NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|209156877|gb|ACI39930|]
View 

tat protein [Human immunodeficiency virus 1]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Tat super family cl08273
Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. ...
 2-63 6.50e-17

Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.


The actual alignment was detected with superfamily member pfam00539:

Pssm-ID: 306921  Cd Length: 64  Bit Score: 68.36  E-value: 6.50e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 209156877    2 EIVDPKLEPWNHPGSQPTTPC-NKCYCKRCCFHCYWCFTTKGLGISHGRKKRRQRRRTPQSNQ 63
Cdd:pfam00539   1 EPLDPRLEPWKHPGSQPKTACtNKCYCKKCCFHCQLCFIKKALGISYERKGRRQRRRAHQKSK 63
 
Name Accession Description Interval E-value
Tat pfam00539
Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. ...
 2-63 6.50e-17

Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.


Pssm-ID: 306921  Cd Length: 64  Bit Score: 68.36  E-value: 6.50e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 209156877    2 EIVDPKLEPWNHPGSQPTTPC-NKCYCKRCCFHCYWCFTTKGLGISHGRKKRRQRRRTPQSNQ 63
Cdd:pfam00539   1 EPLDPRLEPWKHPGSQPKTACtNKCYCKKCCFHCQLCFIKKALGISYERKGRRQRRRAHQKSK 63
 
Name Accession Description Interval E-value
Tat pfam00539
Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. ...
 2-63 6.50e-17

Transactivating regulatory protein (Tat); The retroviral Tat protein binds to the Tar RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region.


Pssm-ID: 306921  Cd Length: 64  Bit Score: 68.36  E-value: 6.50e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 209156877    2 EIVDPKLEPWNHPGSQPTTPC-NKCYCKRCCFHCYWCFTTKGLGISHGRKKRRQRRRTPQSNQ 63
Cdd:pfam00539   1 EPLDPRLEPWKHPGSQPKTACtNKCYCKKCCFHCQLCFIKKALGISYERKGRRQRRRAHQKSK 63
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH