GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Pantoea rwandensis LMG 26275

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) HA51_RS18890 HA51_RS15825
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) HA51_RS18895 HA51_RS15830
livH L-phenylalanine ABC transporter, permease component 1 (LivH) HA51_RS18905 HA51_RS15840
livM L-phenylalanine ABC transporter, permease component 2 (LivM) HA51_RS18900 HA51_RS15835
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK HA51_RS18910 HA51_RS15845
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase
QDPR 6,7-dihydropteridine reductase HA51_RS20690 HA51_RS02865
HPD 4-hydroxyphenylpyruvate dioxygenase
hmgA homogentisate dioxygenase
maiA maleylacetoacetate isomerase HA51_RS12325
fahA fumarylacetoacetate hydrolase HA51_RS22395
atoA acetoacetyl-CoA transferase, A subunit HA51_RS19820
atoD acetoacetyl-CoA transferase, B subunit HA51_RS19815
atoB acetyl-CoA C-acetyltransferase HA51_RS19810 HA51_RS26555
Alternative steps:
aacS acetoacetyl-CoA synthetase HA51_RS10660
ARO10 phenylpyruvate decarboxylase HA51_RS10875
ARO8 L-phenylalanine transaminase HA51_RS11850 HA51_RS18705
aroP L-phenylalanine:H+ symporter AroP HA51_RS07520 HA51_RS17310
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HA51_RS14510 HA51_RS03820
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HA51_RS05000
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HA51_RS04965 HA51_RS11045
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 HA51_RS11290
bamH class II benzoyl-CoA reductase, BamH subunit HA51_RS11295
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
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HA51_RS08785
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HA51_RS26560 HA51_RS11045
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HA51_RS26560 HA51_RS11045
gcdH glutaryl-CoA dehydrogenase
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
paaF 2,3-dehydroadipyl-CoA hydratase HA51_RS04965 HA51_RS26560
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HA51_RS05000
paaH 3-hydroxyadipyl-CoA dehydrogenase HA51_RS26560 HA51_RS11045
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase HA51_RS19810 HA51_RS26555
paaJ2 3-oxoadipyl-CoA thiolase HA51_RS19810 HA51_RS26555
paaK phenylacetate-CoA ligase HA51_RS10660
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase HA51_RS01965 HA51_RS23475
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 HA51_RS26555 HA51_RS19810
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase HA51_RS26560 HA51_RS11045
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 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