GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sinorhizobium meliloti 1021

Best path

livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) SMc01948 SMc02358
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) SMc01949 SMc02357
livH L-phenylalanine ABC transporter, permease component 1 (LivH) SMc01951 SMc02359
livM L-phenylalanine ABC transporter, permease component 2 (LivM) SMc01950
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK SMc01946 SMc00078
ARO8 L-phenylalanine transaminase SMc04386 SMc01578
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A SM_b21640
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B SM_b21639
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C SM_b21638
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E SM_b21636 SMc00981
paaG 1,2-epoxyphenylacetyl-CoA isomerase SM_b21633 SMc01669
paaZ1 oxepin-CoA hydrolase SM_b21635
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase SM_b21635
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase SM_b20589 SMc03879
paaF 2,3-dehydroadipyl-CoA hydratase SMc01153 SMc01669
paaH 3-hydroxyadipyl-CoA dehydrogenase SMc02227 SMc00727
paaJ2 3-oxoadipyl-CoA thiolase SM_b20589 SMc03879
Alternative steps:
aacS acetoacetyl-CoA synthetase SMc00774 SMc02162
ARO10 phenylpyruvate decarboxylase
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase SMc03879 SMa1450
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SMc03878 SMc00268
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SMc01669 SMc01153
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SMc01153 SM_b21633
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 SMa1525 SMc02525
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 SM_b21635
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase SMa1400 SM_b21121
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SMc01153 SMc01669
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SMc01153 SMc01669
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SMc02227 SMc00727
fahA fumarylacetoacetate hydrolase SMc03207 SM_b21112
gcdH glutaryl-CoA dehydrogenase SM_b21181 SM_b21121
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase SMc03208
HPD 4-hydroxyphenylpyruvate dioxygenase SMc03211 SM_b20581
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
maiA maleylacetoacetate isomerase SMc03206 SM_b20005
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase SMc00261
pad-dh phenylacetaldehyde dehydrogenase SMa2213 SMc02689
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
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase SMc03834
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase SM_b20589 SMc03879
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase SM_b21632 SMc02227
PPDCalpha phenylpyruvate decarboxylase, alpha subunit SMc03201 SMc01030
PPDCbeta phenylpyruvate decarboxylase, beta subunit SMc03202 SMc01031
QDPR 6,7-dihydropteridine reductase SMa1191

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 Aug 02 2021. The underlying query database was built on Aug 02 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