GapMind for catabolism of small carbon sources


L-phenylalanine catabolism in Herbaspirillum seropedicae SmR1

Best path

livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Also see fitness data for the top candidates


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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) HSERO_RS05975 HSERO_RS00900
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) HSERO_RS05970 HSERO_RS00895
livH L-phenylalanine ABC transporter, permease component 1 (LivH) HSERO_RS05960 HSERO_RS00885
livM L-phenylalanine ABC transporter, permease component 2 (LivM) HSERO_RS08280 HSERO_RS05965
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK HSERO_RS08270 HSERO_RS17350
ARO8 L-phenylalanine transaminase HSERO_RS22025 HSERO_RS15835
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB HSERO_RS21380 HSERO_RS12755
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A HSERO_RS20610
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B HSERO_RS20615
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C HSERO_RS20620
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E HSERO_RS20630
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase HSERO_RS20640 HSERO_RS01270
paaZ1 oxepin-CoA hydrolase HSERO_RS20590 HSERO_RS20640
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase HSERO_RS20590 HSERO_RS20635
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase HSERO_RS20660 HSERO_RS19990
paaF 2,3-dehydroadipyl-CoA hydratase HSERO_RS19405 HSERO_RS20665
paaH 3-hydroxyadipyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS20645
paaJ2 3-oxoadipyl-CoA thiolase HSERO_RS20660 HSERO_RS19990
Alternative steps:
aacS acetoacetyl-CoA synthetase
ARO10 phenylpyruvate decarboxylase
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit HSERO_RS23190 HSERO_RS20000
atoB acetyl-CoA C-acetyltransferase HSERO_RS01180 HSERO_RS04635
atoD acetoacetyl-CoA transferase, B subunit HSERO_RS23185 HSERO_RS19995
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase HSERO_RS05565 HSERO_RS02535
badI 2-ketocyclohexanecarboxyl-CoA hydrolase HSERO_RS19405 HSERO_RS18840
badK cyclohex-1-ene-1-carboxyl-CoA hydratase HSERO_RS19405 HSERO_RS20665
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 HSERO_RS07420
bamH class II benzoyl-CoA reductase, BamH subunit HSERO_RS07425 HSERO_RS08845
bamI class II benzoyl-CoA reductase, BamI subunit HSERO_RS08850
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 HSERO_RS20590
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase HSERO_RS04640 HSERO_RS12750
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase HSERO_RS19405 HSERO_RS12745
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase HSERO_RS19405 HSERO_RS20665
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase HSERO_RS01260 HSERO_RS04630
fahA fumarylacetoacetate hydrolase HSERO_RS05610 HSERO_RS05065
gcdH glutaryl-CoA dehydrogenase HSERO_RS23440 HSERO_RS04640
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase HSERO_RS05605
HPD 4-hydroxyphenylpyruvate dioxygenase HSERO_RS08335 HSERO_RS18800
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit HSERO_RS12755 HSERO_RS21380
maiA maleylacetoacetate isomerase HSERO_RS05615 HSERO_RS20230
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase HSERO_RS20655 HSERO_RS19285
pad-dh phenylacetaldehyde dehydrogenase HSERO_RS17620 HSERO_RS19755
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 HSERO_RS21390
PCBD pterin-4-alpha-carbinoalamine dehydratase HSERO_RS07200
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase HSERO_RS01265 HSERO_RS01180
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit HSERO_RS14055
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit
PPDCbeta phenylpyruvate decarboxylase, beta subunit
QDPR 6,7-dihydropteridine reductase HSERO_RS18815 HSERO_RS12535

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 (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