GapMind for catabolism of small carbon sources


L-phenylalanine catabolism in Pseudomonas fluorescens GW456-L13

Best path

livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB

Also see fitness data for the top candidates


Overview: Phenylalanine utilization in GapMind is based on MetaCyc pathway L-phenylalanine degradation I (aerobic, via tyrosine, link), pathway II (anaerobic, via phenylacetaldehyde dehydrogenase, link), degradation via phenylpyruvate:ferredoxin oxidoreductase (PMC3346364), or degradation via phenylacetaldehyde:ferredoxin oxidoreductase (PMID:24214948). (MetaCyc describes additional pathways, but they do not result in carbon incorporation or are not reported in prokaryotes, so they are not included in GapMind.)

76 steps (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) PfGW456L13_4611 PfGW456L13_120
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) PfGW456L13_4610 PfGW456L13_121
livH L-phenylalanine ABC transporter, permease component 1 (LivH) PfGW456L13_4608 PfGW456L13_123
livM L-phenylalanine ABC transporter, permease component 2 (LivM) PfGW456L13_4609 PfGW456L13_122
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK PfGW456L13_4606 PfGW456L13_124
PAH phenylalanine 4-monooxygenase PfGW456L13_4394
PCBD pterin-4-alpha-carbinoalamine dehydratase PfGW456L13_4395
QDPR 6,7-dihydropteridine reductase PfGW456L13_4977 PfGW456L13_4938
HPD 4-hydroxyphenylpyruvate dioxygenase PfGW456L13_2935 PfGW456L13_1425
hmgA homogentisate dioxygenase PfGW456L13_4962
maiA maleylacetoacetate isomerase PfGW456L13_4960 PfGW456L13_1835
fahA fumarylacetoacetate hydrolase PfGW456L13_4961
aacS acetoacetyl-CoA synthetase PfGW456L13_2872 PfGW456L13_2593
atoB acetyl-CoA C-acetyltransferase PfGW456L13_2411 PfGW456L13_2982
Alternative steps:
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase PfGW456L13_4396 PfGW456L13_3960
aroP L-phenylalanine:H+ symporter AroP PfGW456L13_4291 PfGW456L13_4400
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PfGW456L13_3458 PfGW456L13_2522
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PfGW456L13_2433 PfGW456L13_2984
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PfGW456L13_1104
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit PfGW456L13_4886 PfGW456L13_2629
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit
boxA benzoyl-CoA epoxidase, subunit A
boxB benzoyl-CoA epoxidase, subunit B
boxC 2,3-epoxybenzoyl-CoA dihydrolase
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase PfGW456L13_2419
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PfGW456L13_2983 PfGW456L13_1630
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PfGW456L13_2984 PfGW456L13_2434
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PfGW456L13_2984 PfGW456L13_2434
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_3873
gcdH glutaryl-CoA dehydrogenase PfGW456L13_554 PfGW456L13_2591
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB PfGW456L13_3456
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PfGW456L13_2984
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PfGW456L13_2427
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PfGW456L13_2426
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PfGW456L13_2425
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PfGW456L13_2423 PfGW456L13_2523
paaF 2,3-dehydroadipyl-CoA hydratase PfGW456L13_2434 PfGW456L13_2984
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PfGW456L13_2433 PfGW456L13_3388
paaH 3-hydroxyadipyl-CoA dehydrogenase PfGW456L13_4041 PfGW456L13_2432
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PfGW456L13_2430 PfGW456L13_4590
paaJ2 3-oxoadipyl-CoA thiolase PfGW456L13_4590 PfGW456L13_2430
paaK phenylacetate-CoA ligase PfGW456L13_2428 PfGW456L13_1910
paaZ1 oxepin-CoA hydrolase PfGW456L13_2419 PfGW456L13_2433
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PfGW456L13_2419
pad-dh phenylacetaldehyde dehydrogenase PfGW456L13_2360 PfGW456L13_2690
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit
padD phenylacetyl-CoA dehydrogenase, PadD subunit
padE phenylglyoxylate dehydrogenase, gamma subunit
padF phenylglyoxylate dehydrogenase, delta subunit
padG phenylglyoxylate dehydrogenase, alpha subunit
padH phenylglyoxylate dehydrogenase, epsilon subunit
padI phenylglyoxylate dehydrogenase, beta subunit
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PfGW456L13_2498 PfGW456L13_2157
pimC pimeloyl-CoA dehydrogenase, small subunit PfGW456L13_2494
pimD pimeloyl-CoA dehydrogenase, large subunit PfGW456L13_2495 PfGW456L13_2536
pimF 6-carboxyhex-2-enoyl-CoA hydratase PfGW456L13_412 PfGW456L13_4041
PPDCalpha phenylpyruvate decarboxylase, alpha subunit PfGW456L13_3540
PPDCbeta phenylpyruvate decarboxylase, beta subunit PfGW456L13_3541

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory