YRC Public Data Repository - Protein Structure Prediction

Protein:	CDX1_RAT
Organism:	Rattus norvegicus
Length:	123 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 CDX1_RAT.

Description	E-value	Query Range	Subject Range
Rx-PA - The gene Retinal Homeobox is referred to in FlyBase by the symbol Dmel\Rx (CG10052, FBgn0020617). It... gi\|220960168 - gi\|220960168\|gb\|ACL92620.1\| Rx-PA [synthetic construct]	120.0	[0..3]	[123..526]
gi\|9621907 - gi\|9621907\|gb\|AAF89581.1\|AF165886_1 paired-box transcription factor [Branchiostoma floridae]	118.0	[0..3]	[122..187]
gi\|41615361 - gi\|41615361\|gb\|AAS09957.1\| Pax7 transcription factor [Ambystoma mexicanum]	118.0	[0..3]	[122..216]
gi\|91087879 - gi\|91087879\|ref\|XP_969925.1\| PREDICTED: similar to transcription factor protein [Tribolium castaneum...	117.0	[0..3]	[97..44]
gi\|15625548 - gi\|15625548\|gb\|AAL04156.1\|AF411465_1 transcription factor Pax7 [Petromyzon marinus]	115.0	[0..3]	[122..208]
gi\|53125916 - gi\|53125916\|emb\|CAG25520.1\| paired box protein 7 [Salvelinus alpinus]	115.0	[0..3]	[122..225]
gi\|41581181 - gi\|41581181\|emb\|CAF02090.1\| paired box protein 7 [Salmo salar]	115.0	[0..3]	[122..231]

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Predicted Domain #1

Region A:
Residues: [1-123]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KTRTKDKYRV VYTDHQRLEL EKEFHYSRYI TIRRKSELAA NLGLTERQVK IWFQNRRAKE  60
   61 RKVNKKKQQQ QQQQQQQPMP PTQLPLPLDG TPTPSGHPGS LCPTNAGLLG TPSPVPVKEE 120
  121 FLP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.522879
Match:	1homA
Description:	DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ANTENNAPEDIA HOMEODOMAIN FROM DROSOPHILA IN SOLUTION BY 1H NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.57523737355937	bayes_pls_golite062009
DNA binding	3.00143272905695	bayes_pls_golite062009
nucleic acid binding	2.89825020286436	bayes_pls_golite062009
transcription factor activity	2.53664874743748	bayes_pls_golite062009
binding	1.68817361068715	bayes_pls_golite062009
sequence-specific DNA binding	1.56629498736977	bayes_pls_golite062009
transcription activator activity	1.26247803652791	bayes_pls_golite062009
protein binding	1.16239587634422	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.14821760889085	bayes_pls_golite062009
transcription repressor activity	0.20862059645422	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: