GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Herbaspirillum seropedicae SmR1

Best path

susB, mglA, mglB, mglC, glk

Also see fitness data for the top candidates

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 (40 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
susB alpha-glucosidase (maltase) HSERO_RS20525 HSERO_RS11645
mglA glucose ABC transporter, ATP-binding component (MglA) HSERO_RS05195 HSERO_RS05250
mglB glucose ABC transporter, substrate-binding component HSERO_RS05190 HSERO_RS22460
mglC glucose ABC transporter, permease component (MglC) HSERO_RS05200 HSERO_RS05325
glk glucokinase HSERO_RS17870
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) HSERO_RS01335 HSERO_RS22745
aglG' glucose ABC transporter, permease component 2 (AglG) HSERO_RS01335 HSERO_RS22745
aglK maltose ABC transporter, ATPase component AglK HSERO_RS22750 HSERO_RS02210
aglK' glucose ABC transporter, ATPase component (AglK) HSERO_RS01355 HSERO_RS02210
bglF glucose PTS, enzyme II (BCA components, BglF)
crr glucose PTS, enzyme IIA
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase HSERO_RS05525 HSERO_RS05155
edd phosphogluconate dehydratase HSERO_RS05520 HSERO_RS16705
gadh1 gluconate 2-dehydrogenase flavoprotein subunit HSERO_RS22385 HSERO_RS16740
gadh2 gluconate 2-dehydrogenase cytochrome c subunit HSERO_RS16735 HSERO_RS22390
gadh3 gluconate 2-dehydrogenase subunit 3 HSERO_RS16745 HSERO_RS22380
gdh quinoprotein glucose dehydrogenase
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) HSERO_RS11145 HSERO_RS22750
gnl gluconolactonase HSERO_RS20090 HSERO_RS19370
gtsA glucose ABC transporter, substrate-binding component (GtsA) HSERO_RS22730
gtsB glucose ABC transporter, permease component 1 (GtsB) HSERO_RS18950 HSERO_RS01340
gtsC glucose ABC transporter, permease component 2 (GtsC) HSERO_RS01335 HSERO_RS22745
gtsD glucose ABC transporter, ATPase component (GtsD) HSERO_RS16715 HSERO_RS02210
kguD 2-keto-6-phosphogluconate reductase HSERO_RS07550 HSERO_RS08110
kguK 2-ketogluconokinase HSERO_RS07545
kguT 2-ketogluconate transporter HSERO_RS21145 HSERO_RS22270
MAL11 maltose permease
malA 6-phospho-alphaglucosidase
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)
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715
malEIICBA maltose phosphotransferase system, EII-CBA components
malF maltose ABC transporter, permease component 1 (MalF) HSERO_RS18950 HSERO_RS16725
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 HSERO_RS16725
malF_Sm maltose ABC transporter, permease component 1
malF_Ss maltose ABC transporter, permease component 1
malG maltose ABC transporter, permease component 2 (MalG) HSERO_RS16730 HSERO_RS16725
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 HSERO_RS16730
malG_Bb maltose ABC transporter, permease component 2 HSERO_RS16730
malG_Sm maltose ABC transporter, permease component 2 HSERO_RS16730
malG_Ss maltose ABC transporter, permease component 2
malI maltose transporter
malK maltose ABC transporter, ATPase component MalK HSERO_RS02210 HSERO_RS01355
malK1 maltose ABC transporter, ATPase component HSERO_RS16715 HSERO_RS18940
malK_Aa maltose ABC transporter, ATPase component HSERO_RS18940 HSERO_RS16715
malK_Bb maltose ABC transporter, ATPase component HSERO_RS18940 HSERO_RS22750
malK_Sm maltose ABC transporter, ATPase component HSERO_RS16715 HSERO_RS02210
malK_Ss maltose ABC transporter, ATPase component HSERO_RS07880 HSERO_RS15940
malP maltose phosphorylase
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC
manZ glucose PTS, enzyme EIID
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily
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 HSERO_RS16715 HSERO_RS18940
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase HSERO_RS00780
ptsG glucose PTS, enzyme IICB
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG)
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) HSERO_RS15495 HSERO_RS16725
thuG maltose ABC transporter, permease component 2 (ThuG) HSERO_RS16730 HSERO_RS02200
thuK maltose ABC transporter, ATPase component ThuK HSERO_RS22750 HSERO_RS02210

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:

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