GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Marinobacter guineae M3B

Best path

livF, livG, livH, livM, livJ, ARO8, iorAB, 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 (47 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) CLH62_RS07860 CLH62_RS05520
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) CLH62_RS07855 CLH62_RS05525
livH L-phenylalanine ABC transporter, permease component 1 (LivH) CLH62_RS07845 CLH62_RS05535
livM L-phenylalanine ABC transporter, permease component 2 (LivM) CLH62_RS07850 CLH62_RS05530
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK CLH62_RS07840
ARO8 L-phenylalanine transaminase CLH62_RS16190 CLH62_RS17740
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB CLH62_RS16185
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A CLH62_RS05490
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B CLH62_RS05495
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C CLH62_RS05500
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E CLH62_RS05510
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CLH62_RS05465 CLH62_RS09255
paaZ1 oxepin-CoA hydrolase CLH62_RS05515 CLH62_RS09255
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase CLH62_RS05515
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase CLH62_RS05480 CLH62_RS07455
paaF 2,3-dehydroadipyl-CoA hydratase CLH62_RS15970 CLH62_RS05465
paaH 3-hydroxyadipyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS05470
paaJ2 3-oxoadipyl-CoA thiolase CLH62_RS05480 CLH62_RS07455
Alternative steps:
aacS acetoacetyl-CoA synthetase CLH62_RS11015 CLH62_RS15470
ARO10 phenylpyruvate decarboxylase
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit CLH62_RS15680 CLH62_RS11885
atoB acetyl-CoA C-acetyltransferase CLH62_RS07455 CLH62_RS15420
atoD acetoacetyl-CoA transferase, B subunit CLH62_RS11890 CLH62_RS15675
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CLH62_RS11700 CLH62_RS00510
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CLH62_RS11695 CLH62_RS05465
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CLH62_RS05465 CLH62_RS00910
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 CLH62_RS10835 CLH62_RS00205
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 CLH62_RS05515 CLH62_RS10190
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CLH62_RS15975 CLH62_RS15440
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CLH62_RS15970 CLH62_RS00910
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CLH62_RS15970 CLH62_RS10205
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CLH62_RS18530 CLH62_RS10205
fahA fumarylacetoacetate hydrolase CLH62_RS08990
gcdH glutaryl-CoA dehydrogenase CLH62_RS10225 CLH62_RS15440
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase CLH62_RS08985
HPD 4-hydroxyphenylpyruvate dioxygenase CLH62_RS09000
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
maiA maleylacetoacetate isomerase CLH62_RS08995
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase CLH62_RS05485 CLH62_RS14380
pad-dh phenylacetaldehyde dehydrogenase CLH62_RS15810 CLH62_RS14090
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit CLH62_RS09095
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
PCBD pterin-4-alpha-carbinoalamine dehydratase CLH62_RS19670
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CLH62_RS10200 CLH62_RS18535
pimC pimeloyl-CoA dehydrogenase, small subunit CLH62_RS10235
pimD pimeloyl-CoA dehydrogenase, large subunit CLH62_RS10230 CLH62_RS04855
pimF 6-carboxyhex-2-enoyl-CoA hydratase CLH62_RS10205 CLH62_RS18530
PPDCalpha phenylpyruvate decarboxylase, alpha subunit CLH62_RS08825
PPDCbeta phenylpyruvate decarboxylase, beta subunit CLH62_RS08830
QDPR 6,7-dihydropteridine reductase CLH62_RS11465

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