YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|208968513
Organism:	synthetic construct
Length:	260 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

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 gi|208968513.

Description	E-value	Query Range	Subject Range
gi\|109482992 - gi\|109482992\|ref\|XP_001069410.1\| PREDICTED: similar to Homeobox protein Hox-C9 (Hox-3.2) isoform 1 [...	5.0E-38	[1..258]	[1..249]
gi\|109096999 - gi\|109096999\|ref\|XP_001108363.1\| PREDICTED: similar to Homeobox protein Hox-C9 (Hox-3.2) isoform 3 [...	2.0E-37	[1..258]	[1..249]
gi\|114644440 - gi\|114644440\|ref\|XP_001136284.1\| PREDICTED: hypothetical protein isoform 1 [Pan troglodytes]	2.0E-37	[1..258]	[1..249]
gi\|47228655 - gi\|47228655\|emb\|CAG07387.1\| unnamed protein product [Tetraodon nigroviridis]	1.0E-36	[1..259]	[1..253]
tr\|G3HV27\|G3HV27... - Homeobox protein Hox-C9 OS=Cricetulus griseus GN=I79_014803 PE=4 SV=1 gi\|109097003, gi... - gi\|109097003\|ref\|XP_001108312.1\| PREDICTED: similar to Homeobox protein Hox-C9 (Hox-3.2) isoform 2 [... gi\|76617586, gi\|... - gi\|76617588\|ref\|XP_878887.1\| PREDICTED: similar to Hox-3.2 isoform 2 [Bos taurus], gi\|76617586\|ref\|X... tr\|M3WTV0\|M3WTV0... - Homeobox C9 OS=Felis catus GN=HOXC9 PE=4 SV=1 HXC9_MOUSE - Homeobox protein Hox-C9 OS=Mus musculus GN=Hoxc9 PE=2 SV=2 gi\|109482994, gi... - gi\|62653137\|ref\|XP_217059.3\| PREDICTED: similar to Hox-3.2 [Rattus norvegicus], gi\|149031892\|gb\|EDL8...	3.0E-33	[1..260]	[1..260]
gi\|113171686 - gi\|113171686\|gb\|ABI30949.1\| homeobox C9 [Capra hircus]	7.0E-33	[1..260]	[1..260]
gi\|21619213 - gi\|21619213\|gb\|AAH32769.1\| HOXC9 protein [Homo sapiens]	3.0E-32	[2..260]	[5..263]
gi\|66476113 - gi\|66476113\|gb\|AAX63764.2\| HoxC9bi [Oncorhynchus mykiss]	5.0E-32	[4..251]	[1..247]

Back

Predicted Domain #1

Region A:
Residues: [1-190]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSATGPISNY YVDSLISHDN EDLLASRFPA TGAHPAAARP SGLVPDCSDF PSCSFAPKPA  60
   61 VFSTSWAPVP SQSSVVYHPY GPQPHLGADT RYMRTWLEPL SGAVSFPSFP AGGRHYALKP 120
  121 DAYPGRRADC GPGEGRSYPD YMYGSPGELR DRAPQTLPSP EADALAGSKH KEEKADLDPS 180
  181 NPVANWIHAR

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	107.823909
Match:	PF04617.4
Description:	No description for PF04617.4 was found.

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

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [191-260]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STRKKRCPYT KYQTLELEKE FLFNMYLTRD RRYEVARVLN LTERQVKIWF QNRRMKMKKM  60
   61 NKEKTDKEQS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	25.30103
Match:	1pufA
Description:	Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	5.13863038737912	bayes_pls_golite062009
DNA binding	4.66369707598026	bayes_pls_golite062009
nucleic acid binding	4.51452285155271	bayes_pls_golite062009
transcription factor activity	4.06706589695599	bayes_pls_golite062009
sequence-specific DNA binding	3.5139760613123	bayes_pls_golite062009
RNA polymerase II transcription factor activity	3.16896789933192	bayes_pls_golite062009
transcription activator activity	3.10621734076555	bayes_pls_golite062009
binding	3.02779747447702	bayes_pls_golite062009
transcription repressor activity	1.91962622287073	bayes_pls_golite062009
protein binding	1.88087411289001	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	1.73068440195944	bayes_pls_golite062009
chromatin binding	1.68956710349366	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	1.62096064323298	bayes_pls_golite062009
transcription factor binding	1.40653841901929	bayes_pls_golite062009
transcription cofactor activity	0.84983974758882	bayes_pls_golite062009
transcription coactivator activity	0.2679415219517	bayes_pls_golite062009
transcription corepressor activity	0.25931464844298	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: