GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas fluorescens FW300-N2C3

Best path

aroP, tnaA

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP AO356_18530 AO356_17670
tnaA tryptophanase
Alternative steps:
ackA acetate kinase AO356_17605
acs acetyl-CoA synthetase, AMP-forming AO356_18695 AO356_16045
adh acetaldehyde dehydrogenase (not acylating) AO356_28025 AO356_15225
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa AO356_30130 AO356_10780
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb AO356_26095
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC AO356_16950
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI) AO356_04940
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) AO356_04935
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component AO356_09255 AO356_12905
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component AO356_12905 AO356_10670
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 AO356_25565 AO356_28650
mhpE 4-hydroxy-2-oxovalerate aldolase AO356_25560 AO356_26150
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase AO356_25585 AO356_13795
nbaF 2-aminomuconate deaminase AO356_09120 AO356_07140
nbaG 2-oxo-3-hexenedioate decarboxylase AO356_25565 AO356_28650
pcaD 3-oxoadipate enol-lactone hydrolase AO356_04905 AO356_02885
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AO356_04930 AO356_21640
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AO356_21650
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AO356_21645
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AO356_25585 AO356_13795
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase AO356_25565 AO356_28650
pta phosphate acetyltransferase AO356_16680
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease AO356_15120 AO356_11625
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 AO356_29165
xylF 2-hydroxymuconate semialdehyde hydrolase AO356_24890

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.

Links

Downloads

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 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