GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sphingomonas indica Dd16

Best path

aroP, ARO8, iorAB, 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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
ARO8 L-phenylalanine transaminase B9N75_RS08135 B9N75_RS12985
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A B9N75_RS12940
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B B9N75_RS14135
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C B9N75_RS12930
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E B9N75_RS12920
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase B9N75_RS12955 B9N75_RS06800
paaZ1 oxepin-CoA hydrolase B9N75_RS12960 B9N75_RS12955
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase B9N75_RS12960 B9N75_RS03395
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase B9N75_RS12945 B9N75_RS12685
paaF 2,3-dehydroadipyl-CoA hydratase B9N75_RS13460 B9N75_RS12955
paaH 3-hydroxyadipyl-CoA dehydrogenase B9N75_RS08655 B9N75_RS11255
paaJ2 3-oxoadipyl-CoA thiolase B9N75_RS12945 B9N75_RS12685
Alternative steps:
aacS acetoacetyl-CoA synthetase B9N75_RS06405 B9N75_RS03355
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit B9N75_RS11125
atoB acetyl-CoA C-acetyltransferase B9N75_RS12685 B9N75_RS02915
atoD acetoacetyl-CoA transferase, B subunit B9N75_RS11140
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase B9N75_RS08485 B9N75_RS10580
badI 2-ketocyclohexanecarboxyl-CoA hydrolase B9N75_RS13460 B9N75_RS12955
badK cyclohex-1-ene-1-carboxyl-CoA hydratase B9N75_RS13460 B9N75_RS12955
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 B9N75_RS11655
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 B9N75_RS12960
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase B9N75_RS13445 B9N75_RS08665
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase B9N75_RS11255 B9N75_RS13460
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase B9N75_RS13460 B9N75_RS11255
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase B9N75_RS08655 B9N75_RS11255
fahA fumarylacetoacetate hydrolase B9N75_RS13430
gcdH glutaryl-CoA dehydrogenase B9N75_RS12195 B9N75_RS13160
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase B9N75_RS01885
HPD 4-hydroxyphenylpyruvate dioxygenase B9N75_RS11495
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) B9N75_RS06875 B9N75_RS12805
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) B9N75_RS06875 B9N75_RS06650
livH L-phenylalanine ABC transporter, permease component 1 (LivH)
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM)
maiA maleylacetoacetate isomerase B9N75_RS06210
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase B9N75_RS08475
paaK phenylacetate-CoA ligase
pad-dh phenylacetaldehyde dehydrogenase B9N75_RS04360 B9N75_RS13435
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 B9N75_RS05675
PCBD pterin-4-alpha-carbinoalamine dehydratase B9N75_RS08785
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase B9N75_RS04110 B9N75_RS12945
pimC pimeloyl-CoA dehydrogenase, small subunit B9N75_RS11320
pimD pimeloyl-CoA dehydrogenase, large subunit B9N75_RS11315
pimF 6-carboxyhex-2-enoyl-CoA hydratase B9N75_RS11255
PPDCalpha phenylpyruvate decarboxylase, alpha subunit B9N75_RS09025
PPDCbeta phenylpyruvate decarboxylase, beta subunit B9N75_RS09030 B9N75_RS12980
QDPR 6,7-dihydropteridine reductase

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 24 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