GapMind for catabolism of small carbon sources


lactose catabolism in Azospirillum brasilense Sp245

Best path

lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk

Also see fitness data for the top candidates


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.)

74 steps (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) AZOBR_RS31660 AZOBR_RS16895
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) AZOBR_RS31255 AZOBR_RS29790
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) AZOBR_RS22710 AZOBR_RS31230
dgoD D-galactonate dehydratase AZOBR_RS31260 AZOBR_RS04900
dgoK 2-dehydro-3-deoxygalactonokinase AZOBR_RS29860
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase AZOBR_RS22730 AZOBR_RS29850
glk glucokinase AZOBR_RS05405 AZOBR_RS11685
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) AZOBR_RS18175
aglG' glucose ABC transporter, permease component 2 (AglG) AZOBR_RS25890
aglK' glucose ABC transporter, ATPase component (AglK) AZOBR_RS25595 AZOBR_RS00060
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AZOBR_RS29850 AZOBR_RS22730
edd phosphogluconate dehydratase AZOBR_RS31260 AZOBR_RS15015
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit AZOBR_RS04080
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase AZOBR_RS22395 AZOBR_RS33705
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)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase AZOBR_RS31355
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) AZOBR_RS30790 AZOBR_RS15495
gnl gluconolactonase AZOBR_RS31230
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC) AZOBR_RS25590 AZOBR_RS27985
gtsD glucose ABC transporter, ATPase component (GtsD) AZOBR_RS25595 AZOBR_RS00060
kguD 2-keto-6-phosphogluconate reductase AZOBR_RS01325 AZOBR_RS15695
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit AZOBR_RS31645
lacB galactose-6-phosphate isomerase, lacB subunit AZOBR_RS10010
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) AZOBR_RS14870
lacC D-tagatose-6-phosphate kinase AZOBR_RS06155 AZOBR_RS30840
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1 AZOBR_RS25585
lacG lactose ABC transporter, permease component 2 AZOBR_RS00065
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
lacK lactose ABC transporter, ATPase component AZOBR_RS25595 AZOBR_RS27980
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
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) AZOBR_RS31245 AZOBR_RS31210
mglB glucose ABC transporter, substrate-binding component AZOBR_RS31240
mglC glucose ABC transporter, permease component (MglC) AZOBR_RS31250 AZOBR_RS31200
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase AZOBR_RS16895 AZOBR_RS26030
pgmA alpha-phosphoglucomutase AZOBR_RS02670 AZOBR_RS33725
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 AZOBR_RS03885 AZOBR_RS30960

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.



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:

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:

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