GapMind for catabolism of small carbon sources

 

lactose catabolism in Halomonas xinjiangensis TRM 0175

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 (31 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) JH15_RS10325 JH15_RS12765
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) JH15_RS06165 JH15_RS10355
dgoD D-galactonate dehydratase JH15_RS06180 JH15_RS10350
dgoK 2-dehydro-3-deoxygalactonokinase JH15_RS06175 JH15_RS14595
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase JH15_RS04935 JH15_RS06170
glk glucokinase JH15_RS04905
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) JH15_RS04280
aglG' glucose ABC transporter, permease component 2 (AglG) JH15_RS04275
aglK' glucose ABC transporter, ATPase component (AglK) JH15_RS03500 JH15_RS04270
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
eda 2-keto-3-deoxygluconate 6-phosphate aldolase JH15_RS04935 JH15_RS06170
edd phosphogluconate dehydratase JH15_RS04900 JH15_RS09690
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit JH15_RS11025
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase JH15_RS15910 JH15_RS14925
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) JH15_RS17390
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase JH15_RS09990 JH15_RS12590
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) JH15_RS09915 JH15_RS07285
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) JH15_RS04285
gtsB glucose ABC transporter, permease component 1 (GtsB) JH15_RS04280
gtsC glucose ABC transporter, permease component 2 (GtsC) JH15_RS04275
gtsD glucose ABC transporter, ATPase component (GtsD) JH15_RS04270 JH15_RS03500
kguD 2-keto-6-phosphogluconate reductase JH15_RS14590 JH15_RS13015
kguK 2-ketogluconokinase JH15_RS14595
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)
lacC D-tagatose-6-phosphate kinase JH15_RS05185
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 JH15_RS09925 JH15_RS03490
lacG lactose ABC transporter, permease component 2 JH15_RS03495
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 JH15_RS03500 JH15_RS04270
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) JH15_RS10190 JH15_RS10340
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) JH15_RS10185 JH15_RS10345
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase
pgmA alpha-phosphoglucomutase JH15_RS08030 JH15_RS12400
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter JH15_RS04255 JH15_RS10615
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase JH15_RS12395 JH15_RS17385

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