GapMind for catabolism of small carbon sources

 

lactose catabolism in Pseudovibrio axinellae Ad2

Best path

lacA', lacC', lacB', klh, gtsA, gtsB, gtsC, gtsD, 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 (30 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacC' periplasmic lactose 3-dehydrogenase, LacC subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) PsAD2_RS09320
klh periplasmic 3'-ketolactose hydrolase
gtsA glucose ABC transporter, substrate-binding component (GtsA) PsAD2_RS21535 PsAD2_RS14045
gtsB glucose ABC transporter, permease component 1 (GtsB) PsAD2_RS21540 PsAD2_RS14040
gtsC glucose ABC transporter, permease component 2 (GtsC) PsAD2_RS21545 PsAD2_RS14035
gtsD glucose ABC transporter, ATPase component (GtsD) PsAD2_RS21550 PsAD2_RS04510
glk glucokinase PsAD2_RS00270 PsAD2_RS05040
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) PsAD2_RS14035 PsAD2_RS21545
aglK' glucose ABC transporter, ATPase component (AglK) PsAD2_RS13385 PsAD2_RS21760
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA PsAD2_RS17650
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase PsAD2_RS03420
dgoD D-galactonate dehydratase
dgoK 2-dehydro-3-deoxygalactonokinase
eda 2-keto-3-deoxygluconate 6-phosphate aldolase PsAD2_RS03420
edd phosphogluconate dehydratase PsAD2_RS04990
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) PsAD2_RS03450
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) PsAD2_RS20325 PsAD2_RS06355
galE UDP-glucose 4-epimerase PsAD2_RS10675 PsAD2_RS21375
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) PsAD2_RS21785
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) PsAD2_RS12885 PsAD2_RS23270
gnl gluconolactonase PsAD2_RS03450
kguD 2-keto-6-phosphogluconate reductase PsAD2_RS07650
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
lacA galactose-6-phosphate isomerase, lacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit
lacC D-tagatose-6-phosphate kinase
lacD D-tagatose-1,6-bisphosphate aldolase (monomeric)
lacE lactose ABC transporter, substrate-binding component
lacF lactose ABC transporter, permease component 1 PsAD2_RS09065
lacG lactose ABC transporter, permease component 2 PsAD2_RS09060
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 PsAD2_RS13385 PsAD2_RS21760
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) PsAD2_RS20100
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
MFS-glucose glucose transporter, MFS superfamily PsAD2_RS21425 PsAD2_RS22100
mglA glucose ABC transporter, ATP-binding component (MglA) PsAD2_RS00555 PsAD2_RS19320
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) PsAD2_RS00560 PsAD2_RS19325
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase PsAD2_RS05080 PsAD2_RS06585
ptsG glucose PTS, enzyme IICB PsAD2_RS17655
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) PsAD2_RS17655
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase PsAD2_RS01615 PsAD2_RS06470

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