GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Rhizorhabdus wittichii RW1

Best path

aroP, ARO8, ARO10, pad-dh, 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
aroP L-phenylalanine:H+ symporter AroP SWIT_RS03485
ARO8 L-phenylalanine transaminase SWIT_RS17960 SWIT_RS23660
ARO10 phenylpyruvate decarboxylase
pad-dh phenylacetaldehyde dehydrogenase SWIT_RS16360 SWIT_RS03735
paaK phenylacetate-CoA ligase SWIT_RS07330 SWIT_RS21155
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A SWIT_RS03840
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B SWIT_RS03845
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C SWIT_RS03850
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E SWIT_RS03860
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase SWIT_RS03820 SWIT_RS10100
paaZ1 oxepin-CoA hydrolase SWIT_RS03815 SWIT_RS18205
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase SWIT_RS03815
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase SWIT_RS03835 SWIT_RS26185
paaF 2,3-dehydroadipyl-CoA hydratase SWIT_RS03865 SWIT_RS03300
paaH 3-hydroxyadipyl-CoA dehydrogenase SWIT_RS03825 SWIT_RS14665
paaJ2 3-oxoadipyl-CoA thiolase SWIT_RS26185 SWIT_RS03835
Alternative steps:
aacS acetoacetyl-CoA synthetase SWIT_RS07325 SWIT_RS22105
atoA acetoacetyl-CoA transferase, A subunit SWIT_RS04890 SWIT_RS26985
atoB acetyl-CoA C-acetyltransferase SWIT_RS03220 SWIT_RS10105
atoD acetoacetyl-CoA transferase, B subunit SWIT_RS26190 SWIT_RS04885
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SWIT_RS10635 SWIT_RS16780
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SWIT_RS09250 SWIT_RS05165
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SWIT_RS03300 SWIT_RS09105
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 SWIT_RS07470
bamH class II benzoyl-CoA reductase, BamH subunit SWIT_RS07465 SWIT_RS15110
bamI class II benzoyl-CoA reductase, BamI subunit SWIT_RS07460
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 SWIT_RS03815
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase SWIT_RS03310 SWIT_RS08910
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SWIT_RS27240 SWIT_RS09625
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SWIT_RS09105 SWIT_RS03300
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SWIT_RS14665 SWIT_RS10110
fahA fumarylacetoacetate hydrolase SWIT_RS19525 SWIT_RS08515
gcdH glutaryl-CoA dehydrogenase SWIT_RS04185 SWIT_RS21415
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase SWIT_RS19530 SWIT_RS07895
HPD 4-hydroxyphenylpyruvate dioxygenase SWIT_RS19535
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB SWIT_RS05980 SWIT_RS15320
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) SWIT_RS14705 SWIT_RS04010
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) SWIT_RS14705 SWIT_RS13320
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)
maiA maleylacetoacetate isomerase SWIT_RS27930 SWIT_RS15455
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
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
PCBD pterin-4-alpha-carbinoalamine dehydratase SWIT_RS07175
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase SWIT_RS18385 SWIT_RS01725
pimC pimeloyl-CoA dehydrogenase, small subunit SWIT_RS01590 SWIT_RS01875
pimD pimeloyl-CoA dehydrogenase, large subunit SWIT_RS01585 SWIT_RS01880
pimF 6-carboxyhex-2-enoyl-CoA hydratase SWIT_RS01610 SWIT_RS04215
PPDCalpha phenylpyruvate decarboxylase, alpha subunit SWIT_RS10830 SWIT_RS03985
PPDCbeta phenylpyruvate decarboxylase, beta subunit SWIT_RS03980 SWIT_RS10825
QDPR 6,7-dihydropteridine reductase SWIT_RS16025 SWIT_RS07255

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 Apr 09 2024. 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