GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Caulobacter crescentus NA1000

Best path

aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

Also see fitness data for the top candidates

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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase CCNA_01684
PCBD pterin-4-alpha-carbinoalamine dehydratase CCNA_00245
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase CCNA_02616
hmgA homogentisate dioxygenase CCNA_02615
maiA maleylacetoacetate isomerase CCNA_03683 CCNA_02569
fahA fumarylacetoacetate hydrolase CCNA_02614
atoA acetoacetyl-CoA transferase, A subunit CCNA_00206 CCNA_02488
atoD acetoacetyl-CoA transferase, B subunit CCNA_00207 CCNA_02489
atoB acetyl-CoA C-acetyltransferase CCNA_00820 CCNA_00544
Alternative steps:
aacS acetoacetyl-CoA synthetase CCNA_01017 CCNA_01382
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase CCNA_01603 CCNA_03323
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase CCNA_00545 CCNA_01885
badI 2-ketocyclohexanecarboxyl-CoA hydrolase CCNA_00006 CCNA_01794
badK cyclohex-1-ene-1-carboxyl-CoA hydratase CCNA_00006 CCNA_02658
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 CCNA_02024
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 CCNA_01412 CCNA_02254
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase CCNA_00006 CCNA_01891
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase CCNA_00006 CCNA_01794
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase CCNA_00123 CCNA_03293
gcdH glutaryl-CoA dehydrogenase CCNA_02254 CCNA_01412
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB CCNA_03280
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) CCNA_03714 CCNA_03235
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) CCNA_03714 CCNA_03235
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
paaF 2,3-dehydroadipyl-CoA hydratase CCNA_00006 CCNA_02658
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase CCNA_01927 CCNA_02658
paaH 3-hydroxyadipyl-CoA dehydrogenase CCNA_00123 CCNA_03293
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase CCNA_02490 CCNA_01168
paaJ2 3-oxoadipyl-CoA thiolase CCNA_02490 CCNA_01168
paaK phenylacetate-CoA ligase CCNA_01382 CCNA_03292
paaZ1 oxepin-CoA hydrolase CCNA_02658 CCNA_00006
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase CCNA_03243 CCNA_03695
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 CCNA_03575 CCNA_00544
pimC pimeloyl-CoA dehydrogenase, small subunit CCNA_01369 CCNA_01884
pimD pimeloyl-CoA dehydrogenase, large subunit CCNA_01368 CCNA_02215
pimF 6-carboxyhex-2-enoyl-CoA hydratase CCNA_03293 CCNA_00074
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit CCNA_01800

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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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