GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Shewanella amazonensis SB2B

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase Sama_2222
PCBD pterin-4-alpha-carbinoalamine dehydratase Sama_2221
QDPR 6,7-dihydropteridine reductase Sama_2932
HPD 4-hydroxyphenylpyruvate dioxygenase Sama_1568
hmgA homogentisate dioxygenase Sama_1569
maiA maleylacetoacetate isomerase Sama_2218
fahA fumarylacetoacetate hydrolase Sama_2219
atoA acetoacetyl-CoA transferase, A subunit Sama_0518 Sama_1357
atoD acetoacetyl-CoA transferase, B subunit Sama_1356 Sama_0519
atoB acetyl-CoA C-acetyltransferase Sama_1375 Sama_0031
Alternative steps:
aacS acetoacetyl-CoA synthetase Sama_1904 Sama_2897
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Sama_1805 Sama_1733
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Sama_1980 Sama_3393
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Sama_3635
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Sama_1378 Sama_2167
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 Sama_1377 Sama_1362
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Sama_1378 Sama_0032
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Sama_1378 Sama_0032
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Sama_0032 Sama_2167
gcdH glutaryl-CoA dehydrogenase Sama_2796 Sama_1362
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) Sama_3087 Sama_3588
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Sama_3087 Sama_1969
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
paaF 2,3-dehydroadipyl-CoA hydratase Sama_1378 Sama_2167
paaG 1,2-epoxyphenylacetyl-CoA isomerase Sama_3052 Sama_3135
paaH 3-hydroxyadipyl-CoA dehydrogenase Sama_0032 Sama_2167
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Sama_0031 Sama_1375
paaJ2 3-oxoadipyl-CoA thiolase Sama_0031 Sama_1375
paaK phenylacetate-CoA ligase Sama_1934 Sama_2897
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Sama_2648 Sama_3435
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Sama_2903 Sama_3176
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 Sama_0031 Sama_1375
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Sama_1362
pimF 6-carboxyhex-2-enoyl-CoA hydratase Sama_2167 Sama_0032
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Sama_1709
PPDCbeta phenylpyruvate decarboxylase, beta subunit Sama_1710 Sama_2795

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.

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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