GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Moritella dasanensis ArB 0140

Best path

aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, 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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase A923_RS0103220
PCBD pterin-4-alpha-carbinoalamine dehydratase A923_RS0103215
QDPR 6,7-dihydropteridine reductase A923_RS0102630 A923_RS0106390
HPD 4-hydroxyphenylpyruvate dioxygenase A923_RS0114560
hmgA homogentisate dioxygenase A923_RS0114555
maiA maleylacetoacetate isomerase A923_RS0114545
fahA fumarylacetoacetate hydrolase A923_RS0114550
aacS acetoacetyl-CoA synthetase A923_RS0100990 A923_RS0104565
atoB acetyl-CoA C-acetyltransferase A923_RS0119275 A923_RS0119825
Alternative steps:
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase A923_RS0100145 A923_RS0120455
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase A923_RS0119400 A923_RS0108700
badI 2-ketocyclohexanecarboxyl-CoA hydrolase A923_RS0112940
badK cyclohex-1-ene-1-carboxyl-CoA hydratase A923_RS0104120 A923_RS0112940
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
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase A923_RS0101015
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A923_RS0104120 A923_RS0110330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A923_RS0119830 A923_RS0104120
gcdH glutaryl-CoA dehydrogenase A923_RS0101015
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) A923_RS0116415 A923_RS0110810
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) A923_RS0116420 A923_RS0110810
livH L-phenylalanine ABC transporter, permease component 1 (LivH) A923_RS0116430
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
paaF 2,3-dehydroadipyl-CoA hydratase A923_RS0110330 A923_RS0112940
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase A923_RS0116325 A923_RS0110330
paaH 3-hydroxyadipyl-CoA dehydrogenase A923_RS0119830 A923_RS0104120
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase A923_RS0119825 A923_RS0119275
paaJ2 3-oxoadipyl-CoA thiolase A923_RS0119825 A923_RS0119275
paaK phenylacetate-CoA ligase A923_RS0104565 A923_RS0113825
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase A923_RS0108515 A923_RS0109940
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit A923_RS0109435 A923_RS0111315
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 A923_RS0119825 A923_RS0119275
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase A923_RS0104120 A923_RS0119830
PPDCalpha phenylpyruvate decarboxylase, alpha subunit A923_RS0101130
PPDCbeta phenylpyruvate decarboxylase, beta subunit A923_RS0101135

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