GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Dokdonella koreensis DS-123

Best path

aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

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 (38 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase I596_RS16375
PCBD pterin-4-alpha-carbinoalamine dehydratase I596_RS12135
QDPR 6,7-dihydropteridine reductase I596_RS11280
HPD 4-hydroxyphenylpyruvate dioxygenase I596_RS04065
hmgA homogentisate dioxygenase I596_RS04070
maiA maleylacetoacetate isomerase I596_RS04080 I596_RS11190
fahA fumarylacetoacetate hydrolase I596_RS04075 I596_RS05080
atoA acetoacetyl-CoA transferase, A subunit I596_RS14240
atoD acetoacetyl-CoA transferase, B subunit I596_RS14240
atoB acetyl-CoA C-acetyltransferase I596_RS05370 I596_RS06325
Alternative steps:
aacS acetoacetyl-CoA synthetase I596_RS17305 I596_RS05290
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase I596_RS14430 I596_RS00600
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase I596_RS10645 I596_RS05500
badI 2-ketocyclohexanecarboxyl-CoA hydrolase I596_RS12940 I596_RS08905
badK cyclohex-1-ene-1-carboxyl-CoA hydratase I596_RS12940 I596_RS04715
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 I596_RS00985 I596_RS06180
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 I596_RS15670 I596_RS04710
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase I596_RS12940 I596_RS04715
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase I596_RS12940 I596_RS02240
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase I596_RS06330 I596_RS02240
gcdH glutaryl-CoA dehydrogenase I596_RS15145 I596_RS15670
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase I596_RS08115
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB I596_RS10685
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) I596_RS07805 I596_RS02480
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) I596_RS07805 I596_RS15380
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 I596_RS12940 I596_RS04715
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase I596_RS12940 I596_RS08905
paaH 3-hydroxyadipyl-CoA dehydrogenase I596_RS06330 I596_RS02240
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase I596_RS06325 I596_RS05370
paaJ2 3-oxoadipyl-CoA thiolase I596_RS06325 I596_RS05370
paaK phenylacetate-CoA ligase I596_RS07565
paaZ1 oxepin-CoA hydrolase I596_RS04715 I596_RS08905
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase I596_RS04570 I596_RS02225
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 I596_RS06325 I596_RS05370
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit I596_RS15145
pimF 6-carboxyhex-2-enoyl-CoA hydratase I596_RS02240
PPDCalpha phenylpyruvate decarboxylase, alpha subunit I596_RS04045
PPDCbeta phenylpyruvate decarboxylase, beta subunit I596_RS04040 I596_RS15125

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 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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