YRC Public Data Repository - Protein Structure Prediction

Protein:	HMS2
Organism:	Saccharomyces cerevisiae
Length:	358 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 HMS2.

Description	E-value	Query Range	Subject Range
HMS2 - Protein with similarity to heat shock transcription factors; overexpression suppresses the pseudohyp... HMS2_YEAST - Probable transcription factor HMS2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=HMS2 ...	0.0	[1..358]	[1..358]
HSF8_SOLLC - Heat shock factor protein HSF8 OS=Solanum lycopersicum GN=HSF8 PE=3 SV=1	4.0E-67	[6..229]	[33..251]
HSF1 - heat shock transcription factor 1 gi\|61362382, gi\|... - gi\|61362386\|gb\|AAX42211.1\| heat shock transcription factor 1 [synthetic construct], gi\|61362382\|gb\|A...	8.0E-63	[3..227]	[8..227]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	1.0E-62	[3..227]	[8..227]
gi\|16118447 - gi\|16118447\|gb\|AAL12248.1\| heat shock transcription factor [Phaseolus acutifolius]	1.0E-61	[2..239]	[3..221]
HSF8_SOLPE - Heat shock factor protein HSF8 OS=Solanum peruvianum GN=HSF8 PE=2 SV=1	1.0E-61	[6..229]	[35..253]
gi\|17061849 - gi\|17061849\|dbj\|BAB72174.1\| heat shock transcription factor mutant [synthetic construct]	2.0E-61	[6..243]	[14..250]
gi\|17061843 - gi\|17061843\|dbj\|BAB72171.1\| heat shock transcription factor [Danio rerio]	2.0E-61	[6..243]	[14..250]
HSF1_MOUSE - Heat shock factor protein 1 OS=Mus musculus GN=Hsf1 PE=1 SV=2	3.0E-61	[3..227]	[8..227]

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Predicted Domain #1

Region A:
Residues: [1-113]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDATSRMEQP DVFVSKLYHL LQGNAYSNII QWSTDGSKLV IWNPDQFTKV ILERFFGIHT  60
   61 FAAFVKQLSK YNFQKAGRPD CVEFSNIHFQ KDNINSLSLV KAHQSAATPN VAA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	86.124002
Match:	3htsB_
Description:	Heat-shock transcription factor
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.50995556050336	bayes_pls_golite062009
binding	3.33026160538031	bayes_pls_golite062009
DNA binding	3.22637331076146	bayes_pls_golite062009
nucleic acid binding	3.05427098674	bayes_pls_golite062009
transcription factor activity	2.60537570879007	bayes_pls_golite062009
sequence-specific DNA binding	1.32971938164691	bayes_pls_golite062009
transcription activator activity	1.09351769815632	bayes_pls_golite062009
transcription repressor activity	0.97608021324937	bayes_pls_golite062009
protein binding	0.653872239015235	bayes_pls_golite062009
RNA polymerase II transcription factor activity	0.29742933266479	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [114-253]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VNNMNKQCTF HWDPFKVNSI LSKAIGKPSF EKLVKNVDRL QGNLDELKST NADSLRIIRE  60
   61 INASLQTISY HQFHAYQTAN FLQENFEAIK KVVCPDSCLQ HQQRQPKRPK RYSLLLLIPN 120
  121 ASELSETPLM RFAGVFEFMN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.261	0.295	pseudohyphal growth	a.1.1	Globin-like
View	Download	0.271	0.174	pseudohyphal growth	a.133.1	Phospholipase A2, PLA2
View	Download	0.268	0.064	pseudohyphal growth	a.77.1	DEATH domain
View	Download	0.236	0.038	pseudohyphal growth	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.271	N/A	N/A	a.133.1	Phospholipase A2, PLA2
View	Download	0.268	N/A	N/A	a.77.1	DEATH domain
View	Download	0.261	N/A	N/A	a.1.1	Globin-like
View	Download	0.236	N/A	N/A	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.234	N/A	N/A	a.121.1	Tetracyclin repressor-like, C-terminal domain
View	Download	0.234	N/A	N/A	a.121.1	Tetracyclin repressor-like, C-terminal domain
View	Download	0.231	N/A	N/A	a.1.1	Globin-like

Predicted Domain #3

Region A:
Residues: [254-358]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CSLDTATQWH PQLHPEAYDL LFVTVSPNMQ QEHLIYFKRL RNLLPSFPVI AIINRPVSPQ  60
   61 DTSIAPSNYS RYYFHHFLQL GFSDILVSPF TPTQLITLLS KHLRT

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.899	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.899	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.889	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.878	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.874	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.860	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.860	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.830	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.745	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.479	0.840	pseudohyphal growth	d.68.1	Translation initiation factor IF3, C-terminal domain
View	Download	0.438	0.840	pseudohyphal growth	c.47.2	RNA 3'-terminal phosphate cyclase, RPTC, insert domain
View	Download	0.417	0.840	pseudohyphal growth	c.23.1	CheY-like
View	Download	0.404	0.840	pseudohyphal growth	c.25.1	Ferredoxin reductase-like, C-terminal NADP-linked domain
View	Download	0.400	0.840	pseudohyphal growth	c.25.1	Ferredoxin reductase-like, C-terminal NADP-linked domain
View	Download	0.391	0.840	pseudohyphal growth	c.84.1	Phosphoglucomutase, first 3 domains
View	Download	0.377	0.840	pseudohyphal growth	c.37.1	P-loop containing nucleoside triphosphate hydrolases
View	Download	0.351	0.840	pseudohyphal growth	c.10.1	RNI-like
View	Download	0.342	0.840	pseudohyphal growth	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.333	0.840	pseudohyphal growth	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.318	0.840	pseudohyphal growth	c.37.1	P-loop containing nucleoside triphosphate hydrolases
View	Download	0.308	0.840	pseudohyphal growth	c.51.1	Anticodon-binding domain of Class II aaRS
View	Download	0.306	0.840	pseudohyphal growth	c.10.1	RNI-like
View	Download	0.303	0.840	pseudohyphal growth	a.71.2	Helical domain of Sec23/24
View	Download	0.298	0.840	pseudohyphal growth	c.23.6	Cobalamin (vitamin B12)-binding domain
View	Download	0.297	0.840	pseudohyphal growth	c.84.1	Phosphoglucomutase, first 3 domains
View	Download	0.274	0.840	pseudohyphal growth	c.3.1	FAD/NAD(P)-binding domain
View	Download	0.252	0.840	pseudohyphal growth	d.68.1	Translation initiation factor IF3, C-terminal domain
View	Download	0.250	0.840	pseudohyphal growth	d.16.1	FAD-linked reductases, C-terminal domain
View	Download	0.241	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.231	0.840	pseudohyphal growth	c.26.2	Adenine nucleotide alpha hydrolases-like
View	Download	0.230	0.840	pseudohyphal growth	g.45.1	Pyk2-associated protein beta ARF-GAP domain
View	Download	0.221	0.840	pseudohyphal growth	c.23.4	Succinyl-CoA synthetase domains
View	Download	0.219	0.840	pseudohyphal growth	c.15.1	BRCT domain
View	Download	0.217	0.840	pseudohyphal growth	c.59.1	MurD-like peptide ligases, peptide-binding domain
View	Download	0.215	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.215	0.840	pseudohyphal growth	c.114.1	YchN-like
View	Download	0.213	0.840	pseudohyphal growth	d.68.4	YhbY-like
View	Download	0.213	0.840	pseudohyphal growth	d.74.4	Prokaryotic AspRS, insert domain
View	Download	0.213	0.840	pseudohyphal growth	c.47.1	Thioredoxin-like
View	Download	0.213	0.840	pseudohyphal growth	c.114.1	YchN-like
View	Download	0.209	0.840	pseudohyphal growth	c.84.1	Phosphoglucomutase, first 3 domains
View	Download	0.208	0.840	pseudohyphal growth	c.57.1	Molybdenum cofactor biosynthesis proteins
View	Download	0.203	0.840	pseudohyphal growth	c.23.1	CheY-like

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: