GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Desulfobacter vibrioformis DSM 8776

Best path

aroP, ARO8, iorA, iorB, 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
ARO8 L-phenylalanine transaminase Q366_RS13815 Q366_RS04965
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit Q366_RS12990 Q366_RS00625
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit Q366_RS12985 Q366_RS00630
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
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Q366_RS18135 Q366_RS07650
paaZ1 oxepin-CoA hydrolase Q366_RS07650 Q366_RS18135
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Q366_RS00870 Q366_RS02505
paaF 2,3-dehydroadipyl-CoA hydratase Q366_RS18135 Q366_RS07650
paaH 3-hydroxyadipyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
paaJ2 3-oxoadipyl-CoA thiolase Q366_RS02505 Q366_RS00870
Alternative steps:
aacS acetoacetyl-CoA synthetase Q366_RS10425 Q366_RS17165
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase Q366_RS09305 Q366_RS02505
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Q366_RS09470 Q366_RS02355
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Q366_RS13010 Q366_RS18135
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Q366_RS18135 Q366_RS13010
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Q366_RS10555
bamE class II benzoyl-CoA reductase, BamE subunit Q366_RS03515 Q366_RS02775
bamF class II benzoyl-CoA reductase, BamF subunit Q366_RS03510
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit Q366_RS04805
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit Q366_RS02065 Q366_RS05275
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit Q366_RS02070
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit Q366_RS02075
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit Q366_RS02060 Q366_RS05275
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 Q366_RS11450 Q366_RS06780
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Q366_RS18135 Q366_RS07650
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q366_RS18135 Q366_RS13010
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q366_RS00865 Q366_RS00395
fahA fumarylacetoacetate hydrolase Q366_RS17640
gcdH glutaryl-CoA dehydrogenase Q366_RS06780 Q366_RS11450
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Q366_RS04640 Q366_RS13540
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Q366_RS04645 Q366_RS00600
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Q366_RS04655 Q366_RS13525
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Q366_RS04650 Q366_RS13530
maiA maleylacetoacetate isomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase Q366_RS18140 Q366_RS00635
pad-dh phenylacetaldehyde dehydrogenase Q366_RS12840 Q366_RS10385
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Q366_RS19755 Q366_RS07265
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
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Q366_RS00870 Q366_RS09305
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit
QDPR 6,7-dihydropteridine reductase

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 Apr 09 2024. 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