YRC Public Data Repository - Protein Structure Prediction

Protein:	HMGB1_RAT
Organism:	Rattus norvegicus
Length:	215 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 HMGB1_RAT.

Description	E-value	Query Range	Subject Range
gi\|109503316 - gi\|109503316\|ref\|XP_573903.2\| PREDICTED: similar to High mobility group protein 2 (HMG-2) [Rattus no...	178.0	[0..1]	[186..127]
gi\|114596859 - gi\|114596859\|ref\|XP_517538.2\| PREDICTED: similar to HMGB2 protein [Pan troglodytes]	176.0	[0..1]	[186..167]
gi\|109076196 - gi\|109076196\|ref\|XP_001085665.1\| PREDICTED: similar to high-mobility group box 2 [Macaca mulatta]	159.0	[0..3]	[186..117]
gi\|94383594 - gi\|94383594\|ref\|XP_001052174.1\| PREDICTED: high mobility group box 2 [Mus musculus]	159.0	[0..1]	[186..77]
gi\|76609479 - gi\|76609479\|ref\|XP_610926.2\| PREDICTED: similar to high-mobility group box 3 [Bos taurus]	157.0	[0..13]	[198..364]
gi\|91080287 - gi\|91080287\|ref\|XP_973934.1\| PREDICTED: similar to High mobility group protein DSP1 (Dorsal switch p...	148.0	[0..2]	[165..689]

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Predicted Domain #1

Region A:
Residues: [1-215]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK TMSAKEKGKF  60
   61 EDMAKADKAR YEREMKTYIP PKGETKKKFK DPNAPKRPPS AFFLFCSEYR PKIKGEHPGL 120
  121 SIGDVAKKLG EMWNNTAADD KQPYEKKAAK LKEKYEKDIA AYRAKGKPDA AKKGVVKAEK 180
  181 SKKKKEEEDD EEDEEDEEEE EEEEDEDEEE DDDDE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	26.522879
Match:	2gzkA
Description:	No description for 2gzkA was found.

Predicted functions:

Term	Confidence	Notes
binding	0.927928103499335	bayes_pls_golite062009
nucleic acid binding	0.38664561645052	bayes_pls_golite062009
DNA binding	0.37554038880732	bayes_pls_golite062009

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

Predicted functions: