GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Marinobacter adhaerens HP15

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta

Also see fitness data for the top candidates

Rules

Overview: Tryptophan degradation in GapMind is based on MetaCyc degradation pathways I via anthranilate (link), II via pyruvate (link), or IX via 3-hydroxyanthranilate (link). Pathway XII (link) overlaps with pathway I and is also represented. The other MetaCyc pathways do not yield fixed carbon or are not reported in prokaryotes, and are not included. For example, pathway IV yields indole-3-lactate, which could potentially be oxidized to indole-3-acetate, which has a known catabolic pathway, but no prokaryotes are known to consume tryptophan this way. Pathway VIII yields tryptophol (also known as indole-3-ethanol), which could potentially be oxidized to indole-3-acetate and consumed. Pathways X and XIII yield indole-3-propionate, which may spontaneously oxidize to kynurate, but kynurate catabolism is not reported.

47 steps (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA HP15_1106 HP15_39
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC HP15_1107 HP15_4029
xylE catechol 2,3-dioxygenase HP15_4031 HP15_1110
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase HP15_4032 HP15_1111
praC 2-hydroxymuconate tautomerase HP15_4038 HP15_1117
praD 2-oxohex-3-enedioate decarboxylase HP15_4037 HP15_1116
mhpD 2-hydroxypentadienoate hydratase HP15_4034 HP15_1113
mhpE 4-hydroxy-2-oxovalerate aldolase HP15_1115 HP15_4036
adh acetaldehyde dehydrogenase (not acylating) HP15_3144 HP15_3039
ackA acetate kinase HP15_1245 HP15_1499
pta phosphate acetyltransferase HP15_1498
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming HP15_811 HP15_2053
ald-dh-CoA acetaldehyde dehydrogenase, acylating HP15_4035 HP15_1114
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa HP15_27 HP15_3349
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component HP15_4062 HP15_4067
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component HP15_1347 HP15_2920
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase HP15_1111 HP15_4032
nbaF 2-aminomuconate deaminase HP15_3543 HP15_2596
nbaG 2-oxo-3-hexenedioate decarboxylase HP15_4037 HP15_1116
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase HP15_2695 HP15_5
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT HP15_857
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylF 2-hydroxymuconate semialdehyde hydrolase HP15_4033 HP15_1112

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 17 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 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