GapMind for catabolism of small carbon sources

 

lactose catabolism in Cereibacter sphaeroides ATCC 17029

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 (34 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) RSPH17029_RS07690
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) RSPH17029_RS00190 RSPH17029_RS04240
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) RSPH17029_RS19585
dgoD D-galactonate dehydratase RSPH17029_RS18320 RSPH17029_RS09155
dgoK 2-dehydro-3-deoxygalactonokinase RSPH17029_RS18270 RSPH17029_RS00195
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase RSPH17029_RS18275 RSPH17029_RS20365
glk glucokinase RSPH17029_RS07695 RSPH17029_RS00375
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE) RSPH17029_RS07685
aglF' glucose ABC transporter, permease component 1 (AglF) RSPH17029_RS07680
aglG' glucose ABC transporter, permease component 2 (AglG) RSPH17029_RS07675 RSPH17029_RS06705
aglK' glucose ABC transporter, ATPase component (AglK) RSPH17029_RS07670 RSPH17029_RS00495
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase RSPH17029_RS06600 RSPH17029_RS20365
edd phosphogluconate dehydratase RSPH17029_RS06605 RSPH17029_RS18285
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit RSPH17029_RS07210
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase RSPH17029_RS09070 RSPH17029_RS11635
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) RSPH17029_RS20210 RSPH17029_RS14840
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase RSPH17029_RS06740 RSPH17029_RS17905
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) RSPH17029_RS08750 RSPH17029_RS00495
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) RSPH17029_RS20300
gtsC glucose ABC transporter, permease component 2 (GtsC) RSPH17029_RS07675
gtsD glucose ABC transporter, ATPase component (GtsD) RSPH17029_RS20290 RSPH17029_RS17190
kguD 2-keto-6-phosphogluconate reductase RSPH17029_RS15170 RSPH17029_RS05035
kguK 2-ketogluconokinase RSPH17029_RS10785
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) RSPH17029_RS06265
lacC D-tagatose-6-phosphate kinase RSPH17029_RS05145 RSPH17029_RS02210
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 RSPH17029_RS20300 RSPH17029_RS00485
lacG lactose ABC transporter, permease component 2 RSPH17029_RS20295
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 RSPH17029_RS00495 RSPH17029_RS20290
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) RSPH17029_RS14320 RSPH17029_RS14655
mglB glucose ABC transporter, substrate-binding component RSPH17029_RS14330 RSPH17029_RS17310
mglC glucose ABC transporter, permease component (MglC) RSPH17029_RS14325 RSPH17029_RS13365
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase RSPH17029_RS07690
pgmA alpha-phosphoglucomutase RSPH17029_RS07735 RSPH17029_RS12575
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 RSPH17029_RS03035 RSPH17029_RS05860

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 Apr 10 2024. 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