GapMind for catabolism of small carbon sources

 

lactose catabolism in Phyllobacterium leguminum ORS 1419

Best path

lacP, 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 (33 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric)
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) C7477_RS04415 C7477_RS09435
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) C7477_RS04400 C7477_RS00245
dgoD D-galactonate dehydratase C7477_RS13890 C7477_RS13745
dgoK 2-dehydro-3-deoxygalactonokinase C7477_RS04410 C7477_RS02015
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase C7477_RS04405 C7477_RS10820
glk glucokinase C7477_RS11585 C7477_RS02345
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) C7477_RS15025
aglF' glucose ABC transporter, permease component 1 (AglF) C7477_RS15030
aglG' glucose ABC transporter, permease component 2 (AglG) C7477_RS15035 C7477_RS15005
aglK' glucose ABC transporter, ATPase component (AglK) C7477_RS15040 C7477_RS15575
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase C7477_RS10820 C7477_RS04405
edd phosphogluconate dehydratase C7477_RS00080 C7477_RS13890
gadh1 gluconate 2-dehydrogenase flavoprotein subunit C7477_RS09995 C7477_RS10280
gadh2 gluconate 2-dehydrogenase cytochrome c subunit C7477_RS10000
gadh3 gluconate 2-dehydrogenase subunit 3 C7477_RS09990
galE UDP-glucose 4-epimerase C7477_RS16345 C7477_RS17420
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)
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase C7477_RS17580 C7477_RS15800
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) C7477_RS15035
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) C7477_RS13775 C7477_RS10760
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) C7477_RS00540 C7477_RS15020
gtsB glucose ABC transporter, permease component 1 (GtsB) C7477_RS00550 C7477_RS15010
gtsC glucose ABC transporter, permease component 2 (GtsC) C7477_RS00555 C7477_RS15005
gtsD glucose ABC transporter, ATPase component (GtsD) C7477_RS00560 C7477_RS15040
kguD 2-keto-6-phosphogluconate reductase C7477_RS04785 C7477_RS06885
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
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) C7477_RS04840
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 C7477_RS13785 C7477_RS00785
lacG lactose ABC transporter, permease component 2 C7477_RS13780 C7477_RS00790
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 C7477_RS00800 C7477_RS09770
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) C7477_RS14925 C7477_RS16705
mglB glucose ABC transporter, substrate-binding component C7477_RS14930 C7477_RS16695
mglC glucose ABC transporter, permease component (MglC) C7477_RS14920 C7477_RS16700
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase C7477_RS05195 C7477_RS06840
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 C7477_RS08980 C7477_RS06610

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