GapMind for catabolism of small carbon sources


L-tryptophan catabolism in Acidovorax sp. GW101-3H11

Best path

aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs

Also see fitness data for the top candidates


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 (28 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
kynA tryptophan 2,3-dioxygenase Ac3H11_1156
kynB kynurenine formamidase Ac3H11_1158 Ac3H11_1663
kyn kynureninase Ac3H11_1157
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa Ac3H11_214 Ac3H11_2771
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb Ac3H11_215
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc Ac3H11_217
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd Ac3H11_216
xylE catechol 2,3-dioxygenase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Ac3H11_4805 Ac3H11_1486
praC 2-hydroxymuconate tautomerase Ac3H11_4833 Ac3H11_2374
praD 2-oxohex-3-enedioate decarboxylase Ac3H11_1483 Ac3H11_4809
mhpD 2-hydroxypentadienoate hydratase Ac3H11_1483 Ac3H11_4809
mhpE 4-hydroxy-2-oxovalerate aldolase Ac3H11_1482 Ac3H11_3372
adh acetaldehyde dehydrogenase (not acylating) Ac3H11_4393 Ac3H11_4184
acs acetyl-CoA synthetase, AMP-forming Ac3H11_951 Ac3H11_191
Alternative steps:
ackA acetate kinase Ac3H11_4666
ald-dh-CoA acetaldehyde dehydrogenase, acylating
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Ac3H11_2750 Ac3H11_2755
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Ac3H11_209
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 Ac3H11_631 Ac3H11_2553
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component Ac3H11_2058 Ac3H11_909
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 Ac3H11_2743
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase Ac3H11_1486 Ac3H11_4805
nbaF 2-aminomuconate deaminase Ac3H11_417 Ac3H11_3338
nbaG 2-oxo-3-hexenedioate decarboxylase Ac3H11_1483 Ac3H11_4809
pcaD 3-oxoadipate enol-lactone hydrolase
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Ac3H11_3920 Ac3H11_178
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Ac3H11_3922 Ac3H11_132
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Ac3H11_3921 Ac3H11_131
pta phosphate acetyltransferase Ac3H11_1079 Ac3H11_4331
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylF 2-hydroxymuconate semialdehyde hydrolase Ac3H11_413

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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