YRC Public Data Repository - Protein Structure Prediction

Protein:	CHA4
Organism:	Saccharomyces cerevisiae
Length:	648 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 CHA4.

Description	E-value	Query Range	Subject Range
CHA4 - DNA binding transcriptional activator, mediates serine/threonine activation of the catabolic L-serin... CHA4_YEAST - Activatory protein CHA4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CHA4 PE=1 SV=1	0.0	[1..648]	[1..648]
gi\|245224 - gi\|245224\|gb\|AAB21394.1\| NIT4=protein product involved in nitrate assimilation [Neurospora intermedi... NIT4_NEUCR - Nitrogen assimilation transcription factor nit-4 - Neurospora crassa	5.0E-99	[2..628]	[8..654]
gi\|6901427 - gi\|6901427\|emb\|CAB71797.1\| pathway-specific nitrogen regulator [Tolypocladium inflatum]	1.0E-96	[4..624]	[30..666]
NIRA_EMENI - Nitrogen assimilation transcription factor nirA OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 ... NIRA_EMENI - Nitrogen assimilation transcription factor nirA OS=Emericella nidulans GN=nirA PE=4 SV=1	7.0E-89	[2..625]	[1..630]
YJ74_SCHPO - Uncharacterized transcriptional regulatory protein C757.04 OS=Schizosaccharomyces pombe (strain 972 ... SPCC757.04 - transcription factor	8.0E-83	[52..602]	[66..599]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	8.0E-78	[31..617]	[26..635]

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Predicted Domain #1

Region A:
Residues: [1-118]

      1          11         21         31         41         51         
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    1 MMLEPSPPPL TTTVTPSLPS SLKKSVTDND QNNNNVPRKR KLACQNCRRR RRKCNMEKPC  60
   61 SNCIKFRTEC VFTQQDLRNK RYSTTYVEAL QSQIRSLKEQ LQILSSSSST IASNALSS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.30103
Match:	1cld__
Description:	CD2-Lac9
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	4.56444258780502	bayes_pls_golite062009
DNA binding	4.26146437716972	bayes_pls_golite062009
nucleic acid binding	4.17369933547911	bayes_pls_golite062009
transcription factor activity	3.049435548132	bayes_pls_golite062009
binding	2.91929847152301	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.03201524223606	bayes_pls_golite062009
sequence-specific DNA binding	1.87955444697212	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	1.86200506906385	bayes_pls_golite062009
transcription activator activity	0.915626626047549	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [119-173]

      1          11         21         31         41         51         
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    1 LKNNSDHGDA PNEKILKYGE TAQSALPSSE SNDENESDAF TKKMPSESPP PVGTN

[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	0.389	a.4.11	RNA polymerase subunit RPB10
View	Download	0.354	a.144.1	PABC (PABP) domain
View	Download	0.337	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.379	a.5.7	4-hydroxy-2-oxovalerate aldolase DmpG, communication domain
View	Download	0.296	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.273	a.5.1	DNA helicase RuvA subunit, C-terminal domain
View	Download	0.260	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.225	a.60.2	RuvA domain 2-like
View	Download	0.213	a.144.1	PABC (PABP) domain

Predicted Domain #3

Region A:
Residues: [174-202]

      1          11         21         31         41         51         
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    1 SIYPSNSLSI IKKKTDGSTR YQQQQVSLK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [374-648]

      1          11         21         31         41         51         
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    1 WGCYIADHLI AILFGRSTSL RLSNSTVPET DELPEIETGI EEYIYDPKVI LSTANPLKKL  60
   61 IVLSRITEIF ASKIFSPNET LLQRSEYLAK FNLEVYNWRR DLPPELQWTK RSLMEMTDFN 120
  121 PTIAYVWFHY YIVLISYNKP FIYEIKQSRE LVEGYVDELY YLLKVWKNKF KTFEKATIYM 180
  181 IYSAILAIQC MKSNLIKKDR KQDFLNFLSA PTLNYELARK FIENSEDALH NSETMDLLGT 240
  241 LSHGNDFALE YNFDFTLLNE IDMLIGGNTN DGLSK

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.23
Match:	1n1bA
Description:	(+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [203-221]

      1          11         21         31         41         51         
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    1 NLSRSPLILR SLSLFFKWL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [238-248]

      1          11         21         31         41         51         
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    1 FFGDTNTKSY Y

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [347-373]

      1          11         21         31         41         51         
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    1 HLNPEAWSNV YEDELSIMDF EVRSRIY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.23
Match:	1n1bA
Description:	(+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [222-237]

      1          11         21         31         41         51         
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    1 YPGHYLFIHR ETFLSA

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [249-346]

      1          11         21         31         41         51         
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    1 CSEELVFAIA ALGSLISYKS ETELFQQSEV FYQRAKTIVL KKIFQLEDSS LAESSSSSKL  60
   61 AIIQTLLCLA FYDIGSGENP MAWYLSGLAF RIAHEIGL

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.23
Match:	1n1bA
Description:	(+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

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: