GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudomonas fluorescens FW300-N2C3

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) AO356_05340 AO356_08480
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) AO356_05335 AO356_08485
livH L-phenylalanine ABC transporter, permease component 1 (LivH) AO356_05325 AO356_08495
livM L-phenylalanine ABC transporter, permease component 2 (LivM) AO356_05330 AO356_08490
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK AO356_05320 AO356_08500
PAH phenylalanine 4-monooxygenase AO356_03975
PCBD pterin-4-alpha-carbinoalamine dehydratase AO356_03980
QDPR 6,7-dihydropteridine reductase AO356_16745 AO356_16950
HPD 4-hydroxyphenylpyruvate dioxygenase AO356_22845 AO356_15580
hmgA homogentisate dioxygenase AO356_16825
maiA maleylacetoacetate isomerase AO356_16835 AO356_11540
fahA fumarylacetoacetate hydrolase AO356_16830 AO356_29105
atoA acetoacetyl-CoA transferase, A subunit AO356_21650
atoD acetoacetyl-CoA transferase, B subunit AO356_21645
atoB acetyl-CoA C-acetyltransferase AO356_21640 AO356_26350
Alternative steps:
aacS acetoacetyl-CoA synthetase AO356_00425 AO356_01575
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase AO356_03985 AO356_25355
aroP L-phenylalanine:H+ symporter AroP AO356_18530 AO356_17670
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AO356_25515 AO356_27985
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AO356_30355 AO356_26360
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AO356_26360 AO356_30355
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit AO356_13910
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 AO356_24165 AO356_22050
bamI class II benzoyl-CoA reductase, BamI subunit AO356_24170
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 AO356_26355 AO356_17045
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AO356_26360 AO356_30295
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AO356_26360 AO356_02330
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AO356_02330 AO356_29995
gcdH glutaryl-CoA dehydrogenase AO356_10850 AO356_01580
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase AO356_14000
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 AO356_16950
paaF 2,3-dehydroadipyl-CoA hydratase AO356_26360 AO356_30355
paaG 1,2-epoxyphenylacetyl-CoA isomerase AO356_30355 AO356_26360
paaH 3-hydroxyadipyl-CoA dehydrogenase AO356_02330 AO356_29995
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AO356_04930 AO356_21640
paaJ2 3-oxoadipyl-CoA thiolase AO356_04930 AO356_21640
paaK phenylacetate-CoA ligase AO356_05105 AO356_05100
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase AO356_28710 AO356_28685
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 AO356_03560 AO356_04930
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase AO356_30295 AO356_02330
PPDCalpha phenylpyruvate decarboxylase, alpha subunit AO356_22990 AO356_24880
PPDCbeta phenylpyruvate decarboxylase, beta subunit AO356_22985 AO356_24885

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