GapMind for catabolism of small carbon sources

 

D-maltose catabolism in Photobacterium jeanii R-40508

Best path

malE, malF, malG, malK, susB, 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 (46 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
malE maltose ABC transporter, substrate-binding component MalE A3K86_RS19480
malF maltose ABC transporter, permease component 1 (MalF) A3K86_RS19485 A3K86_RS19335
malG maltose ABC transporter, permease component 2 (MalG) A3K86_RS19490
malK maltose ABC transporter, ATPase component MalK A3K86_RS19475 A3K86_RS19360
susB alpha-glucosidase (maltase) A3K86_RS14095 A3K86_RS15650
glk glucokinase A3K86_RS19100 A3K86_RS03930
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) A3K86_RS19490
aglG' glucose ABC transporter, permease component 2 (AglG) A3K86_RS19490
aglK maltose ABC transporter, ATPase component AglK A3K86_RS19475 A3K86_RS19360
aglK' glucose ABC transporter, ATPase component (AglK) A3K86_RS19475 A3K86_RS19360
bglF glucose PTS, enzyme II (BCA components, BglF) A3K86_RS20820
crr glucose PTS, enzyme IIA A3K86_RS12910
cscB maltose permease
eda 2-keto-3-deoxygluconate 6-phosphate aldolase A3K86_RS14285 A3K86_RS16310
edd phosphogluconate dehydratase A3K86_RS17170
gadh1 gluconate 2-dehydrogenase flavoprotein subunit
gadh2 gluconate 2-dehydrogenase cytochrome c subunit
gadh3 gluconate 2-dehydrogenase subunit 3
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) A3K86_RS19475 A3K86_RS02885
gnl gluconolactonase
gtsA glucose ABC transporter, substrate-binding component (GtsA) A3K86_RS02915
gtsB glucose ABC transporter, permease component 1 (GtsB)
gtsC glucose ABC transporter, permease component 2 (GtsC)
gtsD glucose ABC transporter, ATPase component (GtsD) A3K86_RS19360 A3K86_RS19475
kguD 2-keto-6-phosphogluconate reductase A3K86_RS17455 A3K86_RS13295
kguK 2-ketogluconokinase A3K86_RS20825
kguT 2-ketogluconate transporter
MAL11 maltose permease
malA 6-phospho-alphaglucosidase A3K86_RS01480
malAP maltose permease
malE1 maltose ABC transporter, substrate-binding component (MalE1/MalE2) A3K86_RS19480
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) A3K86_RS02900 A3K86_RS05470
malEIICB maltose phosphotransferase system, EII-CB components curated:SwissProt::P54715 A3K86_RS02900 A3K86_RS05470
malEIICBA maltose phosphotransferase system, EII-CBA components A3K86_RS02900 A3K86_RS05470
malF1 maltose ABC transporter, permease component 1 (MalF1)
malF_Aa maltose ABC transporter, permease component 1 A3K86_RS19485
malF_Sm maltose ABC transporter, permease component 1 A3K86_RS19485
malF_Ss maltose ABC transporter, permease component 1
malG1 maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa maltose ABC transporter, permease component 2 A3K86_RS19490
malG_Bb maltose ABC transporter, permease component 2 A3K86_RS19490
malG_Sm maltose ABC transporter, permease component 2 A3K86_RS19490
malG_Ss maltose ABC transporter, permease component 2 A3K86_RS10965
malI maltose transporter A3K86_RS04685
malK1 maltose ABC transporter, ATPase component A3K86_RS19360 A3K86_RS19475
malK_Aa maltose ABC transporter, ATPase component A3K86_RS19360 A3K86_RS19475
malK_Bb maltose ABC transporter, ATPase component A3K86_RS19475 A3K86_RS19360
malK_Sm maltose ABC transporter, ATPase component A3K86_RS19360 A3K86_RS19475
malK_Ss maltose ABC transporter, ATPase component A3K86_RS10960 A3K86_RS05795
malP maltose phosphorylase
malX_Sm maltose ABC transporter, substrate-binding component
manX glucose PTS, enzyme EIIAB
manY glucose PTS, enzyme EIIC A3K86_RS16385
manZ glucose PTS, enzyme EIID A3K86_RS16380
mapP maltose 6'-phosphate phosphatase
MFS-glucose glucose transporter, MFS superfamily
mglA glucose ABC transporter, ATP-binding component (MglA) A3K86_RS19615 A3K86_RS15085
mglB glucose ABC transporter, substrate-binding component
mglC glucose ABC transporter, permease component (MglC) A3K86_RS19610
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 A3K86_RS19360 A3K86_RS19475
PAST-A proton-associated sugar transporter A
pgmB beta-phosphoglucomutase
ptsG glucose PTS, enzyme IICB A3K86_RS05470 A3K86_RS02900
ptsG-crr glucose PTS, enzyme II (CBA components, PtsG) A3K86_RS02900 A3K86_RS05470
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) A3K86_RS19335 A3K86_RS19485
thuG maltose ABC transporter, permease component 2 (ThuG) A3K86_RS19490 A3K86_RS19340
thuK maltose ABC transporter, ATPase component ThuK A3K86_RS19360 A3K86_RS19475

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