GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Pantoea rwandensis LMG 26275

Best path

susB, mglA, mglB, mglC, glk

Rules

Overview: Maltose utilization in GapMind is based on the MetaCyc pathway via maltose phosphorylase (link), or a phosphotransferase system followed by 6-phospho-alphaglucosidase, or a phosphotransferase system followed by a phosphatase back to maltose followed by maltose phosphorylase, or hydrolysis by alpha-glucosidase after uptake, or periplasmic hydrolysis by alpha-glucosidase followed by glucose utilization.

89 steps (49 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
susB alpha-glucosidase (maltase) HA51_RS16955
mglA glucose ABC transporter, ATP-binding component (MglA) HA51_RS22600 HA51_RS15895
mglB glucose ABC transporter, substrate-binding component HA51_RS22605 HA51_RS05640
mglC glucose ABC transporter, permease component (MglC) HA51_RS22595 HA51_RS05185
glk glucokinase HA51_RS10880 HA51_RS17370
Alternative steps:
aglE maltose ABC transporter, substrate-binding component AglK
aglE' glucose ABC transporter, substrate-binding component (AglE)
aglF maltose ABC transporter, permease component 1 (AglF)
aglF' glucose ABC transporter, permease component 1 (AglF)
aglG maltose ABC transporter, permease component 2 (AglG) HA51_RS18875
aglG' glucose ABC transporter, permease component 2 (AglG) HA51_RS18875
aglK maltose ABC transporter, ATPase component AglK HA51_RS09990 HA51_RS18870
aglK' glucose ABC transporter, ATPase component (AglK) HA51_RS09990 HA51_RS18870
bglF glucose PTS, enzyme II (BCA components, BglF) HA51_RS20050 HA51_RS04935
crr glucose PTS, enzyme IIA HA51_RS26435
cscB maltose permease HA51_RS03945 HA51_RS04815
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HA51_RS10460 HA51_RS05430
edd phosphogluconate dehydratase HA51_RS25625
gadh1 gluconate 2-dehydrogenase flavoprotein subunit HA51_RS18510 HA51_RS25120
gadh2 gluconate 2-dehydrogenase cytochrome c subunit HA51_RS18505 HA51_RS25125
gadh3 gluconate 2-dehydrogenase subunit 3 HA51_RS18515 HA51_RS25115
gdh quinoprotein glucose dehydrogenase HA51_RS10020 HA51_RS19005
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) HA51_RS18870 HA51_RS00345
gnl gluconolactonase HA51_RS02640 HA51_RS19865
gtsA glucose ABC transporter, substrate-binding component (GtsA)
gtsB glucose ABC transporter, permease component 1 (GtsB) HA51_RS09975
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) HA51_RS18870 HA51_RS03335
kguD 2-keto-6-phosphogluconate reductase HA51_RS05510 HA51_RS25715
kguK 2-ketogluconokinase HA51_RS05520 HA51_RS00260
kguT 2-ketogluconate transporter HA51_RS05515 HA51_RS02315
MAL11 maltose permease
malA 6-phospho-alphaglucosidase HA51_RS12315
malAP maltose permease
malE maltose ABC transporter, substrate-binding component MalE
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2)
malE_Aa maltose ABC transporter, substrate-binding component
malE_Ss maltose ABC transporter, substrate-binding component
malEF_Bb maltose ABC transporter, fused substrate-binding and permease component 1
malEIIA maltose phosphotransferase system, EII-A component (PtsG/YpqE/GamP) HA51_RS02255 HA51_RS14550
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 HA51_RS02255 HA51_RS14550
malEIICBA maltose phosphotransferase system, EII-CBA components HA51_RS02255 HA51_RS14550
malF maltose ABC transporter, permease component 1 (MalF) HA51_RS18880
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 HA51_RS03320
malF_Sm maltose ABC transporter, permease component 1 HA51_RS03320
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG)
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2
malG_Bb maltose ABC transporter, permease component 2 HA51_RS03325
malG_Sm maltose ABC transporter, permease component 2
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK HA51_RS18870 HA51_RS09990
malK1 maltose ABC transporter, ATPase component HA51_RS18870 HA51_RS03335
malK_Aa maltose ABC transporter, ATPase component HA51_RS18870 HA51_RS03335
malK_Bb maltose ABC transporter, ATPase component HA51_RS18870 HA51_RS03335
malK_Sm maltose ABC transporter, ATPase component HA51_RS18870 HA51_RS09990
malK_Ss maltose ABC transporter, ATPase component HA51_RS08550
malP maltose phosphorylase
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB HA51_RS10605
manY glucose PTS, enzyme EIIC HA51_RS10600
manZ glucose PTS, enzyme EIID HA51_RS10595
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily HA51_RS21365 HA51_RS04135
musE maltose ABC transporter, substrate-binding component MusE
musF maltose ABC transporter, permease component 1 (MusF)
musG maltose ABC transporter, permease component 2 (MusG)
musI maltose ABC transporter, uncharacterized membrane component MusI
musK maltose ABC transporter, ATPase component MusK HA51_RS18870 HA51_RS09990
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
ptsG glucose PTS, enzyme IICB HA51_RS14550 HA51_RS02255
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) HA51_RS02255 HA51_RS14550
SemiSWEET Sugar transporter SemiSWEET
SSS-glucose Sodium/glucose cotransporter
SUC2 maltose:H+ symporter
SUT1 maltose:H+ symporter
SWEET1 bidirectional sugar transporter SWEET1
thuE maltose ABC transporter, substrate-binding component ThuE
thuF maltose ABC transporter, permease component 1 (ThuF) HA51_RS03320 HA51_RS12960
thuG maltose ABC transporter, permease component 2 (ThuG) HA51_RS09970 HA51_RS03325
thuK maltose ABC transporter, ATPase component ThuK HA51_RS09990 HA51_RS18870

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