GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Acidovorax sp. GW101-3H11

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 (44 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Ac3H11_1692 Ac3H11_1936
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Ac3H11_1693 Ac3H11_4983
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Ac3H11_1695 Ac3H11_4984
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Ac3H11_1694 Ac3H11_4628
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Ac3H11_2396 Ac3H11_552
PAH phenylalanine 4-monooxygenase Ac3H11_1847
PCBD pterin-4-alpha-carbinoalamine dehydratase Ac3H11_1679
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase Ac3H11_1849 Ac3H11_1225
hmgA homogentisate dioxygenase
maiA maleylacetoacetate isomerase Ac3H11_2306 Ac3H11_210
fahA fumarylacetoacetate hydrolase Ac3H11_4507 Ac3H11_3715
atoA acetoacetyl-CoA transferase, A subunit Ac3H11_132 Ac3H11_3922
atoD acetoacetyl-CoA transferase, B subunit Ac3H11_131 Ac3H11_3921
atoB acetyl-CoA C-acetyltransferase Ac3H11_178 Ac3H11_2303
Alternative steps:
aacS acetoacetyl-CoA synthetase Ac3H11_3009 Ac3H11_4867
ARO10 phenylpyruvate decarboxylase Ac3H11_3309
ARO8 L-phenylalanine transaminase Ac3H11_1015 Ac3H11_1602
aroP L-phenylalanine:H+ symporter AroP
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Ac3H11_2074 Ac3H11_2257
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Ac3H11_4006 Ac3H11_2775
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Ac3H11_4006 Ac3H11_2775
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 Ac3H11_1447 Ac3H11_3809
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 Ac3H11_3083
boxB benzoyl-CoA epoxidase, subunit B Ac3H11_3084
boxC 2,3-epoxybenzoyl-CoA dihydrolase Ac3H11_3085
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase Ac3H11_3089
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Ac3H11_2996 Ac3H11_2359
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Ac3H11_4006 Ac3H11_3192
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ac3H11_4006 Ac3H11_2775
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
gcdH glutaryl-CoA dehydrogenase Ac3H11_3533 Ac3H11_2991
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB Ac3H11_2707 Ac3H11_1196
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
paaF 2,3-dehydroadipyl-CoA hydratase Ac3H11_4006 Ac3H11_2775
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Ac3H11_2719 Ac3H11_4989
paaH 3-hydroxyadipyl-CoA dehydrogenase Ac3H11_1914 Ac3H11_4658
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Ac3H11_3920 Ac3H11_178
paaJ2 3-oxoadipyl-CoA thiolase Ac3H11_3920 Ac3H11_178
paaK phenylacetate-CoA ligase Ac3H11_4625 Ac3H11_964
paaZ1 oxepin-CoA hydrolase Ac3H11_1055 Ac3H11_3089
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Ac3H11_3089
pad-dh phenylacetaldehyde dehydrogenase Ac3H11_1496 Ac3H11_4393
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Ac3H11_3802
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 Ac3H11_2522 Ac3H11_1916
pimC pimeloyl-CoA dehydrogenase, small subunit Ac3H11_1712
pimD pimeloyl-CoA dehydrogenase, large subunit Ac3H11_1711 Ac3H11_2717
pimF 6-carboxyhex-2-enoyl-CoA hydratase Ac3H11_2523 Ac3H11_1931
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit

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