GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Algoriphagus machipongonensis PR1

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 ALPR1_RS06765
PCBD pterin-4-alpha-carbinoalamine dehydratase ALPR1_RS00415
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase ALPR1_RS10690
hmgA homogentisate dioxygenase ALPR1_RS17960
maiA maleylacetoacetate isomerase
fahA fumarylacetoacetate hydrolase ALPR1_RS07280 ALPR1_RS13845
atoA acetoacetyl-CoA transferase, A subunit ALPR1_RS11165
atoD acetoacetyl-CoA transferase, B subunit ALPR1_RS11160
atoB acetyl-CoA C-acetyltransferase ALPR1_RS13240 ALPR1_RS01085
Alternative steps:
aacS acetoacetyl-CoA synthetase ALPR1_RS09835 ALPR1_RS10080
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase ALPR1_RS18160 ALPR1_RS09570
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase ALPR1_RS17925 ALPR1_RS14805
badI 2-ketocyclohexanecarboxyl-CoA hydrolase ALPR1_RS07745
badK cyclohex-1-ene-1-carboxyl-CoA hydratase ALPR1_RS16285
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit ALPR1_RS19450
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase ALPR1_RS02465 ALPR1_RS19205
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase ALPR1_RS16285 ALPR1_RS05015
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase ALPR1_RS16285 ALPR1_RS07745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase ALPR1_RS01095 ALPR1_RS10470
gcdH glutaryl-CoA dehydrogenase ALPR1_RS12195 ALPR1_RS19490
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) ALPR1_RS03040 ALPR1_RS06390
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) ALPR1_RS03040 ALPR1_RS09775
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 ALPR1_RS16785
paaF 2,3-dehydroadipyl-CoA hydratase ALPR1_RS16285
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase ALPR1_RS16285 ALPR1_RS05015
paaH 3-hydroxyadipyl-CoA dehydrogenase ALPR1_RS01095 ALPR1_RS10470
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase ALPR1_RS01085 ALPR1_RS13240
paaJ2 3-oxoadipyl-CoA thiolase ALPR1_RS01085 ALPR1_RS13240
paaK phenylacetate-CoA ligase ALPR1_RS19255
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase ALPR1_RS01205 ALPR1_RS06860
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit ALPR1_RS06270
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 ALPR1_RS01085 ALPR1_RS13240
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit ALPR1_RS18330
PPDCbeta phenylpyruvate decarboxylase, beta subunit ALPR1_RS06440 ALPR1_RS18330

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