sucrose catabolism in Amycolatopsis halophila YIM 93223

GapMind for catabolism of small carbon sources

sucrose catabolism in Amycolatopsis halophila YIM 93223

Best path

Rules

Overview: Sucrose utilization in GapMind is based on MetaCyc pathways sucrose degradation I via sucrose 6-phosphate hydrolase (link), pathway II via sucrose synthase (link), pathway III via invertase (link), and pathway IV via sucrose phosphorylase (link). Pathway V is similar to pathway III and is not reported in prokaryotes, so it is not included. There is no pathway VI. Pathway VII (via sucrose 3-dehydrogenase, link) is too poorly understood to include in GapMind.

all:

sucrose-PTS, scrB and scrK
or sucrose-transport, SUS, scrK, galU and pgmA
or sucrose-transport, ams, scrK and glk
or sucrose-transport, scrP, scrK and pgmA
or ams and glucose-utilization
or ams and fructose-utilization
Comment: In pathway I, a phosphotransferase system forms sucrose 6-phosphate, the hydrolyase scrB forms glucose-6-phosphate and fructose, and fructokinase forms fructose 6-phosphate. In pathway II, transport is followed by sucrose synthase (SUS) in reverse, forming fructose and UDP-glucose; the fructose is phosphorylated by scrK, while the UDP-glucose is transformed to glucose-6-phosphate by uridylyltransferase galU and phosphoglucomutase (pgmA). In pathway III, transport is followed by cleavage to glucose and fructose and phosphorylation of each. In pathway IV, transport is followed by phosphorylase scrP, producing fructose and glucose 1-phosphate, which are transformed by kinase scrK and phosphoglucomutase pgmA. Alternatively, sucrose can be hydrolyzed in the periplasm, followed by utilization of the glucose or fructose.

fructose-utilization:

fructose-PTS-6-phosphate
or fructose-transport and scrK
or fructose-PTS-1-phosphate, 1pfk, fba and tpi
Comment: For a PTS forming fructose 6-phosphate, no further steps are needed to reach central metabolism. For direct transport, the usual pathway is fructokinase (scrK), forming fructose 6-phosphate. For PTS forming fructose 1-phosphate, the usual path is phosphorylation (1pfk) and cleavage by fructose 1,6-bisphosphate aldolase (fba); triose-phosphate isomerase (tpi) converts the glycerone phosphate to D-glyceraldehyde 3-phosphate, which is a central metabolic intermediate.

fructose-PTS-1-phosphate:

fruA and fruB
or fruA and fruI
or fruA and fruD
or fruII-A, fruII-B and fruII-C
or fruII-ABC *
Comment: Fructose 1-phosphate forming PTS systems contain FruA with either FruB, FruI, or FruD. FruA has EII-B'BC components; the other genes all have E-IIA but their domain content varies. FruB has E-IIA and Hpr components; FruI has EI-Hpr-IIA components; and FruD has E-IIA only.

fructose-transport:

araV, araU, araT and araS
or fruE, fruF, fruG and fruK
or frcA, frcB and frcC
or Slc2a5
or ffz
or glcP
or ght6
or STP6
or THT2A
or frt1
or fruP
or BT1758
Comment: Transporters and PTS systems (forming -1-phosphate or -6-phosphate) were found using query: transporter:fructose:D-fructose:BETA-D-FRUCTOSE.

fructose-PTS-6-phosphate:

levD, levE, levF and levG
or levDE, levF and levG

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

sucrose-PTS:

sacP
or ptsS
Comment: PTS form sucrose 6-phosphate.

sucrose-transport:

thuE, thuF, thuG and thuK
or aglE, aglF, aglG and aglK
or TMT1 and TMT2
or sut
or SLC45A2
or scrT
or sut1
or cscB
or SLC45A3
or SLC45A4
Comment: Transporters and PTS systems were analyzed using query: transporter:sucrose

101 steps (43 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
ams	sucrose hydrolase (invertase)	AMYHA_RS21080	AMYHA_RS07415
fruII-ABC *	fructose-specific PTS system (fructose 1-phosphate forming), EII-ABC components	AMYHA_RS23550 with AMYHA_RS23555
1pfk	1-phosphofructokinase	AMYHA_RS23560	AMYHA_RS12935
fba	fructose 1,6-bisphosphate aldolase	AMYHA_RS04045
tpi	triose-phosphate isomerase	AMYHA_RS11495	AMYHA_RS11490
Alternative steps:
aglE	sucrose ABC transporter, substrate-binding component AglK	AMYHA_RS24835
aglE'	glucose ABC transporter, substrate-binding component (AglE)	AMYHA_RS24835
aglF	sucrose ABC transporter, permease component 1 (AglF)	AMYHA_RS24830
aglF'	glucose ABC transporter, permease component 1 (AglF)	AMYHA_RS24830
aglG	sucrose ABC transporter, permease component 2 (AglG)	AMYHA_RS24825	AMYHA_RS07420
aglG'	glucose ABC transporter, permease component 2 (AglG)	AMYHA_RS24825	AMYHA_RS17665
aglK	sucrose ABC transporter, ATPase component AglK	AMYHA_RS07215	AMYHA_RS24840
aglK'	glucose ABC transporter, ATPase component (AglK)	AMYHA_RS24840	AMYHA_RS07215
araS	fructose ABC transporter, substrate-binding component AraS
araT	fructose ABC transporter, permease component 2 (AraT)
araU	fructose ABC transporter, permease component 1 (AraU)
araV	fructose ABC transporter, ATPase component AraV	AMYHA_RS07215	AMYHA_RS07160
bglF	glucose PTS, enzyme II (BCA components, BglF)
BT1758	fructose transporter
crr	glucose PTS, enzyme IIA
cscB	sucrose:H+ symporter CscB
eda	2-keto-3-deoxygluconate 6-phosphate aldolase	AMYHA_RS05505
edd	phosphogluconate dehydratase	AMYHA_RS05510	AMYHA_RS04685
ffz	fructose facilitator (uniporter)
frcA	fructose ABC transporter, ATPase component FrcA	AMYHA_RS08560	AMYHA_RS17865
frcB	fructose ABC transporter, substrate-binding component FrcB
frcC	fructose ABC transporter, permease component FrcC	AMYHA_RS08565
frt1	fructose:H+ symporter Frt1
fruA	fructose-specific PTS system (fructose 1-phosphate forming), EII-B'BC components	AMYHA_RS23550
fruB	fructose-specific PTS system (fructose 1-phosphate forming), Hpr and EII-A components
fruD	fructose-specific PTS system (fructose 1-phosphate forming), EII-A component
fruE	fructose ABC transporter, substrate-binding component FruE
fruF	fructose ABC transporter, permease component 1 (FruF)	AMYHA_RS08565
fruG	fructose ABC transporter, permease component 2 (FruG)	AMYHA_RS08565
fruI	fructose-specific PTS system (fructose 1-phosphate forming), EI, Hpr, and EII-A components	AMYHA_RS23540
fruII-A	fructose-specific PTS system (fructose 1-phosphate forming), EII-A component	AMYHA_RS23555
fruII-B	fructose-specific PTS system (fructose 1-phosphate forming), EII-B component	AMYHA_RS23550
fruII-C	fructose-specific PTS system (fructose 1-phosphate forming), EII-C component	AMYHA_RS23550
fruK	fructose ABC transporter, ATPase component FruK	AMYHA_RS08560	AMYHA_RS00100
fruP	fructose porter FruP
gadh1	gluconate 2-dehydrogenase flavoprotein subunit
gadh2	gluconate 2-dehydrogenase cytochrome c subunit
gadh3	gluconate 2-dehydrogenase subunit 3
galU	glucose 1-phosphate uridylyltransferase	AMYHA_RS08220	AMYHA_RS01120
gdh	quinoprotein glucose dehydrogenase	AMYHA_RS08780
ght6	high-affinity fructose transporter ght6
glcP	fructose:H+ symporter GlcP
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)	AMYHA_RS07160	AMYHA_RS24840
glk	glucokinase	AMYHA_RS17830	AMYHA_RS17900
gnl	gluconolactonase	AMYHA_RS07310	AMYHA_RS17305
gtsA	glucose ABC transporter, substrate-binding component (GtsA)
gtsB	glucose ABC transporter, permease component 1 (GtsB)
gtsC	glucose ABC transporter, permease component 2 (GtsC)	AMYHA_RS24825	AMYHA_RS21320
gtsD	glucose ABC transporter, ATPase component (GtsD)	AMYHA_RS07215	AMYHA_RS24840
kguD	2-keto-6-phosphogluconate reductase	AMYHA_RS07360	AMYHA_RS20260
kguK	2-ketogluconokinase
kguT	2-ketogluconate transporter
levD	fructose PTS system (fructose 6-phosphate forming), EII-A component
levDE	fructose PTS system (fructose 6-phosphate forming), EII-AB component
levE	fructose PTS system (fructose 6-phosphate forming), EII-B component
levF	fructose PTS system (fructose 6-phosphate forming), EII-C component
levG	fructose PTS system (fructose 6-phosphate forming), EII-D component
manX	glucose PTS, enzyme EIIAB
manY	glucose PTS, enzyme EIIC
manZ	glucose PTS, enzyme EIID
MFS-glucose	glucose transporter, MFS superfamily	AMYHA_RS07370
mglA	glucose ABC transporter, ATP-binding component (MglA)	AMYHA_RS08560	AMYHA_RS17865
mglB	glucose ABC transporter, substrate-binding component	AMYHA_RS17870
mglC	glucose ABC transporter, permease component (MglC)	AMYHA_RS08565
PAST-A	proton-associated sugar transporter A
pgmA	alpha-phosphoglucomutase	AMYHA_RS09340	AMYHA_RS25290
ptsG	glucose PTS, enzyme IICB
ptsG-crr	glucose PTS, enzyme II (CBA components, PtsG)
ptsS	sucrose phosphotransferase enzyme EII-BCA
sacP	sucrose phosphotransferase enzyme EII-BC
scrB	sucrose-6-phosphate hydrolase
scrK	fructokinase	AMYHA_RS23955	AMYHA_RS17900
scrP	sucrose phosphorylase
scrT	sucrose permease ScrT
SemiSWEET	Sugar transporter SemiSWEET
Slc2a5	fructose:H+ symporter
SLC45A2	sucrose transporter
SLC45A3	sucrose:H+ symporter
SLC45A4	sucrose:H+ symporter
SSS-glucose	Sodium/glucose cotransporter
STP6	sugar transport protein 6
SUS	sucrose synthase
sut	sucrose:proton symporter SUT/SUC
sut1	alpha-glucoside permease Sut1
SWEET1	bidirectional sugar transporter SWEET1
THT2A	fructose THT2A
thuE	sucrose ABC transporter, substrate-binding component ThuE
thuF	sucrose ABC transporter, permease component 1 (ThuF)	AMYHA_RS07165	AMYHA_RS07245
thuG	sucrose ABC transporter, permease component 2 (ThuG)	AMYHA_RS21320	AMYHA_RS14440
thuK	sucrose ABC transporter, ATPase component ThuK	AMYHA_RS07215	AMYHA_RS24840
TMT1	heteromeric sucrose:H+ symporter, TMT1 component
TMT2	heteromeric sucrose:H+ symporter, TMT2 component

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