GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Streptacidiphilus oryzae TH49

Best path

aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs

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 BS73_RS10785 BS73_RS16535
kynA tryptophan 2,3-dioxygenase BS73_RS22015
kynB kynurenine formamidase BS73_RS18345 BS73_RS16710
kyn kynureninase BS73_RS18350
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa BS73_RS21365 BS73_RS33040
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb BS73_RS12335 BS73_RS21365
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
xylE catechol 2,3-dioxygenase BS73_RS31835 BS73_RS01220
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase BS73_RS01225 BS73_RS23595
praC 2-hydroxymuconate tautomerase BS73_RS17890 BS73_RS04070
praD 2-oxohex-3-enedioate decarboxylase BS73_RS04080 BS73_RS37045
mhpD 2-hydroxypentadienoate hydratase BS73_RS04080 BS73_RS37045
mhpE 4-hydroxy-2-oxovalerate aldolase BS73_RS11375
adh acetaldehyde dehydrogenase (not acylating) BS73_RS04090 BS73_RS01745
acs acetyl-CoA synthetase, AMP-forming BS73_RS20690 BS73_RS01530
Alternative steps:
ackA acetate kinase BS73_RS15005
ald-dh-CoA acetaldehyde dehydrogenase, acylating
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA BS73_RS04050
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 BS73_RS32780 BS73_RS10015
catB muconate cycloisomerase
catC muconolactone isomerase
catI 3-oxoadipate CoA-transferase subunit A (CatI)
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) BS73_RS10355
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component BS73_RS09120 BS73_RS25510
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component BS73_RS25510 BS73_RS01465
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent BS73_RS01240
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase BS73_RS04105
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase BS73_RS01225 BS73_RS24675
nbaF 2-aminomuconate deaminase BS73_RS10995 BS73_RS19445
nbaG 2-oxo-3-hexenedioate decarboxylase BS73_RS04080 BS73_RS37045
pcaD 3-oxoadipate enol-lactone hydrolase BS73_RS09995 BS73_RS15110
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase BS73_RS12600 BS73_RS30630
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) BS73_RS10025
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) BS73_RS10020
pta phosphate acetyltransferase
sibC L-kynurenine 3-monooxygenase BS73_RS29215
TAT tryptophan permease BS73_RS25710
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
tnaT tryptophan:Na+ symporter TnaT
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylF 2-hydroxymuconate semialdehyde hydrolase BS73_RS00370

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 24 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