YRC Public Data Repository - Protein Structure Prediction

Protein:	GDH1
Organism:	Saccharomyces cerevisiae
Length:	454 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 GDH1.

Description	E-value	Query Range	Subject Range
gi\|190407665 - gi\|190407665\|gb\|EDV10932.1\| NADP-specific glutamate dehydrogenase [Saccharomyces cerevisiae RM11-1a] GDH1 - NADP(+)-dependent glutamate dehydrogenase, synthesizes glutamate from ammonia and alpha-ketoglutarat... DHE4_YEAST - NADP-specific glutamate dehydrogenase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=... gi\|151945450 - gi\|151945450\|gb\|EDN63693.1\| NADP-dependent glutamate dehydrogenase [Saccharomyces cerevisiae YJM789]	0.0	[1..454]	[1..454]
gi\|11348602 - pir\|\|H83072 glutamate dehydrogenase PA4588 [imported] - Pseudomonas aeruginosa (strain PAO1) gi\|46165034, gi\|... - gi\|46165034\|ref\|ZP_00138144.2\| COG0334: Glutamate dehydrogenase/leucine dehydrogenase [Pseudomonas a... gi\|218773911, gi... - gi\|218893683\|ref\|YP_002442552.1\| glutamate dehydrogenase [Pseudomonas aeruginosa LESB58], gi\|2187739... gi\|15599784, gi\|... - gi\|9950836\|gb\|AAG07976.1\|AE004872_7 glutamate dehydrogenase [Pseudomonas aeruginosa PAO1], gi\|155997... gi\|84323381, gi\|... - gi\|84323381\|ref\|ZP_00971454.1\| COG0334: Glutamate dehydrogenase/leucine dehydrogenase [Pseudomonas a...	0.0	[2..453]	[18..445]
DHE4_SACU7 - NADP-specific glutamate dehydrogenase 1 OS=Saccharomyces uvarum (strain ATCC 76518 / CBS 7001 / CLIB... gi\|48686489, gi\|... - gi\|48686495\|emb\|CAF29498.1\| NADP-specific glutamate dehydrogenase 1 [Saccharomyces uvarum], gi\|48686... DHE4_SACBA - NADP-specific glutamate dehydrogenase 1 OS=Saccharomyces bayanus GN=GDH1 PE=3 SV=1	0.0	[1..454]	[1..454]
gi\|24982069, gi\|... - gi\|26987411\|ref\|NP_742836.1\| glutamate dehydrogenase [Pseudomonas putida KT2440], gi\|24982069\|gb\|AAN...	0.0	[3..453]	[22..449]
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	[3..453]	[21..447]
gi\|154085\|gb\|AAA... - glutamate dehydrogenase (EC 1.4.1.4) gi\|154085 - gi\|154085\|gb\|AAA27131.1\| glutamate dehydrogenase (EC 1.4.1.4) [Salmonella enterica subsp. enterica s...	0.0	[3..453]	[21..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	[3..453]	[21..447]
gi\|4239787\|emb\|C... - NADP-glutamate dehydrogenase [Pseudomonas aeruginosa] gi\|4239787, gi\|4... - gi\|4239791\|emb\|CAA77192.1\| NADP-glutamate dehydrogenase [Pseudomonas aeruginosa], gi\|4239787\|emb\|CAA...	0.0	[2..453]	[18..445]

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Predicted Domain #1

Region A:
Residues: [1-187]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEPEFQQAY EEVVSSLEDS TLFEQHPEYR KVLPIVSVPE RIIQFRVTWE NDKGEQEVAQ  60
   61 GYRVQYNSAK GPYKGGLRFH PSVNLSILKF LGFEQIFKNS LTGLDMGGGK GGLCVDLKGR 120
  121 SNNEIRRICY AFMRELSRHI GQDTDVPAGD IGVGGREIGY LFGAYRSYKN SWEGVLTGKG 180
  181 LNWGGSL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [378-394]

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

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [436-454]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NIASFIKVSD AMFDQGDVF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1242.0
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, acting on the CH-NH2 group of donors, NAD or NADP as acceptor	4.08697502437308	bayes_pls_golite062009
oxidoreductase activity	3.54983447672782	bayes_pls_golite062009
oxidoreductase activity, acting on CH-OH group of donors	2.66605122152932	bayes_pls_golite062009
malate dehydrogenase activity	2.43636049081724	bayes_pls_golite062009
catalytic activity	2.0643953589843	bayes_pls_golite062009
binding	1.77370305872094	bayes_pls_golite062009
DNA binding	1.61355789916908	bayes_pls_golite062009
transcription regulator activity	1.55390653047158	bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	1.54527841865655	bayes_pls_golite062009
nucleic acid binding	1.48478425318425	bayes_pls_golite062009
malic enzyme activity	1.39067036188188	bayes_pls_golite062009
glutamate dehydrogenase [NAD(P)+] activity	0.994926158034199	bayes_pls_golite062009
transcription factor activity	0.91090893050278	bayes_pls_golite062009
structural molecule activity	0.345975336806588	bayes_pls_golite062009
NAD or NADH binding	0.0664389065992004	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [188-377]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IRPEATGYGL VYYTQAMIDY ATNGKESFEG KRVTISGSGN VAQYAALKVI ELGGTVVSLS  60
   61 DSKGCIISET GITSEQVADI SSAKVNFKSL EQIVNEYSTF SENKVQYIAG ARPWTHVQKV 120
  121 DIALPCATQN EVSGEEAKAL VAQGVKFIAE GSNMGSTPEA IAVFETARST ATGPSEAVWY 180
  181 GPPKAANLGG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [395-435]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TSERVDQELK RIMINCFNEC IDYAKKYTKD GKVLPSLVKG A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1242.0
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: