YRC Public Data Repository - Protein Structure Prediction

Protein:	YLL054C
Organism:	Saccharomyces cerevisiae
Length:	769 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 YLL054C.

Description	E-value	Query Range	Subject Range
YLL054C - Putative protein of unknown function with similarity to Pip2p, an oleate-specific transcriptional ac...	0.0	[1..769]	[1..769]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[4..673]	[28..641]
THI1_SCHPO - Thiamine repressible genes regulatory protein thi1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 2... thi1 - transcription factor Thi1	0.0	[4..673]	[28..641]
SPAC3C7.04 - transcription factor YF54_SCHPO - Uncharacterized transcriptional regulatory protein C3C7.04 OS=Schizosaccharomyces pombe (strain 972 ...	7.0E-80	[7..621]	[32..603]

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Predicted Domain #1

Region A:
Residues: [1-150]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSIASQKKVK PSFVCLRCKQ RKIKCDKLWP TCSKCKASSS ICSYEVEPGR INKSPTIENA  60
   61 PHRDIRNITP ASMSASGSFT SILNPSTKDW EMKNFAMNLS NAHDKLVVMN NTTIVDSPFA 120
  121 FHSILQHDLY AKALTTCIHE RILIDVERHR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	14.522879
Match:	1pyiA_
Description:	PPR1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	4.16002381293778	bayes_pls_golite062009
DNA binding	3.92936270801133	bayes_pls_golite062009
nucleic acid binding	3.76909067702445	bayes_pls_golite062009
binding	2.91929847152301	bayes_pls_golite062009
transcription factor activity	2.76608547022152	bayes_pls_golite062009
sequence-specific DNA binding	1.80020012839068	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	1.69026374220371	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.54700248976411	bayes_pls_golite062009
transcription activator activity	0.778623988601299	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [151-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ENVSANNKKR ELNLTIGDIG PLFFIDKAAL KFIENTSKTS KLYPPIDFLY NTYDYEQAHP  60
   61

[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	SCOP Match	SCOP Description
View	Download	0.391	b.40.4	Nucleic acid-binding proteins
View	Download	0.322	d.15.7	Immunoglobulin-binding domains
View	Download	0.236	d.109.1	Actin depolymerizing proteins
View	Download	0.356	d.68.7	R3H domain
View	Download	0.221	d.58.24	CheY-binding domain of CheA
View	Download	0.391	b.40.4	Nucleic acid-binding proteins
View	Download	0.356	d.68.7	R3H domain
View	Download	0.322	d.15.7	Immunoglobulin-binding domains
View	Download	0.236	d.109.1	Actin depolymerizing proteins
View	Download	0.221	d.58.24	CheY-binding domain of CheA
View	Download	0.208	d.58.49	YajQ-like

Predicted Domain #3

Region A:
Residues: [211-230]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EENNDKISIN ILLEELSKYF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [244-254]

      1          11         21         31         41         51         
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    1 YKTIYPVYPL L

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [388-415]

      1          11         21         31         41         51         
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    1 NEEPFQYTRY VSESDDYPRL FNLRRKLW

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.29
Match:	1n1bA
Description:	(+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [231-243]

      1          11         21         31         41         51         
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    1 LNKNEVDGLI VDF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [255-387]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EISLFEDNIR ELLQLNEFNG YNIVFAGKDS RRKLETITLL TIILAFSYRR LSLSTSHSFK  60
   61 ESFGVKSNNL TLLAHKLLAL MNVFQYVNEH TLCCLLYFFI LRYLNPDQAD MYPTHSDILN 120
  121 LKFLENVAIK LGL

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [416-705]

      1          11         21         31         41         51         
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    1 LGVQFLKFGI LIPEGDSDIL SLEYLRSFMK TDESLPELFE RNYASTNNLD LSLMATAENI  60
   61 YHLHLSLQVL LTSCFPINGP SYLKEVLDNI DKTKDFLNQK FPLILSSLGE PRMKSLHINV 120
  121 PSSLANEESF DFSTFEENET FIANVISYTC TMNIYDSLSL HFENQCFKNA LEYKTYYHRF 180
  181 TFTAIQDYLT LLKLISEYFN GSLLHLREPF GFATQKVVRF SIHRLLIFQA TLLVRLFYKK 240
  241 DTCDRSSAAM GMLNDRNGRL SRVIEKMIKL MSYHMKLLVE IVISKLEKSY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.29
Match:	1n1bA
Description:	(+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [706-769]

      1          11         21         31         41         51         
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    1 LGSFISVSIF RYIIYLVDTD ALSAFISDYW KSDAVMDERY SRIHRIVGLK WGMGRDKSFS  60
   61 FTQN

[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	0.745	0.802	transcription activator activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.745	0.802	transcription activator activity	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.728	0.802	transcription activator activity	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.713	0.802	transcription activator activity	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.680	0.802	transcription activator activity	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.676	0.802	transcription activator activity	a.65.1	Annexin
View	Download	0.627	0.802	transcription activator activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.520	0.802	transcription activator activity	a.144.2	Ribosomal protein L20
View	Download	0.516	0.802	transcription activator activity	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.471	0.802	transcription activator activity	a.4.13	Sigma3 and sigma4 domains of RNA polymerase sigma factors
View	Download	0.439	0.802	transcription activator activity	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.409	0.802	transcription activator activity	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.404	0.802	transcription activator activity	a.112.1	Description not found.
View	Download	0.402	0.802	transcription activator activity	a.2.7	tRNA-binding arm
View	Download	0.376	0.802	transcription activator activity	a.157.1	Skp1 dimerisation domain-like
View	Download	0.373	0.802	transcription activator activity	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.361	0.802	transcription activator activity	a.8.1	Bacterial immunoglobulin/albumin-binding domains
View	Download	0.359	0.802	transcription activator activity	a.30.1	ROP protein
View	Download	0.357	0.802	transcription activator activity	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.346	0.802	transcription activator activity	a.23.5	Hemolysin expression modulating protein HHA
View	Download	0.336	0.802	transcription activator activity	a.28.1	ACP-like
View	Download	0.321	0.802	transcription activator activity	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.319	0.802	transcription activator activity	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.300	0.802	transcription activator activity	a.5.7	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain
View	Download	0.300	0.802	transcription activator activity	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.281	0.802	transcription activator activity	g.53.1	TAZ domain
View	Download	0.279	0.802	transcription activator activity	d.30.1	Allophycocyanin linker chain (domain)
View	Download	0.270	0.802	transcription activator activity	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.265	0.802	transcription activator activity	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.264	0.802	transcription activator activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.262	0.802	transcription activator activity	a.5.2	UBA-like
View	Download	0.261	0.802	transcription activator activity	d.58.18	Regulatory domain in the aminoacid metabolism
View	Download	0.257	0.802	transcription activator activity	a.4.1	Homeodomain-like
View	Download	0.250	0.802	transcription activator activity	a.5.6	Hypothetical protein MTH1615
View	Download	0.236	0.802	transcription activator activity	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.221	0.802	transcription activator activity	a.29.2	Bromodomain
View	Download	0.215	0.802	transcription activator activity	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.211	0.802	transcription activator activity	g.13.1	Crambin-like
View	Download	0.206	0.802	transcription activator activity	d.43.1	Elongation factor Ts (EF-Ts), dimerisation domain
View	Download	0.202	0.802	transcription activator activity	a.77.1	DEATH domain
View	Download	0.201	0.802	transcription activator activity	a.28.1	ACP-like

Predicted Domain #6

Region A:
Residues: [673-769]

      1          11         21         31         41         51         
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    1 GRLSRVIEKM IKLMSYHMKL LVEIVISKLE KSYLGSFISV SIFRYIIYLV DTDALSAFIS  60
   61 DYWKSDAVMD ERYSRIHRIV GLKWGMGRDK SFSFTQN

[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.

Found no 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: