLC 478
Cdd:cd17936      2 LDPSQLEALKHALTSELALIQGPPGTGKTFLGVKLVRallqNQDLSITGPILVVCYTNHALDQFLEGLLDFGPtKIVRLG 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  479 AKsreAIDSPVAFLALHNQVrnmdsvpeLQKLQQ---LKDEQGElsaadekryrslkrncerellqvwnccv*atfalia 555
Cdd:cd17936     82 AR---VIGMTTTGAAKYREL--------LQALGPkvvIVEEAAE------------------------------------ 114

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  556 ysifVIECHLpyLSS*FQNwk*dyfiitIEHH*dIFFG--EQLSVKIFVKKAANAG--LSQSLFERLVVLGIRPIRLQVQ 631
Cdd:cd17936    115 ----VLEAHI--LAALTPS---------TEHL--ILIGdhKQLRPKVNVYELTAKKynLDVSLFERLVKNGLPFVTLNVQ 177


                   .
gi 1005460229  632 Y 632
Cdd:cd17936    178 R 178
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 404-633 3.41e-16

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: 78.79  E-value: 3.41e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  404 LNHSQVYAVKTVLQR--PLSLIQGPPGTGKTVTSASVVYHLAKQNNG------------------------QVLVCAPSN 457
Cdd:cd18042      1 LNESQLEAIASALQNspGITLIQGPPGTGKTKTIVGILSVLLAGKYRkyyekvkkklrklqrnlnnkkkknRILVCAPSN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  458 IAVDQLTEKIHKTGL----------KVVRLCAKS-REAI--DSPVAFLALhnqvrNMDSVPELQKLQQLK-----DE--Q 517
Cdd:cd18042     81 AAVDEIVLRLLSEGFldgdgrsykpNVVRVGRQElRASIlnEADIVCTTL-----SSSGSDLLESLPRGFdtviiDEaaQ 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  518 G-ELSAADEKRYRslkrnCERellqvwncCV*atfaLIAysifviechlpylss*fqnwk*dyfiitiehh*DIffgEQL 596
Cdd:cd18042    156 AvELSTLIPLRLG-----CKR--------LI-----LVG---------------------------------DP---KQL 181

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1005460229  597 SVKIFVKKAANAGLSQSLFERLVVLGIRPIRLQVQYR 633
Cdd:cd18042    182 PATVFSKVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 420-463 3.74e-15

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: 73.04  E-value: 3.74e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1005460229  420 LSLIQGPPGTGKTVTSASVVYHLAKQNNG-QVLVCAPSNIAVDQL 463
Cdd:cd17934      1 ISLIQGPPGTGKTTTIAAIVLQLLKGLRGkRVLVTAQSNVAVDNV 45
ZBD_UPF1_nv_SF1_Hel-like cd21343
Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases ...
 117-206 6.17e-15

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: 70.60  E-value: 6.17e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  117 ACRYCGVHDpasVVQCIQC--KKWFCNgrgntagSHIVNHLVRAKHKEVTLHKdgplgetVLECYNCACRNVFLLGFipa 194
Cdd:cd21343      1 ACYVCGSHT---VVRCGTCirRPWFCN-------SCIYDHLIRTKHKEVLLAS-------PYVCAGCGESDITLLYF--- 60

                           90
                   ....*....|..
gi 1005460229  195 kadSVVVLLCRQ 206
Cdd:cd21343     61 ---GGVSYRCVD 69
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 420-632 9.44e-13

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: 65.97  E-value: 9.44e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  420 LSLIQGPPGTGKTVTSASVVYHLAKQNNGQ---VLVCAPSNIAVDQLTEkihktglkvvrlcaksreaidspvaflalhn 496
Cdd:cd17914      1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGEpgrILLVTPTNKAAAQLDN------------------------------- 49

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  497 qvrnmdsvpelqklqQLKDEQGELSAADekryrslkrncerellqvwnccv*aTFALIAysifviechlpyLSS*FQNWk 576
Cdd:cd17914     50 ---------------ILVDEAAQILEPE-------------------------TSRLID------------LALDQGRV- 76

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1005460229  577 *dyfIITIEHH*diffgeQLSVKIFVKKAANAGLSQSLFERLVVLGIRPIRLQVQY 632
Cdd:cd17914     77 ----ILVGDHD-------QLGPVWRGAVLAKICNEQSLFTRLVRLGVSLIRLQVQY 121
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 404-510 6.86e-12

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: 65.72  E-value: 6.86e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  404 LNHSQVYAVKTVLQ-RPLSLIQGPPGTGKTVTSASVVYHLAKQNNgQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCAKSR 482
Cdd:cd18041      2 LNKDQRQAIKKVLNaKDYALILGMPGTGKTTTIAALVRILVALGK-SVLLTSYTHSAVDNILLKLKKFGVNFLRLGRLKK 80

                           90       100
                   ....*....|....*....|....*...
gi 1005460229  483 eaIDSPVAFLALHNQVRNMDSVPELQKL 510
Cdd:cd18041     81 --IHPDVQEFTLEAILKSCKSVEELESK 106
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 408-469 9.77e-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: 64.11  E-value: 9.77e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1005460229  408 QVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLaKQNNGQVLVCAPSNIAVDQLTEK-------IHK 469
Cdd:cd17933      2 QKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAAL-EAEGKRVVLAAPTGKAAKRLSEStgieastIHR 69
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 366-471 4.22e-11

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: 66.92  E-value: 4.22e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  366 DETSVSGYIyHKLLGHEVEEQVVKCQLPKRFSAQGLpELNHSQVYAVKTVL-QRPLSLIQGPPGTGKTVTSASVVYHLAK 444
Cdd:COG0507     89 AEQRLARRL-RRLARPALDEADVEAALAALEPRAGI-TLSDEQREAVALALtTRRVSVLTGGAGTGKTTTLRALLAALEA 166

                           90       100
                   ....*....|....*....|....*..
gi 1005460229  445 QnNGQVLVCAPSNIAVDQLTEKIHKTG 471
Cdd:COG0507    167 L-GLRVALAAPTGKAAKRLSESTGIEA 192
EEXXQc_AQR cd17935
EEXXQ-box helicase domain of AQR; Aquarius (AQR) is a multifunctional RNA helicase that binds ...
 403-640 6.97e-10

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: 60.13  E-value: 6.97e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA---SVVYHlaKQNNGQVLVCAPSNIAVDQLTEKIHKTGLKVVRLCA 479
Cdd:cd17935      5 KFTPTQIEAIRSGMQPGLTMVVGPPGTGKTDVAVqiiSNLYH--NFPNQRTLIVTHSNQALNQLFEKIMALDIDERHLLR 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  480 KSREAidSPVAFLALHnqvrnmdsvpelqklqqlkdeqgelsaadekryRSLKRNcerELLQVwNCCV*ATFALIAYSIF 559
Cdd:cd17935     83 LGHGA--KIIAMTCTH---------------------------------AALKRG---ELVEL-GFKYDNILMEEAAQIL 123

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  560 VIECHLPYLSS*FQNW--K*DYFIITIEHH*diffgeQLS--VKI-FVKKAANagLSQSLFERLVVLGIRPIRLQVQYRM 634
Cdd:cd17935    124 EIETFIPLLLQNPEDGpnRLKRLIMIGDHH-------QLPpvIKNmAFQKYSN--MEQSLFTRLVRLGVPTVDLDAQGRA 194


                   ....*.
gi 1005460229  635 HPSLSE 640
Cdd:cd17935    195 RASISS 200
DEXXQc_Mov10L1 cd18078
DEXXQ-box helicase domain of Mov10L1; Moloney leukemia virus 10-like protein 1 (Mov10L1) binds ...
 404-482 1.31e-09

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: 59.69  E-value: 1.31e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  404 LNHSQVYAVKTVLQ---RPLS-LIQGPPGTGKTVTSA----SVVYHLAKQnngQVLVCAPSNIAVDQLTEKIHKTGL--- 472
Cdd:cd18078      2 LNELQKEAVKRILGgecRPLPyILFGPPGTGKTVTIIeailQVVYNLPRS---RILVCAPSNSAADLVTSRLHESKVlkp 78

                           90
                   ....*....|.
gi 1005460229  473 -KVVRLCAKSR 482
Cdd:cd18078     79 gDMVRLNAVNR 89
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 405-461 1.06e-08

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: 54.51  E-value: 1.06e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1005460229  405 NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKqNNGQVLVCAPSNIAVD 461
Cdd:cd18043      1 DSSQEAAIISARNGKNVVIQGPPGTGKSQTIANIIANALA-RGKRVLFVSEKKAALD 56
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 403-465 1.62e-08

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: 55.65  E-value: 1.62e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1005460229  403 ELNHSQVYAVKTVL--QRPLSLIQGPPGTGKTvTSASVVYHLAKQNNGQVLVCAPSNIAVDQLTE 465
Cdd:pfam13604    1 TLNAEQAAAVRALLtsGDRVAVLVGPAGTGKT-TALKALREAWEAAGYRVIGLAPTGRAAKVLGE 64
DEXDc smart00487
DEAD-like helicases superfamily;
396-469 4.80e-07

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 51.72  E-value: 4.80e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1005460229   396 FSAQGLPELNHSQVYAVKTVLQRPLS-LIQGPPGTGKTVT-SASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHK 469
Cdd:smart00487    1 IEKFGFEPLRPYQKEAIEALLSGLRDvILAAPTGSGKTLAaLLPALEALKRGKGGRVLVLVPTRELAEQWAEELKK 76
DEXXQc_HELZ cd18077
DEXXQ-box helicase domain of HELZ; Helicase with zinc finger (HELZ) acts as a helicase that ...
 404-461 6.44e-07

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: 51.72  E-value: 6.44e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1005460229  404 LNHSQVYAVkTVLQRPLS------LIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVD 461
Cdd:cd18077      2 LNAKQKEAV-LAITTPLSiqlppvLLIGPFGTGKTFTLAQAVKHILQQPETRILICTHSNSAAD 64
AAA_19 pfam13245
AAA domain;
411-472 6.95e-07

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 49.52  E-value: 6.95e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1005460229  411 AVKTVLQRPLSLIQGPPGTGKTVTSASVVYHLAKQN--NGQVLVCAPSNIAVDQLTEkihKTGL 472
Cdd:pfam13245    4 AVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGgvSFPILLAAPTGRAAKRLSE---RTGL 64
ResIII pfam04851
Type III restriction enzyme, res subunit;
403-478 1.19e-06

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 49.59  E-value: 1.19e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  403 ELNHSQVYAVKTVLQRPLS-----LIQGPPGTGKTVTSASVVYHLAKQNNGQ-VLVCAPSNIAVDQLTEKIHKTGLKVVR 476
Cdd:pfam04851    3 ELRPYQIEAIENLLESIKNgqkrgLIVMATGSGKTLTAAKLIARLFKKGPIKkVLFLVPRKDLLEQALEEFKKFLPNYVE 82


                   ..
gi 1005460229  477 LC 478
Cdd:pfam04851   83 IG 84
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 370-495 2.65e-06

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: 51.68  E-value: 2.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  370 VSGYIYHKLLGHEvEEQVVKcQLPKRFSAQGLP-------------ELNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA 436
Cdd:TIGR01447  100 CDGRLYLRRYWRE-EEKLAA-KLRTLLEARKRTapsailenlfpllNEQNWRKTAVALALKSNFSLITGGPGTGKTTTVA 177

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1005460229  437 ----SVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHKtglKVVRLCAKSREAIDSPVAFLALH 495
Cdd:TIGR01447  178 rlllALVKQSPKQGKLRIALAAPTGKAAARLAESLRK---AVKNLAAAEALIAALPSEAVTIH 237
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1019-1128 1.27e-05

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 49.77  E-value: 1.27e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1019 TIPPAAAARIPVPVGMFIPPVPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHPHQPMTYAPHM-PASQAS-QDASQ 1096
Cdd:pfam03154  189 PGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQRLPSPHPPLQPMTQPpPPSQVSpQPLPQ 268

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1005460229 1097 PLSQGPMTQGGMS-------MSQPMASQPLSQPDLSQDS 1128
Cdd:pfam03154  269 PSLHGQMPPMPHSlqtgpshMQHPVPPQPFPLTPQSSQS 307
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
422-509 3.30e-04

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 44.63  E-value: 3.30e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  422 LIQGPPGTGKTVTSASVVYHLakQNNGQVLVCAPSNIAVDQLTEKIHK-TGLKVVRLCAKSreaIDSPVAFlALHNQVRN 500
Cdd:COG1061    104 LVVAPTGTGKTVLALALAAEL--LRGKRVLVLVPRRELLEQWAEELRRfLGDPLAGGGKKD---SDAPITV-ATYQSLAR 177


                   ....*....
gi 1005460229  501 MDSVPELQK 509
Cdd:COG1061    178 RAHLDELGD 186
KLF1_2_4_N-like cd22056
N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of ...
 1037-1120 7.34e-04

N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of Kruppel-like factor (KLF)1, KLF2, and KLF4; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domains of an unknown subfamily of KLFs, predominantly found in fish, related to the N-terminal domains of KLF1, KLF2, and KLF4.


Pssm-ID: 409231 [Multi-domain]  Cd Length: 339  Bit Score: 43.11  E-value: 7.34e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1037 PPVPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHPHQPMTYAPHMPASQASQDASQPLSQ-----------GPMTQ 1105
Cdd:cd22056    215 SVHPQAFTHHQAAGPGALQGRGGRGGPDCHLLHSSHHHHHHHHLQYQYMNAPYPPHYAHQGAPQfhgqysvfrepMRVHH 294

                           90
                   ....*....|....*..
gi 1005460229 1106 GGMSMSQ--PMASQPLS 1120
Cdd:cd22056    295 QGHPGSMltPPSSPPLL 311
SOBP pfam15279
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ...
 1014-1126 1.06e-03

Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein.


Pssm-ID: 464609 [Multi-domain]  Cd Length: 325  Bit Score: 42.49  E-value: 1.06e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1014 IGAERTIPPAAAARIPVPVGMFIPP--VPPPHHNFFGQPLAGRMPPHGRPVQQPRQRNQRNHHP-HQPMtYAPHMPASQA 1090
Cdd:pfam15279  174 LGKPQQHPPPSPLPAFMEPSSMPPPflRPPPSIPQPNSPLSNPMLPGIGPPPKPPRNLGPPSNPmHRPP-FSPHHPPPPP 252

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1005460229 1091 SQDASQPLSQGPMTQGGMSMSQPmASQPLSQPDLSQ 1126
Cdd:pfam15279  253 TPPGPPPGLPPPPPRGFTPPFGP-PFPPVNMMPNPP 287
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 1029-1122 2.20e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 42.33  E-value: 2.20e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1029 PVPVGMFIPPVPPPHHNffgQPLAGRMPPHGRPVQQPRQRNQR---NHHPHQPMTYAPHMPASQASQDASQPLSQGPMTQ 1105
Cdd:pfam09770  213 QPAPAPAQPPAAPPAQQ---AQQQQQFPPQIQQQQQPQQQPQQpqqHPGQGHPVTILQRPQSPQPDPAQPSIQPQAQQFH 289

                           90
                   ....*....|....*..
gi 1005460229 1106 GGMSMSQPMASQPLSQP 1122
Cdd:pfam09770  290 QQPPPVPVQPTQILQNP 306
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 729-751 2.81e-03

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: 38.19  E-value: 2.81e-03
                           10        20
                   ....*....|....*....|...
gi 1005460229  729 FLNDPRRLNVALTRAKYGIIVIG 751
Cdd:cd18786     67 NSLTPRRLYVALTRARKRLVIYD 89
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 1016-1132 2.92e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 41.62  E-value: 2.92e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229 1016 AERTIPPAAAARIPVPVGMFIPPVPPPhhnffgqplAGRMPPhgrPVQQPRQRNQRNHHPHQPMtyAPHMPASQASQDAS 1095
Cdd:PRK14951   392 APVAQAAAAPAPAAAPAAAASAPAAPP---------AAAPPA---PVAAPAAAAPAAAPAAAPA--AVALAPAPPAQAAP 457

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 1005460229 1096 QPLSQGPMTQGGMSM-SQPMASQPLSQPDLSQDSYLGD 1132
Cdd:PRK14951   458 ETVAIPVRVAPEPAVaSAAPAPAAAPAAARLTPTEEGD 495
DEXXQc_HELZ2-N cd18076
N-terminal DEXXQ-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 419-469 3.77e-03

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: 40.26  E-value: 3.77e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1005460229  419 PLsLIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVD-QLTEKIHK 469
Cdd:cd18076     25 PL-LIYGPFGTGKTFTLAMAALEVIREPGTKVLICTHTNSAADiYIREYFHP 75
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 422-465 4.92e-03

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 38.92  E-value: 4.92e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 1005460229  422 LIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSN-IAVDQLTE 465
Cdd:cd00046      5 LITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKaLALQTAER 49
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 408-504 7.10e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 38.64  E-value: 7.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005460229  408 QVYAVKTVLQRPLS------LIQGPPGTGKTVTSASVVYHLAKQNNGQVLVCAPSNIAVDQLTEKIHKTGLkVVRLCAKS 481
Cdd:pfam13191    8 ELEQLLDALDRVRSgrppsvLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDENLPYSPLLEALTREGL-LRQLLDEL 86

                           90       100
                   ....*....|....*....|....*
gi 1005460229  482 REAIDS--PVAFLALHNQVRNMDSV 504
Cdd:pfam13191   87 ESSLLEawRAALLEALAPVPELPGD 111
ZBD_mv_SF1_Hel-like cd21402
Cys/His rich zinc-binding domain (CH/ZBD) of mesnidovirus SF1 helicase and related proteins; ...
 116-165 9.29e-03

Cys/His rich zinc-binding domain (CH/ZBD) of mesnidovirus SF1 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. This mesnidovirus group includes the Bontag Baru virus (BBaV) replication helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), 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.


Pssm-ID: 394809  Cd Length: 111  Bit Score: 37.11  E-value: 9.29e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1005460229  116 YACRYCGVHdpaSVVQCIQCKKWFCNGRGNTAGSHIVNHLVRAKHKEVTL 165
Cdd:cd21402      1 YNCYVCGEN---AYLTCATCERAFCNSADTNHGSHIEQHLQYSGHTCLYL 47
 
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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