GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Mucilaginibacter mallensis MP1X4

Best path

aroP, 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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase BLU33_RS04185
PCBD pterin-4-alpha-carbinoalamine dehydratase
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase BLU33_RS04115
hmgA homogentisate dioxygenase BLU33_RS04120
maiA maleylacetoacetate isomerase
fahA fumarylacetoacetate hydrolase
atoA acetoacetyl-CoA transferase, A subunit BLU33_RS08095
atoD acetoacetyl-CoA transferase, B subunit BLU33_RS08100
atoB acetyl-CoA C-acetyltransferase BLU33_RS09250 BLU33_RS24945
Alternative steps:
aacS acetoacetyl-CoA synthetase
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase BLU33_RS14885 BLU33_RS20880
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BLU33_RS06255 BLU33_RS09730
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BLU33_RS22635
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BLU33_RS22635
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit BLU33_RS03415
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 BLU33_RS01435
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 BLU33_RS24850 BLU33_RS17775
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BLU33_RS22635
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BLU33_RS22635
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BLU33_RS00005 BLU33_RS11455
gcdH glutaryl-CoA dehydrogenase BLU33_RS08585 BLU33_RS24850
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
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) BLU33_RS23120 BLU33_RS15970
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) BLU33_RS23120 BLU33_RS19505
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)
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 BLU33_RS17665 BLU33_RS18820
paaF 2,3-dehydroadipyl-CoA hydratase BLU33_RS22635
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase BLU33_RS22635
paaH 3-hydroxyadipyl-CoA dehydrogenase BLU33_RS00005 BLU33_RS11455
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BLU33_RS24945 BLU33_RS09250
paaJ2 3-oxoadipyl-CoA thiolase BLU33_RS24945 BLU33_RS09250
paaK phenylacetate-CoA ligase
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase BLU33_RS06915 BLU33_RS10385
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 BLU33_RS24945 BLU33_RS09250
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit BLU33_RS24660
PPDCbeta phenylpyruvate decarboxylase, beta subunit BLU33_RS24660 BLU33_RS18750

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