lactose catabolism in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

lactose catabolism in Sinorhizobium fredii NGR234

Best path

lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk

Rules

Overview: Lactose utilization in GapMind is based on MetaCyc pathway lactose degradation II via 3'-ketolactose (link), pathway III via beta-galactosidase (link), or uptake by a PTS system followed by hydrolysis of lactose 6'-phosphate. (There is no pathway I.)

all:

lactose-transport, beta-galactosidase, galactose-degradation and glk
or lactose-PTS, pbgal, galactose-6-phosphate-degradation and glk
or lacA', lacC', lacB', klh and glucose-utilization
Comment: In pathway III, lactose is taken up and cleaved to galactose and glucose by beta-galactosidase; the glucose is consumed by kinase glk. (The galactose 1-epimerase galM, EC 5.1.3.3, is not included in galactose degradation; it is important for lactose utilization in E. coli (PMID:7966338), but not in Sinorhizobium meliloti or in Bacteroides thetaiotaomicron, which also use this pathway.) Or, a PTS forms lactose 6'-phosphate and phosphogalactosidase (pbgal) forms galactose 6-phosphate and glucose. Or, lactose is oxidized to 3'-ketolactose by a periplasmic 3-component dehydrogenase (lacACB'), and then hydrolyzed by a periplasmic enzyme (klh) to 3-keto-beta-D-galactose and D-glucopyranose, and hypothetical reduction of the 3-ketogalactose. Liberation of glucose is probably sufficient for growth.

beta-galactosidase:

lacZ
or lacL and lacM
Comment: Most lactases are homomeric, but Lactobacillus have a heteromeric enzyme LacLM. (There is also a heteromeric beta-galactosidase in barley, see BGAL_HORVU, but it is not included. Also, "evolved beta-galactosidase" ebgA from E. coli is more active with its partner ebgC, but it retains activity on its own, so it is included in step lacZ instead.)

glucose-utilization:

glucose-transport and glk
or glucose-PTS
or gdh, gnl, gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: Glucose can be taken up and then phosphorylated to glucose 6-phosphate by the kinase glk. Or, both uptake and phosphorylation are catalyzed by a PTS system. Or, glucose is oxidized to glucono-1,5-lactone in the periplasm (by gdh), hydrolyzed to gluconate (by gnl), oxidized to 2-ketogluconate (by gadh123), taken up by kguT, phosphorylated to 2-dehydro-6-phosphogluconate (by kguK), reduced to gluconate 6-phosphate (by kguD), dehydrated by edd to 2-dehydro-3-deoxy-gluconate 6-phosphate, and cleaved by aldolase eda to pyruvate and D-glyceraldehyde 3-phosphate.

glucose-PTS:

ptsG-crr
or bglF
or ptsG and crr
or manX, manY and manZ

glucose-transport:

MFS-glucose
or SSS-glucose
or glcU'
or PAST-A
or SemiSWEET
or SWEET1
or mglA, mglB and mglC
or gtsA, gtsB, gtsC and gtsD
or glcS, glcT, glcU and glcV
or aglE', aglF', aglG' and aglK'
Comment: Transporters and PTS systems were analyzed uzing query: transporter:glucose:D-glucose:D-glucopyranose:ALPHA-GLUCOSE:GLC:CPD-15374

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)

lactose-PTS:

lacIIA, lacIIB and lacIIC
or lacIIA and lacIICB
Comment: PTS systems forming lactose 6'-phosphate. Klebsiella pneumoniae has a EIIA,B,C in three separate proteins. The other characterized PTS systems have EIIA and EIICB

lactose-transport:

lacE, lacF, lacG and lacK
or lacP
or lacS
or lacY
Comment: Transporters and PTS systems were identified using query: transporter:lactose:alpha-lactose:CPD-15971

74 steps (41 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
lacE	lactose ABC transporter, substrate-binding component	NGR_RS01325
lacF	lactose ABC transporter, permease component 1	NGR_RS01320	NGR_RS05360
lacG	lactose ABC transporter, permease component 2	NGR_RS01315	NGR_RS29500
lacK	lactose ABC transporter, ATPase component	NGR_RS01305	NGR_RS08900
lacZ	lactase (homomeric)	NGR_RS01310	NGR_RS25855
galdh	D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones)	NGR_RS15815	NGR_RS13555
galactonolactonase	galactonolactonase (either 1,4- or 1,5-lactone)	NGR_RS13540	NGR_RS10650
dgoD	D-galactonate dehydratase	NGR_RS23200	NGR_RS13535
dgoK	2-dehydro-3-deoxygalactonokinase	NGR_RS13550	NGR_RS23025
dgoA	2-dehydro-3-deoxy-6-phosphogalactonate aldolase	NGR_RS13545	NGR_RS25805
glk	glucokinase	NGR_RS28545	NGR_RS26390
Alternative steps:
aglE'	glucose ABC transporter, substrate-binding component (AglE)	NGR_RS12915
aglF'	glucose ABC transporter, permease component 1 (AglF)	NGR_RS12920	NGR_RS30985
aglG'	glucose ABC transporter, permease component 2 (AglG)	NGR_RS12925	NGR_RS20150
aglK'	glucose ABC transporter, ATPase component (AglK)	NGR_RS12935	NGR_RS01305
bglF	glucose PTS, enzyme II (BCA components, BglF)
crr	glucose PTS, enzyme IIA
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	NGR_RS25805	NGR_RS13545
edd	phosphogluconate dehydratase	NGR_RS12950	NGR_RS24345
gadh1	gluconate 2-dehydrogenase flavoprotein subunit	NGR_RS00555
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	NGR_RS15000
gadh3	gluconate 2-dehydrogenase subunit 3	NGR_RS00550	NGR_RS00545
galE	UDP-glucose 4-epimerase	NGR_RS12315	NGR_RS06395
galK	galactokinase (-1-phosphate forming)
galT	UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase
gatY	D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY)	NGR_RS06555	NGR_RS14610
gatZ	D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)	NGR_RS00570
gdh	quinoprotein glucose dehydrogenase	NGR_RS15020	NGR_RS22565
glcS	glucose ABC transporter, substrate-binding component (GlcS)
glcT	glucose ABC transporter, permease component 1 (GlcT)
glcU	glucose ABC transporter, permease component 2 (GlcU)
glcU'	Glucose uptake protein GlcU
glcV	glucose ABC transporter, ATPase component (GclV)	NGR_RS09940	NGR_RS01050
gnl	gluconolactonase	NGR_RS10695	NGR_RS02200
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	NGR_RS27655	NGR_RS07700
gtsB	glucose ABC transporter, permease component 1 (GtsB)	NGR_RS27660	NGR_RS07695
gtsC	glucose ABC transporter, permease component 2 (GtsC)	NGR_RS07690	NGR_RS27665
gtsD	glucose ABC transporter, ATPase component (GtsD)	NGR_RS07685	NGR_RS05625
kguD	2-keto-6-phosphogluconate reductase	NGR_RS25005	NGR_RS25725
kguK	2-ketogluconokinase
kguT	2-ketogluconate transporter	NGR_RS09750
klh	periplasmic 3'-ketolactose hydrolase
lacA	galactose-6-phosphate isomerase, lacA subunit	NGR_RS08350	NGR_RS14625
lacA'	periplasmic lactose 3-dehydrogenase, LacA subunit	NGR_RS00540
lacB	galactose-6-phosphate isomerase, lacB subunit	NGR_RS08350	NGR_RS14625
lacB'	periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
lacC	D-tagatose-6-phosphate kinase
lacC'	periplasmic lactose 3-dehydrogenase, LacC subunit
lacD	D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacIIA	lactose PTS system, EIIA component
lacIIB	lactose PTS system, EIIB component
lacIIC	lactose PTS system, EIIC component
lacIICB	lactose PTS system, fused EIIC and EIIB components
lacL	heteromeric lactase, large subunit
lacM	heteromeric lactase, small subunit
lacP	lactose permease LacP
lacS	lactose permease LacS
lacY	lactose:proton symporter LacY
manX	glucose PTS, enzyme EIIAB
manY	glucose PTS, enzyme EIIC
manZ	glucose PTS, enzyme EIID
MFS-glucose	glucose transporter, MFS superfamily
mglA	glucose ABC transporter, ATP-binding component (MglA)	NGR_RS23220	NGR_RS00525
mglB	glucose ABC transporter, substrate-binding component	NGR_RS23225	NGR_RS23260
mglC	glucose ABC transporter, permease component (MglC)	NGR_RS23215	NGR_RS23265
PAST-A	proton-associated sugar transporter A
pbgal	phospho-beta-galactosidase	NGR_RS25855
pgmA	alpha-phosphoglucomutase	NGR_RS25635	NGR_RS06645
ptsG	glucose PTS, enzyme IICB
ptsG-crr	glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET	Sugar transporter SemiSWEET
SSS-glucose	Sodium/glucose cotransporter
SWEET1	bidirectional sugar transporter SWEET1
tpi	triose-phosphate isomerase	NGR_RS17645	NGR_RS14620

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 Apr 09 2024. 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 2024 update 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