Protein Info for GFF4255 in Pseudomonas sp. DMC3
Annotation: 5-aminovalerate aminotransferase DavT
These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.
Protein Families and Features
Best Hits
Swiss-Prot: 85% identical to DAVT_PSEPK: 5-aminovalerate aminotransferase DavT (davT) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
KEGG orthology group: K14268, 5-aminovalerate aminotransferase [EC: 2.6.1.48] (inferred from 99% identity to pfo:Pfl01_0188)MetaCyc: 97% identical to 4-aminobutyrate transaminase subunit (Pseudomonas fluorescens)
4-aminobutyrate transaminase. [EC: 2.6.1.19]
Predicted SEED Role
"5-aminovalerate aminotransferase (EC 2.6.1.48) / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)" in subsystem Lysine degradation (EC 2.6.1.19, EC 2.6.1.48)
MetaCyc Pathways
- L-lysine degradation IV (5/5 steps found)
- superpathway of L-arginine and L-ornithine degradation (10/13 steps found)
- 4-aminobutanoate degradation I (2/2 steps found)
- 4-aminobutanoate degradation III (2/2 steps found)
- GABA shunt II (3/4 steps found)
- superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation (8/11 steps found)
- superpathway of 4-aminobutanoate degradation (2/3 steps found)
- L-lysine degradation X (4/6 steps found)
- 4-aminobutanoate degradation II (1/2 steps found)
- GABA shunt I (2/4 steps found)
- L-lysine degradation I (3/7 steps found)
- L-lysine degradation III (2/6 steps found)
- 4-aminobutanoate degradation V (2/7 steps found)
- nicotine degradation I (pyridine pathway) (6/17 steps found)
- superpathway of L-lysine degradation (16/43 steps found)
KEGG Metabolic Maps
- Alanine and aspartate metabolism
- Butanoate metabolism
- Glutamate metabolism
- Lysine degradation
- Propanoate metabolism
- beta-Alanine metabolism
Isozymes
Compare fitness of predicted isozymes for: 2.6.1.19
Use Curated BLAST to search for 2.6.1.19 or 2.6.1.48
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
Find the best match in UniProt
Protein Sequence (425 amino acids)
>GFF4255 5-aminovalerate aminotransferase DavT (Pseudomonas sp. DMC3) MSKTNAELMARRTNAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS IDDSIASIERIFKNDAEPKDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA GSPIACAAALAVMEVFEEEQLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVEL FENGDSHKPNPTAVAAVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDEQLDKGLAIIEE CFSEL