GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudomonas putida KT2440

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 (48 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) PP_1137 PP_4863
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) PP_1138 PP_2767
livH L-phenylalanine ABC transporter, permease component 1 (LivH) PP_1140 PP_4866
livM L-phenylalanine ABC transporter, permease component 2 (LivM) PP_1139 PP_4865
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK PP_1141 PP_4867
PAH phenylalanine 4-monooxygenase PP_4490
PCBD pterin-4-alpha-carbinoalamine dehydratase PP_4491
QDPR 6,7-dihydropteridine reductase PP_2432 PP_4632
HPD 4-hydroxyphenylpyruvate dioxygenase PP_3433 PP_2554
hmgA homogentisate dioxygenase PP_4621
maiA maleylacetoacetate isomerase PP_4619 PP_1320
fahA fumarylacetoacetate hydrolase PP_4620 PP_3205
atoA acetoacetyl-CoA transferase, A subunit PP_3122 PP_3951
atoD acetoacetyl-CoA transferase, B subunit PP_3123 PP_3952
atoB acetyl-CoA C-acetyltransferase PP_2215 PP_4636
Alternative steps:
aacS acetoacetyl-CoA synthetase PP_3071 PP_3458
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase PP_3590 PP_1972
aroP L-phenylalanine:H+ symporter AroP PP_0927 PP_4495
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PP_1946 PP_1852
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PP_3283 PP_2217
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PP_2217 PP_3284
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PP_0311
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 PP_2184 PP_4123
bamI class II benzoyl-CoA reductase, BamI subunit PP_2185
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 PP_3270 PP_0708
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PP_2216 PP_4064
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PP_2217 PP_3284
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PP_2217 PP_3284
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PP_2136 PP_3755
gcdH glutaryl-CoA dehydrogenase PP_0158 PP_4064
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PP_2217
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PP_3278
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PP_3277
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PP_3276
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PP_3274 PP_1163
paaF 2,3-dehydroadipyl-CoA hydratase PP_3284 PP_2217
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PP_3283 PP_3726
paaH 3-hydroxyadipyl-CoA dehydrogenase PP_2136 PP_3282
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PP_3280 PP_1377
paaJ2 3-oxoadipyl-CoA thiolase PP_1377 PP_3280
paaK phenylacetate-CoA ligase PP_3279 PP_4550
paaZ1 oxepin-CoA hydrolase PP_3270 PP_3283
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PP_3270
pad-dh phenylacetaldehyde dehydrogenase PP_3463 PP_5278
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 PP_2051 PP_2137
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase PP_2136 PP_2047
PPDCalpha phenylpyruvate decarboxylase, alpha subunit PP_4401 PP_0555
PPDCbeta phenylpyruvate decarboxylase, beta subunit PP_4402 PP_0554

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