GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Rhizobium etli CFN 42

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 RHE_RS25845
tnaA tryptophanase
Alternative steps:
ackA acetate kinase RHE_RS17585
acs acetyl-CoA synthetase, AMP-forming RHE_RS21025 RHE_RS21035
adh acetaldehyde dehydrogenase (not acylating) RHE_RS19035 RHE_RS20725
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa RHE_RS26340 RHE_RS06885
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb RHE_RS09105
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 RHE_RS11745 RHE_RS24310
catB muconate cycloisomerase
catC muconolactone isomerase
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 RHE_RS22810 RHE_RS28485
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component RHE_RS10870 RHE_RS07460
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 RHE_RS28320
mhpD 2-hydroxypentadienoate hydratase RHE_RS11750
mhpE 4-hydroxy-2-oxovalerate aldolase RHE_RS11755 RHE_RS25735
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase RHE_RS19035 RHE_RS05810
nbaF 2-aminomuconate deaminase RHE_RS25710 RHE_RS24625
nbaG 2-oxo-3-hexenedioate decarboxylase RHE_RS11750
pcaD 3-oxoadipate enol-lactone hydrolase RHE_RS24320 RHE_RS27440
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase RHE_RS25075 RHE_RS20545
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) RHE_RS25065
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) RHE_RS25070
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase RHE_RS08800 RHE_RS19035
praC 2-hydroxymuconate tautomerase RHE_RS24720
praD 2-oxohex-3-enedioate decarboxylase RHE_RS11750
pta phosphate acetyltransferase RHE_RS01970 RHE_RS12030
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease RHE_RS25845
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 RHE_RS06315
xylF 2-hydroxymuconate semialdehyde hydrolase RHE_RS09715 RHE_RS18070

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