GapMind for catabolism of small carbon sources


L-tryptophan catabolism in Burkholderia phytofirmans PsJN

Best path

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

Also see fitness data for the top candidates


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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP BPHYT_RS15500 BPHYT_RS07280
kynA tryptophan 2,3-dioxygenase BPHYT_RS16035
kynB kynurenine formamidase BPHYT_RS16025
kyn kynureninase BPHYT_RS16030 BPHYT_RS07275
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC 3-hydroxyanthranilate 3,4-dioxygenase BPHYT_RS07265
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase BPHYT_RS07270
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase BPHYT_RS07235 BPHYT_RS28885
nbaF 2-aminomuconate deaminase BPHYT_RS07260 BPHYT_RS15070
nbaG 2-oxo-3-hexenedioate decarboxylase BPHYT_RS07255 BPHYT_RS28900
mhpD 2-hydroxypentadienoate hydratase BPHYT_RS07240 BPHYT_RS28900
mhpE 4-hydroxy-2-oxovalerate aldolase BPHYT_RS07250 BPHYT_RS28905
adh acetaldehyde dehydrogenase (not acylating) BPHYT_RS25810 BPHYT_RS00120
ackA acetate kinase BPHYT_RS06125 BPHYT_RS26200
pta phosphate acetyltransferase BPHYT_RS21700 BPHYT_RS27695
Alternative steps:
acs acetyl-CoA synthetase, AMP-forming BPHYT_RS07000 BPHYT_RS27780
ald-dh-CoA acetaldehyde dehydrogenase, acylating BPHYT_RS07245 BPHYT_RS21770
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa BPHYT_RS34990 BPHYT_RS21090
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb BPHYT_RS34930
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc BPHYT_RS10690 BPHYT_RS07855
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BPHYT_RS07855 BPHYT_RS10690
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB BPHYT_RS07860
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC BPHYT_RS07865 BPHYT_RS15575
catA catechol 1,2-dioxygenase BPHYT_RS07850 BPHYT_RS10670
catB muconate cycloisomerase BPHYT_RS07840 BPHYT_RS10675
catC muconolactone isomerase BPHYT_RS07835 BPHYT_RS10665
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 BPHYT_RS22535 BPHYT_RS11445
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component BPHYT_RS13580 BPHYT_RS05495
ecfT energy-coupling factor transporter, transmembrane (T) component
pcaD 3-oxoadipate enol-lactone hydrolase BPHYT_RS21430 BPHYT_RS02320
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BPHYT_RS29385 BPHYT_RS17345
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BPHYT_RS21415 BPHYT_RS13675
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BPHYT_RS21420 BPHYT_RS13670
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BPHYT_RS07235 BPHYT_RS28885
praC 2-hydroxymuconate tautomerase BPHYT_RS24200 BPHYT_RS10700
praD 2-oxohex-3-enedioate decarboxylase BPHYT_RS07255 BPHYT_RS28900
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease BPHYT_RS15500 BPHYT_RS07280
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
xylF 2-hydroxymuconate semialdehyde hydrolase BPHYT_RS23610

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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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