GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sphingomonas koreensis DSMZ 15582

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase Ga0059261_1314
PCBD pterin-4-alpha-carbinoalamine dehydratase Ga0059261_1993
QDPR 6,7-dihydropteridine reductase Ga0059261_2819
HPD 4-hydroxyphenylpyruvate dioxygenase Ga0059261_2984
hmgA homogentisate dioxygenase Ga0059261_1694
maiA maleylacetoacetate isomerase Ga0059261_0507 Ga0059261_2015
fahA fumarylacetoacetate hydrolase Ga0059261_1693 Ga0059261_2473
atoA acetoacetyl-CoA transferase, A subunit Ga0059261_0265
atoD acetoacetyl-CoA transferase, B subunit Ga0059261_0263
atoB acetyl-CoA C-acetyltransferase Ga0059261_0982 Ga0059261_2888
Alternative steps:
aacS acetoacetyl-CoA synthetase Ga0059261_0771 Ga0059261_0835
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Ga0059261_2226 Ga0059261_2265
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Ga0059261_0364 Ga0059261_1451
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Ga0059261_2668 Ga0059261_3685
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Ga0059261_3685 Ga0059261_0837
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 Ga0059261_0704
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 Ga0059261_3681 Ga0059261_4052
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Ga0059261_3685 Ga0059261_2908
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Ga0059261_3685 Ga0059261_2668
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Ga0059261_2816 Ga0059261_0837
gcdH glutaryl-CoA dehydrogenase Ga0059261_2164 Ga0059261_4052
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) Ga0059261_2542 Ga0059261_4235
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Ga0059261_2542 Ga0059261_2250
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 Ga0059261_3685 Ga0059261_2668
paaG 1,2-epoxyphenylacetyl-CoA isomerase Ga0059261_3986 Ga0059261_2887
paaH 3-hydroxyadipyl-CoA dehydrogenase Ga0059261_2816 Ga0059261_0837
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Ga0059261_2888 Ga0059261_0982
paaJ2 3-oxoadipyl-CoA thiolase Ga0059261_0982 Ga0059261_2888
paaK phenylacetate-CoA ligase Ga0059261_0835
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Ga0059261_1680 Ga0059261_3374
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 Ga0059261_3284 Ga0059261_2160
pimC pimeloyl-CoA dehydrogenase, small subunit Ga0059261_2860 Ga0059261_0840
pimD pimeloyl-CoA dehydrogenase, large subunit Ga0059261_2859 Ga0059261_0839
pimF 6-carboxyhex-2-enoyl-CoA hydratase Ga0059261_0837 Ga0059261_2827
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Ga0059261_2273 Ga0059261_0016
PPDCbeta phenylpyruvate decarboxylase, beta subunit Ga0059261_2272 Ga0059261_0017

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