D-maltose catabolism in Phyllobacterium endophyticum PEPV15

GapMind for catabolism of small carbon sources

D-maltose catabolism in Phyllobacterium endophyticum PEPV15

Best path

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.

all:

maltose-transport, malP, pgmB and glk
or maltose-PTS, malA and glk
or maltose-PTS, mapP, malP, pgmB and glk
or maltose-transport, susB and glk
or susB and glucose-utilization
Comment: In the phosphorylase pathway, malP forms beta-glucose-1-phosphate and glucose, and beta-phosphoglucomutase forms glucose-6-phosphate, a central metabolite; glucokinase (glk) is also needed to feed the released glucose into central metabolism. Alternatively, PTS systems produce maltose 6'-phosphate, which can be cleaved by 6-phospho-alpha-glucosidase to glucose and glucose-6-phosphate. Alternatively, maltose can be hydrolyzed by alpha-glucosidase (EC 3.2.1.20) in the cytoplasm. Alternatively, maltose can be hydrolyzed by alpha-glucosidase (EC 3.2.1.20) in the periplasm, as in Bacteroides thetaiotaomicron, followed by glucose utilization.

glucose-utilization:

glucose-transport and glk
or glucose-PTS
or gdh, gnl, gadh1, gadh2, gadh3, kguT, kguK, kguD, edd and eda
Comment: Glucose can be taken up and then phosphorylated to glucose 6-phosphate by the kinase glk. Or, both uptake and phosphorylation are catalyzed by a PTS system. Or, glucose is oxidized to glucono-1,5-lactone in the periplasm (by gdh), hydrolyzed to gluconate (by gnl), oxidized to 2-ketogluconate (by gadh123), taken up by kguT, phosphorylated to 2-dehydro-6-phosphogluconate (by kguK), reduced to gluconate 6-phosphate (by kguD), dehydrated by edd to 2-dehydro-3-deoxy-gluconate 6-phosphate, and cleaved by aldolase eda to pyruvate and D-glyceraldehyde 3-phosphate.

glucose-PTS:

ptsG-crr
or bglF
or ptsG and crr
or manX, manY and manZ

glucose-transport:

MFS-glucose
or SSS-glucose
or glcU'
or PAST-A
or SemiSWEET
or SWEET1
or mglA, mglB and mglC
or gtsA, gtsB, gtsC and gtsD
or glcS, glcT, glcU and glcV
or aglE', aglF', aglG' and aglK'
Comment: Transporters and PTS systems were analyzed uzing query: transporter:glucose:D-glucose:D-glucopyranose:ALPHA-GLUCOSE:GLC:CPD-15374

maltose-PTS:

malEIICBA
or malEIICB and malEIIA
Comment: PTS systems form maltose 6'-phosphate

maltose-transport:

malE, malF, malG and malK
or thuE, thuF, thuG and thuK
or malE1, malF1, malG1 and malK1
or malX_Sm, malF_Sm, malG_Sm and malK_Sm
or musE, musF, musG, musK and musI
or malE_Aa, malF_Aa, malG_Aa and malK_Aa
or aglE, aglF, aglG and aglK
or malEF_Bb, malG_Bb and malK_Bb
or malE_Ss, malF_Ss, malG_Ss and malK_Ss
or MAL11
or SUC2
or SUT1
or cscB
or malAP
or malI
Comment: Transporters and PTS systems identified using: query: transporter:maltose:ALPHA-MALTOSE:CPD-15717

89 steps (41 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
susB	alpha-glucosidase (maltase)	CU100_RS19730	CU100_RS19680
gtsA	glucose ABC transporter, substrate-binding component (GtsA)	CU100_RS02575	CU100_RS17275
gtsB	glucose ABC transporter, permease component 1 (GtsB)	CU100_RS02580	CU100_RS17270
gtsC	glucose ABC transporter, permease component 2 (GtsC)	CU100_RS02585	CU100_RS17265
gtsD	glucose ABC transporter, ATPase component (GtsD)	CU100_RS02590	CU100_RS20770
glk	glucokinase	CU100_RS02105	CU100_RS18345
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)	CU100_RS21710	CU100_RS17270
aglF'	glucose ABC transporter, permease component 1 (AglF)	CU100_RS17270
aglG	maltose ABC transporter, permease component 2 (AglG)	CU100_RS06950	CU100_RS17355
aglG'	glucose ABC transporter, permease component 2 (AglG)	CU100_RS06950	CU100_RS04710
aglK	maltose ABC transporter, ATPase component AglK	CU100_RS06970	CU100_RS15040
aglK'	glucose ABC transporter, ATPase component (AglK)	CU100_RS06970	CU100_RS15040
bglF	glucose PTS, enzyme II (BCA components, BglF)
crr	glucose PTS, enzyme IIA
cscB	maltose permease
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	CU100_RS25210	CU100_RS16395
edd	phosphogluconate dehydratase	CU100_RS05480	CU100_RS02435
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit	CU100_RS07320
gadh3	gluconate 2-dehydrogenase subunit 3
gdh	quinoprotein glucose dehydrogenase	CU100_RS18900	CU100_RS17405
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)	CU100_RS25090	CU100_RS20600
gnl	gluconolactonase	CU100_RS16105	CU100_RS11440
kguD	2-keto-6-phosphogluconate reductase	CU100_RS04245	CU100_RS23850
kguK	2-ketogluconokinase
kguT	2-ketogluconate transporter
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)	CU100_RS16725
malF1	maltose ABC transporter, permease component 1 (MalF1)
malF_Aa	maltose ABC transporter, permease component 1	CU100_RS00665	CU100_RS16725
malF_Sm	maltose ABC transporter, permease component 1
malF_Ss	maltose ABC transporter, permease component 1	CU100_RS07000
malG	maltose ABC transporter, permease component 2 (MalG)	CU100_RS16720	CU100_RS24945
malG1	maltose ABC transporter, permease component 2 (MalG1/MalG2)
malG_Aa	maltose ABC transporter, permease component 2	CU100_RS16720	CU100_RS15065
malG_Bb	maltose ABC transporter, permease component 2	CU100_RS15065	CU100_RS16720
malG_Sm	maltose ABC transporter, permease component 2	CU100_RS16720	CU100_RS15065
malG_Ss	maltose ABC transporter, permease component 2	CU100_RS03585
malI	maltose transporter
malK	maltose ABC transporter, ATPase component MalK	CU100_RS06970	CU100_RS15040
malK1	maltose ABC transporter, ATPase component	CU100_RS02485	CU100_RS24940
malK_Aa	maltose ABC transporter, ATPase component	CU100_RS02485	CU100_RS00650
malK_Bb	maltose ABC transporter, ATPase component	CU100_RS20770	CU100_RS02485
malK_Sm	maltose ABC transporter, ATPase component	CU100_RS02485	CU100_RS15040
malK_Ss	maltose ABC transporter, ATPase component	CU100_RS14775	CU100_RS26070
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
mglA	glucose ABC transporter, ATP-binding component (MglA)	CU100_RS21645	CU100_RS06140
mglB	glucose ABC transporter, substrate-binding component	CU100_RS21650	CU100_RS03130
mglC	glucose ABC transporter, permease component (MglC)	CU100_RS21640	CU100_RS03135
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	CU100_RS16715	CU100_RS02485
PAST-A	proton-associated sugar transporter A
pgmB	beta-phosphoglucomutase
ptsG	glucose PTS, enzyme IICB
ptsG-crr	glucose PTS, enzyme II (CBA components, PtsG)
SemiSWEET	Sugar transporter SemiSWEET	CU100_RS21085
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)	CU100_RS15060	CU100_RS21710
thuG	maltose ABC transporter, permease component 2 (ThuG)	CU100_RS15065	CU100_RS02470
thuK	maltose ABC transporter, ATPase component ThuK	CU100_RS06970	CU100_RS15040

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources