GapMind for catabolism of small carbon sources

 

lactose catabolism in Rhizobium leguminosarum 3841

Best path

lacE, lacF, lacG, lacK, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk

Rules

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 (41 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1 RL_RS27260 RL_RS36235
lacG lactose ABC transporter, permease component 2 RL_RS27255 RL_RS36230
lacK lactose ABC transporter, ATPase component RL_RS27250 RL_RS33515
lacZ lactase (homomeric) RL_RS21895 RL_RS21495
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) RL_RS08160 RL_RS04790
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) RL_RS04775 RL_RS30660
dgoD D-galactonate dehydratase RL_RS18610 RL_RS21820
dgoK 2-dehydro-3-deoxygalactonokinase RL_RS04785 RL_RS18270
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase RL_RS04780 RL_RS21465
glk glucokinase RL_RS33105 RL_RS00960
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) RL_RS03905
aglF' glucose ABC transporter, permease component 1 (AglF) RL_RS03910 RL_RS36315
aglG' glucose ABC transporter, permease component 2 (AglG) RL_RS03915 RL_RS14430
aglK' glucose ABC transporter, ATPase component (AglK) RL_RS03925 RL_RS36360
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RL_RS21465 RL_RS04780
edd phosphogluconate dehydratase RL_RS03935 RL_RS09390
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit RL_RS07020
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase RL_RS03165 RL_RS23980
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) RL_RS33900
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) RL_RS34165 RL_RS03390
gdh quinoprotein glucose dehydrogenase RL_RS07055 RL_RS19755
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT) RL_RS08605
glcU glucose ABC transporter, permease component 2 (GlcU) RL_RS34830 RL_RS03915
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) RL_RS33780 RL_RS03350
gnl gluconolactonase RL_RS21855 RL_RS34365
gtsA glucose ABC transporter, substrate-binding component (GtsA) RL_RS21915 RL_RS09500
gtsB glucose ABC transporter, permease component 1 (GtsB) RL_RS21910 RL_RS14435
gtsC glucose ABC transporter, permease component 2 (GtsC) RL_RS21905 RL_RS09510
gtsD glucose ABC transporter, ATPase component (GtsD) RL_RS36220 RL_RS21900
kguD 2-keto-6-phosphogluconate reductase RL_RS00780 RL_RS35850
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter RL_RS36000 RL_RS05180
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit RL_RS33975
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit RL_RS29625
lacB galactose-6-phosphate isomerase, lacB subunit RL_RS13125 RL_RS33975
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) RL_RS12870 RL_RS00760
lacC D-tagatose-6-phosphate kinase
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
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
lacL heteromeric lactase, large subunit
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
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) RL_RS18630 RL_RS18680
mglB glucose ABC transporter, substrate-binding component RL_RS18635 RL_RS18670
mglC glucose ABC transporter, permease component (MglC) RL_RS18625 RL_RS18675
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase RL_RS21495
pgmA alpha-phosphoglucomutase RL_RS21240 RL_RS20450
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 RL_RS12945 RL_RS33970

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