GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Xenophilus azovorans DSM 13620

Best path

livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, 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 (51 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) Q392_RS11630 Q392_RS20790
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) Q392_RS11635 Q392_RS20785
livH L-phenylalanine ABC transporter, permease component 1 (LivH) Q392_RS11645 Q392_RS07410
livM L-phenylalanine ABC transporter, permease component 2 (LivM) Q392_RS11640 Q392_RS07415
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK Q392_RS28895 Q392_RS05395
ARO8 L-phenylalanine transaminase Q392_RS20965 Q392_RS16690
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB Q392_RS04890
paaA phenylacetyl-CoA 1,2-epoxidase, subunit A Q392_RS30145
paaB phenylacetyl-CoA 1,2-epoxidase, subunit B Q392_RS30140
paaC phenylacetyl-CoA 1,2-epoxidase, subunit C Q392_RS30135
paaE phenylacetyl-CoA 1,2-epoxidase, subunit E Q392_RS30125 Q392_RS05600
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Q392_RS30160 Q392_RS00330
paaZ1 oxepin-CoA hydrolase Q392_RS14950 Q392_RS25260
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase Q392_RS20100
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase Q392_RS13480 Q392_RS19235
paaF 2,3-dehydroadipyl-CoA hydratase Q392_RS17990 Q392_RS02545
paaH 3-hydroxyadipyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
paaJ2 3-oxoadipyl-CoA thiolase Q392_RS19235 Q392_RS13480
Alternative steps:
aacS acetoacetyl-CoA synthetase Q392_RS27260 Q392_RS21080
ARO10 phenylpyruvate decarboxylase
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit Q392_RS06750 Q392_RS29045
atoB acetyl-CoA C-acetyltransferase Q392_RS11095 Q392_RS22590
atoD acetoacetyl-CoA transferase, B subunit Q392_RS06755 Q392_RS29040
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase Q392_RS13490 Q392_RS01930
badI 2-ketocyclohexanecarboxyl-CoA hydrolase Q392_RS13495 Q392_RS01935
badK cyclohex-1-ene-1-carboxyl-CoA hydratase Q392_RS17990 Q392_RS02545
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 Q392_RS16650 Q392_RS14130
bamI class II benzoyl-CoA reductase, BamI subunit Q392_RS16645
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 Q392_RS20125
boxB benzoyl-CoA epoxidase, subunit B Q392_RS20120
boxC 2,3-epoxybenzoyl-CoA dihydrolase Q392_RS20115
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase Q392_RS20100 Q392_RS25475
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase Q392_RS02180 Q392_RS27255
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase Q392_RS02515 Q392_RS08845
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase Q392_RS17990 Q392_RS02545
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase Q392_RS25280 Q392_RS25070
fahA fumarylacetoacetate hydrolase Q392_RS20155 Q392_RS01235
gcdH glutaryl-CoA dehydrogenase Q392_RS20240 Q392_RS27255
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase
hmgA homogentisate dioxygenase Q392_RS01240
HPD 4-hydroxyphenylpyruvate dioxygenase Q392_RS19565
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit
maiA maleylacetoacetate isomerase Q392_RS22570 Q392_RS20475
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
paaK phenylacetate-CoA ligase Q392_RS30150 Q392_RS00310
pad-dh phenylacetaldehyde dehydrogenase Q392_RS25600 Q392_RS19250
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 Q392_RS19570
PCBD pterin-4-alpha-carbinoalamine dehydratase Q392_RS29625
pfor phenylacetaldeyde:ferredoxin oxidoreductase
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase Q392_RS27910 Q392_RS25275
pimC pimeloyl-CoA dehydrogenase, small subunit Q392_RS25265 Q392_RS11710
pimD pimeloyl-CoA dehydrogenase, large subunit Q392_RS25270 Q392_RS11705
pimF 6-carboxyhex-2-enoyl-CoA hydratase Q392_RS27900 Q392_RS25280
PPDCalpha phenylpyruvate decarboxylase, alpha subunit Q392_RS02555 Q392_RS04360
PPDCbeta phenylpyruvate decarboxylase, beta subunit Q392_RS02550 Q392_RS28345
QDPR 6,7-dihydropteridine reductase Q392_RS25205

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