GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Geobacter uraniireducens Rf4

Best path

aroP, ARO8, iorA, iorB, 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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
ARO8 L-phenylalanine transaminase GURA_RS12735 GURA_RS04390
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit GURA_RS10825
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit GURA_RS10820 GURA_RS11105
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
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase GURA_RS08130 GURA_RS15480
paaZ1 oxepin-CoA hydrolase
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase GURA_RS08100 GURA_RS15490
paaF 2,3-dehydroadipyl-CoA hydratase GURA_RS15480 GURA_RS08130
paaH 3-hydroxyadipyl-CoA dehydrogenase GURA_RS08095 GURA_RS15485
paaJ2 3-oxoadipyl-CoA thiolase GURA_RS08100 GURA_RS15490
Alternative steps:
aacS acetoacetyl-CoA synthetase GURA_RS08015
ARO10 phenylpyruvate decarboxylase
atoA acetoacetyl-CoA transferase, A subunit GURA_RS22155
atoB acetyl-CoA C-acetyltransferase GURA_RS15490 GURA_RS08100
atoD acetoacetyl-CoA transferase, B subunit GURA_RS22150
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase GURA_RS09505 GURA_RS18385
badI 2-ketocyclohexanecarboxyl-CoA hydrolase GURA_RS15480
badK cyclohex-1-ene-1-carboxyl-CoA hydratase GURA_RS15480 GURA_RS08130
bamB class II benzoyl-CoA reductase, BamB subunit
bamC class II benzoyl-CoA reductase, BamC subunit
bamD class II benzoyl-CoA reductase, BamD subunit GURA_RS12275 GURA_RS06195
bamE class II benzoyl-CoA reductase, BamE subunit
bamF class II benzoyl-CoA reductase, BamF subunit GURA_RS18270
bamG class II benzoyl-CoA reductase, BamG subunit GURA_RS21560
bamH class II benzoyl-CoA reductase, BamH subunit GURA_RS21555 GURA_RS01690
bamI class II benzoyl-CoA reductase, BamI subunit GURA_RS21550 GURA_RS18545
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit GURA_RS19745 GURA_RS02480
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit GURA_RS19745
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 GURA_RS15475 GURA_RS15455
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase GURA_RS15480
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase GURA_RS15480 GURA_RS08130
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase GURA_RS08095 GURA_RS15485
fahA fumarylacetoacetate hydrolase
gcdH glutaryl-CoA dehydrogenase GURA_RS16870 GURA_RS15475
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) GURA_RS10775 GURA_RS00570
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) GURA_RS10785 GURA_RS00575
livH L-phenylalanine ABC transporter, permease component 1 (LivH) GURA_RS10795
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) GURA_RS10790
maiA maleylacetoacetate isomerase
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase GURA_RS10815 GURA_RS10770
pad-dh phenylacetaldehyde dehydrogenase GURA_RS00565 GURA_RS16875
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit GURA_RS14115 GURA_RS02430
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 GURA_RS12690
padI phenylglyoxylate dehydrogenase, beta subunit
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase
pfor phenylacetaldeyde:ferredoxin oxidoreductase GURA_RS16635 GURA_RS12315
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase GURA_RS08100 GURA_RS15490
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit GURA_RS14760 GURA_RS06460
PPDCbeta phenylpyruvate decarboxylase, beta subunit GURA_RS14755 GURA_RS06465
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