D-galactose catabolism in Succinatimonas hippei YIT 12066

GapMind for catabolism of small carbon sources

D-galactose catabolism in Succinatimonas hippei YIT 12066

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 (27 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
ytfQ	galactose ABC transporter, substrate-binding component	HMPREF9444_RS00050
ytfR	galactose ABC transporter, ATPase component	HMPREF9444_RS00045	HMPREF9444_RS09995
ytfT	galactose ABC transporter, permease component 1	HMPREF9444_RS00040	HMPREF9444_RS09990
yjtF	galactose ABC transporter, permease component 2	HMPREF9444_RS00035	HMPREF9444_RS09990
galK	galactokinase (-1-phosphate forming)	HMPREF9444_RS01005
galT	UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase	HMPREF9444_RS01000
galE	UDP-glucose 4-epimerase	HMPREF9444_RS00995	HMPREF9444_RS09280
pgmA	alpha-phosphoglucomutase	HMPREF9444_RS05690	HMPREF9444_RS04310
Alternative steps:
BPHYT_RS16925	galactose ABC transporter, permease component	HMPREF9444_RS09990
BPHYT_RS16930	galactose ABC transporter, ATPase component	HMPREF9444_RS09995	HMPREF9444_RS07215
BPHYT_RS16935	galactose ABC transporter, substrate-binding component
CeSWEET1	galactose transporter
chvE	galactose ABC transporter, substrate-binding component ChvE	HMPREF9444_RS07210
dgoA	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	HMPREF9444_RS07790	HMPREF9444_RS09345
dgoD	D-galactonate dehydratase	HMPREF9444_RS09355	HMPREF9444_RS09830
dgoK	2-dehydro-3-deoxygalactonokinase	HMPREF9444_RS09350	HMPREF9444_RS07795
gal2	galactose transporter
galactonolactonase	galactonolactonase (either 1,4- or 1,5-lactone)
galdh	D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones)	HMPREF9444_RS08900	HMPREF9444_RS01835
galP	galactose:H+ symporter GalP	HMPREF9444_RS05050
gatY	D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)
gatZ	D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gguA	galactose ABC transporter, ATPase component GguA	HMPREF9444_RS07215	HMPREF9444_RS09995
gguB	galactose ABC transporter, permease component GguB	HMPREF9444_RS07220	HMPREF9444_RS09990
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)	HMPREF9444_RS01090	HMPREF9444_RS07965
HP1174	Na+-dependent galactose transporter
lacA	galactose-6-phosphate isomerase, lacA subunit
lacB	galactose-6-phosphate isomerase, lacB subunit
lacC	D-tagatose-6-phosphate kinase	HMPREF9444_RS02515
lacD	D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacP	galactose:H+ symporter
mglA	galactose ABC transporter, ATPase component MglA	HMPREF9444_RS09995	HMPREF9444_RS07215
mglB	galactose ABC transporter, substrate-binding component MglB	HMPREF9444_RS10015
mglC	galactose ABC transporter, permease component MglC	HMPREF9444_RS09990	HMPREF9444_RS07220
MST1	galactose:H+ symporter
PfGW456L13_1894	ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
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	HMPREF9444_RS01090	HMPREF9444_RS07965
ptcA	galactose PTS system, EIIA component
ptcB	galactose PTS system, EIIB component
ptcEIIC	galactose PTS system, EIIC component
sglS	sodium/galactose cotransporter	HMPREF9444_RS07925	HMPREF9444_RS06520
SGLT1	sodium/galactose cotransporter	HMPREF9444_RS07925
tpi	triose-phosphate isomerase	HMPREF9444_RS02520	HMPREF9444_RS09140

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