GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Methylibium petroleiphilum PM1

Best path

livF, livG, livH, livM, livJ, ARO8, ARO10, pfor, 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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) MPE_RS05645 MPE_RS22245
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) MPE_RS05640 MPE_RS18955
livH L-phenylalanine ABC transporter, permease component 1 (LivH) MPE_RS05630 MPE_RS18565
livM L-phenylalanine ABC transporter, permease component 2 (LivM) MPE_RS05635
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK MPE_RS09770
ARO8 L-phenylalanine transaminase MPE_RS18605 MPE_RS11575
ARO10 phenylpyruvate decarboxylase
pfor phenylacetaldeyde:ferredoxin oxidoreductase MPE_RS13010
paaK phenylacetate-CoA ligase MPE_RS04925 MPE_RS22130
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A MPE_RS04930
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B MPE_RS04935
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C MPE_RS04940
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E MPE_RS04950
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase MPE_RS04915 MPE_RS04455
paaZ1 oxepin-CoA hydrolase MPE_RS09815 MPE_RS04915
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase MPE_RS04385 MPE_RS07750
paaF 2,3-dehydroadipyl-CoA hydratase MPE_RS03005 MPE_RS02065
paaH 3-hydroxyadipyl-CoA dehydrogenase MPE_RS02080 MPE_RS22170
paaJ2 3-oxoadipyl-CoA thiolase MPE_RS04385 MPE_RS09410
Alternative steps:
aacS acetoacetyl-CoA synthetase MPE_RS01745 MPE_RS04460
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit MPE_RS07345
atoB acetyl-CoA C-acetyltransferase MPE_RS09410 MPE_RS07750
atoD acetoacetyl-CoA transferase, B subunit MPE_RS07350
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase MPE_RS06685 MPE_RS03210
badI 2-ketocyclohexanecarboxyl-CoA hydrolase MPE_RS03005
badK cyclohex-1-ene-1-carboxyl-CoA hydratase MPE_RS03005 MPE_RS04915
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 MPE_RS18740 MPE_RS07105
bamI class II benzoyl-CoA reductase, BamI subunit MPE_RS01710
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 MPE_RS16960 MPE_RS09835
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase MPE_RS04395 MPE_RS04915
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase MPE_RS03005 MPE_RS08935
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase MPE_RS02080 MPE_RS22170
fahA fumarylacetoacetate hydrolase MPE_RS18355 MPE_RS01695
gcdH glutaryl-CoA dehydrogenase MPE_RS16000 MPE_RS16960
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase MPE_RS04370
HPD 4-hydroxyphenylpyruvate dioxygenase MPE_RS01755
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB MPE_RS17710
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit MPE_RS17710
maiA maleylacetoacetate isomerase MPE_RS09425 MPE_RS04250
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
pad-dh phenylacetaldehyde dehydrogenase MPE_RS09615 MPE_RS03015
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit MPE_RS04285 MPE_RS05880
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 MPE_RS01760
PCBD pterin-4-alpha-carbinoalamine dehydratase MPE_RS14695 MPE_RS15325
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase MPE_RS08940 MPE_RS02075
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase MPE_RS08935
PPDCalpha phenylpyruvate decarboxylase, alpha subunit MPE_RS08080
PPDCbeta phenylpyruvate decarboxylase, beta subunit MPE_RS08075
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