GapMind for catabolism of small carbon sources


lactose catabolism in Algoriphagus machipongonensis PR1

Best path

lacA', lacC', lacB', klh, SSS-glucose, 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 (31 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit ALPR1_RS17985 ALPR1_RS18965
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit ALPR1_RS17980 ALPR1_RS18960
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) ALPR1_RS18010 ALPR1_RS11665
klh periplasmic 3'-ketolactose hydrolase ALPR1_RS07255 ALPR1_RS15135
SSS-glucose Sodium/glucose cotransporter ALPR1_RS12485 ALPR1_RS16525
glk glucokinase ALPR1_RS14545 ALPR1_RS05845
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)
aglK' glucose ABC transporter, ATPase component (AglK) ALPR1_RS06390 ALPR1_RS04965
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase ALPR1_RS11100
dgoD D-galactonate dehydratase ALPR1_RS18915 ALPR1_RS04550
dgoK 2-dehydro-3-deoxygalactonokinase ALPR1_RS11095
eda 2-keto-3-deoxygluconate 6-phosphate aldolase ALPR1_RS11100
edd phosphogluconate dehydratase ALPR1_RS04550 ALPR1_RS18915
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit ALPR1_RS05995
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) ALPR1_RS08520 ALPR1_RS03685
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) ALPR1_RS16160 ALPR1_RS17925
galE UDP-glucose 4-epimerase ALPR1_RS09655 ALPR1_RS09845
galK galactokinase (-1-phosphate forming) ALPR1_RS05775
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 ALPR1_RS19260 ALPR1_RS04230
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) ALPR1_RS06390 ALPR1_RS08010
gnl gluconolactonase ALPR1_RS05665 ALPR1_RS08520
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) ALPR1_RS06390 ALPR1_RS13410
kguD 2-keto-6-phosphogluconate reductase ALPR1_RS11040
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit ALPR1_RS00375
lacB galactose-6-phosphate isomerase, lacB subunit ALPR1_RS00375
lacC D-tagatose-6-phosphate kinase ALPR1_RS13560 ALPR1_RS14310
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1
lacG lactose ABC transporter, permease component 2
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 ALPR1_RS06390 ALPR1_RS07820
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY
lacZ lactase (homomeric) ALPR1_RS01940
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily ALPR1_RS10185 ALPR1_RS12850
mglA glucose ABC transporter, ATP-binding component (MglA) ALPR1_RS07820
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC)
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase ALPR1_RS10665 ALPR1_RS02605
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase ALPR1_RS03020 ALPR1_RS05050

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.



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