GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Herbaspirillum aquaticum IEH 4430

Best path

livF, livG, livH, livM, livJ, 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 (47 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) CEJ45_RS22555 CEJ45_RS04965
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) CEJ45_RS22550 CEJ45_RS04960
livH L-phenylalanine ABC transporter, permease component 1 (LivH) CEJ45_RS11220 CEJ45_RS04950
livM L-phenylalanine ABC transporter, permease component 2 (LivM) CEJ45_RS04955 CEJ45_RS05575
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK CEJ45_RS04945 CEJ45_RS12295
ARO8 L-phenylalanine transaminase CEJ45_RS11070 CEJ45_RS21015
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB CEJ45_RS10405 CEJ45_RS06400
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A CEJ45_RS20075
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B CEJ45_RS20070
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C CEJ45_RS20065
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E CEJ45_RS20055
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CEJ45_RS20050 CEJ45_RS14465
paaZ1 oxepin-CoA hydrolase CEJ45_RS20095 CEJ45_RS11490
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase CEJ45_RS20095
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase CEJ45_RS20030 CEJ45_RS16030
paaF 2,3-dehydroadipyl-CoA hydratase CEJ45_RS16530 CEJ45_RS06410
paaH 3-hydroxyadipyl-CoA dehydrogenase CEJ45_RS14455 CEJ45_RS11470
paaJ2 3-oxoadipyl-CoA thiolase CEJ45_RS20030 CEJ45_RS16030
Alternative steps:
aacS acetoacetyl-CoA synthetase CEJ45_RS14175
ARO10 phenylpyruvate decarboxylase
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit CEJ45_RS12845 CEJ45_RS16020
atoB acetyl-CoA C-acetyltransferase CEJ45_RS14415 CEJ45_RS09425
atoD acetoacetyl-CoA transferase, B subunit CEJ45_RS12850 CEJ45_RS16025
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CEJ45_RS11695 CEJ45_RS09675
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CEJ45_RS16530 CEJ45_RS00250
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CEJ45_RS16530 CEJ45_RS20050
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 CEJ45_RS23980
bamH class II benzoyl-CoA reductase, BamH subunit CEJ45_RS23985 CEJ45_RS05500
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 CEJ45_RS20095
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase CEJ45_RS06405 CEJ45_RS12595
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CEJ45_RS06410 CEJ45_RS16530
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CEJ45_RS16530 CEJ45_RS06410
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CEJ45_RS14455 CEJ45_RS11470
fahA fumarylacetoacetate hydrolase CEJ45_RS11650 CEJ45_RS12230
gcdH glutaryl-CoA dehydrogenase CEJ45_RS11500 CEJ45_RS12595
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase CEJ45_RS11655
HPD 4-hydroxyphenylpyruvate dioxygenase CEJ45_RS05000 CEJ45_RS13640
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit CEJ45_RS06400
maiA maleylacetoacetate isomerase CEJ45_RS11645 CEJ45_RS20325
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase CEJ45_RS20035 CEJ45_RS14175
pad-dh phenylacetaldehyde dehydrogenase CEJ45_RS01220 CEJ45_RS06185
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 CEJ45_RS10410
PCBD pterin-4-alpha-carbinoalamine dehydratase CEJ45_RS15375
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase CEJ45_RS11475 CEJ45_RS14460
pimC pimeloyl-CoA dehydrogenase, small subunit CEJ45_RS11485
pimD pimeloyl-CoA dehydrogenase, large subunit CEJ45_RS11480 CEJ45_RS01415
pimF 6-carboxyhex-2-enoyl-CoA hydratase CEJ45_RS11470
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit
QDPR 6,7-dihydropteridine reductase CEJ45_RS13655 CEJ45_RS06640

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.

Links

Downloads

Related tools

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