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View Structure Prediction Details

Protein: PABP6_ARATH
Organism: Arabidopsis thaliana
Length: 537 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 PABP6_ARATH.

Description E-value Query
Range		 Subject
Range
gi|73976799 - gi|73976799|ref|XP_857739.1| PREDICTED: similar to poly(A) binding protein, cytoplasmic 4 isoform 2 ...
 462.0 [0..11] [537..1]

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Predicted Domain #1
Region A:
Residues: [1-88] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALVKTETQA LGNHQHSSRF GSLYVGDLSP DVTEKDLIDK FSLNVPVVSV HLCRNSVTGK  60
   61 SMCYAYINFD SPFSASNAMT RLNHSDLK

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 48.69897
Match: 1cvjA
Description: Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #2
Region A:
Residues: [89-211] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GKAMRIMWSQ RDLAYRRRTR TGFANLYVKN LDSSITSSCL ERMFCPFGSI LSCKVVEENG  60
   61 QSKGFGFVQF DTEQSAVSAR SALHGSMVYG KKLFVAKFIN KDERAAMAGN QDSTNVYVKN 120
  121 LIE

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 9.045757
Match: 1sjrA
Description: NMR Structure of RRM2 from Human Polypyrimidine Tract Binding Protein Isoform 1 (PTB1)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 5.15097136329571 bayes_pls_golite062009
nucleic acid binding 4.92126426323641 bayes_pls_golite062009
mRNA binding 4.05281507540116 bayes_pls_golite062009
binding 3.64400841800969 bayes_pls_golite062009
2.60920363363072 bayes_pls_golite062009
protein binding 2.17260848225967 bayes_pls_golite062009
transcription regulator activity 1.92450390013691 bayes_pls_golite062009
DNA binding 1.8021593476478 bayes_pls_golite062009
single-stranded RNA binding 1.46469774223879 bayes_pls_golite062009
poly-pyrimidine tract binding 1.36691748240059 bayes_pls_golite062009
transcription factor activity 1.15127506309683 bayes_pls_golite062009
transcription repressor activity 0.998305828880243 bayes_pls_golite062009
mRNA 3'-UTR binding 0.824614388276642 bayes_pls_golite062009
mRNA 5'-UTR binding 0.625848256054783 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.461000905454505 bayes_pls_golite062009
sequence-specific DNA binding 0.383589644462932 bayes_pls_golite062009
translation regulator activity 0.38120065819101 bayes_pls_golite062009
structural molecule activity 0.166336846372115 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.128616879457381 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [212-297] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TVTDDCLHTL FSQYGTVSSV VVMRDGMGRS RGFGFVNFCN PENAKKAMES LCGLQLGSKK  60
   61 LFVGKALKKD ERREMLKQKF SDNFIA

[Run NCBI BLAST on this sequence.]

Detection Method: FFAS03
Confidence: 3.69
Match: 1p1tA
Description: NMR Structure of the N-terminal RRM domain of Cleavage stimulation factor 64 KDa subunit
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
RNA binding 4.74219150342477 bayes_pls_golite062009
nucleic acid binding 4.65259034341669 bayes_pls_golite062009
mRNA binding 3.63162433534903 bayes_pls_golite062009
binding 3.48033873254013 bayes_pls_golite062009
2.38034004712143 bayes_pls_golite062009
protein binding 2.10850948869511 bayes_pls_golite062009
transcription regulator activity 1.94691250607537 bayes_pls_golite062009
DNA binding 1.80828042019548 bayes_pls_golite062009
transcription factor activity 1.17242427495624 bayes_pls_golite062009
single-stranded RNA binding 1.08300488237934 bayes_pls_golite062009
transcription repressor activity 1.00459347347517 bayes_pls_golite062009
poly-pyrimidine tract binding 0.960399311787502 bayes_pls_golite062009
mRNA 3'-UTR binding 0.462558743683805 bayes_pls_golite062009
sequence-specific DNA binding 0.327072171076297 bayes_pls_golite062009
mRNA 5'-UTR binding 0.271234585816403 bayes_pls_golite062009
translation regulator activity 0.246220338604608 bayes_pls_golite062009
structural molecule activity 0.175217083426707 bayes_pls_golite062009
translation repressor activity, nucleic acid binding 0.147208072406136 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.0127733116412899 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [298-381] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPNMRWSNLY VKNLSESMNE TRLREIFGCY GQIVSAKVMC HENGRSKGFG FVCFSNCEES  60
   61 KQAKRYLNGF LVDGKPIVVR VAER

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 22.154902
Match: 2d9pA
Description: No description for 2d9pA was found.

Predicted Domain #5
Region A:
Residues: [382-537] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KEDRIKRLQQ YFQAQPRQYT QAPSAPSPAQ PVLSYVSSSY GCFQPFQVGT SYYYMGNQVP  60
   61 QMSGHQNITT YVPAGKVPLK ERRSMHLVYK HPAYPVAKRG AKQTLVFKGE VNRNLEAATC 120
  121 SKATTSEENR KEERRLTLSG KLSPEVKVEE SGKQLQ

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 3.30103
Match: 1m2vB
Description: Sec24
Matching Structure (courtesy of the PDB):
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Created and Maintained by: Michael Riffle