D-mannitol catabolism in Nocardiopsis gilva YIM 90087

GapMind for catabolism of small carbon sources

D-mannitol catabolism in Nocardiopsis gilva YIM 90087

Best path

Rules

Overview: Mannitol degradation in GapMind is based on MetaCyc pathway mannitol degradation I via a phosphotransferase system (link), pathway II via mannitol 1-dehydrogenase (link), or another oxidative pathway with mannitol 2-dehydrogenase (PMID:8254318).

all:

mannitol-PTS and mtlD
or mannitol-transport, mt1d, mak and manA
or mannitol-transport, mt2d and scrK
Comment: In pathway I, the phosphotransferase system forms mannitol 1-phosphate and 5-dehydrogenase (mtlD) forms fructose 6-phosphate. In pathway II, mannitol is oxidized to mannose by mt1d, phosphorylated to mannose 6-phosphate, and isomerized to fructose 6-phosphate. Alternatively, mannitol 2-dehydrogenase (mt2d) forms fructose, and fructokinase (scrK) forms fructose 6-phosphate.

mannitol-transport:

mtlE, mtlF, mtlG and mtlK
or PLT5
Comment: Transporters and PTS systems were identified using query: transporter:mannitol:D-mannitol

mannitol-PTS:

mtlA
or cmtA * and cmtB
or gutB, gutE and gutA
Comment: PTS systems forming mannitol 1-phosphate

17 steps (11 with candidates)

Or see definitions of steps

Step	Description	Best candidate	2nd candidate
mtlE	polyol ABC transporter, substrate-binding component MtlE/SmoE	CDO52_RS17255
mtlF	polyol ABC transporter, permease component 1 (MtlF/SmoF)	CDO52_RS17260	CDO52_RS20065
mtlG	polyol ABC transporter, permease component 2 (MtlG/SmoG)	CDO52_RS17265	CDO52_RS16285
mtlK	polyol ABC transporter, ATP component MtlK/SmoG	CDO52_RS13845	CDO52_RS13825
mt2d	mannitol 2-dehydrogenase	CDO52_RS17250	CDO52_RS17480
scrK	fructokinase	CDO52_RS22090	CDO52_RS05430
Alternative steps:
cmtA *	mannitol phosphotransferase system, EII-CB component CmtA/MtlF	CDO52_RS15520 with CDO52_RS15525
cmtB	mannitol phosphotransferase system, EII-A component CmtB/MtlF	CDO52_RS23885	CDO52_RS21195
gutA	mannitol PTS system, EII-C2 component GutA
gutB	mannitol PTS system, EII-A component GutB
gutE	mannitol PTS system, EII-BC1 component GutE
mak	mannose kinase	CDO52_RS11555
manA	mannose-6-phosphate isomerase	CDO52_RS10720
mt1d	mannitol 1-dehydrogenase
mtlA	mannitol phosphotransferase system, EII-CBA components	CDO52_RS15520
mtlD	mannitol-1-phosphate 5-dehydrogenase
PLT5	polyol transporter PLT5

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.

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