GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Shewanella oneidensis MR-1

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 (37 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase SO1666
PCBD pterin-4-alpha-carbinoalamine dehydratase SO1667
QDPR 6,7-dihydropteridine reductase SO0772 SO3715
HPD 4-hydroxyphenylpyruvate dioxygenase SO1962
hmgA homogentisate dioxygenase SO1963
maiA maleylacetoacetate isomerase SO1671 SO4697
fahA fumarylacetoacetate hydrolase SO1670
atoA acetoacetyl-CoA transferase, A subunit SO1892
atoD acetoacetyl-CoA transferase, B subunit SO1891
atoB acetyl-CoA C-acetyltransferase SO1677 SO0020
Alternative steps:
aacS acetoacetyl-CoA synthetase SO1971 SO3664
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase SO2350 SO2406
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SO4382 SO2776
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SO4739
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SO1680 SO3908
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 SO1017
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 SO1679 SO1897
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SO0021
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SO3088 SO1680
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SO0021 SO3088
gcdH glutaryl-CoA dehydrogenase SO1897 SO1679
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) SO3960 SO4655
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) SO3960 SO3602
livH L-phenylalanine ABC transporter, permease component 1 (LivH)
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM)
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 SO1364
paaF 2,3-dehydroadipyl-CoA hydratase SO1680 SO3908
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase SO3908 SO4739
paaH 3-hydroxyadipyl-CoA dehydrogenase SO0021 SO3088
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase SO0020 SO1677
paaJ2 3-oxoadipyl-CoA thiolase SO0020 SO1677
paaK phenylacetate-CoA ligase SO2581
paaZ1 oxepin-CoA hydrolase SO1680 SO3088
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase SO3496 SO4480
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit SO4061 SO4357
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 SO0020 SO1677
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase SO3088 SO0021
PPDCalpha phenylpyruvate decarboxylase, alpha subunit SO2339
PPDCbeta phenylpyruvate decarboxylase, beta subunit SO2340

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