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Conserved domains on  [gi|36310352|gb|AAQ85514|]
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NS5A, partial [Hepacivirus hominis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HCV_NS5a_C super family cl15181
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 31-254 6.85e-93

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


The actual alignment was detected with superfamily member pfam12941:

Pssm-ID: 289693  Cd Length: 242  Bit Score: 273.35  E-value: 6.85e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352    31 SHITAETAKRRLARGSPPSLASSSASQLSAPSLKATCTTHHDSPDADLIEANLLWRQEMGGNITRVESENKVVILDSFDP 110
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352   111 LRAEEDEGEISVPAEILRKSRKFPPAMPIWARPDYNPPLLESWKDPDYVPPVVHGCPLPPARAPPIPPPRRKRTVVLTES 190
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 36310352   191 TVSSALAELATKAFGSSGlSSADSGTATAPPDQPSDDG-DTRSDVESYSSMPPLEGEPGDPDLSD 254
Cdd:pfam12941 161 TLPTALAELATKSFGSSS-TSGITGDNTTTSSEPAPSGcPPDSDVESYSSMPPLEGEPGDPDLSD 224
HCV_NS5a_1b super family cl07057
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 1-20 1.27e-03

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


The actual alignment was detected with superfamily member pfam08301:

Pssm-ID: 149382  Cd Length: 102  Bit Score: 37.34  E-value: 1.27e-03
                          10        20
                  ....*....|....*....|
gi 36310352     1 VGLNQYLVGSQLPCEPEPDV 20
Cdd:pfam08301  83 VGLDGYGVRSQLPCELEPDV 102
 
Name Accession Description Interval E-value
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 31-254 6.85e-93

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 273.35  E-value: 6.85e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352    31 SHITAETAKRRLARGSPPSLASSSASQLSAPSLKATCTTHHDSPDADLIEANLLWRQEMGGNITRVESENKVVILDSFDP 110
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352   111 LRAEEDEGEISVPAEILRKSRKFPPAMPIWARPDYNPPLLESWKDPDYVPPVVHGCPLPPARAPPIPPPRRKRTVVLTES 190
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 36310352   191 TVSSALAELATKAFGSSGlSSADSGTATAPPDQPSDDG-DTRSDVESYSSMPPLEGEPGDPDLSD 254
Cdd:pfam12941 161 TLPTALAELATKSFGSSS-TSGITGDNTTTSSEPAPSGcPPDSDVESYSSMPPLEGEPGDPDLSD 224
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 1-20 1.27e-03

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 37.34  E-value: 1.27e-03
                          10        20
                  ....*....|....*....|
gi 36310352     1 VGLNQYLVGSQLPCEPEPDV 20
Cdd:pfam08301  83 VGLDGYGVRSQLPCELEPDV 102
 
Name Accession Description Interval E-value
HCV_NS5a_C pfam12941
HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C ...
 31-254 6.85e-93

HCV NS5a protein C-terminal region; This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR.


Pssm-ID: 289693  Cd Length: 242  Bit Score: 273.35  E-value: 6.85e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352    31 SHITAETAKRRLARGSPPSLASSSASQLSAPSLKATCTTHHDSPDADLIEANLLWRQEMGGNITRVESENKVVILDSFDP 110
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 36310352   111 LRAEEDEGEISVPAEILRKSRKFPPAMPIWARPDYNPPLLESWKDPDYVPPVVHGCPLPPARAPPIPPPRRKRTVVLTES 190
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSRRFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTES 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 36310352   191 TVSSALAELATKAFGSSGlSSADSGTATAPPDQPSDDG-DTRSDVESYSSMPPLEGEPGDPDLSD 254
Cdd:pfam12941 161 TLPTALAELATKSFGSSS-TSGITGDNTTTSSEPAPSGcPPDSDVESYSSMPPLEGEPGDPDLSD 224
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 1-20 1.27e-03

Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain.


Pssm-ID: 149382  Cd Length: 102  Bit Score: 37.34  E-value: 1.27e-03
                          10        20
                  ....*....|....*....|
gi 36310352     1 VGLNQYLVGSQLPCEPEPDV 20
Cdd:pfam08301  83 VGLDGYGVRSQLPCELEPDV 102
 
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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