YRC Public Data Repository - Protein Structure Prediction

Protein:	PABP8_ARATH
Organism:	Arabidopsis thaliana
Length:	671 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 PABP8_ARATH.

Description	E-value	Query Range	Subject Range
gi\|41388837 - gi\|41388837\|gb\|AAH65540.1\| PABPC4 protein [Homo sapiens]	517.0	[0..36]	[666..2]
PABP1_BOVIN - Polyadenylate-binding protein 1 OS=Bos taurus GN=PABPC1 PE=2 SV=1 gi\|109087089 - gi\|109087089\|ref\|XP_001098239.1\| PREDICTED: poly(A) binding protein, cytoplasmic 1 isoform 2 [Macaca... gi\|123993665, gi... - gi\|168278070\|dbj\|BAG11013.1\| polyadenylate-binding protein 1 [synthetic construct], gi\|123999981\|gb\|... gi\|194036975 - gi\|194036975\|ref\|XP_001927782.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-bind... PABPC1 - poly(A) binding protein, cytoplasmic 1 gi\|73974130, gi\|... - gi\|73974178\|ref\|XP_857695.1\| PREDICTED: similar to Polyadenylate-binding protein 1 (Poly(A)-binding ...	516.0	[0..36]	[662..2]
gi\|26354649 - gi\|26354649\|dbj\|BAC40951.1\| unnamed protein product [Mus musculus]	516.0	[0..36]	[662..2]
gi\|73976771 - gi\|73976771\|ref\|XP_857168.1\| PREDICTED: similar to poly(A) binding protein, cytoplasmic 4 isoform 1 ...	515.0	[0..36]	[666..2]
gi\|197097606 - gi\|197097606\|ref\|NP_001126097.1\| poly(A) binding protein, cytoplasmic 1 [Pongo abelii] gi\|55730342 - gi\|55730342\|emb\|CAH91893.1\| hypothetical protein [Pongo abelii]	515.0	[0..36]	[662..2]
PABP1_RAT - Polyadenylate-binding protein 1 OS=Rattus norvegicus GN=Pabpc1 PE=1 SV=1	514.0	[0..36]	[662..2]

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Predicted Domain #1

Region A:
Residues: [1-216]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAQIQHQGQN ANGGVAVPGA AAAEAAAAAA GAAAAAAGAA QQGTTSLYVG DLDATVTDSQ  60
   61 LFEAFTQAGQ VVSVRVCRDM TTRRSLGYGY VNYATPQDAS RALNELNFMA LNGRAIRVMY 120
  121 SVRDPSLRKS GVGNIFIKNL DKSIDHKALH ETFSAFGPIL SCKVAVDPSG QSKGYGFVQY 180
  181 DTDEAAQGAI DKLNGMLLND KQVYVGPFVH KLQRDP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	52.09691
Match:	1cvjA
Description:	Poly(A)-binding protein
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [217-322]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGEKVKFTNV YVKNLSESLS DEELNKVFGE FGVTTSCVIM RDGEGKSKGF GFVNFENSDD  60
   61 AARAVDALNG KTFDDKEWFV GKAQKKSERE TELKQKFEQS LKEAAD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	16.221849
Match:	2d9pA
Description:	No description for 2d9pA was found.

Predicted Domain #3

Region A:
Residues: [323-409]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KSQGSNLYVK NLDESVTDDK LREHFAPFGT ITSCKVMRDP SGVSRGSGFV AFSTPEEATR  60
   61 AITEMNGKMI VTKPLYVALA QRKEDRK

[Run NCBI BLAST on this sequence.]

Detection Method:	FFAS03
Confidence:	4.49
Match:	2f3jA
Description:	No description for 2f3jA was found.

Predicted Domain #4

Region A:
Residues: [410-520]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ARLQAQFSQM RPVNMPPAVG PRMQMYPPGG PPMGQQLFYG QGPPAMIPQP GFGYQQQLVP  60
   61 GMRPGGSPMP NFFMPMMQQG QQQQQQQQQQ QRPGGGRRGA LPQPQQPSPM M

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #5

Region A:
Residues: [521-671]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QQQMHPRGRM YRYPQRDVNT MPGPTQNMLS VPYDVSSGGG VHHRDSPTSQ PVPIVALATR  60
   61 LANAAPEQQR TMLGENLYPL VEQLEPESAA KVTGMLLEMD QTEVLHLLES PEALKAKVTE 120
  121 AMDVLRSVAQ QQAGGAADQL ASLSLGDNIV P

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	32.522879
Match:	1g9lA
Description:	poly(A) binding protein
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits