GapMind for catabolism of small carbon sources

 

lactose catabolism in Ochrobactrum thiophenivorans DSM 7216

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 (35 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) CEV31_RS02605 CEV31_RS03445
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) CEV31_RS05370
dgoD D-galactonate dehydratase CEV31_RS20170 CEV31_RS02600
dgoK 2-dehydro-3-deoxygalactonokinase CEV31_RS02595 CEV31_RS18540
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase CEV31_RS02590 CEV31_RS20745
glk glucokinase CEV31_RS07005 CEV31_RS18970
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) CEV31_RS07180
aglG' glucose ABC transporter, permease component 2 (AglG) CEV31_RS16735 CEV31_RS14070
aglK' glucose ABC transporter, ATPase component (AglK) CEV31_RS15275 CEV31_RS06775
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA CEV31_RS13155
eda 2-keto-3-deoxygluconate 6-phosphate aldolase CEV31_RS20745 CEV31_RS18545
edd phosphogluconate dehydratase CEV31_RS15685 CEV31_RS06110
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit CEV31_RS09840 CEV31_RS08410
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase CEV31_RS11660 CEV31_RS08270
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) CEV31_RS08915
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) CEV31_RS16790
gdh quinoprotein glucose dehydrogenase CEV31_RS06685 CEV31_RS03435
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) CEV31_RS14655 CEV31_RS17415
gnl gluconolactonase CEV31_RS19470 CEV31_RS14210
gtsA glucose ABC transporter, substrate-binding component (GtsA) CEV31_RS09330
gtsB glucose ABC transporter, permease component 1 (GtsB) CEV31_RS09335 CEV31_RS14435
gtsC glucose ABC transporter, permease component 2 (GtsC) CEV31_RS09340 CEV31_RS07125
gtsD glucose ABC transporter, ATPase component (GtsD) CEV31_RS09345 CEV31_RS17415
kguD 2-keto-6-phosphogluconate reductase CEV31_RS03240 CEV31_RS05585
kguK 2-ketogluconokinase
kguT 2-ketogluconate transporter
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit CEV31_RS08920
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB galactose-6-phosphate isomerase, lacB subunit CEV31_RS08920
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 CEV31_RS14435 CEV31_RS14075
lacG lactose ABC transporter, permease component 2 CEV31_RS14660 CEV31_RS07185
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 CEV31_RS15275 CEV31_RS17415
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 CEV31_RS19855
mglA glucose ABC transporter, ATP-binding component (MglA) CEV31_RS02580 CEV31_RS17305
mglB glucose ABC transporter, substrate-binding component CEV31_RS02585 CEV31_RS17260
mglC glucose ABC transporter, permease component (MglC) CEV31_RS02575 CEV31_RS09010
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase CEV31_RS05910 CEV31_RS03255
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 CEV31_RS12005 CEV31_RS08925

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.

Links

Downloads

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