GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Kocuria flava HO-9041

Best path

aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 AS188_RS01250 AS188_RS03395
ARO8 L-phenylalanine transaminase AS188_RS14185 AS188_RS05075
PPDCalpha phenylpyruvate decarboxylase, alpha subunit AS188_RS05140 AS188_RS00100
PPDCbeta phenylpyruvate decarboxylase, beta subunit AS188_RS05135 AS188_RS00095
pad-dh phenylacetaldehyde dehydrogenase AS188_RS11615 AS188_RS00910
paaK phenylacetate-CoA ligase AS188_RS01180 AS188_RS08645
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A AS188_RS01190
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B AS188_RS01195
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C AS188_RS01200
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E AS188_RS01210
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AS188_RS02285 AS188_RS15810
paaZ1 oxepin-CoA hydrolase AS188_RS01170 AS188_RS01390
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AS188_RS01170
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AS188_RS15780 AS188_RS14085
paaF 2,3-dehydroadipyl-CoA hydratase AS188_RS01390 AS188_RS02285
paaH 3-hydroxyadipyl-CoA dehydrogenase AS188_RS02280 AS188_RS15805
paaJ2 3-oxoadipyl-CoA thiolase AS188_RS15780 AS188_RS14085
Alternative steps:
aacS acetoacetyl-CoA synthetase AS188_RS02550 AS188_RS00055
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit AS188_RS00810 AS188_RS14080
atoB acetyl-CoA C-acetyltransferase AS188_RS00800 AS188_RS15780
atoD acetoacetyl-CoA transferase, B subunit AS188_RS00805 AS188_RS14075
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AS188_RS04345 AS188_RS04270
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AS188_RS14545 AS188_RS15810
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AS188_RS01390 AS188_RS15810
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
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 AS188_RS01170 AS188_RS04315
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AS188_RS04445 AS188_RS04425
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AS188_RS01390 AS188_RS15810
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AS188_RS01390 AS188_RS15810
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AS188_RS02280 AS188_RS15805
fahA fumarylacetoacetate hydrolase
gcdH glutaryl-CoA dehydrogenase AS188_RS02305 AS188_RS15830
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
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) AS188_RS02965 AS188_RS12245
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) AS188_RS09695 AS188_RS12245
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
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 AS188_RS03580
padI phenylglyoxylate dehydrogenase, beta subunit
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AS188_RS15780 AS188_RS14085
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase AS188_RS05240
QDPR 6,7-dihydropteridine reductase AS188_RS05670 AS188_RS03230

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