Protein Info for SO1275 in Shewanella oneidensis MR-1

Name: gabD
Updated annotation (from data): succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16]
Rationale: Specifically important for: L-Isoleucine. Also very important with putrescine as the N source. The more specific KEGG annotation is consistent its role on N putrescine (which is converted to 4-aminobutyrate and then to succinate semialdehyde). Its role on isoleucine is unclear but a close homolog, Shewana3_3092, also has this phenotype (albeit milder). Also note that isoleucine is catabolized to propionyl-CoA and Shewana3_3092 is very important for propionate utilization. The annotation of son:SO_1275 in KEGG has been updated to list glutarate-semialdehyde as an additional substrate. (KEGG_correct)
Original annotation: succinate-semialdehyde dehydrogenase (NCBI ptt file)

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

• PF00171: Aldedh
  • amino acids 19 to 478 (460 residues), 561.6 bits, E=6.1e-173
• TIGR01780: succinate-semialdehyde dehydrogenase
  • amino acids 30 to 476 (447 residues), 744.4 bits, E=2.2e-228

Best Hits

Swiss-Prot: 73% identical to DAVD_PSEPK: Glutarate-semialdehyde dehydrogenase (davD) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K00135, succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (inferred from 100% identity to son:SO_1275)

MetaCyc: 71% identical to glutarate semialdehyde dehydrogenase (Pseudomonas aeruginosa)
Glutarate-semialdehyde dehydrogenase. [EC: 1.2.1.20]

Predicted SEED Role

"Aldehyde dehydrogenase B (EC 1.2.1.22)" in subsystem Glycerolipid and Glycerophospholipid Metabolism in Bacteria or Methylglyoxal Metabolism (EC 1.2.1.22)

MetaCyc Pathways

• 4-aminobutanoate degradation III (2/2 steps found)
• methylglyoxal degradation V (2/3 steps found)
• L-lactaldehyde degradation (aerobic) (1/2 steps found)
• methylglyoxal degradation IV (1/3 steps found)
• L-lysine degradation IV (2/5 steps found)
• lactate biosynthesis (archaea) (2/5 steps found)
• superpathway of methylglyoxal degradation (4/8 steps found)
• L-lysine degradation III (2/6 steps found)
• L-lysine degradation X (2/6 steps found)
• L-lysine degradation I (2/7 steps found)
• L-rhamnose degradation II (2/8 steps found)
• superpathway of fucose and rhamnose degradation (3/12 steps found)
• superpathway of L-lysine degradation (8/43 steps found)

KEGG Metabolic Maps

• Butanoate metabolism
• Glutamate metabolism
• Lysine degradation
• Pyruvate metabolism
• Tyrosine metabolism

Isozymes

No predicted isozymes

Use Curated BLAST to search for 1.2.1.16 or 1.2.1.20 or 1.2.1.22

Sequence Analysis Tools

See Q8EHE8 at UniProt or InterPro

Protein Sequence (482 amino acids)

>SO1275 succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (Shewanella oneidensis MR-1)
MLLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAA
LPAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFA
EEAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVK
PAPQTPFTALALAVLAERAGIPAGVFSVITGDAIAIGNEMCTNPIVRKLSFTGSTNVGIK
LMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAG
VYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKV
HELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYG
RDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM
SV