GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Erythrobacter marinus HWDM-33

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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase AAV99_RS03335
PCBD pterin-4-alpha-carbinoalamine dehydratase AAV99_RS00755
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase AAV99_RS09625
hmgA homogentisate dioxygenase AAV99_RS11990
maiA maleylacetoacetate isomerase AAV99_RS11995
fahA fumarylacetoacetate hydrolase AAV99_RS11985
atoA acetoacetyl-CoA transferase, A subunit AAV99_RS05295
atoD acetoacetyl-CoA transferase, B subunit AAV99_RS05285
atoB acetyl-CoA C-acetyltransferase AAV99_RS12435 AAV99_RS09865
Alternative steps:
aacS acetoacetyl-CoA synthetase AAV99_RS02765 AAV99_RS12450
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase AAV99_RS06500 AAV99_RS03255
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AAV99_RS03635 AAV99_RS08075
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AAV99_RS05725
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AAV99_RS05725 AAV99_RS05720
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 AAV99_RS09825
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 AAV99_RS13300 AAV99_RS03120
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AAV99_RS05725
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AAV99_RS05725 AAV99_RS12275
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AAV99_RS07705 AAV99_RS00990
gcdH glutaryl-CoA dehydrogenase AAV99_RS06380 AAV99_RS03120
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) AAV99_RS05200 AAV99_RS12745
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) AAV99_RS05200 AAV99_RS12745
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 AAV99_RS05725 AAV99_RS05720
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AAV99_RS05720 AAV99_RS05725
paaH 3-hydroxyadipyl-CoA dehydrogenase AAV99_RS07705 AAV99_RS00990
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AAV99_RS12435 AAV99_RS07710
paaJ2 3-oxoadipyl-CoA thiolase AAV99_RS12435 AAV99_RS07710
paaK phenylacetate-CoA ligase AAV99_RS07715 AAV99_RS12450
paaZ1 oxepin-CoA hydrolase AAV99_RS05725
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase AAV99_RS09860 AAV99_RS05570
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 AAV99_RS07710 AAV99_RS12435
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit AAV99_RS08475 AAV99_RS09615
PPDCbeta phenylpyruvate decarboxylase, beta subunit AAV99_RS08480 AAV99_RS06250

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