GapMind for catabolism of small carbon sources


lactose catabolism in Herbaspirillum seropedicae SmR1

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) HSERO_RS01350 HSERO_RS23930
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) HSERO_RS13590 HSERO_RS05210
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) HSERO_RS05225 HSERO_RS19370
dgoD D-galactonate dehydratase HSERO_RS05150 HSERO_RS16705
dgoK 2-dehydro-3-deoxygalactonokinase HSERO_RS05160 HSERO_RS07545
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase HSERO_RS05525 HSERO_RS05155
glk glucokinase HSERO_RS17870
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) HSERO_RS01335 HSERO_RS22745
aglK' glucose ABC transporter, ATPase component (AglK) HSERO_RS01355 HSERO_RS02210
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HSERO_RS05525 HSERO_RS05155
edd phosphogluconate dehydratase HSERO_RS05520 HSERO_RS16705
gadh1 gluconate 2-dehydrogenase flavoprotein subunit HSERO_RS22385 HSERO_RS16740
gadh2 gluconate 2-dehydrogenase cytochrome c subunit HSERO_RS16735 HSERO_RS22390
gadh3 gluconate 2-dehydrogenase subunit 3 HSERO_RS16745 HSERO_RS22380
galE UDP-glucose 4-epimerase HSERO_RS21095 HSERO_RS22045
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) HSERO_RS03355
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase
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) HSERO_RS11145 HSERO_RS22750
gnl gluconolactonase HSERO_RS20090 HSERO_RS19370
gtsA glucose ABC transporter, substrate-binding component (GtsA) HSERO_RS22730
gtsB glucose ABC transporter, permease component 1 (GtsB) HSERO_RS18950 HSERO_RS01340
gtsC glucose ABC transporter, permease component 2 (GtsC) HSERO_RS01335 HSERO_RS22745
gtsD glucose ABC transporter, ATPase component (GtsD) HSERO_RS16715 HSERO_RS02210
kguD 2-keto-6-phosphogluconate reductase HSERO_RS07550 HSERO_RS08110
kguK 2-ketogluconokinase HSERO_RS07545
kguT 2-ketogluconate transporter HSERO_RS21145 HSERO_RS22270
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) HSERO_RS23110 HSERO_RS05540
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 HSERO_RS15495 HSERO_RS16725
lacG lactose ABC transporter, permease component 2 HSERO_RS18945 HSERO_RS15500
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 HSERO_RS02210 HSERO_RS22750
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) HSERO_RS05195 HSERO_RS05250
mglB glucose ABC transporter, substrate-binding component HSERO_RS05190 HSERO_RS22460
mglC glucose ABC transporter, permease component (MglC) HSERO_RS05200 HSERO_RS05325
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase HSERO_RS13360 HSERO_RS02355
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 HSERO_RS08805 HSERO_RS03345

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