GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Sinorhizobium fredii NGR234

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 (26 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP NGR_RS11085
tnaA tryptophanase
Alternative steps:
ackA acetate kinase NGR_RS06510
acs acetyl-CoA synthetase, AMP-forming NGR_RS27780 NGR_RS27800
adh acetaldehyde dehydrogenase (not acylating) NGR_RS06135 NGR_RS22740
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa NGR_RS08215 NGR_RS13400
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb NGR_RS05415
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 NGR_RS03590
catA catechol 1,2-dioxygenase NGR_RS02870 NGR_RS10185
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI) NGR_RS10280
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) NGR_RS10285
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component NGR_RS13010 NGR_RS03315
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component NGR_RS10745 NGR_RS05570
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent NGR_RS09635
kyn kynureninase
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase NGR_RS21580
mhpD 2-hydroxypentadienoate hydratase NGR_RS09670 NGR_RS02865
mhpE 4-hydroxy-2-oxovalerate aldolase NGR_RS02860 NGR_RS09675
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase NGR_RS09650 NGR_RS14830
nbaF 2-aminomuconate deaminase NGR_RS28790 NGR_RS27105
nbaG 2-oxo-3-hexenedioate decarboxylase NGR_RS02865 NGR_RS09670
pcaD 3-oxoadipate enol-lactone hydrolase NGR_RS10195 NGR_RS08195
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase NGR_RS10290 NGR_RS27475
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase NGR_RS09650 NGR_RS26215
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase NGR_RS02865 NGR_RS09670
pta phosphate acetyltransferase NGR_RS06505 NGR_RS11510
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease NGR_RS11085
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 NGR_RS15045 NGR_RS02050
xylF 2-hydroxymuconate semialdehyde hydrolase

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