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.
Or see definitions of steps
| Step | Description | Best candidate | 2nd candidate |
|---|---|---|---|
| aroP | tryptophan:H+ symporter AroP | ||
| tnaA | tryptophanase | ||
| Alternative steps: | |||
| ackA | acetate kinase | BIND_RS00995 | |
| acs | acetyl-CoA synthetase, AMP-forming | BIND_RS00265 | BIND_RS03160 |
| adh | acetaldehyde dehydrogenase (not acylating) | BIND_RS14385 | BIND_RS16960 |
| ald-dh-CoA | acetaldehyde dehydrogenase, acylating | ||
| andAa | anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa | BIND_RS12575 | BIND_RS14375 |
| andAb | anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb | BIND_RS13965 | |
| 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 | BIND_RS17235 | |
| catA | catechol 1,2-dioxygenase | ||
| 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 | BIND_RS12425 | BIND_RS12440 |
| ecfA2 | energy-coupling factor transporter, ATPase 2 (A2) component | BIND_RS12425 | BIND_RS11405 |
| 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 | ||
| mhpD | 2-hydroxypentadienoate hydratase | ||
| mhpE | 4-hydroxy-2-oxovalerate aldolase | BIND_RS14270 | BIND_RS02470 |
| nbaC | 3-hydroxyanthranilate 3,4-dioxygenase | ||
| nbaD | 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase | ||
| nbaE | 2-aminomuconate 6-semialdehyde dehydrogenase | BIND_RS14385 | BIND_RS16960 |
| nbaF | 2-aminomuconate deaminase | ||
| nbaG | 2-oxo-3-hexenedioate decarboxylase | ||
| pcaD | 3-oxoadipate enol-lactone hydrolase | BIND_RS14645 | |
| pcaF | succinyl-CoA:acetyl-CoA C-succinyltransferase | BIND_RS02165 | BIND_RS15490 |
| pcaI | 3-oxoadipate CoA-transferase subunit A (PcaI) | BIND_RS05800 | BIND_RS16610 |
| pcaJ | 3-oxoadipate CoA-transferase subunit B (PcaJ) | BIND_RS05795 | BIND_RS16615 |
| praB | 2-hydroxymuconate 6-semialdehyde dehydrogenase | BIND_RS14385 | BIND_RS16960 |
| praC | 2-hydroxymuconate tautomerase | ||
| praD | 2-oxohex-3-enedioate decarboxylase | ||
| pta | phosphate acetyltransferase | BIND_RS01000 | BIND_RS12405 |
| 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 | ||
| 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 24 2021. The underlying query database was built on Sep 17 2021.
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:
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