GapMind for catabolism of small carbon sources


L-tryptophan catabolism in Pseudomonas fluorescens FW300-N2E2

Best path

aroP, tnaA

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 (29 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP Pf6N2E2_5633 Pf6N2E2_5459
tnaA tryptophanase
Alternative steps:
ackA acetate kinase Pf6N2E2_5444
acs acetyl-CoA synthetase, AMP-forming Pf6N2E2_5659 Pf6N2E2_5149
adh acetaldehyde dehydrogenase (not acylating) Pf6N2E2_1381 Pf6N2E2_4979
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa Pf6N2E2_1861 Pf6N2E2_4027
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb Pf6N2E2_1092
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc Pf6N2E2_1863
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Pf6N2E2_1863
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Pf6N2E2_5315
catA catechol 1,2-dioxygenase Pf6N2E2_997
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI) Pf6N2E2_2837
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) Pf6N2E2_2836
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component Pf6N2E2_3801 Pf6N2E2_4515
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component Pf6N2E2_4455 Pf6N2E2_4002
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
kyn kynureninase
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
mhpD 2-hydroxypentadienoate hydratase Pf6N2E2_1313
mhpE 4-hydroxy-2-oxovalerate aldolase Pf6N2E2_1314 Pf6N2E2_1103
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase Pf6N2E2_1309 Pf6N2E2_4679
nbaF 2-aminomuconate deaminase Pf6N2E2_3403 Pf6N2E2_3707
nbaG 2-oxo-3-hexenedioate decarboxylase Pf6N2E2_1313
pcaD 3-oxoadipate enol-lactone hydrolase Pf6N2E2_2830 Pf6N2E2_2401
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase Pf6N2E2_2835 Pf6N2E2_2113
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) Pf6N2E2_2111
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) Pf6N2E2_2112
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase Pf6N2E2_1309 Pf6N2E2_4679
praC 2-hydroxymuconate tautomerase Pf6N2E2_687
praD 2-oxohex-3-enedioate decarboxylase Pf6N2E2_1313
pta phosphate acetyltransferase Pf6N2E2_5260
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease Pf6N2E2_4959 Pf6N2E2_4195
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylE catechol 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase Pf6N2E2_5281 Pf6N2E2_667

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.



Related tools

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