YRC Public Data Repository - Protein Structure Prediction

Protein:	HDA2
Organism:	Saccharomyces cerevisiae
Length:	674 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 HDA2.

Description	E-value	Query Range	Subject Range
MYH4_PIG - Myosin-4 OS=Sus scrofa GN=MYH4 PE=2 SV=1	5.0E-62	[73..668]	[843..1442]
MYH2_BOVIN - Myosin-2 OS=Bos taurus GN=MYH2 PE=2 SV=1	4.0E-61	[73..668]	[846..1445]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	1.0E-60	[73..668]	[57..656]
gi\|14250231, gi\|... - ref\|NP_659210.1\| myosin, heavy polypeptide 2, skeletal muscle, adult [Mus musculus], gi\|14250231\|gb...	2.0E-60	[73..668]	[848..1447]
gi\|179508, gi\|10... - sp\|P12883\|MYH7_HUMAN Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta), gi\|4557773\|ref\|NP...	2.0E-60	[73..668]	[841..1440]

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Predicted Domain #1

Region A:
Residues: [1-59]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSRKNSKKLK VYYLPVTLTQ FQKDLSEILI SLHAKSFKAS IIGEPQADAV NKPSGLPAG

[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: [60-391]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PETHPYPTLS QRQLTYIFDS NIRAIANHPS LLVDHYMPRQ LLRMEPTESS IAGSHKFQVL  60
   61 NQLINSICFR DREGSPNEVI KCAIIAHSIK ELDLLEGLIL GKKFRTKRLS GTSLYNEKHK 120
  121 FPNLPTVDST INKDGTPNSV SSTSSNSNST SYTGYSKDDY DYSVKRNLKK RKINTDDWLF 180
  181 LATTKHLKHD QYLLANYDID MIISFDPMLE VELPALQVLR NNANKDIPII KLLVQNSPDH 240
  241 YLLDSEIKNS SVKSSHLSNN GHVDDSQEYE EIKSSLLYFL QARNAPVNNC EIDYIKLVKC 300
  301 CLEGKDCNNI LPVLDLITLD EASKDSSDSG FW

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	17.154902
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [392-498]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QPQLTKLQYS STELPLWDGP LDIKTYQTEL MHRAVIRLRD IQDEYAKGTV PLYEKRLNET  60
   61 QRQNQLDEIK NSVGLTFKKK QEVEKSINDS EKRLKHAMTE STKLQNK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	8.69897
Match:	1c1gA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
protein deacetylase activity	6.89067246450687	bayes_pls_golite062009
histone deacetylase activity	6.72973102400173	bayes_pls_golite062009
deacetylase activity	6.17788760083229	bayes_pls_golite062009
transcription regulator activity	5.13863038737912	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	5.08778624990141	bayes_pls_golite062009
DNA binding	4.66369707598026	bayes_pls_golite062009
nucleic acid binding	4.51452285155271	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	4.31765999651746	bayes_pls_golite062009
transcription factor activity	4.06706589695599	bayes_pls_golite062009
transcription repressor activity	3.55154985983449	bayes_pls_golite062009
RNA polymerase II transcription factor activity	3.16896789933192	bayes_pls_golite062009
binding	3.02779747447702	bayes_pls_golite062009
sequence-specific DNA binding	2.41271657675151	bayes_pls_golite062009
lysine N-acetyltransferase activity	1.90369937566383	bayes_pls_golite062009
histone acetyltransferase activity	1.90369937566383	bayes_pls_golite062009
transcription activator activity	1.77700860354597	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 corepressor activity	1.49423102874486	bayes_pls_golite062009
transcription factor binding	1.40653841901929	bayes_pls_golite062009
transcription cofactor activity	0.84983974758882	bayes_pls_golite062009
protein binding	0.830419844171551	bayes_pls_golite062009
N-acyltransferase activity	0.712553030350746	bayes_pls_golite062009
histone binding	0.557787598121402	bayes_pls_golite062009
N-acetyltransferase activity	0.474709214154094	bayes_pls_golite062009
transcription coactivator activity	0.2679415219517	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.141400887946529	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [499-674]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 INHLLKNRQE LENFNKLPSN TISSENHLEE GSALADKLKE YIDKNATLFN KLKELQQANA  60
   61 EKSKLNDELR SKYQIESSKA AESAQTLKIL QESMKSLENE VNGPLTKFST ESLKKELERL 120
  121 QNDFQSLKAR NKFLKNYITL MNRQYDLKNK NNVQVEKAAA NGTRFRSTRS NTPNYT

[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

Predicted functions: