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Conserved domains on  [gi|296881924|gb|ADH82393|]
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nonstructural 5a protein, partial [Hepatitis C virus subtype 6f]

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 ...
 207-455 7.58e-86

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: 262.95  E-value: 7.58e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  207 SHITAETAGRRLARGSPPSLASSSASQLSAPSLKATCTTADRHPDAELIEANLLWRQEVGGNITRVESENKVIILDSFDP 286
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  287 LVAETDDREISVAAECHRPPRpKYPPALPIWARPDYNPPVLETWKKPDYDPPTVAGCALPPSGQPPVPPPRRKRTVLLDS 366
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  367 STVSQALAELAQKSFPEGSTAS-RAESGIDCSVPSSDVVPPlgeddaGSEAGSFSSMPPLEGEPGDPDLSSGSWSTVSDE 445
Cdd:pfam12941 160 STLPTALAELATKSFGSSSTSGiTGDNTTTSSEPAPSGCPP------DSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSG 233

                         250
                  ....*....|
gi 296881924  446 DDAHsSVVCC 455
Cdd:pfam12941 234 ADTE-DVVCC 242
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 96-196 2.12e-48

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: 160.99  E-value: 2.12e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924   96 GPSVPIPSPNYHKALWRVAAEEYVEVVRHGDNHYIVAATSDNLkCPCQVPSPEFF--TEVDGVRLHRYAPACRPLLRDEI 173
Cdd:pfam08301   1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                          90       100
                  ....*....|....*....|...
gi 296881924  174 TYSVGLSTYIIGSQLPCEPEPDV 196
Cdd:pfam08301  80 GQSVGLDGYGVRSQLPCELEPDV 102
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
 3-24 2.76e-09

Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


:

Pssm-ID: 366682  Cd Length: 23  Bit Score: 52.21  E-value: 2.76e-09
                          10        20
                  ....*....|....*....|..
gi 296881924    3 SWLRDIWDWVCTVLSDFKTWLK 24
Cdd:pfam01506   2 SWLWDIWDWVCRVLRDFKNWLK 23
 
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 ...
 207-455 7.58e-86

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: 262.95  E-value: 7.58e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  207 SHITAETAGRRLARGSPPSLASSSASQLSAPSLKATCTTADRHPDAELIEANLLWRQEVGGNITRVESENKVIILDSFDP 286
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  287 LVAETDDREISVAAECHRPPRpKYPPALPIWARPDYNPPVLETWKKPDYDPPTVAGCALPPSGQPPVPPPRRKRTVLLDS 366
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  367 STVSQALAELAQKSFPEGSTAS-RAESGIDCSVPSSDVVPPlgeddaGSEAGSFSSMPPLEGEPGDPDLSSGSWSTVSDE 445
Cdd:pfam12941 160 STLPTALAELATKSFGSSSTSGiTGDNTTTSSEPAPSGCPP------DSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSG 233

                         250
                  ....*....|
gi 296881924  446 DDAHsSVVCC 455
Cdd:pfam12941 234 ADTE-DVVCC 242
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 96-196 2.12e-48

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: 160.99  E-value: 2.12e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924   96 GPSVPIPSPNYHKALWRVAAEEYVEVVRHGDNHYIVAATSDNLkCPCQVPSPEFF--TEVDGVRLHRYAPACRPLLRDEI 173
Cdd:pfam08301   1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                          90       100
                  ....*....|....*....|...
gi 296881924  174 TYSVGLSTYIIGSQLPCEPEPDV 196
Cdd:pfam08301  80 GQSVGLDGYGVRSQLPCELEPDV 102
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
 3-24 2.76e-09

Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


Pssm-ID: 366682  Cd Length: 23  Bit Score: 52.21  E-value: 2.76e-09
                          10        20
                  ....*....|....*....|..
gi 296881924    3 SWLRDIWDWVCTVLSDFKTWLK 24
Cdd:pfam01506   2 SWLWDIWDWVCRVLRDFKNWLK 23
 
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 ...
 207-455 7.58e-86

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: 262.95  E-value: 7.58e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  207 SHITAETAGRRLARGSPPSLASSSASQLSAPSLKATCTTADRHPDAELIEANLLWRQEVGGNITRVESENKVIILDSFDP 286
Cdd:pfam12941   1 SHITAEAAGRRLARGSPPSMASSSASQLSAPSLKATCTANHDSPDAELIEANLLWRQEMGGNITRVESENKVVILDSFDP 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  287 LVAETDDREISVAAECHRPPRpKYPPALPIWARPDYNPPVLETWKKPDYDPPTVAGCALPPSGQPPVPPPRRKRTVLLDS 366
Cdd:pfam12941  81 LVAEEDEREVSVPAEILRKSR-RFAPALPVWARPDYNPLLVETWKKPDYEPPVVHGCPLPPPRSPPVPPPRKKRTVVLTE 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924  367 STVSQALAELAQKSFPEGSTAS-RAESGIDCSVPSSDVVPPlgeddaGSEAGSFSSMPPLEGEPGDPDLSSGSWSTVSDE 445
Cdd:pfam12941 160 STLPTALAELATKSFGSSSTSGiTGDNTTTSSEPAPSGCPP------DSDVESYSSMPPLEGEPGDPDLSDGSWSTVSSG 233

                         250
                  ....*....|
gi 296881924  446 DDAHsSVVCC 455
Cdd:pfam12941 234 ADTE-DVVCC 242
HCV_NS5a_1b pfam08301
Hepatitis C virus non-structural 5a domain 1b; The molecular function of the non-structural 5a ...
 96-196 2.12e-48

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: 160.99  E-value: 2.12e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 296881924   96 GPSVPIPSPNYHKALWRVAAEEYVEVVRHGDNHYIVAATSDNLkCPCQVPSPEFF--TEVDGVRLHRYAPACRPLLRDEI 173
Cdd:pfam08301   1 GPAVPLPPPNYGPALWRVGAEDYVEVVRVGDTHYVTATSCYNL-CPCQVPRPEFFapTEVDGVRVSWYAPPCKPLLVYEV 79

                          90       100
                  ....*....|....*....|...
gi 296881924  174 TYSVGLSTYIIGSQLPCEPEPDV 196
Cdd:pfam08301  80 GQSVGLDGYGVRSQLPCELEPDV 102
HCV_NS5a pfam01506
Hepatitis C virus non-structural 5a protein membrane anchor; The molecular function of the ...
 3-24 2.76e-09

Hepatitis C virus non-structural 5a protein membrane anchor; 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 N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous.


Pssm-ID: 366682  Cd Length: 23  Bit Score: 52.21  E-value: 2.76e-09
                          10        20
                  ....*....|....*....|..
gi 296881924    3 SWLRDIWDWVCTVLSDFKTWLK 24
Cdd:pfam01506   2 SWLWDIWDWVCRVLRDFKNWLK 23
 
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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