GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Phaeobacter inhibens BS107

Best path

aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 (47 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
ARO8 L-phenylalanine transaminase PGA1_c29420 PGA1_c21250
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB PGA1_c04490 PGA1_c17080
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A PGA1_c04080
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B PGA1_c04070
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C PGA1_c04060
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E PGA1_c04040
paaG 1,2-epoxyphenylacetyl-CoA isomerase PGA1_c26820 PGA1_c16990
paaZ1 oxepin-CoA hydrolase PGA1_c26830 PGA1_262p00800
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PGA1_c26830 PGA1_262p00800
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PGA1_c04090 PGA1_c34350
paaF 2,3-dehydroadipyl-CoA hydratase PGA1_c36500 PGA1_262p01980
paaH 3-hydroxyadipyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
paaJ2 3-oxoadipyl-CoA thiolase PGA1_c04090 PGA1_c34350
Alternative steps:
aacS acetoacetyl-CoA synthetase PGA1_262p01840 PGA1_c34070
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit PGA1_c06210
atoB acetyl-CoA C-acetyltransferase PGA1_c03400 PGA1_c33180
atoD acetoacetyl-CoA transferase, B subunit PGA1_c06200
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PGA1_c17930 PGA1_c03390
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PGA1_262p01980 PGA1_c26820
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
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 PGA1_c10430 PGA1_c25750
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 PGA1_c26830 PGA1_262p00800
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase PGA1_c10280 PGA1_c17340
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PGA1_c36500 PGA1_262p01980
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PGA1_c36500 PGA1_262p01980
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PGA1_c04110 PGA1_c11320
fahA fumarylacetoacetate hydrolase PGA1_c00430 PGA1_c04530
gcdH glutaryl-CoA dehydrogenase PGA1_c15710 PGA1_c10280
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase PGA1_c00440
HPD 4-hydroxyphenylpyruvate dioxygenase PGA1_c07610
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) PGA1_c16520 PGA1_c02620
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) PGA1_c02610 PGA1_c32620
livH L-phenylalanine ABC transporter, permease component 1 (LivH) PGA1_c02590
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) PGA1_c32580 PGA1_c02600
maiA maleylacetoacetate isomerase PGA1_c00380 PGA1_c32680
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase PGA1_c36500
paaK phenylacetate-CoA ligase PGA1_c26800 PGA1_c34070
pad-dh phenylacetaldehyde dehydrogenase PGA1_c21670 PGA1_c32120
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit PGA1_c28890 PGA1_c27640
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
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase PGA1_c29290
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PGA1_c22730 PGA1_c04120
pimC pimeloyl-CoA dehydrogenase, small subunit PGA1_c04140
pimD pimeloyl-CoA dehydrogenase, large subunit PGA1_c04130 PGA1_c12060
pimF 6-carboxyhex-2-enoyl-CoA hydratase PGA1_c22740 PGA1_c04110
PPDCalpha phenylpyruvate decarboxylase, alpha subunit PGA1_c17550
PPDCbeta phenylpyruvate decarboxylase, beta subunit PGA1_c23150 PGA1_c17560
QDPR 6,7-dihydropteridine reductase PGA1_78p00100

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 Aug 02 2021. The underlying query database was built on Aug 02 2021.

Links

Downloads

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 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