GapMind for catabolism of small carbon sources

 

lactose catabolism in Klebsiella michiganensis M5al

Best path

lacIIA, lacIIB, lacIIC, pbgal, lacA, lacB, lacC, gatY, gatZ, tpi, 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 (52 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
lacIIA lactose PTS system, EIIA component BWI76_RS01515 BWI76_RS11735
lacIIB lactose PTS system, EIIB component BWI76_RS02945 BWI76_RS01520
lacIIC lactose PTS system, EIIC component BWI76_RS23350 BWI76_RS14945
pbgal phospho-beta-galactosidase BWI76_RS22380 BWI76_RS07295
lacA galactose-6-phosphate isomerase, lacA subunit BWI76_RS02175
lacB galactose-6-phosphate isomerase, lacB subunit BWI76_RS02175
lacC D-tagatose-6-phosphate kinase BWI76_RS00735 BWI76_RS17175
gatY D-tagatose-1,6-bisphosphate aldolase, catalytic subunit (GatY/KbaY) BWI76_RS24855 BWI76_RS11550
gatZ D-tagatose-1,6-bisphosphate aldolase, chaperone subunit (GatZ/KbaZ) BWI76_RS24875
tpi triose-phosphate isomerase BWI76_RS27465 BWI76_RS23980
glk glucokinase BWI76_RS20510 BWI76_RS22415
Alternative steps:
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF' glucose ABC transporter, permease component 1 (AglF) BWI76_RS03135
aglG' glucose ABC transporter, permease component 2 (AglG) BWI76_RS01820
aglK' glucose ABC transporter, ATPase component (AglK) BWI76_RS01840 BWI76_RS06690
bglF glucose PTS, enzyme II (BCA components, BglF) BWI76_RS19555 BWI76_RS07290
crr glucose PTS, enzyme IIA BWI76_RS20655 BWI76_RS08220
dgoA 2-dehydro-3-deoxy-6-phosphogalactonate aldolase BWI76_RS18095 BWI76_RS27940
dgoD D-galactonate dehydratase BWI76_RS27935 BWI76_RS15895
dgoK 2-dehydro-3-deoxygalactonokinase BWI76_RS27945 BWI76_RS03905
eda 2-keto-3-deoxygluconate 6-phosphate aldolase BWI76_RS18095 BWI76_RS27940
edd phosphogluconate dehydratase BWI76_RS18100 BWI76_RS00975
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) BWI76_RS21760 BWI76_RS14780
galdh D-galactose 1-dehydrogenase (forming 1,4- or 1,5-lactones) BWI76_RS07640 BWI76_RS13720
galE UDP-glucose 4-epimerase BWI76_RS18995 BWI76_RS19065
galK galactokinase (-1-phosphate forming) BWI76_RS08615
galT UDP-glucose:alpha-D-galactose-1-phosphate uridylyltransferase BWI76_RS08620
gdh quinoprotein glucose dehydrogenase BWI76_RS04950 BWI76_RS13270
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) BWI76_RS09465 BWI76_RS06035
gnl gluconolactonase BWI76_RS23720 BWI76_RS21470
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) BWI76_RS23380
gtsC glucose ABC transporter, permease component 2 (GtsC) BWI76_RS17835 BWI76_RS06705
gtsD glucose ABC transporter, ATPase component (GtsD) BWI76_RS03270 BWI76_RS06690
kguD 2-keto-6-phosphogluconate reductase BWI76_RS26960 BWI76_RS27925
kguK 2-ketogluconokinase BWI76_RS26950 BWI76_RS07325
kguT 2-ketogluconate transporter BWI76_RS26955 BWI76_RS06145
klh periplasmic 3'-ketolactose hydrolase
lacA' periplasmic lactose 3-dehydrogenase, LacA subunit
lacB' periplasmic lactose 3-dehydrogenase, cytochrome c component (LacB)
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 BWI76_RS23380 BWI76_RS26300
lacG lactose ABC transporter, permease component 2 BWI76_RS17835
lacIICB lactose PTS system, fused EIIC and EIIB components BWI76_RS22405 BWI76_RS04045
lacK lactose ABC transporter, ATPase component BWI76_RS06690 BWI76_RS01840
lacL heteromeric lactase, large subunit BWI76_RS15420
lacM heteromeric lactase, small subunit
lacP lactose permease LacP
lacS lactose permease LacS
lacY lactose:proton symporter LacY BWI76_RS00610 BWI76_RS10315
lacZ lactase (homomeric) BWI76_RS15420 BWI76_RS06715
manX glucose PTS, enzyme EIIAB BWI76_RS17890 BWI76_RS01735
manY glucose PTS, enzyme EIIC BWI76_RS17895 BWI76_RS01730
manZ glucose PTS, enzyme EIID BWI76_RS17900 BWI76_RS01725
MFS-glucose glucose transporter, MFS superfamily BWI76_RS24055 BWI76_RS17580
mglA glucose ABC transporter, ATP-binding component (MglA) BWI76_RS19640 BWI76_RS07240
mglB glucose ABC transporter, substrate-binding component BWI76_RS19645 BWI76_RS27030
mglC glucose ABC transporter, permease component (MglC) BWI76_RS19635 BWI76_RS14865
PAST-A proton-associated sugar transporter A
pgmA alpha-phosphoglucomutase BWI76_RS08290 BWI76_RS25130
ptsG glucose PTS, enzyme IICB BWI76_RS11130 BWI76_RS08220
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) BWI76_RS11130 BWI76_RS08220
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SWEET1 bidirectional sugar transporter SWEET1

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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