GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Xanthobacter autotrophicus Py2

Best path

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

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
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase XAUT_RS03260
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA XAUT_RS05690
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB XAUT_RS05695
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC XAUT_RS05700 XAUT_RS05285
catA catechol 1,2-dioxygenase XAUT_RS22065 XAUT_RS05685
catB muconate cycloisomerase XAUT_RS22070 XAUT_RS05680
catC muconolactone isomerase XAUT_RS05625
pcaD 3-oxoadipate enol-lactone hydrolase XAUT_RS05610 XAUT_RS17525
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) XAUT_RS05620 XAUT_RS11815
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) XAUT_RS05615 XAUT_RS11820
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase XAUT_RS04530 XAUT_RS04615
Alternative steps:
ackA acetate kinase XAUT_RS16350
acs acetyl-CoA synthetase, AMP-forming XAUT_RS07400 XAUT_RS12385
adh acetaldehyde dehydrogenase (not acylating) XAUT_RS01855 XAUT_RS03370
ald-dh-CoA acetaldehyde dehydrogenase, acylating XAUT_RS04720
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa XAUT_RS13165 XAUT_RS24895
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
catI 3-oxoadipate CoA-transferase subunit A (CatI) XAUT_RS25720
catJ 3-oxoadipate CoA-transferase subunit B (CatJ)
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component XAUT_RS05745 XAUT_RS14810
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component XAUT_RS12270 XAUT_RS05745
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent XAUT_RS01910
mhpD 2-hydroxypentadienoate hydratase XAUT_RS04715
mhpE 4-hydroxy-2-oxovalerate aldolase XAUT_RS04725 XAUT_RS06660
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase XAUT_RS10335
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase XAUT_RS01855 XAUT_RS13710
nbaF 2-aminomuconate deaminase XAUT_RS01900 XAUT_RS23580
nbaG 2-oxo-3-hexenedioate decarboxylase XAUT_RS04715
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase XAUT_RS13710 XAUT_RS01855
praC 2-hydroxymuconate tautomerase XAUT_RS08555 XAUT_RS04780
praD 2-oxohex-3-enedioate decarboxylase XAUT_RS04715
pta phosphate acetyltransferase XAUT_RS16345 XAUT_RS15790
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 XAUT_RS06015 XAUT_RS04680
xylF 2-hydroxymuconate semialdehyde hydrolase XAUT_RS04710 XAUT_RS07330

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