GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Rhizorhabdus wittichii RW1

Best path

aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs

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 (35 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP SWIT_RS03485
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase SWIT_RS23890 SWIT_RS07320
kyn kynureninase SWIT_RS03465
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase SWIT_RS17820
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase SWIT_RS17825 SWIT_RS08505
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase SWIT_RS17800 SWIT_RS21770
nbaF 2-aminomuconate deaminase SWIT_RS17815 SWIT_RS04520
nbaG 2-oxo-3-hexenedioate decarboxylase SWIT_RS04645 SWIT_RS17810
mhpD 2-hydroxypentadienoate hydratase SWIT_RS17805 SWIT_RS04640
mhpE 4-hydroxy-2-oxovalerate aldolase SWIT_RS10670 SWIT_RS26325
adh acetaldehyde dehydrogenase (not acylating) SWIT_RS03590 SWIT_RS08815
acs acetyl-CoA synthetase, AMP-forming SWIT_RS17565 SWIT_RS03515
Alternative steps:
ackA acetate kinase SWIT_RS22145
ald-dh-CoA acetaldehyde dehydrogenase, acylating SWIT_RS26330 SWIT_RS10665
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa SWIT_RS04575 SWIT_RS10380
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc SWIT_RS04565 SWIT_RS15445
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd SWIT_RS15450
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA SWIT_RS13380 SWIT_RS08880
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB SWIT_RS13385
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC
catA catechol 1,2-dioxygenase SWIT_RS04980 SWIT_RS26980
catB muconate cycloisomerase SWIT_RS04970
catC muconolactone isomerase SWIT_RS04975
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) SWIT_RS16640
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component SWIT_RS04010 SWIT_RS00070
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component SWIT_RS13320 SWIT_RS04010
ecfT energy-coupling factor transporter, transmembrane (T) component
pcaD 3-oxoadipate enol-lactone hydrolase SWIT_RS04985 SWIT_RS05450
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase SWIT_RS26185 SWIT_RS21925
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) SWIT_RS21935 SWIT_RS04890
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) SWIT_RS21930 SWIT_RS26190
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase SWIT_RS17800 SWIT_RS08815
praC 2-hydroxymuconate tautomerase SWIT_RS19285
praD 2-oxohex-3-enedioate decarboxylase SWIT_RS04645 SWIT_RS17810
pta phosphate acetyltransferase SWIT_RS13975
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
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 SWIT_RS04555 SWIT_RS15400
xylF 2-hydroxymuconate semialdehyde hydrolase SWIT_RS08860 SWIT_RS26215

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 Apr 09 2024. 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