GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism in Oceanisphaera arctica V1-41

Best path

tnaT, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF

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 (27 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
tnaT tryptophan:Na+ symporter TnaT UN63_RS01905 UN63_RS09940
kynA tryptophan 2,3-dioxygenase
kynB kynurenine formamidase
kyn kynureninase
antA anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA UN63_RS00170
antB anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB UN63_RS00165
antC anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC UN63_RS00160
catA catechol 1,2-dioxygenase UN63_RS00175
catB muconate cycloisomerase UN63_RS00185
catC muconolactone isomerase UN63_RS00180
pcaD 3-oxoadipate enol-lactone hydrolase UN63_RS00235
catI 3-oxoadipate CoA-transferase subunit A (CatI) UN63_RS00220
catJ 3-oxoadipate CoA-transferase subunit B (CatJ) UN63_RS00225
pcaF succinyl-CoA:acetyl-CoA C-succinyltransferase UN63_RS10730 UN63_RS00230
Alternative steps:
ackA acetate kinase UN63_RS08110 UN63_RS08075
acs acetyl-CoA synthetase, AMP-forming UN63_RS07990 UN63_RS15435
adh acetaldehyde dehydrogenase (not acylating) UN63_RS03525 UN63_RS03450
ald-dh-CoA acetaldehyde dehydrogenase, acylating
andAa anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa UN63_RS16200
andAb anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb
andAc anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc UN63_RS00170
andAd athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
aroP tryptophan:H+ symporter AroP
ecfA1 energy-coupling factor transporter, ATPase 1 (A1) component UN63_RS03975 UN63_RS02300
ecfA2 energy-coupling factor transporter, ATPase 2 (A2) component UN63_RS12580 UN63_RS12840
ecfT energy-coupling factor transporter, transmembrane (T) component
hpaH anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
mhpD 2-hydroxypentadienoate hydratase
mhpE 4-hydroxy-2-oxovalerate aldolase UN63_RS15145
nbaC 3-hydroxyanthranilate 3,4-dioxygenase
nbaD 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
nbaE 2-aminomuconate 6-semialdehyde dehydrogenase UN63_RS14965 UN63_RS08090
nbaF 2-aminomuconate deaminase UN63_RS06865 UN63_RS11400
nbaG 2-oxo-3-hexenedioate decarboxylase
pcaI 3-oxoadipate CoA-transferase subunit A (PcaI) UN63_RS00285
pcaJ 3-oxoadipate CoA-transferase subunit B (PcaJ) UN63_RS00280
praB 2-hydroxymuconate 6-semialdehyde dehydrogenase UN63_RS14965 UN63_RS03450
praC 2-hydroxymuconate tautomerase UN63_RS05920
praD 2-oxohex-3-enedioate decarboxylase
pta phosphate acetyltransferase UN63_RS08115 UN63_RS06755
sibC L-kynurenine 3-monooxygenase
TAT tryptophan permease
tnaA tryptophanase
tnaB tryptophan:H+ symporter TnaB
trpP energy-coupling factor transporter, tryptophan-specific (S) component TrpP
xylE catechol 2,3-dioxygenase
xylF 2-hydroxymuconate semialdehyde hydrolase UN63_RS09155

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