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View Structure Prediction Details

Protein: GDH2
Organism: Saccharomyces cerevisiae
Length: 1092 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 GDH2.

Description E-value Query
Range
Subject
Range
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
0.0 [25..1087] [44..1025]
GDH2 - NAD(+)-dependent glutamate dehydrogenase, degrades glutamate to ammonia and alpha-ketoglutarate; exp...
DHE2_YEAST - NAD-specific glutamate dehydrogenase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GDH...
0.0 [1..1092] [1..1092]
gi|4584518 - gi|4584518|emb|CAB40797.1| NAD-specific glutamate dehydrogenase [Agaricus bisporus]
0.0 [24..1086] [23..1029]
SPCC132.04c - NAD-dependent glutamate dehydrogenase
GDH2_SCHPO - Probable NAD-specific glutamate dehydrogenase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843)...
0.0 [29..1081] [92..1096]
gi|4106519 - gi|4106519|gb|AAD02872.1| glutamate dehydrogenase [Trypanosoma brucei]
0.0 [231..1082] [161..982]
gi|46396076 - gi|46396076|sp||P82953_1 [Segment 1 of 7] Mannose-specific lectin (Agglutinin)
0.0 [405..1087] [1..670]
gi|7576911 - gi|7576911|gb|AAF64047.1|AF241225_1 glutamate dehydrogenase [Plasmodium falciparum]
0.0 [40..660] [34..677]
gi|15076346 - gi|15076346|emb|CAC47899.1| Conserved hypothetical protein [Sinorhizobium meliloti 1021]
gi|15967073 - gi|15967073|ref|NP_387426.1| hypothetical protein SMc04085 [Sinorhizobium meliloti 1021]
0.0 [352..1068] [548..1303]

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Predicted Domain #1
Region A:
Residues: [1-377]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLFDNKNRGA LNSLNTPDIA SLSISSMSDY HVFDFPGKDL QREEVIDLLD QQGFIPDDLI  60
   61 EQEVDWFYNS LGIDDLFFSR ESPQLISNII HSLYASKLDF FAKSKFNGIQ PRLFSIKNKI 120
  121 ITNDNHAIFM ESNTGVSISD SQQKNFKFAS DAVGNDTLEH GKDTIKKNRI EMDDSCPPYE 180
  181 LDSEIDDLFL DNKSQKNCRL VSFWAPESEL KLTFVYESVY PNDDPAGVDI SSQDLLKGDI 240
  241 ESISDKTMYK VSSNENKKLY GLLLKLVKER EGPVIKTTRS VENKDEIRLL VAYKRFTTKR 300
  301 YYSALNSLFH YYKLKPSKFY LESFNVKDDD IIIFSVYLNE NQQLEDVLLH DVEAALKQVE 360
  361 REASLLYAIP NNSFHEV

[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.

Found no structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [378-471]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YQRRQFSPKE AIYAHIGAIF INHFVNRLGS DYQNLLSQIT IKRNDTTLLE IVENLKRKLR  60
   61 NETLTQQTII NIMSKHYTII SKLYKNFAQI HYYH

[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 0.564 a.4.1 Homeodomain-like
View Download 0.565 a.100.1 6-phosphogluconate dehydrogenase C-terminal domain-like
View Download 0.495 a.77.1 DEATH domain
View Download 0.488 a.58.1 Chemotaxis receptor methyltransferase CheR, N-terminal domain
View Download 0.452 a.77.1 DEATH domain
View Download 0.410 i.1.1 Ribosome and ribosomal fragments
View Download 0.382 a.39.1 EF-hand
View Download 0.344 a.77.1 DEATH domain
View Download 0.329 a.4.5 "Winged helix" DNA-binding domain
View Download 0.318 a.3.1 Cytochrome c
View Download 0.318 d.54.1 Enolase N-terminal domain-like
View Download 0.309 a.24.17 Group V grass pollen allergen
View Download 0.306 a.4.1 Homeodomain-like
View Download 0.300 a.12.1 Kix domain of CBP (creb binding protein)
View Download 0.285 a.3.1 Cytochrome c
View Download 0.285 a.76.1 Iron-dependent represor protein, dimerization domain
View Download 0.280 a.74.1 Cyclin-like
View Download 0.276 a.16.1 S15/NS1 RNA-binding domain
View Download 0.266 c.47.1 Thioredoxin-like
View Download 0.253 d.93.1 SH2 domain
View Download 0.249 a.116.1 GTPase activation domain, GAP
View Download 0.244 d.164.1 SMAD MH1 domain
View Download 0.240 a.40.1 Calponin-homology domain, CH-domain
View Download 0.226 a.144.1 PABC (PABP) domain
View Download 0.223 a.48.3 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View Download 0.221 a.7.6 Ribosomal protein S20
View Download 0.218 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.214 c.47.1 Thioredoxin-like
View Download 0.213 a.6.1 Putative DNA-binding domain
View Download 0.206 a.68.1 Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View Download 0.201 a.4.12 TrpR-like

Predicted Domain #3
Region A:
Residues: [472-719]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSTKDMEKTL SFQRLEKVEP FKNDQEFEAY LNKFIPNDSP DLLILKTLNI FNKSILKTNF  60
   61 FITRKVAISF RLDPSLVMTK FEYPETPYGI FFVVGNTFKG FHIRFRDIAR GGIRIVCSRN 120
  121 QDIYDLNSKN VIDENYQLAS TQQRKNKDIP EGGSKGVILL NPGLVEHDQT FVAFSQYVDA 180
  181 MIDILINDPL KENYVNLLPK EEILFFGPDE GTAGFVDWAT NHARVRNCPW WKSFLTGKSP 240
  241 SLGGIPHD

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [921-940]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GVTSSSMEVL ASLALNDNDF 

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [971-1015]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AELEFGQLWN LNQLNGTHIS EISNQLSFTI NKLNDDLVAS QELWL

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 117.0
Match: 1euzA_
Description: Glutamate dehydrogenase
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [720-920]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EYGMTSLGVR AYVNKIYETL NLTNSTVYKF QTGGPDGDLG SNEILLSSPN ECYLAILDGS  60
   61 GVLCDPKGLD KDELCRLAHE RKMISDFDTS KLSNNGFFVS VDAMDIMLPN GTIVANGTTF 120
  121 RNTFHTQIFK FVDHVDIFVP CGGRPNSITL NNLHYFVDEK TGKCKIPYIV EGANLFITQP 180
  181 AKNALEEHGC ILFKDASANK G

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [941-970]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VHKFIGDVSG ERSALYKSYV VEVQSRIQKN 

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 117.0
Match: 1euzA_
Description: Glutamate dehydrogenase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
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
glutamate dehydrogenase (NADP+) activity 2.29316799437014 bayes_pls_golite062009
catalytic activity 2.0643953589843 bayes_pls_golite062009
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 1.54527841865655 bayes_pls_golite062009
malic enzyme activity 1.39067036188188 bayes_pls_golite062009
glutamate dehydrogenase [NAD(P)+] activity 0.994926158034199 bayes_pls_golite062009

Predicted Domain #5
Region A:
Residues: [1016-1092]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NDLKLRNYLL LDKIIPKILI DVAGPQSVLE NIPESYLKVL LSSYLSSTFV YQNGIDVNIG  60
   61 KFLEFIGGLK REAEASA

[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 0.538 a.3.1 Cytochrome c
View Download 0.638 a.64.1 Saposin
View Download 0.621 a.48.3 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View Download 0.480 a.68.1 Wiscott-Aldrich syndrome protein, WASP, C-terminal domain
View Download 0.465 a.3.1 Cytochrome c
View Download 0.424 f.28.1 Nonheme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
View Download 0.418 a.5.6 Hypothetical protein MTH1615
View Download 0.406 a.27.1 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View Download 0.400 a.35.1 lambda repressor-like DNA-binding domains
View Download 0.389 a.80.1 DNA polymerase III clamp loader subunits, C-terminal domain
View Download 0.376 a.4.5 "Winged helix" DNA-binding domain
View Download 0.375 a.28.1 ACP-like
View Download 0.369 a.3.1 Cytochrome c
View Download 0.333 a.4.1 Homeodomain-like
View Download 0.324 a.24.7 FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View Download 0.313 a.61.1 Retroviral matrix proteins
View Download 0.311 a.4.5 "Winged helix" DNA-binding domain
View Download 0.311 d.42.1 POZ domain
View Download 0.307 a.3.1 Cytochrome c
View Download 0.303 a.28.1 ACP-like
View Download 0.288 a.37.1 A DNA-binding domain in eukaryotic transcription factors
View Download 0.264 a.46.1 Methionine synthase domain
View Download 0.263 a.4.7 Ribosomal protein L11, C-terminal domain
View Download 0.257 d.95.2 Homing endonucleases
View Download 0.253 a.28.1 ACP-like
View Download 0.247 a.61.1 Retroviral matrix proteins
View Download 0.246 a.181.1 Antibiotic binding domain of TipA-like multidrug resistance regulators
View Download 0.238 a.4.5 "Winged helix" DNA-binding domain
View Download 0.233 a.38.1 Helix-loop-helix DNA-binding domain
View Download 0.228 a.30.2 Homodimeric domain of signal transducing histidine kinase
View Download 0.226 a.28.1 ACP-like
View Download 0.226 a.4.5 "Winged helix" DNA-binding domain
View Download 0.226 a.4.1 Homeodomain-like
View Download 0.223 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.219 d.51.1 Eukaryotic type KH-domain (KH-domain type I)
View Download 0.219 a.8.3 Families 57/38 glycoside transferase middle domain
View Download 0.218 a.4.5 "Winged helix" DNA-binding domain
View Download 0.218 d.75.1 tRNA splicing endonuclease EdnA, N-terminal domain
View Download 0.215 a.100.1 6-phosphogluconate dehydrogenase C-terminal domain-like
View Download 0.214 a.4.1 Homeodomain-like
View Download 0.214 a.13.1 alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View Download 0.209 a.24.17 Group V grass pollen allergen
View Download 0.206 a.64.1 Saposin
View Download 0.205 a.77.1 DEATH domain
View Download 0.204 a.118.14 FliG
View Download 0.202 a.134.1 Fungal elicitin


YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle