GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism in Sulfuritalea hydrogenivorans sk43H DSM 22779

Best path

livF, livG, livH, livM, livJ, ARO8, iorAB, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, 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 (58 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
livF L-phenylalanine ABC transporter, ATPase component 1 (LivF) SUTH_RS01360 SUTH_RS06110
livG L-phenylalanine ABC transporter, ATPase component 2 (LivG) SUTH_RS01365 SUTH_RS10320
livH L-phenylalanine ABC transporter, permease component 1 (LivH) SUTH_RS01375 SUTH_RS00445
livM L-phenylalanine ABC transporter, permease component 2 (LivM) SUTH_RS01370 SUTH_RS03125
livJ L-phenylalanine ABC transporter, substrate-binding component LivJ/LivK SUTH_RS01380
ARO8 L-phenylalanine transaminase SUTH_RS08465 SUTH_RS09875
iorAB phenylpyruvate:ferredoxin oxidoreductase, fused IorA/IorB SUTH_RS10720 SUTH_RS03175
padB phenylacetyl-CoA dehydrogenase, PadB subunit SUTH_RS08060
padC phenylacetyl-CoA dehydrogenase, PadC subunit SUTH_RS08065 SUTH_RS02110
padD phenylacetyl-CoA dehydrogenase, PadD subunit SUTH_RS08070
padG phenylglyoxylate dehydrogenase, alpha subunit SUTH_RS08085 SUTH_RS14785
padI phenylglyoxylate dehydrogenase, beta subunit SUTH_RS08095 SUTH_RS14790
padE phenylglyoxylate dehydrogenase, gamma subunit SUTH_RS08075 SUTH_RS14785
padF phenylglyoxylate dehydrogenase, delta subunit SUTH_RS08080
padH phenylglyoxylate dehydrogenase, epsilon subunit SUTH_RS08090
bcrA ATP-dependent benzoyl-CoA reductase, alpha subunit SUTH_RS08185 SUTH_RS08180
bcrB ATP-dependent benzoyl-CoA reductase, beta subunit SUTH_RS08175
bcrC ATP-dependent benzoyl-CoA reductase, gamma subunit SUTH_RS08170
bcrD ATP-dependent benzoyl-CoA reductase, delta subunit SUTH_RS08180 SUTH_RS08185
dch cyclohexa-1,5-diene-1-carboxyl-CoA hydratase SUTH_RS08215 SUTH_RS08545
had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase SUTH_RS08220
oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase SUTH_RS08225
pimB 3-oxopimeloyl-CoA:CoA acetyltransferase SUTH_RS05630 SUTH_RS07380
gcdH glutaryl-CoA dehydrogenase SUTH_RS08235 SUTH_RS02660
ech (S)-3-hydroxybutanoyl-CoA hydro-lyase SUTH_RS15075 SUTH_RS08215
fadB (S)-3-hydroxybutanoyl-CoA dehydrogenase SUTH_RS07375 SUTH_RS03100
atoB acetyl-CoA C-acetyltransferase SUTH_RS02650 SUTH_RS05575
Alternative steps:
aacS acetoacetyl-CoA synthetase SUTH_RS07420 SUTH_RS00825
ARO10 phenylpyruvate decarboxylase SUTH_RS10350
aroP L-phenylalanine:H+ symporter AroP
atoA acetoacetyl-CoA transferase, A subunit
atoD acetoacetyl-CoA transferase, B subunit
badH 2-hydroxy-cyclohexanecarboxyl-CoA dehydrogenase SUTH_RS08230 SUTH_RS10940
badI 2-ketocyclohexanecarboxyl-CoA hydrolase SUTH_RS08545 SUTH_RS15075
badK cyclohex-1-ene-1-carboxyl-CoA hydratase SUTH_RS15075 SUTH_RS13975
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 SUTH_RS13775
bamG class II benzoyl-CoA reductase, BamG subunit
bamH class II benzoyl-CoA reductase, BamH subunit SUTH_RS06865 SUTH_RS10170
bamI class II benzoyl-CoA reductase, BamI subunit SUTH_RS06870 SUTH_RS10175
boxA benzoyl-CoA epoxidase, subunit A SUTH_RS08150
boxB benzoyl-CoA epoxidase, subunit B SUTH_RS08155
boxC 2,3-epoxybenzoyl-CoA dihydrolase SUTH_RS08160
boxD 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Ch1CoA cyclohex-1-ene-1-carbonyl-CoA dehydrogenase SUTH_RS02660 SUTH_RS02630
fahA fumarylacetoacetate hydrolase SUTH_RS14020 SUTH_RS13665
hmgA homogentisate dioxygenase
HPD 4-hydroxyphenylpyruvate dioxygenase
iorA phenylpyruvate:ferredoxin oxidoreductase, IorA subunit SUTH_RS14875
iorB phenylpyruvate:ferredoxin oxidoreductase, IorB subunit SUTH_RS14880 SUTH_RS03175
maiA maleylacetoacetate isomerase SUTH_RS14010 SUTH_RS10260
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 SUTH_RS15075 SUTH_RS10290
paaG 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase SUTH_RS13975 SUTH_RS10290
paaH 3-hydroxyadipyl-CoA dehydrogenase SUTH_RS07375 SUTH_RS03100
paaJ1 3-oxo-5,6-dehydrosuberyl-CoA thiolase SUTH_RS13985 SUTH_RS01990
paaJ2 3-oxoadipyl-CoA thiolase SUTH_RS13985 SUTH_RS01990
paaK phenylacetate-CoA ligase SUTH_RS08100 SUTH_RS03140
paaZ1 oxepin-CoA hydrolase SUTH_RS10290 SUTH_RS13975
paaZ2 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
pad-dh phenylacetaldehyde dehydrogenase SUTH_RS08615 SUTH_RS05840
PAH phenylalanine 4-monooxygenase
PCBD pterin-4-alpha-carbinoalamine dehydratase SUTH_RS06375
pfor phenylacetaldeyde:ferredoxin oxidoreductase SUTH_RS10560
pimC pimeloyl-CoA dehydrogenase, small subunit SUTH_RS11550 SUTH_RS11645
pimD pimeloyl-CoA dehydrogenase, large subunit SUTH_RS11545 SUTH_RS11640
pimF 6-carboxyhex-2-enoyl-CoA hydratase SUTH_RS05635 SUTH_RS00440
PPDCalpha phenylpyruvate decarboxylase, alpha subunit SUTH_RS14825
PPDCbeta phenylpyruvate decarboxylase, beta subunit SUTH_RS14830
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