GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudomonas stutzeri RCH2

Best path

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

Also see fitness data for the top candidates

Rules

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Psest_1308 Psest_3854
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Psest_1309 Psest_1089
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Psest_1311 Psest_1092
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Psest_1310 Psest_1093
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Psest_1312
PAH phenylalanine 4-monooxygenase Psest_0781
PCBD pterin-4-alpha-carbinoalamine dehydratase Psest_0780
QDPR 6,7-dihydropteridine reductase Psest_0930 Psest_3204
HPD 4-hydroxyphenylpyruvate dioxygenase Psest_3514 Psest_4071
hmgA homogentisate dioxygenase Psest_3513
maiA maleylacetoacetate isomerase Psest_3511 Psest_3276
fahA fumarylacetoacetate hydrolase Psest_3512
atoA acetoacetyl-CoA transferase, A subunit Psest_1078
atoD acetoacetyl-CoA transferase, B subunit Psest_1077
atoB acetyl-CoA C-acetyltransferase Psest_1076 Psest_2446
Alternative steps:
aacS acetoacetyl-CoA synthetase Psest_1086 Psest_1334
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Psest_0779 Psest_1295
aroP L-phenylalanine:H+ symporter AroP Psest_1697
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Psest_2358 Psest_1147
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Psest_2437
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Psest_2437 Psest_3109
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit
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
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Psest_1084 Psest_2445
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Psest_2437 Psest_3109
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Psest_2437 Psest_3109
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Psest_2654 Psest_4235
gcdH glutaryl-CoA dehydrogenase Psest_3830 Psest_2440
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB Psest_3517
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Psest_3453
paaF 2,3-dehydroadipyl-CoA hydratase Psest_2437 Psest_3109
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Psest_2437 Psest_3109
paaH 3-hydroxyadipyl-CoA dehydrogenase Psest_2654 Psest_3800
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Psest_3070 Psest_1076
paaJ2 3-oxoadipyl-CoA thiolase Psest_3070 Psest_1076
paaK phenylacetate-CoA ligase Psest_1335 Psest_4228
paaZ1 oxepin-CoA hydrolase Psest_3109 Psest_2437
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Psest_4305 Psest_0905
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 Psest_1829 Psest_3070
pimC pimeloyl-CoA dehydrogenase, small subunit Psest_4233
pimD pimeloyl-CoA dehydrogenase, large subunit Psest_4234 Psest_2669
pimF 6-carboxyhex-2-enoyl-CoA hydratase Psest_4235 Psest_2654
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Psest_1429 Psest_2219
PPDCbeta phenylpyruvate decarboxylase, beta subunit Psest_2218 Psest_1427

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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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