GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Stutzerimonas stutzeri A1501

Best path

livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) PST_RS14970 PST_RS02165
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) PST_RS14965 PST_RS16095
livH L-phenylalanine ABC transporter, permease component 1 (LivH) PST_RS14955 PST_RS16080
livM L-phenylalanine ABC transporter, permease component 2 (LivM) PST_RS14960 PST_RS16075
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK PST_RS14950
PAH phenylalanine 4-monooxygenase PST_RS17755
PCBD pterin-4-alpha-carbinoalamine dehydratase PST_RS17760
QDPR 6,7-dihydropteridine reductase PST_RS05785 PST_RS15650
HPD 4-hydroxyphenylpyruvate dioxygenase PST_RS04445 PST_RS01035
hmgA homogentisate dioxygenase PST_RS04450
maiA maleylacetoacetate isomerase PST_RS04460 PST_RS12720
fahA fumarylacetoacetate hydrolase PST_RS04455
atoA acetoacetyl-CoA transferase, A subunit PST_RS16145
atoD acetoacetyl-CoA transferase, B subunit PST_RS16150
atoB acetyl-CoA C-acetyltransferase PST_RS03530 PST_RS16155
Alternative steps:
aacS acetoacetyl-CoA synthetase PST_RS16110 PST_RS14850
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase PST_RS17765 PST_RS15035
aroP L-phenylalanine:H+ symporter AroP PST_RS13100
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase PST_RS10135 PST_RS03535
badI 2-ketocyclohexanecarboxyl-CoA hydrolase PST_RS09740
badK cyclohex-1-ene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS03120
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
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 PST_RS16120 PST_RS09700
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase PST_RS09740 PST_RS06175
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase PST_RS09740 PST_RS06175
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase PST_RS08735 PST_RS00510
gcdH glutaryl-CoA dehydrogenase PST_RS02285 PST_RS09725
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase PST_RS04505
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB PST_RS04430
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 PST_RS09740 PST_RS06175
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase PST_RS03120 PST_RS09740
paaH 3-hydroxyadipyl-CoA dehydrogenase PST_RS08735 PST_RS00510
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase PST_RS06390 PST_RS16155
paaJ2 3-oxoadipyl-CoA thiolase PST_RS06390 PST_RS16155
paaK phenylacetate-CoA ligase PST_RS14845 PST_RS00545
paaZ1 oxepin-CoA hydrolase PST_RS08835 PST_RS03120
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase PST_RS08835
pad-dh phenylacetaldehyde dehydrogenase PST_RS00240 PST_RS08835
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit PST_RS18400
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 PST_RS12565 PST_RS06390
pimC pimeloyl-CoA dehydrogenase, small subunit PST_RS00520
pimD pimeloyl-CoA dehydrogenase, large subunit PST_RS00515 PST_RS08590
pimF 6-carboxyhex-2-enoyl-CoA hydratase PST_RS00510 PST_RS08735
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit

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 Apr 09 2024. 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