GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudomonas simiae WCS417

Best path

livF, livG, livH, livM, livJ, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) PS417_06595 PS417_02675
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) PS417_06600 PS417_02670
livH L-phenylalanine ABC transporter, permease component 1 (LivH) PS417_06610 PS417_02660
livM L-phenylalanine ABC transporter, permease component 2 (LivM) PS417_06605 PS417_02665
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK PS417_06615 PS417_02655
PAH phenylalanine 4-monooxygenase PS417_19900
PCBD pterin-4-alpha-carbinoalamine dehydratase PS417_19905
QDPR 6,7-dihydropteridine reductase PS417_23490 PS417_23400
HPD 4-hydroxyphenylpyruvate dioxygenase PS417_14005 PS417_24445
hmgA homogentisate dioxygenase PS417_05015
maiA maleylacetoacetate isomerase PS417_05025 PS417_17970
fahA fumarylacetoacetate hydrolase PS417_05020 PS417_18185
atoA acetoacetyl-CoA transferase, A subunit PS417_10525
atoD acetoacetyl-CoA transferase, B subunit PS417_10520
atoB acetyl-CoA C-acetyltransferase PS417_10515 PS417_13855
Alternative steps:
aacS acetoacetyl-CoA synthetase PS417_12145 PS417_17010
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase PS417_19910 PS417_18690
aroP L-phenylalanine:H+ symporter AroP PS417_22235 PS417_23700
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PS417_11520 PS417_09065
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PS417_13845 PS417_13835
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PS417_13845 PS417_10680
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit PS417_26235
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 PS417_16595
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 PS417_13850 PS417_04135
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PS417_13845 PS417_07575
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PS417_13845 PS417_07575
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PS417_07575 PS417_21215
gcdH glutaryl-CoA dehydrogenase PS417_00580 PS417_17015
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
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 PS417_23400
paaF 2,3-dehydroadipyl-CoA hydratase PS417_13845 PS417_10680
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PS417_10680 PS417_13845
paaH 3-hydroxyadipyl-CoA dehydrogenase PS417_07575 PS417_21215
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PS417_06710 PS417_10515
paaJ2 3-oxoadipyl-CoA thiolase PS417_06710 PS417_10515
paaK phenylacetate-CoA ligase PS417_15170 PS417_22070
paaZ1 oxepin-CoA hydrolase PS417_13845 PS417_10680
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase PS417_17930 PS417_27745
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
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase PS417_19210 PS417_07580
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit PS417_14930
pimF 6-carboxyhex-2-enoyl-CoA hydratase PS417_07575 PS417_21215
PPDCalpha phenylpyruvate decarboxylase, alpha subunit PS417_17545
PPDCbeta phenylpyruvate decarboxylase, beta subunit PS417_17550 PS417_11770

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