GapMind for catabolism of small carbon sources


lactose catabolism in Marinomonas arctica 328

Best path

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


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 (36 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) DK187_RS11890 DK187_RS16825
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) DK187_RS20570 DK187_RS11910
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) DK187_RS11895 DK187_RS03545
dgoD D-galactonate dehydratase DK187_RS20575 DK187_RS11915
dgoK 2-dehydro-3-deoxygalactonokinase DK187_RS11905 DK187_RS16375
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase DK187_RS01530 DK187_RS11900
glk glucokinase DK187_RS01540
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) DK187_RS03320
aglF' glucose ABC transporter, permease component 1 (AglF) DK187_RS03325 DK187_RS04620
aglG' glucose ABC transporter, permease component 2 (AglG) DK187_RS03330 DK187_RS17250
aglK' glucose ABC transporter, ATPase component (AglK) DK187_RS03335 DK187_RS11940
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase DK187_RS01530 DK187_RS11900
edd phosphogluconate dehydratase DK187_RS13445 DK187_RS19975
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase DK187_RS01255 DK187_RS19820
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) DK187_RS03465
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase DK187_RS01750 DK187_RS10780
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) DK187_RS16035 DK187_RS18225
gnl gluconolactonase DK187_RS03545 DK187_RS11895
gtsA glucose ABC transporter, substrate-binding component (GtsA) DK187_RS03300 DK187_RS17240
gtsB glucose ABC transporter, permease component 1 (GtsB) DK187_RS03295 DK187_RS17245
gtsC glucose ABC transporter, permease component 2 (GtsC) DK187_RS03290 DK187_RS17250
gtsD glucose ABC transporter, ATPase component (GtsD) DK187_RS03285 DK187_RS04605
kguD 2-keto-6-phosphogluconate reductase DK187_RS16380 DK187_RS15435
kguK 2-ketogluconokinase DK187_RS16375
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit DK187_RS05020
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit DK187_RS05020
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)
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1 DK187_RS09385 DK187_RS20425
lacG lactose ABC transporter, permease component 2 DK187_RS11925 DK187_RS16030
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 DK187_RS11940 DK187_RS09450
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 DK187_RS15015 DK187_RS08940
mglA glucose ABC transporter, ATP-binding component (MglA) DK187_RS20555 DK187_RS16470
mglB glucose ABC transporter, substrate-binding component DK187_RS20550 DK187_RS04280
mglC glucose ABC transporter, permease component (MglC) DK187_RS20560 DK187_RS04270
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase DK187_RS17390
pgmA alpha-phosphoglucomutase DK187_RS12930 DK187_RS01620
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 DK187_RS01615 DK187_RS05025

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.



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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