GapMind for catabolism of small carbon sources


L-phenylalanine catabolism in Pseudomonas fluorescens FW300-N1B4

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


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) Pf1N1B4_3214 Pf1N1B4_1378
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Pf1N1B4_3215 Pf1N1B4_1379
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Pf1N1B4_3217 Pf1N1B4_1381
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Pf1N1B4_3216 Pf1N1B4_1380
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Pf1N1B4_3218 Pf1N1B4_1382
PAH phenylalanine 4-monooxygenase Pf1N1B4_3566
PCBD pterin-4-alpha-carbinoalamine dehydratase Pf1N1B4_3565
QDPR 6,7-dihydropteridine reductase Pf1N1B4_1040 Pf1N1B4_925
HPD 4-hydroxyphenylpyruvate dioxygenase Pf1N1B4_5003 Pf1N1B4_2747
hmgA homogentisate dioxygenase Pf1N1B4_1025
maiA maleylacetoacetate isomerase Pf1N1B4_1023 Pf1N1B4_1955
fahA fumarylacetoacetate hydrolase Pf1N1B4_1024
atoA acetoacetyl-CoA transferase, A subunit Pf1N1B4_5833
atoD acetoacetyl-CoA transferase, B subunit Pf1N1B4_5834
atoB acetyl-CoA C-acetyltransferase Pf1N1B4_4786 Pf1N1B4_5835
Alternative steps:
aacS acetoacetyl-CoA synthetase Pf1N1B4_5634 Pf1N1B4_3988
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase Pf1N1B4_3564 Pf1N1B4_5070
aroP L-phenylalanine:H+ symporter AroP Pf1N1B4_3559 Pf1N1B4_801
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Pf1N1B4_5039 Pf1N1B4_512
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Pf1N1B4_4788 Pf1N1B4_5593
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_679
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit Pf1N1B4_2440
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 Pf1N1B4_2989 Pf1N1B4_4037
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 Pf1N1B4_966 Pf1N1B4_4787
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_3903
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Pf1N1B4_4788 Pf1N1B4_3903
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
gcdH glutaryl-CoA dehydrogenase Pf1N1B4_1816 Pf1N1B4_3987
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 Pf1N1B4_925
paaF 2,3-dehydroadipyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_4777
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Pf1N1B4_4788 Pf1N1B4_679
paaH 3-hydroxyadipyl-CoA dehydrogenase Pf1N1B4_3903 Pf1N1B4_5134
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Pf1N1B4_3234 Pf1N1B4_5835
paaJ2 3-oxoadipyl-CoA thiolase Pf1N1B4_3234 Pf1N1B4_5835
paaK phenylacetate-CoA ligase Pf1N1B4_575 Pf1N1B4_572
paaZ1 oxepin-CoA hydrolase Pf1N1B4_4788 Pf1N1B4_679
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase Pf1N1B4_171 Pf1N1B4_2132
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 Pf1N1B4_371 Pf1N1B4_3234
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit Pf1N1B4_5610 Pf1N1B4_966
pimF 6-carboxyhex-2-enoyl-CoA hydratase Pf1N1B4_3903 Pf1N1B4_1787
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Pf1N1B4_1020 Pf1N1B4_4480
PPDCbeta phenylpyruvate decarboxylase, beta subunit Pf1N1B4_1019 Pf1N1B4_4479

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 (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