GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Mesorhizobium ciceri WSM1271

Best path

livF, livG, livH, livM, livJ, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Mesci_1237 Mesci_6239
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Mesci_1236 Mesci_6238
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Mesci_1234 Mesci_6236
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Mesci_1235 Mesci_6237
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Mesci_1239 Mesci_4851
PAH phenylalanine 4-monooxygenase Mesci_0618
PCBD pterin-4-alpha-carbinoalamine dehydratase Mesci_0958 Mesci_4256
QDPR 6,7-dihydropteridine reductase Mesci_2598
HPD 4-hydroxyphenylpyruvate dioxygenase Mesci_4543
hmgA homogentisate dioxygenase Mesci_4549
maiA maleylacetoacetate isomerase Mesci_3453 Mesci_4357
fahA fumarylacetoacetate hydrolase Mesci_4547 Mesci_0703
aacS acetoacetyl-CoA synthetase Mesci_2424 Mesci_2534
atoB acetyl-CoA C-acetyltransferase Mesci_1329 Mesci_1095
Alternative steps:
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Mesci_2249 Mesci_1303
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Mesci_2838 Mesci_2477
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Mesci_6037 Mesci_4665
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Mesci_6037 Mesci_4665
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 Mesci_0140 Mesci_3289
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 Mesci_3403 Mesci_4845
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Mesci_6037 Mesci_1071
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Mesci_6037 Mesci_4665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Mesci_1071 Mesci_6001
gcdH glutaryl-CoA dehydrogenase Mesci_1983 Mesci_4845
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB Mesci_0337
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
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 Mesci_6037 Mesci_4665
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Mesci_0108 Mesci_4665
paaH 3-hydroxyadipyl-CoA dehydrogenase Mesci_1071 Mesci_6001
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Mesci_1095 Mesci_1329
paaJ2 3-oxoadipyl-CoA thiolase Mesci_1095 Mesci_1329
paaK phenylacetate-CoA ligase Mesci_0122 Mesci_0716
paaZ1 oxepin-CoA hydrolase Mesci_6037 Mesci_4665
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Mesci_5394 Mesci_4924
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 Mesci_0043
padI phenylglyoxylate dehydrogenase, beta subunit
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Mesci_1329 Mesci_1095
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Mesci_6214 Mesci_6003
pimF 6-carboxyhex-2-enoyl-CoA hydratase Mesci_1071 Mesci_6001
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Mesci_0881 Mesci_1463
PPDCbeta phenylpyruvate decarboxylase, beta subunit Mesci_0882 Mesci_1464

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