GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Pseudarthrobacter sulfonivorans Ar51

Best path

aroP, kynA, kynB, kyn, antA, antB, antC, xylE, xylF, mhpD, mhpE, adh, ackA, pta

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 (32 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP AU252_RS05225 AU252_RS18980
kynA tryptophan 2,3-dioxygenase AU252_RS03240
kynB kynurenine formamidase AU252_RS09345
kyn kynureninase AU252_RS03235
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA AU252_RS22725
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB AU252_RS22720
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC AU252_RS22715
xylE catechol 2,3-dioxygenase AU252_RS19380 AU252_RS22415
xylF 2-hydroxymuconate semialdehyde hydrolase AU252_RS17320 AU252_RS22250
mhpD 2-hydroxypentadienoate hydratase AU252_RS17315 AU252_RS22420
mhpE 4-hydroxy-2-oxovalerate aldolase AU252_RS17305 AU252_RS22425
adh acetaldehyde dehydrogenase (not acylating) AU252_RS16200 AU252_RS12650
ackA acetate kinase AU252_RS15110
pta phosphate acetyltransferase AU252_RS15080
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming AU252_RS14440 AU252_RS07515
ald-dh-CoA acetaldehyde dehydrogenase, acylating AU252_RS17310
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa AU252_RS18125 AU252_RS12505
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
catA catechol 1,2-dioxygenase AU252_RS00595 AU252_RS22730
catB muconate cycloisomerase AU252_RS00520 AU252_RS22735
catC muconolactone isomerase AU252_RS12265 AU252_RS22740
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 AU252_RS17960 AU252_RS13340
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component AU252_RS17760 AU252_RS13385
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase AU252_RS22410 AU252_RS11515
nbaF 2-aminomuconate deaminase AU252_RS22345 AU252_RS24575
nbaG 2-oxo-3-hexenedioate decarboxylase AU252_RS22420 AU252_RS17315
pcaD 3-oxoadipate enol-lactone hydrolase AU252_RS16275 AU252_RS10755
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase AU252_RS15005 AU252_RS00310
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) AU252_RS10770 AU252_RS07725
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) AU252_RS10775 AU252_RS03410
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase AU252_RS22410 AU252_RS11515
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase AU252_RS22420 AU252_RS17315
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease AU252_RS04790 AU252_RS08100
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP

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.

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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 (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