L-tryptophan catabolism in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

L-tryptophan catabolism in Burkholderia phytofirmans PsJN

Best path

aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta

Also see fitness data for the top candidates

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.

all:

tryptophan-transport, kynA, kynB, kyn and anthranilate-degradation
or tryptophan-transport and tnaA
or tryptophan-transport, kynA, kynB, sibC, kyn and 3-hydroxyanthranilate-degradation
Comment: In pathway I, dioxygenase kynA opens the non-aromatic ring, to N-formyl-L-kynureine, a hydrolase yields L-kynurenine (and formate), and a hydrolase yields anthranilate and L-alanine. In pathway II, the tryptophan is hydrolyzed to indole and pyruvate, and the indole may be secreted (as in E. coli). In pathway IX, dioxygenase kynA forms N-formyl-L-kynurenine and a hydrolase forms L-kynurenine, as in pathway I; then, oxygenase sibC forms 3-hydroxy-L-kynurenine, which is hydrolyzed to L-alanine and 3-hydroxyanthranilate.

anthranilate-degradation:

anthranilate-dioxygenase and catechol-degradation
or hpaH and 3-hydroxyanthranilate-degradation
Comment: In MetaCyc pathway anthranilate degradation I (link), a dioxygenase cleaves off carbon dioxide and ammonia, leaving catechol. In MetaCyc pathway anthranilate degradation IV (link), anthranilate hydroxylase/monooxygenase (hpaH) yields 3-hydroxyanthranilate. Additional pathways are not included: the fate of 2-amino-5-oxocyclohex-1-enecarboxyl-CoA is not known (link), and anthraniloyl-CoA reductase (the only anaerobic route known, link) has not been linked to sequence.

anthranilate-dioxygenase:

antA, antB and antC
or andAa, andAb, andAc and andAd
Comment: There are two forms of anthranilate dioxygenase, 3-subunit antABC or 4-subunit andAabcd.

3-hydroxyanthranilate-degradation: nbaC, nbaD, nbaE, nbaF, nbaG and 2-hydroxypenta-2,4-dienoate-degradation

Comment: 3-hydroxyanthranilate degradation is part of L-tryptophan degradation pathway XII (link). Dioxygenase NbaC cleaves the aromatic ring, yielding 2-amino-3-carboxymuconate 6-semialdehyde, a decarboxylase forms (2Z,4E)-2-aminomuconate semialdehyde, a dehydrogenase forms (2Z,4E)-2-aminomuconate, a deaminase forms (3E)-2-oxo-3-hexenedioate (also known as 2-oxalocrotonate), and a decarboxylase forms (2Z)-2-hydroxypenta-2,4-dienoate (HPD).

catechol-degradation:

xylE and 2-hydroxymuconate-6-semialdehyde-degradation
or catA, catB, catC, pcaD and 3-oxoadipate-degradation
Comment: In MetaCyc pathway catechol degradation to HPD I (meta-cleavage, link), dioxygenase xylE converts catechol to (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate (also known as 2-hydroxymuconate 6-semialdehyde). (Catechol degradation to HPD II also involves xylE and HPD, link.) In MetaCyc pathway catechol degradation III (ortho-cleavage, link), the 1,2-dioxygenase catA forms cis,cis-muconate, a cycloisomerase forms (+)-muconolactone, an isomerase converts this to (4,5-dihydro-5-oxofuran-2-yl)-acetate (also known as 3-oxoadipate enol lactone), and a hydrolase cleaves this to 3-oxoadipate.

3-oxoadipate-degradation: 3-oxodipate-CoA-transferase and pcaF

Comment: MetaCyc pathway 3-oxoadipate degradation (link) involves activation by CoA (using succinyl-CoA) and a thiolase (succinyltransferase) reaction that splits it to acetyl-CoA and succinyl-CoA.

2-hydroxymuconate-6-semialdehyde-degradation:

praB, praC, praD and 2-hydroxypenta-2,4-dienoate-degradation
or xylF and 2-hydroxypenta-2,4-dienoate-degradation
Comment: Dehydrogenase praB forms 2-hydroxymuconate, tautomerase praC forms (3E)-2-oxohex-3-enedioate (2-oxalocrotonate), and decarboxylase praD yields 2-hydroxypenta-2,4-dienoate (HPD). (This series of steps is part of protocatechuate para-cleavage, link, or catechol degradation II, link.) Or, hydrolase xylF forms HPD and formate. (This is part of a MetaCyc pathway for catechol degradation, link.)

2-hydroxypenta-2,4-dienoate-degradation: mhpD, mhpE and acetaldehyde-degradation

Comment: (2Z)-2-hydroxypenta-2,4-dienoate (HPD) is a common intermediate in the aerobic degradation of many aromatic compounds. In MetaCyc pathway 2-hydroxypenta-2,4-dienoate degradation (link), HPD is hydrated to (S)-4-hydroxy-2-oxopentanoate and an aldolase cleaves it to pyruvate and acetaldehyde.

3-oxodipate-CoA-transferase:

pcaI and pcaJ
or catI and catJ
Comment: Two different types of 3-oxoadipate CoA-transferases (EC 2.8.3.6) are known. They are both heteromeric with each subunit containing a CoA-transferase domain

acetaldehyde-degradation:

ald-dh-CoA
or adh and acs
or adh, ackA and pta
Comment: Acetaldehyde can be oxidized to acetyl-CoA, or oxidized to acetate and activated to acetyl-CoA by either acetyl-CoA synthetase (acs) or by acetate kinase (ackA) and phosphate acetyltransferase (pta).

tryptophan-transport:

trpP, ecfA1, ecfA2 and ecfT
or aroP
or tnaB
or TAT
or tnaT
Comment: Transporters were identified using query: transporter:tryptophan:L-tryptophan:trp

47 steps (36 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
aroP	tryptophan:H+ symporter AroP	BPHYT_RS15500	BPHYT_RS07280
kynA	tryptophan 2,3-dioxygenase	BPHYT_RS16035
kynB	kynurenine formamidase	BPHYT_RS16025
kyn	kynureninase	BPHYT_RS16030	BPHYT_RS07275
hpaH	anthranilate 3-monooxygenase (hydroxylase), FADH2-dependent
nbaC	3-hydroxyanthranilate 3,4-dioxygenase	BPHYT_RS07265
nbaD	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase	BPHYT_RS07270
nbaE	2-aminomuconate 6-semialdehyde dehydrogenase	BPHYT_RS07235	BPHYT_RS28885
nbaF	2-aminomuconate deaminase	BPHYT_RS07260	BPHYT_RS15070
nbaG	2-oxo-3-hexenedioate decarboxylase	BPHYT_RS07255	BPHYT_RS28900
mhpD	2-hydroxypentadienoate hydratase	BPHYT_RS07240	BPHYT_RS28900
mhpE	4-hydroxy-2-oxovalerate aldolase	BPHYT_RS07250	BPHYT_RS28905
adh	acetaldehyde dehydrogenase (not acylating)	BPHYT_RS25810	BPHYT_RS00120
ackA	acetate kinase	BPHYT_RS06125	BPHYT_RS26200
pta	phosphate acetyltransferase	BPHYT_RS21700	BPHYT_RS27695
Alternative steps:
acs	acetyl-CoA synthetase, AMP-forming	BPHYT_RS07000	BPHYT_RS27780
ald-dh-CoA	acetaldehyde dehydrogenase, acylating	BPHYT_RS07245	BPHYT_RS21770
andAa	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin--NAD(+) reductase component AndAa	BPHYT_RS34990	BPHYT_RS21090
andAb	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), ferredoxin subunit AndAb	BPHYT_RS34930
andAc	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AndAc	BPHYT_RS10690	BPHYT_RS07855
andAd	athranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AndAd
antA	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA	BPHYT_RS07855	BPHYT_RS10690
antB	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB	BPHYT_RS07860
antC	anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC	BPHYT_RS07865	BPHYT_RS15575
catA	catechol 1,2-dioxygenase	BPHYT_RS07850	BPHYT_RS10670
catB	muconate cycloisomerase	BPHYT_RS07840	BPHYT_RS10675
catC	muconolactone isomerase	BPHYT_RS07835	BPHYT_RS10665
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	BPHYT_RS22535	BPHYT_RS11445
ecfA2	energy-coupling factor transporter, ATPase 2 (A2) component	BPHYT_RS13580	BPHYT_RS05495
ecfT	energy-coupling factor transporter, transmembrane (T) component
pcaD	3-oxoadipate enol-lactone hydrolase	BPHYT_RS21430	BPHYT_RS02320
pcaF	succinyl-CoA:acetyl-CoA C-succinyltransferase	BPHYT_RS29385	BPHYT_RS17345
pcaI	3-oxoadipate CoA-transferase subunit A (PcaI)	BPHYT_RS21415	BPHYT_RS13675
pcaJ	3-oxoadipate CoA-transferase subunit B (PcaJ)	BPHYT_RS21420	BPHYT_RS13670
praB	2-hydroxymuconate 6-semialdehyde dehydrogenase	BPHYT_RS07235	BPHYT_RS28885
praC	2-hydroxymuconate tautomerase	BPHYT_RS24200	BPHYT_RS10700
praD	2-oxohex-3-enedioate decarboxylase	BPHYT_RS07255	BPHYT_RS28900
sibC	L-kynurenine 3-monooxygenase
TAT	tryptophan permease	BPHYT_RS15500	BPHYT_RS07280
tnaA	tryptophanase
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	BPHYT_RS23610

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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources