GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Echinicola vietnamensis KMM 6221, DSM 17526

Best path

aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

Also see fitness data for the top candidates

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 Echvi_2513
PCBD pterin-4-alpha-carbinoalamine dehydratase Echvi_0850
QDPR 6,7-dihydropteridine reductase Echvi_4494 Echvi_0893
HPD 4-hydroxyphenylpyruvate dioxygenase Echvi_2983
hmgA homogentisate dioxygenase Echvi_1105
maiA maleylacetoacetate isomerase
fahA fumarylacetoacetate hydrolase Echvi_2481 Echvi_2939
atoA acetoacetyl-CoA transferase, A subunit Echvi_3272
atoD acetoacetyl-CoA transferase, B subunit Echvi_3271
atoB acetyl-CoA C-acetyltransferase Echvi_3705 Echvi_1071
Alternative steps:
aacS acetoacetyl-CoA synthetase
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Echvi_0675 Echvi_2857
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Echvi_3928 Echvi_4610
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Echvi_2341
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Echvi_4069
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Echvi_0731
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 Echvi_1212 Echvi_1473
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Echvi_4069 Echvi_0343
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Echvi_4069 Echvi_0069
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Echvi_1069 Echvi_3304
gcdH glutaryl-CoA dehydrogenase Echvi_2990 Echvi_0738
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) Echvi_1333 Echvi_2909
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Echvi_1333 Echvi_4539
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 Echvi_0363
paaF 2,3-dehydroadipyl-CoA hydratase Echvi_4069 Echvi_0343
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Echvi_0069
paaH 3-hydroxyadipyl-CoA dehydrogenase Echvi_1069 Echvi_3304
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Echvi_1071 Echvi_3705
paaJ2 3-oxoadipyl-CoA thiolase Echvi_1071 Echvi_3705
paaK phenylacetate-CoA ligase Echvi_2567
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Echvi_0481 Echvi_1497
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit Echvi_2097
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 Echvi_1071 Echvi_3705
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Echvi_1750
PPDCbeta phenylpyruvate decarboxylase, beta subunit Echvi_3823 Echvi_1750

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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