GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Klebsiella michiganensis M5al

Best path

livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

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 (45 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) BWI76_RS26330 BWI76_RS07265
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) BWI76_RS26335 BWI76_RS07270
livH L-phenylalanine ABC transporter, permease component 1 (LivH) BWI76_RS26345 BWI76_RS07280
livM L-phenylalanine ABC transporter, permease component 2 (LivM) BWI76_RS26340 BWI76_RS07275
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK BWI76_RS26365 BWI76_RS26350
ARO8 L-phenylalanine transaminase BWI76_RS09870 BWI76_RS01925
ARO10 phenylpyruvate decarboxylase BWI76_RS20520
pad-dh phenylacetaldehyde dehydrogenase BWI76_RS12820 BWI76_RS07615
paaK phenylacetate-CoA ligase BWI76_RS13140 BWI76_RS17800
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A BWI76_RS13090
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B BWI76_RS13095
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C BWI76_RS13100
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E BWI76_RS13110
paaG 1,2-epoxyphenylacetyl-CoA isomerase BWI76_RS13120 BWI76_RS13115
paaZ1 oxepin-CoA hydrolase BWI76_RS13085
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase BWI76_RS13085
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase BWI76_RS13135 BWI76_RS16135
paaF 2,3-dehydroadipyl-CoA hydratase BWI76_RS13115 BWI76_RS13120
paaH 3-hydroxyadipyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
paaJ2 3-oxoadipyl-CoA thiolase BWI76_RS16135 BWI76_RS13135
Alternative steps:
aacS acetoacetyl-CoA synthetase BWI76_RS17800 BWI76_RS23695
aroP L-phenylalanine:H+ symporter AroP BWI76_RS04870 BWI76_RS07360
atoA acetoacetyl-CoA transferase, A subunit BWI76_RS16145
atoB acetyl-CoA C-acetyltransferase BWI76_RS23445 BWI76_RS01360
atoD acetoacetyl-CoA transferase, B subunit BWI76_RS16140
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase BWI76_RS11090 BWI76_RS23705
badI 2-ketocyclohexanecarboxyl-CoA hydrolase BWI76_RS20065
badK cyclohex-1-ene-1-carboxyl-CoA hydratase BWI76_RS13115 BWI76_RS13120
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 BWI76_RS20170
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit BWI76_RS03740
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit BWI76_RS03740
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 BWI76_RS13085
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase BWI76_RS13115
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase BWI76_RS13115 BWI76_RS20455
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase BWI76_RS01365 BWI76_RS20455
fahA fumarylacetoacetate hydrolase BWI76_RS03870
gcdH glutaryl-CoA dehydrogenase
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase BWI76_RS16945
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
maiA maleylacetoacetate isomerase BWI76_RS19575 BWI76_RS25335
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase BWI76_RS20065
padB phenylacetyl-CoA dehydrogenase, PadB subunit
padC phenylacetyl-CoA dehydrogenase, PadC subunit BWI76_RS09685 BWI76_RS15930
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
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase BWI76_RS13135 BWI76_RS16135
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase BWI76_RS01365 BWI76_RS20455
PPDCalpha phenylpyruvate decarboxylase, alpha subunit BWI76_RS14160
PPDCbeta phenylpyruvate decarboxylase, beta subunit BWI76_RS14155
QDPR 6,7-dihydropteridine reductase BWI76_RS21240 BWI76_RS16230

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 Aug 02 2021. The underlying query database was built on Aug 02 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, 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