GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sedimenticola selenatireducens DSM 17993

Best path

livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, padB, padC, padD, padG, padI, padE, padF, padH, boxA, boxB, boxC, boxD, 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 (56 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) A3GO_RS0114200 A3GO_RS0114180
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) A3GO_RS0114175 A3GO_RS0114425
livH L-phenylalanine ABC transporter, permease component 1 (LivH) A3GO_RS0114215 A3GO_RS0114165
livM L-phenylalanine ABC transporter, permease component 2 (LivM) A3GO_RS0114210 A3GO_RS0114170
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK A3GO_RS0114190 A3GO_RS0114160
ARO8 L-phenylalanine transaminase A3GO_RS0103725 A3GO_RS0104720
ARO10 phenylpyruvate decarboxylase A3GO_RS0105735
pad-dh phenylacetaldehyde dehydrogenase A3GO_RS0110905 A3GO_RS0120300
paaK phenylacetate-CoA ligase A3GO_RS0115380 A3GO_RS0115695
padB phenylacetyl-CoA dehydrogenase, PadB subunit A3GO_RS0115735 A3GO_RS0111485
padC phenylacetyl-CoA dehydrogenase, PadC subunit A3GO_RS0115730 A3GO_RS0111480
padD phenylacetyl-CoA dehydrogenase, PadD subunit A3GO_RS0111475 A3GO_RS24140
padG phenylglyoxylate dehydrogenase, alpha subunit A3GO_RS0115710
padI phenylglyoxylate dehydrogenase, beta subunit A3GO_RS0115700
padE phenylglyoxylate dehydrogenase, gamma subunit A3GO_RS0115720
padF phenylglyoxylate dehydrogenase, delta subunit A3GO_RS0115715
padH phenylglyoxylate dehydrogenase, epsilon subunit A3GO_RS0115705 A3GO_RS0107860
boxA benzoyl-CoA epoxidase, subunit A A3GO_RS0113935
boxB benzoyl-CoA epoxidase, subunit B A3GO_RS0118600
boxC 2,3-epoxybenzoyl-CoA dihydrolase A3GO_RS0118595
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase A3GO_RS0115405
paaF 2,3-dehydroadipyl-CoA hydratase A3GO_RS0115400 A3GO_RS0104130
paaH 3-hydroxyadipyl-CoA dehydrogenase A3GO_RS0115390 A3GO_RS0108695
paaJ2 3-oxoadipyl-CoA thiolase A3GO_RS0115675 A3GO_RS0115385
Alternative steps:
aacS acetoacetyl-CoA synthetase A3GO_RS0104365 A3GO_RS0121265
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit
atoB acetyl-CoA C-acetyltransferase A3GO_RS0108835 A3GO_RS0107785
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase A3GO_RS0104110 A3GO_RS0109385
badI 2-ketocyclohexanecarboxyl-CoA hydrolase A3GO_RS0109460 A3GO_RS0105700
badK cyclohex-1-ene-1-carboxyl-CoA hydratase A3GO_RS0104130 A3GO_RS0115400
bamB class II benzoyl-CoA reductase, BamB subunit A3GO_RS0107855
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 A3GO_RS0120600 A3GO_RS0108155
bamI class II benzoyl-CoA reductase, BamI subunit
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit A3GO_RS0115785
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit A3GO_RS0115780
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit A3GO_RS0115775
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit A3GO_RS0115790 A3GO_RS0115785
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase A3GO_RS0114370 A3GO_RS0114380
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase A3GO_RS0115770 A3GO_RS0114405
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase A3GO_RS0114405 A3GO_RS0115400
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase A3GO_RS0108695 A3GO_RS0114400
fahA fumarylacetoacetate hydrolase A3GO_RS0104380
gcdH glutaryl-CoA dehydrogenase A3GO_RS0115815 A3GO_RS0114380
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase A3GO_RS0115760
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit A3GO_RS0108735 A3GO_RS0110745
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB A3GO_RS0106200
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit A3GO_RS0108740
maiA maleylacetoacetate isomerase A3GO_RS0104375
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase A3GO_RS0115765
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
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase A3GO_RS0115395 A3GO_RS0108710
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase A3GO_RS0115385 A3GO_RS0115675
paaZ1 oxepin-CoA hydrolase A3GO_RS0115405 A3GO_RS0115395
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase A3GO_RS0115405
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase A3GO_RS0113255
pfor phenylacetaldeyde:ferredoxin oxidoreductase A3GO_RS0107855
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase A3GO_RS0108690 A3GO_RS0107785
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase
PPDCalpha phenylpyruvate decarboxylase, alpha subunit A3GO_RS0108005
PPDCbeta phenylpyruvate decarboxylase, beta subunit A3GO_RS0108000
QDPR 6,7-dihydropteridine reductase

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