GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP AU252_RS05225 AU252_RS18980
ARO8 L-phenylalanine transaminase AU252_RS16745 AU252_RS10910
PPDCalpha phenylpyruvate decarboxylase, alpha subunit AU252_RS15590 AU252_RS03450
PPDCbeta phenylpyruvate decarboxylase, beta subunit AU252_RS15595 AU252_RS03445
pad-dh phenylacetaldehyde dehydrogenase AU252_RS01160 AU252_RS01555
paaK phenylacetate-CoA ligase AU252_RS15070 AU252_RS01265
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A AU252_RS15420
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B AU252_RS15425
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C AU252_RS15430
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E AU252_RS15440
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase AU252_RS07800 AU252_RS00885
paaZ1 oxepin-CoA hydrolase AU252_RS15050 AU252_RS00745
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase AU252_RS15050
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase AU252_RS15005 AU252_RS00310
paaF 2,3-dehydroadipyl-CoA hydratase AU252_RS07800 AU252_RS00745
paaH 3-hydroxyadipyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
paaJ2 3-oxoadipyl-CoA thiolase AU252_RS15005 AU252_RS00310
Alternative steps:
aacS acetoacetyl-CoA synthetase AU252_RS01520 AU252_RS16370
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit AU252_RS03415 AU252_RS07725
atoB acetyl-CoA C-acetyltransferase AU252_RS00950 AU252_RS16800
atoD acetoacetyl-CoA transferase, B subunit AU252_RS07730 AU252_RS03410
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase AU252_RS12495 AU252_RS01630
badI 2-ketocyclohexanecarboxyl-CoA hydrolase AU252_RS14925 AU252_RS07800
badK cyclohex-1-ene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
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 AU252_RS15050
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase AU252_RS01515 AU252_RS00840
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase AU252_RS07800 AU252_RS00745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase AU252_RS07800 AU252_RS00745
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase AU252_RS02130 AU252_RS07090
fahA fumarylacetoacetate hydrolase AU252_RS19175
gcdH glutaryl-CoA dehydrogenase AU252_RS16430 AU252_RS00305
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) AU252_RS04340 AU252_RS01290
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) AU252_RS04335 AU252_RS00660
livH L-phenylalanine ABC transporter, permease component 1 (LivH) AU252_RS01305 AU252_RS00670
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) AU252_RS04330
maiA maleylacetoacetate isomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
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 AU252_RS17880
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase AU252_RS15005 AU252_RS00785
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit AU252_RS00805
pimF 6-carboxyhex-2-enoyl-CoA hydratase
QDPR 6,7-dihydropteridine reductase AU252_RS06790

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