GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sphingobium czechense LL01

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 (42 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase V473_RS00280
PCBD pterin-4-alpha-carbinoalamine dehydratase V473_RS11445
QDPR 6,7-dihydropteridine reductase V473_RS19685
HPD 4-hydroxyphenylpyruvate dioxygenase V473_RS00275 V473_RS17905
hmgA homogentisate dioxygenase V473_RS00270
maiA maleylacetoacetate isomerase V473_RS00260
fahA fumarylacetoacetate hydrolase V473_RS00265 V473_RS15945
atoA acetoacetyl-CoA transferase, A subunit V473_RS02865 V473_RS08605
atoD acetoacetyl-CoA transferase, B subunit V473_RS00560 V473_RS08315
atoB acetyl-CoA C-acetyltransferase V473_RS07145 V473_RS00635
Alternative steps:
aacS acetoacetyl-CoA synthetase V473_RS14610 V473_RS18475
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase V473_RS02585 V473_RS13990
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase V473_RS12220 V473_RS21655
badI 2-ketocyclohexanecarboxyl-CoA hydrolase V473_RS18555 V473_RS14620
badK cyclohex-1-ene-1-carboxyl-CoA hydratase V473_RS04380 V473_RS05770
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 V473_RS12790
bamH class II benzoyl-CoA reductase, BamH subunit V473_RS07745 V473_RS12785
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 V473_RS08390
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase V473_RS17395 V473_RS04405
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase V473_RS04380 V473_RS18630
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase V473_RS04380 V473_RS05770
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase V473_RS00615 V473_RS18225
gcdH glutaryl-CoA dehydrogenase V473_RS17395 V473_RS17555
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB V473_RS08130
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) V473_RS04120 V473_RS13485
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) V473_RS04115 V473_RS13485
livH L-phenylalanine ABC transporter, permease component 1 (LivH) V473_RS04105
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 V473_RS04380
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 V473_RS05770 V473_RS04380
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase V473_RS18515 V473_RS18080
paaH 3-hydroxyadipyl-CoA dehydrogenase V473_RS00615 V473_RS18225
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase V473_RS08300 V473_RS07145
paaJ2 3-oxoadipyl-CoA thiolase V473_RS08300 V473_RS07145
paaK phenylacetate-CoA ligase V473_RS18160 V473_RS05200
paaZ1 oxepin-CoA hydrolase V473_RS08215 V473_RS05770
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase V473_RS05540 V473_RS05490
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 V473_RS05590 V473_RS08600
pimC pimeloyl-CoA dehydrogenase, small subunit V473_RS05640 V473_RS08240
pimD pimeloyl-CoA dehydrogenase, large subunit V473_RS05635 V473_RS18115
pimF 6-carboxyhex-2-enoyl-CoA hydratase V473_RS18200 V473_RS00615
PPDCalpha phenylpyruvate decarboxylase, alpha subunit V473_RS07890
PPDCbeta phenylpyruvate decarboxylase, beta subunit V473_RS07885 V473_RS09775

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