Protein Info for Pf1N1B4_2429 in Pseudomonas fluorescens FW300-N1B4

Updated annotation (from data): Carnitine 3-dehydrogenase (EC 1.1.1.108)
Rationale: Specifically important for utilizing Carnitine Hydrochloride. Automated validation from mutant phenotype: the predicted function (CARNITINE-3-DEHYDROGENASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Original annotation: Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)

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: 92% identical to LCDH_PSEU2: L-carnitine dehydrogenase (lcdH) from Pseudomonas syringae pv. syringae (strain B728a)

KEGG orthology group: K00074, 3-hydroxybutyryl-CoA dehydrogenase [EC: 1.1.1.157] (inferred from 97% identity to pfo:Pfl01_5232)

MetaCyc: 85% identical to L-carnitine dehydrogenase (Pseudomonas aeruginosa PAO1)
Carnitine 3-dehydrogenase. [EC: 1.1.1.108]

Predicted SEED Role

"Carnitine 3-dehydrogenase (EC 1.1.1.108) @ 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157) @ 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)" (EC 1.1.1.108, EC 1.1.1.157, EC 1.1.1.35)

MetaCyc Pathways

oleate β-oxidation (30/35 steps found)
fatty acid salvage (6/6 steps found)
adipate degradation (5/5 steps found)
2-methyl-branched fatty acid β-oxidation (11/14 steps found)
superpathway of glyoxylate cycle and fatty acid degradation (11/14 steps found)
L-carnitine degradation III (3/3 steps found)
benzoyl-CoA biosynthesis (3/3 steps found)
valproate β-oxidation (7/9 steps found)
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) (4/5 steps found)
4-hydroxybenzoate biosynthesis III (plants) (4/5 steps found)
adipate biosynthesis (4/5 steps found)
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) (19/26 steps found)
fatty acid β-oxidation I (generic) (5/7 steps found)
pyruvate fermentation to butanol II (engineered) (4/6 steps found)
1-butanol autotrophic biosynthesis (engineered) (19/27 steps found)
D-carnitine degradation II (1/2 steps found)
fatty acid β-oxidation II (plant peroxisome) (3/5 steps found)
glutaryl-CoA degradation (3/5 steps found)
pyruvate fermentation to hexanol (engineered) (7/11 steps found)
fatty acid β-oxidation VI (mammalian peroxisome) (4/7 steps found)
L-glutamate degradation V (via hydroxyglutarate) (6/10 steps found)
methyl ketone biosynthesis (engineered) (3/6 steps found)
superpathway of Clostridium acetobutylicum acidogenic fermentation (5/9 steps found)
glycerol degradation to butanol (10/16 steps found)
pyruvate fermentation to butanol I (4/8 steps found)
superpathway of phenylethylamine degradation (6/11 steps found)
benzoyl-CoA degradation I (aerobic) (3/7 steps found)
pyruvate fermentation to butanoate (3/7 steps found)
phenylacetate degradation I (aerobic) (4/9 steps found)
superpathway of Clostridium acetobutylicum solventogenic fermentation (6/13 steps found)
benzoate biosynthesis I (CoA-dependent, β-oxidative) (3/9 steps found)
2-methylpropene degradation (2/8 steps found)
3-hydroxypropanoate/4-hydroxybutanate cycle (9/18 steps found)
3-phenylpropanoate degradation (3/10 steps found)
methyl tert-butyl ether degradation (3/10 steps found)
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation (8/17 steps found)
L-glutamate degradation VII (to butanoate) (3/12 steps found)
crotonate fermentation (to acetate and cyclohexane carboxylate) (4/16 steps found)
L-tryptophan degradation III (eukaryotic) (3/15 steps found)
benzoate fermentation (to acetate and cyclohexane carboxylate) (4/17 steps found)
toluene degradation VI (anaerobic) (4/18 steps found)
cholesterol degradation to androstenedione I (cholesterol oxidase) (3/17 steps found)
androstenedione degradation I (aerobic) (6/25 steps found)
platensimycin biosynthesis (6/26 steps found)
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) (3/22 steps found)
superpathway of testosterone and androsterone degradation (6/28 steps found)
androstenedione degradation II (anaerobic) (4/27 steps found)
superpathway of cholesterol degradation I (cholesterol oxidase) (9/42 steps found)
superpathway of cholesterol degradation II (cholesterol dehydrogenase) (9/47 steps found)
superpathway of cholesterol degradation III (oxidase) (5/49 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.157, 1.1.1.35

Use Curated BLAST to search for 1.1.1.108 or 1.1.1.157 or 1.1.1.35

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

See A0A166NQT5 at UniProt or InterPro

Protein Sequence (321 amino acids)

>Pf1N1B4_2429 Carnitine 3-dehydrogenase (EC 1.1.1.108) (Pseudomonas fluorescens FW300-N1B4)
MSFITDIKTFAALGSGVIGSGWVSRALAHGLDVVAWDPAPGAEAALRKRVANAWGALEKQ
GLAPGASQDRLRFVATIEECVRDADFIQESAPERLELKLELHSKISAAAKPNALIGSSTS
GLLPSEFYESSTHPERCVVGHPFNPVYLLPLVEVVGGKNTAPQAVQAAMKVYESLGMRPL
HVRKEVPGFIADRLLEALWREALHLVNDGVATTGEIDDAIRFGAGLRWSFMGTFLTYTLA
GGDAGMRHFMAQFGPALQLPWTYLPAPELTDKLIDDVVDGTSEQLGKHSISALERYRDDC
LLAVLEAVKTTKEKHGMAFSE