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View Structure Prediction Details

Protein: CSP1_ARATH
Organism: Arabidopsis thaliana
Length: 299 amino acids
Reference: Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16



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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for CSP1_ARATH.

Description E-value Query
Range		 Subject
Range
gi|25167021 - gi|25167021|gb|AAN73790.1|AF484517_1 gag-pol fusion polyprotein [Human immunodeficiency virus 1]
 203.0 [0..4] [208..300]

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Predicted Domain #1
Region A:
Residues: [1-76] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MASEDQSAAR STGKVNWFNA SKGYGFITPD DGSVELFVHQ SSIVSEGYRS LTVGDAVEFA  60
   61 ITQGSDGKTK AVNVTA

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 18.39794
Match: 1mjcA
Description: CRYSTAL STRUCTURE OF CSPA, THE MAJOR COLD SHOCK PROTEIN OF ESCHERICHIA COLI
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
nucleic acid binding 4.29626483284963 bayes_pls_golite062009
DNA binding 3.71771169141041 bayes_pls_golite062009
binding 2.83465364476231 bayes_pls_golite062009
single-stranded DNA binding 2.18907296204914 bayes_pls_golite062009
structural constituent of ribosome 2.13063800565247 bayes_pls_golite062009
transcription regulator activity 2.10110937001387 bayes_pls_golite062009
sequence-specific DNA binding 1.9581702424972 bayes_pls_golite062009
structural molecule activity 1.9177190829469 bayes_pls_golite062009
structure-specific DNA binding 1.81524862921454 bayes_pls_golite062009
transcription activator activity 1.24141936405635 bayes_pls_golite062009
protein binding 1.20309946451799 bayes_pls_golite062009
ribonuclease activity 1.19236946227657 bayes_pls_golite062009
transcription factor activity 1.14242112812892 bayes_pls_golite062009
DNA-directed RNA polymerase activity 0.794634028933139 bayes_pls_golite062009
RNA polymerase activity 0.794634028933139 bayes_pls_golite062009
RNA polymerase II transcription factor activity 0.583085644017496 bayes_pls_golite062009
nuclease activity 0.57381531077345 bayes_pls_golite062009
translation regulator activity 0.31332179848255 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.263197317040851 bayes_pls_golite062009
chromatin binding 0.19409870825073 bayes_pls_golite062009
RNA binding 0.18502033889261 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 0.125256208482441 bayes_pls_golite062009
exoribonuclease activity 0.109774918833391 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [77-218] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGGGSLKKEN NSRGNGARRG GGGSGCYNCG ELGHISKDCG IGGGGGGGER RSRGGEGCYN  60
   61 CGDTGHFARD CTSAGNGDQR GATKGGNDGC YTCGDVGHVA RDCTQKSVGN GDQRGAVKGG 120
  121 NDGCYTCGDV GHFARDCTQK VA

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 15.045757
Match: 1bajA
Description: HIV-1 CAPSID PROTEIN C-TERMINAL FRAGMENT PLUS GAG P2 DOMAIN
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
transcription regulator activity 4.15011217435369 bayes_pls_golite062009
DNA binding 3.53875479816163 bayes_pls_golite062009
nucleic acid binding 3.44034453920031 bayes_pls_golite062009
transcription factor activity 2.85277117704074 bayes_pls_golite062009
transcription activator activity 2.7914489292048 bayes_pls_golite062009
binding 2.66299166397108 bayes_pls_golite062009
protein binding 1.9611027722895 bayes_pls_golite062009
RNA polymerase II transcription factor activity 0.815065790327049 bayes_pls_golite062009
transcription repressor activity 0.574479324767174 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [219-299] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AGNVRSGGGG SGTCYSCGGV GHIARDCATK RQPSRGCYQC GGSGHLARDC DQRGSGGGGN  60
   61 DNACYKCGKE GHFARECSSV A

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 8.221849
Match: 1aafA
Description: NUCLEOCAPSID ZINC FINGERS DETECTED IN RETROVIRUSES: EXAFS STUDIES ON INTACT VIRUSES AND THE SOLUTION-STATE STRUCTURE OF THE NUCLEOCAPSID PROTEIN FROM HIV-1
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle