GapMind for catabolism of small carbon sources

 

lactose catabolism in Paraburkholderia bryophila 376MFSha3.1

Best path

lacP, lacZ, galdh, galactonolactonase, dgoD, dgoK, dgoA, glk

Also see fitness data for the top candidates

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 (39 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacP lactose permease LacP
lacZ lactase (homomeric) H281DRAFT_02633 H281DRAFT_03229
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) H281DRAFT_06300 H281DRAFT_06296
galactonolactonase galactonolactonase (either 1,4- or 1,5-lactone) H281DRAFT_06301 H281DRAFT_00300
dgoD D-galactonate dehydratase H281DRAFT_04215 H281DRAFT_02329
dgoK 2-dehydro-3-deoxygalactonokinase H281DRAFT_06294 H281DRAFT_00856
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase H281DRAFT_06295 H281DRAFT_04277
glk glucokinase H281DRAFT_00163
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) H281DRAFT_00168 H281DRAFT_03232
aglK' glucose ABC transporter, ATPase component (AglK) H281DRAFT_04155 H281DRAFT_03228
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA H281DRAFT_01852 H281DRAFT_01977
eda 2-keto-3-deoxygluconate 6-phosphate aldolase H281DRAFT_04277 H281DRAFT_06295
edd phosphogluconate dehydratase H281DRAFT_04278 H281DRAFT_00127
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit H281DRAFT_04220 H281DRAFT_05401
gadh3 gluconate 2-dehydrogenase subunit 3
galE UDP-glucose 4-epimerase H281DRAFT_00074 H281DRAFT_04849
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) H281DRAFT_04188 H281DRAFT_01311
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ)
gdh quinoprotein glucose dehydrogenase H281DRAFT_03298 H281DRAFT_00328
glcS glucose ABC transporter, substrate-binding component (GlcS)
glcT glucose ABC transporter, permease component 1 (GlcT)
glcU glucose ABC transporter, permease component 2 (GlcU) H281DRAFT_01452 H281DRAFT_00168
glcU' Glucose uptake protein GlcU
glcV glucose ABC transporter, ATPase component (GclV) H281DRAFT_05887 H281DRAFT_05405
gnl gluconolactonase H281DRAFT_00300 H281DRAFT_05949
gtsA glucose ABC transporter, substrate-binding component (GtsA) H281DRAFT_00166 H281DRAFT_01454
gtsB glucose ABC transporter, permease component 1 (GtsB) H281DRAFT_00167 H281DRAFT_01453
gtsC glucose ABC transporter, permease component 2 (GtsC) H281DRAFT_00168 H281DRAFT_01452
gtsD glucose ABC transporter, ATPase component (GtsD) H281DRAFT_00169 H281DRAFT_03749
kguD 2-keto-6-phosphogluconate reductase H281DRAFT_05213 H281DRAFT_04333
kguK 2-ketogluconokinase H281DRAFT_05211
kguT 2-ketogluconate transporter H281DRAFT_05212 H281DRAFT_00211
klh periplasmic 3'-ketolactose hydrolase
lacA galactose-6-phosphate isomerase, lacA subunit
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit H281DRAFT_02427
lacB galactose-6-phosphate isomerase, lacB subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB) H281DRAFT_02148 H281DRAFT_00126
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 H281DRAFT_03746
lacG lactose ABC transporter, permease component 2 H281DRAFT_03232 H281DRAFT_05702
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 H281DRAFT_04155 H281DRAFT_03228
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) H281DRAFT_02712 H281DRAFT_00426
mglB glucose ABC transporter, substrate-binding component H281DRAFT_03877 H281DRAFT_02713
mglC glucose ABC transporter, permease component (MglC) H281DRAFT_02714 H281DRAFT_04148
PAST-A proton-associated sugar transporter A
pbgal phospho-beta-galactosidase H281DRAFT_01455
pgmA alpha-phosphoglucomutase H281DRAFT_00078 H281DRAFT_04410
ptsG glucose PTS, enzyme IICB H281DRAFT_01853 H281DRAFT_01976
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) H281DRAFT_01853 H281DRAFT_01976
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1
tpi triose-phosphate isomerase H281DRAFT_04564 H281DRAFT_04190

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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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