D-galactose catabolism in Yersinia intermedia Y228

GapMind for catabolism of small carbon sources

D-galactose catabolism in Yersinia intermedia Y228

Best path

ytfQ, ytfR, ytfT, yjtF, galK, galT, galE, pgmA

Rules

Overview: Galactose utilization in GapMind is based on MetaCyc pathways lactose and galactose degradation I via tagatose 6-phosphate (link), the Leloir pathway via UDP-galactose (link), and the oxidative pathway via D-galactonate (link). Pathway IV via galactitol (link) is not reported in prokaryotes and is not included. (There is no pathway III.)

all: galactose-utilization
galactose-utilization:

galactose-PTS and galactose-6-phosphate-degradation
or galactose-transport and galactose-degradation

galactose-degradation:

galK, galT, galE and pgmA
or galdh, galactonolactonase, dgoD, dgoK and dgoA
Comment: In the Leloir pathway, galactokinase (galK) forms galactose 1-phosphate, a uridyltransferase (galT) uses glucose 1-phosphate to form UDP-galactose, an epimerase (galE) forms UDP-glucose, and this is converted to glucose 1-phosphate by the same uridyltransferase. (We initially included the 1-epimerase galM, EC 5.1.3.3, in our model of the Leloir pathway, but found that in most bacteria, galM proteins were not important for fitness during growth on galactose; the only exception was Echvi_0697.) The oxidative pathway begins with oxidation to a lactone (by galdh) and hydrolysis to galactonate; galactonate is then dehydrated, phosphorylated, and cleaved by an aldolase.

galactose-6-phosphate-degradation: lacA, lacB, lacC, tag16P-aldolase and tpi

Comment: The tagatose 6-phosphate pathway involves the isomerization of galactose 6-phosphate to tagatose-6-phosphate (by lacAB), phosphorylation to tagatose 1,6-bisphosphate (by lacC), and an aldolase.

tag16P-aldolase:

lacD
or gatY and gatZ
Comment: Two forms of D-tagatose-1,6-phosphate aldolase are known, homomeric (lacD) or heteromeric (gatYZ or kbaYZ)

galactose-PTS: ptcA, ptcB and ptcEIIC
galactose-transport:

mglA, mglB and mglC
or ytfQ, ytfR, ytfT and yjtF
or gguA, gguB and chvE
or glcS, glcT, glcU and glcV
or PfGW456L13_1894, PfGW456L13_1895, PfGW456L13_1896 and PfGW456L13_1897
or BPHYT_RS16935, BPHYT_RS16930 and BPHYT_RS16925
or galP
or HP1174
or gal2
or SGLT1
or CeSWEET1
or sglS
or MST1
or lacP
Comment: Transporters and PTS systems were identified using: query: transporter:galactose:D-galactose:D-galactofuranose:D-galactopyranose:CPD0-2486:CPD0-2485:alpha-d-galactose:CPD-15590

48 steps (36 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
ytfQ	galactose ABC transporter, substrate-binding component	CH53_RS09625
ytfR	galactose ABC transporter, ATPase component	CH53_RS09630	CH53_RS18475
ytfT	galactose ABC transporter, permease component 1	CH53_RS09635	CH53_RS08870
yjtF	galactose ABC transporter, permease component 2	CH53_RS09640	CH53_RS08870
galK	galactokinase (-1-phosphate forming)	CH53_RS15645
galT	UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase	CH53_RS15650
galE	UDP-glucose 4-epimerase	CH53_RS15655	CH53_RS14395
pgmA	alpha-phosphoglucomutase	CH53_RS15380	CH53_RS16330
Alternative steps:
BPHYT_RS16925	galactose ABC transporter, permease component	CH53_RS19470	CH53_RS08870
BPHYT_RS16930	galactose ABC transporter, ATPase component	CH53_RS19465	CH53_RS18475
BPHYT_RS16935	galactose ABC transporter, substrate-binding component	CH53_RS19460
CeSWEET1	galactose transporter
chvE	galactose ABC transporter, substrate-binding component ChvE	CH53_RS08250
dgoA	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	CH53_RS18805	CH53_RS08500
dgoD	D-galactonate dehydratase	CH53_RS08495	CH53_RS19500
dgoK	2-dehydro-3-deoxygalactonokinase	CH53_RS08045	CH53_RS08505
gal2	galactose transporter
galactonolactonase	galactonolactonase (either 1,4- or 1,5-lactone)	CH53_RS14565
galdh	D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones)	CH53_RS21000	CH53_RS01810
galP	galactose:H+ symporter GalP	CH53_RS17075
gatY	D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)	CH53_RS01215
gatZ	D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)	CH53_RS01180
gguA	galactose ABC transporter, ATPase component GguA	CH53_RS08245	CH53_RS18475
gguB	galactose ABC transporter, permease component GguB	CH53_RS08240	CH53_RS04140
glcS	galactose ABC transporter, substrate-binding component GlcS
glcT	galactose ABC transporter, permease component 1 (GlcT)
glcU	galactose ABC transporter, permease component 2 (GlcU)
glcV	galactose ABC transporter, ATPase component (GlcV)	CH53_RS01010	CH53_RS16980
HP1174	Na+-dependent galactose transporter	CH53_RS04195	CH53_RS19800
lacA	galactose-6-phosphate isomerase, lacA subunit	CH53_RS15005
lacB	galactose-6-phosphate isomerase, lacB subunit	CH53_RS15005
lacC	D-tagatose-6-phosphate kinase	CH53_RS09360	CH53_RS12315
lacD	D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP	galactose:H+ symporter
mglA	galactose ABC transporter, ATPase component MglA	CH53_RS16145	CH53_RS18475
mglB	galactose ABC transporter, substrate-binding component MglB	CH53_RS16140
mglC	galactose ABC transporter, permease component MglC	CH53_RS16150	CH53_RS18480
MST1	galactose:H+ symporter
PfGW456L13_1894	ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component	CH53_RS11630
PfGW456L13_1895	ABC transporter for D-Galactose and D-Glucose, permease component 1
PfGW456L13_1896	ABC transporter for D-Galactose and D-Glucose, permease component 2
PfGW456L13_1897	ABC transporter for D-Galactose and D-Glucose, ATPase component	CH53_RS10140	CH53_RS21020
ptcA	galactose PTS system, EIIA component	CH53_RS03550	CH53_RS08560
ptcB	galactose PTS system, EIIB component	CH53_RS18260	CH53_RS08540
ptcEIIC	galactose PTS system, EIIC component	CH53_RS03560
sglS	sodium/galactose cotransporter
SGLT1	sodium/galactose cotransporter
tpi	triose-phosphate isomerase	CH53_RS09370	CH53_RS12865

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.

Downloads

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

Related tools

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