Protein Info for GFF713 in Variovorax sp. SCN45
Annotation: Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.79)
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: 46% identical to GABD_SYNY3: Probable succinate-semialdehyde dehydrogenase [NADP(+)] (gabD) from Synechocystis sp. (strain PCC 6803 / Kazusa)
KEGG orthology group: K08324, aldehyde dehydrogenase family protein [EC: 1.2.1.-] (inferred from 78% identity to bcj:BCAL1183)MetaCyc: 46% identical to NAD-dependent succinate-semialdehyde dehydrogenase (Synechocystis sp. PCC 6803)
Succinate-semialdehyde dehydrogenase. [EC: 1.2.1.24]
Predicted SEED Role
"Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16)" (EC 1.2.1.16, EC 1.2.1.24)
MetaCyc Pathways
- superpathway of 4-aminobutanoate degradation (3/3 steps found)
- 4-aminobutanoate degradation I (2/2 steps found)
- 4-aminobutanoate degradation III (2/2 steps found)
- GABA shunt I (3/4 steps found)
- GABA shunt II (3/4 steps found)
- 4-aminobutanoate degradation IV (1/3 steps found)
- N-methylpyrrolidone degradation (1/3 steps found)
- superpathway of L-arginine and L-ornithine degradation (7/13 steps found)
- superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation (5/11 steps found)
KEGG Metabolic Maps
- 1- and 2-Methylnaphthalene degradation
- Arginine and proline metabolism
- Butanoate metabolism
- Geraniol degradation
- Glutamate metabolism
- Limonene and pinene degradation
- Lysine biosynthesis
- Naphthalene and anthracene degradation
- Tryptophan metabolism
- Tyrosine metabolism
- Urea cycle and metabolism of amino groups
Isozymes
Compare fitness of predicted isozymes for: 1.2.1.-, 1.2.1.16
Use Curated BLAST to search for 1.2.1.- or 1.2.1.16 or 1.2.1.24
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 (461 amino acids)
>GFF713 Succinate-semialdehyde dehydrogenase [NAD] (EC 1.2.1.24); Succinate-semialdehyde dehydrogenase [NADP+] (EC 1.2.1.79) (Variovorax sp. SCN45) MAFPTDIQPAAFQSHNPANGALIEANTGHGSAEIEARIAQSAATWKTWSATPMAERSAML DRLADLLDQRAESYGRLITTEMGKPIGEAIAEVRKAATGARHFAEKGPGYLAPMPIEGMN AHVAYESLGPVFAVMPWNLPFWQVLRFFIPTVLAGNTVLVKHAETVQGCARALEQLVLDA GAPAGLYLNLAIRRGAVAAVVADPRVRCVTVTGSTQAGRAVAAEAGAHGKKAVLELGGSD PFIVLEDADFDRAVQLAVTSRFSNNAQSCIAAKRFFIAEAIAEKFQAAFVERASALRMGD PLLAETQLGPLARADLRESVHAQVQAALEQGGRLLCGGQPAQGPGNFYPPTVIAGLSHDA PIVQEEIFGPVALLFTFKTDEEAIALANATEFGLGATIWSRDLERAHRLASAVEAGAVFI NDFVRSDPRASFGGVKGSGFGRELGALGARELTNAKLVFVG