GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Nocardioides dokdonensis FR1436

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 (27 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
acs acetyl-CoA synthetase, AMP-forming I601_RS07695 I601_RS18315
adh acetaldehyde dehydrogenase (not acylating) I601_RS01590 I601_RS05735
ald-dh-CoA acetaldehyde dehydrogenase, acylating I601_RS02750 I601_RS17195
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa I601_RS05815 I601_RS15705
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb I601_RS16905
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 I601_RS10315
catA catechol 1,2-dioxygenase
catB muconate cycloisomerase I601_RS03945
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) I601_RS03020
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component I601_RS11490 I601_RS01500
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component I601_RS09290 I601_RS10160
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
kyn kynureninase I601_RS12060
kynA tryptophan 2,3-dioxygenase I601_RS10845
kynB kynurenine formamidase I601_RS04420 I601_RS17280
mhpD 2-hydroxypentadienoate hydratase I601_RS02755
mhpE 4-hydroxy-2-oxovalerate aldolase I601_RS02745 I601_RS17190
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase I601_RS01130 I601_RS01380
nbaF 2-aminomuconate deaminase I601_RS12200 I601_RS11970
nbaG 2-oxo-3-hexenedioate decarboxylase I601_RS02755
pcaD 3-oxoadipate enol-lactone hydrolase I601_RS07960
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase I601_RS17535 I601_RS05865
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) I601_RS13875
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) I601_RS13880
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase I601_RS01130 I601_RS01380
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase I601_RS02755
pta phosphate acetyltransferase
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT I601_RS18805
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylE catechol 2,3-dioxygenase I601_RS17175
xylF 2-hydroxymuconate semialdehyde hydrolase I601_RS17180 I601_RS02865

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 24 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 (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:

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