GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sporolactobacillus vineae SL153

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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP RH97_RS12640 RH97_RS11340
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase
hmgA homogentisate dioxygenase
maiA maleylacetoacetate isomerase
fahA fumarylacetoacetate hydrolase
atoA acetoacetyl-CoA transferase, A subunit RH97_RS08945 RH97_RS04720
atoD acetoacetyl-CoA transferase, B subunit RH97_RS08950 RH97_RS04725
atoB acetyl-CoA C-acetyltransferase RH97_RS08940 RH97_RS04710
Alternative steps:
aacS acetoacetyl-CoA synthetase RH97_RS08925
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase RH97_RS04630 RH97_RS07705
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase RH97_RS11210 RH97_RS03700
badI 2-ketocyclohexanecarboxyl-CoA hydrolase RH97_RS07390
badK cyclohex-1-ene-1-carboxyl-CoA hydratase RH97_RS08930 RH97_RS07390
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit RH97_RS08910
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 RH97_RS08905
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase RH97_RS08930
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RH97_RS08930 RH97_RS07390
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RH97_RS08935 RH97_RS05205
gcdH glutaryl-CoA dehydrogenase RH97_RS08905
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) RH97_RS07250 RH97_RS07245
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) RH97_RS07245 RH97_RS01645
livH L-phenylalanine ABC transporter, permease component 1 (LivH) RH97_RS07235
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK RH97_RS07230
livM L-phenylalanine ABC transporter, permease component 2 (LivM) RH97_RS07240
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 RH97_RS08930 RH97_RS07390
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase RH97_RS08930 RH97_RS07390
paaH 3-hydroxyadipyl-CoA dehydrogenase RH97_RS08935 RH97_RS05205
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase RH97_RS08940 RH97_RS04710
paaJ2 3-oxoadipyl-CoA thiolase RH97_RS08940 RH97_RS04710
paaK phenylacetate-CoA ligase RH97_RS07385
paaZ1 oxepin-CoA hydrolase RH97_RS08930
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase RH97_RS02580 RH97_RS06550
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 RH97_RS08940 RH97_RS04710
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit RH97_RS04120 RH97_RS10575
PPDCbeta phenylpyruvate decarboxylase, beta subunit RH97_RS04115 RH97_RS10580

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.

Links

Downloads

Related tools

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