GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Shewanella loihica PV-4

Best path

aroP, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase Shew_1435
PCBD pterin-4-alpha-carbinoalamine dehydratase Shew_1436
QDPR 6,7-dihydropteridine reductase Shew_0688 Shew_0048
HPD 4-hydroxyphenylpyruvate dioxygenase Shew_2155
hmgA homogentisate dioxygenase Shew_2154
maiA maleylacetoacetate isomerase Shew_1439
fahA fumarylacetoacetate hydrolase Shew_1438
atoA acetoacetyl-CoA transferase, A subunit Shew_2575
atoD acetoacetyl-CoA transferase, B subunit Shew_2576
atoB acetyl-CoA C-acetyltransferase Shew_1667 Shew_0018
Alternative steps:
aacS acetoacetyl-CoA synthetase Shew_2593
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Shew_1999 Shew_1951
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Shew_1603 Shew_3525
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Shew_3814 Shew_0540
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Shew_2672 Shew_0540
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 Shew_1669 Shew_2570
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Shew_2672 Shew_2864
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Shew_1670 Shew_0019
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Shew_0019 Shew_2425
gcdH glutaryl-CoA dehydrogenase Shew_0900 Shew_2570
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
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Shew_2606 Shew_3310
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Shew_2611 Shew_3310
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Shew_2609
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Shew_2608
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 Shew_1670 Shew_2864
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Shew_0540 Shew_2672
paaH 3-hydroxyadipyl-CoA dehydrogenase Shew_0019 Shew_2425
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Shew_0018 Shew_2858
paaJ2 3-oxoadipyl-CoA thiolase Shew_0018 Shew_1667
paaK phenylacetate-CoA ligase Shew_2188 Shew_3084
paaZ1 oxepin-CoA hydrolase Shew_2672 Shew_1670
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Shew_0967 Shew_3574
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Shew_0244 Shew_0607
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 Shew_0729
padI phenylglyoxylate dehydrogenase, beta subunit
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Shew_2858 Shew_0018
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Shew_2570
pimF 6-carboxyhex-2-enoyl-CoA hydratase Shew_2864 Shew_2425
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Shew_1925
PPDCbeta phenylpyruvate decarboxylase, beta subunit Shew_1926

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