D-mannose catabolism in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

D-mannose catabolism in Dinoroseobacter shibae DFL-12

Best path

Also see fitness data for the top candidates

Rules

Overview: Mannose utilization in GapMind is based on MetaCyc pathways D-mannose degradation I via a PTS system (link), pathway II via mannose kinase (link), or conversion to fructose by mannose isomerase.

all:

mannose-PTS and manA
or mannose-transport, mannokinase and manA
or mannose-transport, man-isomerase and scrK
Comment: In pathway I, after uptake and phosphorlation by a PTS system, mannose-6-phosphate isomerase (manA) produces fructose-6-phosphate, which is a central metabolic intermediate. In pathway II, after uptake, mannose kinase is followed by isomerization to fructose 6-phosphate. Or, D-mannose isomerase yields fructose, which can be metabolized by fructokinase (scrK).

mannose-transport:

glcS, glcT, glcU and glcV
or TT_C0211, TT_C0327, TT_C0326 and TT_C0328
or TM1746, TM1747, TM1748, TM1749 and TM1750
or frcA, frcB and frcC
or HSERO_RS03635, HSERO_RS03640 and HSERO_RS03645
or STP6
or gluP
or glcP
or MST1
or manMFS
Comment: Transporters and PTS systems were identified using query: transporter:mannose:D-mannose:D-mannopyranose:CPD-13559:CPD-12601

mannose-PTS:

manX, manY and manZ
or manP
Comment: PTS systems form D-mannose 6-phosphate

32 steps (14 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
frcA	mannose ABC transporter, ATPase component FrcA	Dshi_0388	Dshi_1276
frcB	mannose ABC transporter, substrate-binding component FrcB	Dshi_0390
frcC	mannose ABC transporter, permease component FrcC	Dshi_0389	Dshi_2431
man-isomerase	D-mannose isomerase
scrK	fructokinase	Dshi_2797	Dshi_1976
Alternative steps:
glcP	mannose:H+ symporter
glcS	mannose ABC transporter, substrate-binding component GlcS
glcT	mannose ABC transporter, permease component 1 (GlcT)
glcU	mannose ABC transporter, permease component 2 (GlcU)
glcV	mannose ABC transporter, ATPase component GlcV	Dshi_3141	Dshi_2017
gluP	mannose:Na+ symporter
HSERO_RS03635	mannose ABC transporter, substrate-binding component
HSERO_RS03640	mannose ABC transporter, ATPase component	Dshi_2433	Dshi_0530
HSERO_RS03645	mannose ABC transporter, permease component	Dshi_2432	Dshi_0389
manA	mannose-6-phosphate isomerase	Dshi_1897	Dshi_4146
manMFS	mannose transporter, MFS superfamily
mannokinase	D-mannose kinase
manP	mannose PTS system, EII-CBA components
manX	mannose PTS system, EII-AB component ManX/ManL
manY	mannose PTS system, EII-C component ManY/ManM
manZ	mannose PTS system, EII-D component ManZ/ManN
MST1	mannose:H+ symporter
STP6	mannose:H+ symporter
TM1746	mannose ABC transporter, substrate-binding component
TM1747	mannose ABC transporter, permease component 1	Dshi_2598	Dshi_3793
TM1748	mannose ABC transporter, permease component 2	Dshi_0882	Dshi_3794
TM1749	mannose ABC transporter, ATPase component 1	Dshi_0884	Dshi_3796
TM1750	mannose ABC transporter, ATPase component 2	Dshi_3795	Dshi_0885
TT_C0211	mannose ABC transporter, ATPase component MalK1	Dshi_1416	Dshi_1250
TT_C0326	mannose ABC transporter, permease component 2	Dshi_1246	Dshi_1650
TT_C0327	mannose ABC transporter, permease component 1
TT_C0328	mannose ABC transporter, substrate-binding 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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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