GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Sinorhizobium meliloti 1021

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 (20 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
aroP tryptophan:H+ symporter AroP
tnaA tryptophanase
Alternative steps:
ackA acetate kinase SM_b21184
acs acetyl-CoA synthetase, AMP-forming SMc04093 SMc04095
adh acetaldehyde dehydrogenase (not acylating) SM_b21301 SM_b21539
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa SM_b20820 SMc00914
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb SMc01993 SM_b20985
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
catA catechol 1,2-dioxygenase SM_b20576
catB muconate cycloisomerase SMa0056
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI) SM_b20587
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) SM_b20588
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component SMc00962 SMc00771
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component SM_b21130 SMa2067
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
kyn kynureninase
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase SMa0259
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase SMc02778 SMc02546
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase SMc00094 SMc02689
nbaF 2-aminomuconate deaminase SMc02881 SMa1377
nbaG 2-oxo-3-hexenedioate decarboxylase
pcaD 3-oxoadipate enol-lactone hydrolase SM_b20579 SMc04308
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase SM_b20589 SMc03879
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI)
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ)
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase SMa2213 SMc02689
praC 2-hydroxymuconate tautomerase
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase SM_b21532 SMc01126
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
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 SMc00115
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 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:

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