YRC Public Data Repository - Protein Structure Prediction

Protein:	HDA1
Organism:	Saccharomyces cerevisiae
Length:	706 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 HDA1.

Description	E-value	Query Range	Subject Range
gi\|151944501 - gi\|151944501\|gb\|EDN62779.1\| histone deacetylase [Saccharomyces cerevisiae YJM789] HDA1_YEAST - Histone deacetylase HDA1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HDA1 PE=1 SV=1 HDA1 - Putative catalytic subunit of a class II histone deacetylase complex that also contains Hda2p and Hd...	0.0	[1..706]	[1..706]
CLR3_SCHPO - Histone deacetylase clr3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=clr3 PE=1 SV=1 clr3 - histone deacetylase (class II) Clr3	0.0	[12..696]	[23..676]
gi\|18376165 - gi\|18376165\|emb\|CAD21239.1\| related to histone deacetylase A [Neurospora crassa]	0.0	[12..697]	[33..730]
gi\|14190349 - gi\|14190349\|gb\|AAK55655.1\| histone deacetylase HDA1 [Candida albicans]	0.0	[3..535]	[63..610]
gi\|7108921 - gi\|7108921\|gb\|AAF36540.1\| GR AF-1 specific histone deacetylase [Homo sapiens]	0.0	[3..519]	[274..770]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[3..519]	[271..767]
HDAC1_MOUSE - Histone deacetylase 1 OS=Mus musculus GN=Hdac1 PE=1 SV=1	0.0	[65..450]	[10..389]

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Predicted Domain #1

Region A:
Residues: [1-236]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDSVMVKKEV LENPDHDLKR KLEENKEEEN SLSTTSKSKR QVIVPVCMPK IHYSPLKTGL  60
   61 CYDVRMRYHA KIFTSYFEYI DPHPEDPRRI YRIYKILAEN GLINDPTLSG VDDLGDLMLK 120
  121 IPVRAATSEE ILEVHTKEHL EFIESTEKMS REELLKETEK GDSVYFNNDS YASARLPCGG 180
  181 AIEACKAVVE GRVKNSLAVV RPPGHHAEPQ AAGGFCLFSN VAVAAKNILK NYPESV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	288.522879
Match:	1c3pA_
Description:	HDAC homologue
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [237-436]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RRIMILDWDI HHGNGTQKSF YQDDQVLYVS LHRFEMGKYY PGTIQGQYDQ TGEGKGEGFN  60
   61 CNITWPVGGV GDAEYMWAFE QVVMPMGREF KPDLVIISSG FDAADGDTIG QCHVTPSCYG 120
  121 HMTHMLKSLA RGNLCVVLEG GYNLDAIARS ALSVAKVLIG EPPDELPDPL SDPKPEVIEM 180
  181 IDKVIRLQSK YWNCFRRRHA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	288.522879
Match:	1c3pA_
Description:	HDAC homologue
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [437-706]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSGCNFNEPI NDSIISKNFP LQKAIRQQQQ HYLSDEFNFV TLPLVSMDLP DNTVLCTPNI  60
   61 SESNTIIIVV HDTSDIWAKR NVISGTIDLS SSVIIDNSLD FIKWGLDRKY GIIDVNIPLT 120
  121 LFEPDNYSGM ITSQEVLIYL WDNYIKYFPS VAKIAFIGIG DSYSGIVHLL GHRDTRAVTK 180
  181 TVINFLGDKQ LKPLVPLVDE TLSEWYFKNS LIFSNNSHQC WKENESRKPR KKFGRVLRCD 240
  241 TDGLNNIIEE RFEEATDFIL DSFEEWSDEE

[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.

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