GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudomonas putida KT2440

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF

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 (25 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP PP_4495 PP_0927
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA PP_3161
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB PP_3162
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC PP_3163 PP_1163
catA catechol 1,2-dioxygenase PP_3713 PP_3166
catB muconate cycloisomerase PP_3715
catC muconolactone isomerase PP_3714
pcaD 3-oxoadipate enol-lactone hydrolase PP_1380 PP_4540
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PP_3951 PP_3122
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PP_3952 PP_3123
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PP_1377 PP_3280
Alternative steps:
ackA acetate kinase PP_1457
acs acetyl-CoA synthetase, AMP-forming PP_4487 PP_4702
adh acetaldehyde dehydrogenase (not acylating) PP_2680 PP_0545
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa PP_3175 PP_1705
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb PP_3736
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
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 PP_5179 PP_0114
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component PP_4751 PP_5168
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase PP_1791
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase PP_2487 PP_0545
nbaF 2-aminomuconate deaminase PP_0613 PP_0931
nbaG 2-oxo-3-hexenedioate decarboxylase
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PP_2487 PP_5063
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase PP_0774
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease PP_3727 PP_0660
tnaA tryptophanase
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 PP_3197
xylF 2-hydroxymuconate semialdehyde hydrolase

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, the preprint 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