GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Martelella endophytica YC6887

Best path

STP6, man-isomerase, scrK

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.

32 steps (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
STP6 mannose:H+ symporter TM49_RS02240
man-isomerase D-mannose isomerase TM49_RS14740
scrK fructokinase TM49_RS05945 TM49_RS01780
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA TM49_RS11595 TM49_RS05125
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC TM49_RS07030
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) TM49_RS00310
glcV mannose ABC transporter, ATPase component GlcV TM49_RS00315 TM49_RS20910
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component TM49_RS08235 TM49_RS07025
HSERO_RS03645 mannose ABC transporter, permease component TM49_RS09750 TM49_RS07030
manA mannose-6-phosphate isomerase TM49_RS05660
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase TM49_RS01780 TM49_RS17980
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 TM49_RS02240
TM1746 mannose ABC transporter, substrate-binding component TM49_RS12540
TM1747 mannose ABC transporter, permease component 1 TM49_RS12545 TM49_RS12035
TM1748 mannose ABC transporter, permease component 2 TM49_RS12550 TM49_RS15860
TM1749 mannose ABC transporter, ATPase component 1 TM49_RS09995 TM49_RS12555
TM1750 mannose ABC transporter, ATPase component 2 TM49_RS08490 TM49_RS03365
TT_C0211 mannose ABC transporter, ATPase component MalK1 TM49_RS06950 TM49_RS22150
TT_C0326 mannose ABC transporter, permease component 2 TM49_RS05325 TM49_RS13245
TT_C0327 mannose ABC transporter, permease component 1 TM49_RS06265
TT_C0328 mannose ABC transporter, substrate-binding component TM49_RS13235

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.

Links

Downloads

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:

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