GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Phaeobacter inhibens BS107

Best path

aroP, tnaA

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 (23 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
tnaA tryptophanase
Alternative steps:
ackA acetate kinase PGA1_c28840
acs acetyl-CoA synthetase, AMP-forming PGA1_c12950 PGA1_c11900
adh acetaldehyde dehydrogenase (not acylating) PGA1_c32800 PGA1_c29650
ald-dh-CoA acetaldehyde dehydrogenase, acylating PGA1_c19350
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa PGA1_c29270
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
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
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase PGA1_c30470
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 PGA1_c10670 PGA1_c22140
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component PGA1_262p01740 PGA1_c23270
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
kyn kynureninase PGA1_c09980
kynA tryptophan 2,3-dioxygenase PGA1_c09970
kynB kynurenine formamidase
mhpD 2-hydroxypentadienoate hydratase PGA1_c32190
mhpE 4-hydroxy-2-oxovalerate aldolase PGA1_c31400 PGA1_c19370
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase PGA1_c32220 PGA1_c21670
nbaF 2-aminomuconate deaminase PGA1_c33270
nbaG 2-oxo-3-hexenedioate decarboxylase PGA1_c32190
pcaD 3-oxoadipate enol-lactone hydrolase PGA1_c04570
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase PGA1_c04090 PGA1_c34350
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) PGA1_c06210
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) PGA1_c06200
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase PGA1_c32220 PGA1_c21670
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase PGA1_c32190
pta phosphate acetyltransferase PGA1_c28850
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
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 PGA1_c32210
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, 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