GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudomonas fluorescens FW300-N2E2

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 (43 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Pf6N2E2_2926 Pf6N2E2_3576
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Pf6N2E2_2925 Pf6N2E2_3577
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Pf6N2E2_2923 Pf6N2E2_3579
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Pf6N2E2_2924 Pf6N2E2_3578
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Pf6N2E2_2921 Pf6N2E2_3580
PAH phenylalanine 4-monooxygenase Pf6N2E2_2630
PCBD pterin-4-alpha-carbinoalamine dehydratase Pf6N2E2_2631
QDPR 6,7-dihydropteridine reductase Pf6N2E2_5274 Pf6N2E2_5315
HPD 4-hydroxyphenylpyruvate dioxygenase Pf6N2E2_456 Pf6N2E2_5058
hmgA homogentisate dioxygenase Pf6N2E2_5290
maiA maleylacetoacetate isomerase Pf6N2E2_5292 Pf6N2E2_933
fahA fumarylacetoacetate hydrolase Pf6N2E2_5291 Pf6N2E2_1662
atoA acetoacetyl-CoA transferase, A subunit Pf6N2E2_2111
atoD acetoacetyl-CoA transferase, B subunit Pf6N2E2_2112
atoB acetyl-CoA C-acetyltransferase Pf6N2E2_2113 Pf6N2E2_1145
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf6N2E2_2042 Pf6N2E2_2190
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Pf6N2E2_2632 Pf6N2E2_50
aroP L-phenylalanine:H+ symporter AroP Pf6N2E2_5633 Pf6N2E2_5459
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Pf6N2E2_1839 Pf6N2E2_1323
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Pf6N2E2_1934 Pf6N2E2_1147
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1834
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Pf6N2E2_4704
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 Pf6N2E2_1468 Pf6N2E2_273
bamI class II benzoyl-CoA reductase, BamI subunit Pf6N2E2_1467
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 Pf6N2E2_1146 Pf6N2E2_5333
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Pf6N2E2_1147 Pf6N2E2_1922
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf6N2E2_1147 Pf6N2E2_1834
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
gcdH glutaryl-CoA dehydrogenase Pf6N2E2_4036 Pf6N2E2_2191
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase Pf6N2E2_1522
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
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 Pf6N2E2_5315
paaF 2,3-dehydroadipyl-CoA hydratase Pf6N2E2_1834 Pf6N2E2_1147
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Pf6N2E2_1934 Pf6N2E2_1840
paaH 3-hydroxyadipyl-CoA dehydrogenase Pf6N2E2_2290 Pf6N2E2_1922
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Pf6N2E2_2835 Pf6N2E2_2113
paaJ2 3-oxoadipyl-CoA thiolase Pf6N2E2_2835 Pf6N2E2_2113
paaK phenylacetate-CoA ligase Pf6N2E2_2873 Pf6N2E2_2872
paaZ1 oxepin-CoA hydrolase Pf6N2E2_1834 Pf6N2E2_1147
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Pf6N2E2_1329 Pf6N2E2_1878
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 Pf6N2E2_2539 Pf6N2E2_2289
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Pf6N2E2_1922 Pf6N2E2_2290
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Pf6N2E2_481 Pf6N2E2_665
PPDCbeta phenylpyruvate decarboxylase, beta subunit Pf6N2E2_480 Pf6N2E2_666

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