YRC Public Data Repository - Protein Structure Prediction

Protein:	GDH3
Organism:	Saccharomyces cerevisiae
Length:	457 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 GDH3.

Description	E-value	Query Range	Subject Range
gi\|190406708 - gi\|190406708\|gb\|EDV09975.1\| NADP-linked glutamate dehydrogenase [Saccharomyces cerevisiae RM11-1a] gi\|207348058 - gi\|207348058\|gb\|EDZ74033.1\| YAL062Wp-like protein [Saccharomyces cerevisiae AWRI1631] GDH3 - NADP(+)-dependent glutamate dehydrogenase, synthesizes glutamate from ammonia and alpha-ketoglutarat... DHE5_YEAST - NADP-specific glutamate dehydrogenase 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=...	0.0	[1..457]	[1..457]
lcl\|NC_016856.1_... - [gene=gdhA] [protein=glutamate dehydrogenase] [protein_id=YP_005237152.1] [location=complement(13886... DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium GN=gdhA PE=3 SV=2 gi\|167991885, gi... - gi\|205329728\|gb\|EDZ16492.1\| NADP-specific glutamate dehydrogenase [Salmonella enterica subsp. enteri... gi\|197261668, gi... - gi\|197261668\|ref\|ZP_03161742.1\| NADP-specific glutamate dehydrogenase [Salmonella enterica subsp. en... DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium GN=gdhA PE=3 SV=2 DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720... gi\|161363663, gi... - gi\|161614299\|ref\|YP_001588264.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serova...	0.0	[2..456]	[19..447]
lcl\|NC_016856.1_... - [gene=gdhA] [protein=glutamate dehydrogenase] [protein_id=YP_005237152.1] [location=complement(13886... DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium GN=gdhA PE=3 SV=2 gi\|167991885, gi... - gi\|205329728\|gb\|EDZ16492.1\| NADP-specific glutamate dehydrogenase [Salmonella enterica subsp. enteri... gi\|197261668, gi... - gi\|197261668\|ref\|ZP_03161742.1\| NADP-specific glutamate dehydrogenase [Salmonella enterica subsp. en... DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium GN=gdhA PE=3 SV=2 DHE4_SALTY - NADP-specific glutamate dehydrogenase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720... gi\|161363663, gi... - gi\|161614299\|ref\|YP_001588264.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serova...	0.0	[2..456]	[19..447]
gi\|29141644, gi\|... - gi\|29141644\|ref\|NP_804986.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serovar Ty... gi\|16760596 - gi\|16760596\|ref\|NP_456213.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serovar Ty... DHE4_SALTI - NADP-specific glutamate dehydrogenase OS=Salmonella typhi GN=gdhA PE=3 SV=1 gi\|214003054 - gi\|214003054\|ref\|ZP_03413789.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serovar... gi\|213162977 - gi\|213162977\|ref\|ZP_03348687.1\| glutamate dehydrogenase [Salmonella enterica subsp. enterica serovar... DHE4_SALTI - NADP-specific glutamate dehydrogenase OS=Salmonella typhi GN=gdhA PE=3 SV=1	0.0	[2..456]	[19..447]
DHE4_PENCH - NADP-specific glutamate dehydrogenase OS=Penicillium chrysogenum GN=GDH PE=3 SV=1 gi\|211592684 - gi\|211592684\|emb\|CAP99044.1\| glutamate dehydrogenase gdhA-Penicillium chrysogenum [Penicillium chrys...	0.0	[1..457]	[5..461]
gi\|13274574 - gi\|13274574\|gb\|AAK17986.1\|AF332586_2 glutamate dehydrogenase [Klebsiella aerogenes]	0.0	[2..456]	[19..447]
DHE4_EMENI - NADP-specific glutamate dehydrogenase OS=Emericella nidulans GN=gdhA PE=3 SV=1	0.0	[1..457]	[4..459]

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Predicted Domain #1

Region A:
Residues: [1-188]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTSEPEFQQA YDEIVSSVED SKIFEKFPQY KKVLPIVSVP ERIIQFRVTW ENDNGEQEVA  60
   61 QGYRVQFNSA KGPYKGGLRF HPSVNLSILK FLGFEQIFKN ALTGLDMGGG KGGLCVDLKG 120
  121 KSDNEIRRIC YAFMRELSRH IGKDTDVPAG DIGVGGREIG YLFGAYRSYK NSWEGVLTGK 180
  181 GLNWGGSL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [379-395]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VAVSGLEMAQ NSQKVTW

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [439-457]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIASFVMVAD AMLDQGDVF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1208.0
Match:	1bgvA_
Description:	Glutamate dehydrogenase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
glutamate dehydrogenase (NADP+) activity	4.50065200228697	bayes_pls_golite062009
oxidoreductase activity	3.09625241707629	bayes_pls_golite062009
glutamate dehydrogenase [NAD(P)+] activity	2.15778057341677	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor	2.00319512154556	bayes_pls_golite062009
catalytic activity	1.79741889688267	bayes_pls_golite062009
oxidoreductase activity, acting on CH-OH group of donors	1.65338499044318	bayes_pls_golite062009
DNA binding	1.61355789916908	bayes_pls_golite062009
transcription regulator activity	1.55390653047158	bayes_pls_golite062009
nucleic acid binding	1.48478425318425	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	1.47309297191111	bayes_pls_golite062009
binding	0.982999356179965	bayes_pls_golite062009
transcription factor activity	0.91090893050278	bayes_pls_golite062009
structural molecule activity	0.75267483298133	bayes_pls_golite062009
malate dehydrogenase activity	0.63606663166401	bayes_pls_golite062009
coenzyme binding	0.35922330382799	bayes_pls_golite062009
transferase activity, transferring acyl groups	0.0992243118937675	bayes_pls_golite062009
NAD or NADH binding	0.0664389065992004	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [189-378]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IRPEATGFGL VYYTQAMIDY ATNGKESFEG KRVTISGSGN VAQYAALKVI ELGGIVVSLS  60
   61 DSKGCIISET GITSEQIHDI ASAKIRFKSL EEIVDEYSTF SESKMKYVAG ARPWTHVSNV 120
  121 DIALPCATQN EVSGDEAKAL VASGVKFVAE GANMGSTPEA ISVFETARST ATNAKDAVWF 180
  181 GPPKAANLGG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [396-438]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TAERVDQELK KIMINCFNDC IQAAQEYSTE KNTNTLPSLV KGA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1208.0
Match:	1bgvA_
Description:	Glutamate dehydrogenase
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: