GapMind for catabolism of small carbon sources


lactose catabolism in Burkholderia phytofirmans PsJN

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) BPHYT_RS22765 BPHYT_RS29195
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BPHYT_RS16920 BPHYT_RS16940
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) BPHYT_RS16915 BPHYT_RS24170
dgoD D-galactonate dehydratase BPHYT_RS16405 BPHYT_RS19730
dgoK 2-dehydro-3-deoxygalactonokinase BPHYT_RS16950 BPHYT_RS09175
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BPHYT_RS16945 BPHYT_RS16730
glk glucokinase BPHYT_RS05010
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG' glucose ABC transporter, permease component 2 (AglG) BPHYT_RS05035 BPHYT_RS22780
aglK' glucose ABC transporter, ATPase component (AglK) BPHYT_RS16095 BPHYT_RS22760
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA BPHYT_RS02740
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BPHYT_RS16730 BPHYT_RS16945
edd phosphogluconate dehydratase BPHYT_RS16735 BPHYT_RS04815
gadh1 gluconate 2-dehydrogenase flavoprotein subunit BPHYT_RS23025 BPHYT_RS30780
gadh2 gluconate 2-dehydrogenase cytochrome c subunit BPHYT_RS23020 BPHYT_RS01060
gadh3 gluconate 2-dehydrogenase subunit 3 BPHYT_RS23030 BPHYT_RS01070
galE UDP-glucose 4-epimerase BPHYT_RS04450 BPHYT_RS07405
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) BPHYT_RS16260
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase BPHYT_RS08325
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) BPHYT_RS05035
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) BPHYT_RS24660 BPHYT_RS08805
gnl gluconolactonase BPHYT_RS06110 BPHYT_RS21245
gtsA glucose ABC transporter, substrate-binding component (GtsA) BPHYT_RS00415 BPHYT_RS05025
gtsB glucose ABC transporter, permease component 1 (GtsB) BPHYT_RS05030 BPHYT_RS29185
gtsC glucose ABC transporter, permease component 2 (GtsC) BPHYT_RS05035 BPHYT_RS29180
gtsD glucose ABC transporter, ATPase component (GtsD) BPHYT_RS05040 BPHYT_RS35680
kguD 2-keto-6-phosphogluconate reductase BPHYT_RS11290 BPHYT_RS14520
kguK 2-ketogluconokinase BPHYT_RS11300
kguT 2-ketogluconate transporter BPHYT_RS11295 BPHYT_RS10985
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) BPHYT_RS04810 BPHYT_RS01960
lacC D-tagatose-6-phosphate kinase
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 BPHYT_RS35665
lacG lactose ABC transporter, permease component 2 BPHYT_RS22780 BPHYT_RS17465
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 BPHYT_RS16095 BPHYT_RS22760
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) BPHYT_RS27185 BPHYT_RS20740
mglB glucose ABC transporter, substrate-binding component BPHYT_RS32820
mglC glucose ABC transporter, permease component (MglC) BPHYT_RS16055 BPHYT_RS27190
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase BPHYT_RS29195
pgmA alpha-phosphoglucomutase BPHYT_RS04470 BPHYT_RS14155
ptsG glucose PTS, enzyme IICB BPHYT_RS02745
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BPHYT_RS02745
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase BPHYT_RS06610 BPHYT_RS16270

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