GapMind for catabolism of small carbon sources


L-phenylalanine catabolism in Aquimarina macrocephali JAMB N27

Best path

aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2


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
ARO8 L-phenylalanine transaminase Z054_RS0124040 Z054_RS0121930
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A Z054_RS0124820
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B Z054_RS0124815
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C Z054_RS0124810
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Z054_RS0124825 Z054_RS0109240
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Z054_RS0124795 Z054_RS0108580
paaZ1 oxepin-CoA hydrolase Z054_RS0124770
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Z054_RS0124770
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Z054_RS0124775 Z054_RS0115825
paaF 2,3-dehydroadipyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
paaH 3-hydroxyadipyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0124785
paaJ2 3-oxoadipyl-CoA thiolase Z054_RS0124775 Z054_RS0115825
Alternative steps:
aacS acetoacetyl-CoA synthetase
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit Z054_RS0108630
atoB acetyl-CoA C-acetyltransferase Z054_RS0106210 Z054_RS0115825
atoD acetoacetyl-CoA transferase, B subunit Z054_RS0108615
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Z054_RS0106690 Z054_RS0120995
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Z054_RS0106490 Z054_RS0108580
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Z054_RS0105210
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 Z054_RS0106365
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 Z054_RS0124770
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Z054_RS0121070 Z054_RS0104505
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Z054_RS0106865 Z054_RS0108580
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Z054_RS0106865 Z054_RS0108580
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Z054_RS0115830 Z054_RS0112885
fahA fumarylacetoacetate hydrolase Z054_RS0112785 Z054_RS0101655
gcdH glutaryl-CoA dehydrogenase Z054_RS0123520 Z054_RS0121070
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase Z054_RS0101645 Z054_RS0119965
HPD 4-hydroxyphenylpyruvate dioxygenase Z054_RS0101650 Z054_RS0119970
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Z054_RS0104130 Z054_RS0126330
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Z054_RS0104130 Z054_RS0121300
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)
maiA maleylacetoacetate isomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase
pad-dh phenylacetaldehyde dehydrogenase Z054_RS0121915 Z054_RS0104935
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Z054_RS0100525
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
PAH phenylalanine 4-monooxygenase Z054_RS0124845
PCBD pterin-4-alpha-carbinoalamine dehydratase Z054_RS0105275
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Z054_RS0115825 Z054_RS0124775
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase Z054_RS0124785
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Z054_RS0105825
PPDCbeta phenylpyruvate decarboxylase, beta subunit Z054_RS0105825 Z054_RS0113525
QDPR 6,7-dihydropteridine reductase

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