GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Rhodobacter sphaeroides ATCC 17029

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP L-phenylalanine:H+ symporter AroP
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase RSPH17029_RS12900
QDPR 6,7-dihydropteridine reductase
HPD 4-hydroxyphenylpyruvate dioxygenase
hmgA homogentisate dioxygenase
maiA maleylacetoacetate isomerase RSPH17029_RS19405
fahA fumarylacetoacetate hydrolase RSPH17029_RS09140
atoA acetoacetyl-CoA transferase, A subunit RSPH17029_RS02855
atoD acetoacetyl-CoA transferase, B subunit RSPH17029_RS02850
atoB acetyl-CoA C-acetyltransferase RSPH17029_RS12120 RSPH17029_RS19805
Alternative steps:
aacS acetoacetyl-CoA synthetase RSPH17029_RS17960 RSPH17029_RS13630
ARO10 phenylpyruvate decarboxylase
ARO8 L-phenylalanine transaminase RSPH17029_RS12225 RSPH17029_RS12840
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase RSPH17029_RS05725 RSPH17029_RS12125
badI 2-ketocyclohexanecarboxyl-CoA hydrolase RSPH17029_RS00050 RSPH17029_RS05960
badK cyclohex-1-ene-1-carboxyl-CoA hydratase RSPH17029_RS00050 RSPH17029_RS06550
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 RSPH17029_RS13825
bamH class II benzoyl-CoA reductase, BamH subunit RSPH17029_RS13830 RSPH17029_RS05995
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 RSPH17029_RS05935 RSPH17029_RS09050
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase RSPH17029_RS00050 RSPH17029_RS06550
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase RSPH17029_RS00050 RSPH17029_RS17990
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
gcdH glutaryl-CoA dehydrogenase RSPH17029_RS14905 RSPH17029_RS05935
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB RSPH17029_RS08070 RSPH17029_RS18350
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) RSPH17029_RS04835 RSPH17029_RS07940
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) RSPH17029_RS04855 RSPH17029_RS20335
livH L-phenylalanine ABC transporter, permease component 1 (LivH) RSPH17029_RS17970 RSPH17029_RS14875
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK
livM L-phenylalanine ABC transporter, permease component 2 (LivM) RSPH17029_RS17975 RSPH17029_RS04845
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 RSPH17029_RS00050 RSPH17029_RS16015
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase RSPH17029_RS06550 RSPH17029_RS00050
paaH 3-hydroxyadipyl-CoA dehydrogenase RSPH17029_RS16015 RSPH17029_RS04435
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase RSPH17029_RS16020 RSPH17029_RS00115
paaJ2 3-oxoadipyl-CoA thiolase RSPH17029_RS16020 RSPH17029_RS00115
paaK phenylacetate-CoA ligase RSPH17029_RS04830 RSPH17029_RS18475
paaZ1 oxepin-CoA hydrolase RSPH17029_RS05960 RSPH17029_RS06550
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase RSPH17029_RS16005 RSPH17029_RS04350
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 RSPH17029_RS12120 RSPH17029_RS00115
pimC pimeloyl-CoA dehydrogenase, small subunit
pimD pimeloyl-CoA dehydrogenase, large subunit
pimF 6-carboxyhex-2-enoyl-CoA hydratase RSPH17029_RS16015
PPDCalpha phenylpyruvate decarboxylase, alpha subunit RSPH17029_RS05845
PPDCbeta phenylpyruvate decarboxylase, beta subunit RSPH17029_RS05840

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