GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Methyloferula stellata AR4T

Best path

livF, livG, livH, livM, livJ, 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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) A3OQ_RS0120265 A3OQ_RS0108735
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) A3OQ_RS0120260 A3OQ_RS0115155
livH L-phenylalanine ABC transporter, permease component 1 (LivH) A3OQ_RS0120250 A3OQ_RS0115165
livM L-phenylalanine ABC transporter, permease component 2 (LivM) A3OQ_RS0120255 A3OQ_RS0115160
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK A3OQ_RS0120275
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase A3OQ_RS0105795
QDPR 6,7-dihydropteridine reductase A3OQ_RS0116620
HPD 4-hydroxyphenylpyruvate dioxygenase
hmgA homogentisate dioxygenase
maiA maleylacetoacetate isomerase
fahA fumarylacetoacetate hydrolase
atoA acetoacetyl-CoA transferase, A subunit A3OQ_RS0102555
atoD acetoacetyl-CoA transferase, B subunit A3OQ_RS0102560
atoB acetyl-CoA C-acetyltransferase A3OQ_RS0109070 A3OQ_RS0104730
Alternative steps:
aacS acetoacetyl-CoA synthetase
ARO10 phenylpyruvate decarboxylase A3OQ_RS0110765
ARO8 L-phenylalanine transaminase A3OQ_RS0104145 A3OQ_RS0106285
aroP L-phenylalanine:H+ symporter AroP
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase A3OQ_RS0115500 A3OQ_RS0109065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase A3OQ_RS0102705
badK cyclohex-1-ene-1-carboxyl-CoA hydratase A3OQ_RS0102705 A3OQ_RS0109465
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 A3OQ_RS0106995 A3OQ_RS0108510
bamI class II benzoyl-CoA reductase, BamI subunit A3OQ_RS0119725
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
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase A3OQ_RS0102705
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3OQ_RS0102705 A3OQ_RS0109465
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3OQ_RS0104720 A3OQ_RS0103110
gcdH glutaryl-CoA dehydrogenase A3OQ_RS0100300
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB A3OQ_RS0100655
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit A3OQ_RS0100655
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 A3OQ_RS0102705 A3OQ_RS0109465
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase A3OQ_RS0102705 A3OQ_RS0109465
paaH 3-hydroxyadipyl-CoA dehydrogenase A3OQ_RS0104720 A3OQ_RS0103110
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase A3OQ_RS0109070 A3OQ_RS0104730
paaJ2 3-oxoadipyl-CoA thiolase A3OQ_RS0109070 A3OQ_RS0104730
paaK phenylacetate-CoA ligase
paaZ1 oxepin-CoA hydrolase A3OQ_RS0102705 A3OQ_RS0109465
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase A3OQ_RS0112965 A3OQ_RS0101160
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 A3OQ_RS0109070 A3OQ_RS0104730
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase A3OQ_RS0104720
PPDCalpha phenylpyruvate decarboxylase, alpha subunit A3OQ_RS0115430
PPDCbeta phenylpyruvate decarboxylase, beta subunit A3OQ_RS0115435

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