YRC Public Data Repository - Protein Structure Prediction

Protein:	AT13A_ARATH
Organism:	Arabidopsis thaliana
Length:	603 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 AT13A_ARATH.

Description	E-value	Query Range	Subject Range
gi\|7494579 - gi\|7494579\|pir\|\|T29959 DNA-directed RNA polymerase II large subunit ama-1 - Caenorhabditis elegans	290.0	[0..85]	[570..1329]
RPB1_CAEBR - DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2 gi\|157759005 - gi\|157759005\|ref\|XP_001671846.1\| Hypothetical protein CBG05355 [Caenorhabditis briggsae AF16]	283.0	[0..85]	[575..1324]
gi\|54643878\|gb\|E... - GA13798-PA [Drosophila pseudoobscura], RpII215 [Drosophila pseudoobscura pseudoobscura] gi\|54643878, gi\|... - gi\|54643878\|gb\|EAL32621.1\| RpII215 [Drosophila pseudoobscura pseudoobscura], gi\|125983594\|ref\|XP_001...	282.0	[0..87]	[563..1325]
gi\|40217297, gi\|... - gi\|4808164\|emb\|CAB42795.1\| largest subunit of the RNA polymerase II complex [Drosophila guanche], gi...	281.0	[0..87]	[563..1325]
gi\|4808162 - gi\|4808162\|emb\|CAB42796.1\| largest subunit of the RNA polymerase II complex [Drosophila madeirensis]	275.0	[0..87]	[563..1325]
gi\|9587193, gi\|9... - gi\|9587199\|gb\|AAF89203.1\|AF272653_1 RNA polymerase II largest subunit [Drosophila subobscura], gi\|95...	275.0	[0..87]	[563..1325]
gi\|46228363 - gi\|46228363\|gb\|EAK89262.1\| putative DNA-directed RNA polymerase,possible RNA polymerase A/beta'/A'' ... gi\|66359288 - gi\|66359288\|ref\|XP_626822.1\| DNA-directed RNA polymerase,possible RNA polymerase A/beta'/A'' subunit...	268.0	[0..87]	[581..1376]

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Predicted Domain #1

Region A:
Residues: [1-86]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDFPENLPSD IGRLEQIVSH FFPKALHIVL NSRIPSLQSR GRTRERLSGL NVRKSDKWFN  60
   61 LVMGDRPAAL EKLHSWHRNI LDSMII

[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 #2

Region A:
Residues: [87-326]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DIILVHPISN DNLDDDDDHS DSVVRSAETV IERWVVQYEN PLIMSPQSSD SATRYQKVYK  60
   61 KSIILLRSLY AQTRLLPAYR VSRQLSSSLA SSGYDLIYKV SSFSDIFSGP VTETMKEFRF 120
  121 APVEVPPGRL CASVTYRSDL SDFNLGAHIT LPPRIITDYV GSPATDPMRF FPSPGRSVEG 180
  181 HSFTGRAGRP PLTGSSAERP HSWTSGFHRP PAQFATPNQS FSPAQSHQLS PGLHDFHWSR 240
  241

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	35.154902
Match:	1i3qA
Description:	RBP1
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [327-421]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TDAFGDNHQL SPPFSPSGSP STPRYISGGN SPRINVRPGT APVTIPSSAT LNRYVSSNFS  60
   61 EPGRNPLPPF SPKSTRRSPS SQDSLPGIAL YRSSR

[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 #4

Region A:
Residues: [422-603]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGESPSGLMN QYPTQKLSKD SKYDSGRFSG VLSSSDSPRF AFSRSPSRLS SQDDLDDPDC  60
   61 SCPFDFDDVD ESGLQYSHSL DRRKTSSSIS QSLPLGRRSS QDAAVGVLVH MLKTAPPLRQ 120
  121 DSSTYMASMS GVQREGSVSG TESEFSMARS TSDALEELRN YKQLKDLLLS KSKSGSGPTR 180
  181 VH

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

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