GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Rhizobium freirei PRF 81

Best path

frcA, frcB, frcC, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA RHSP_RS18820 RHSP_RS23030
frcB mannose ABC transporter, substrate-binding component FrcB RHSP_RS18810
frcC mannose ABC transporter, permease component FrcC RHSP_RS18815 RHSP_RS23330
man-isomerase D-mannose isomerase RHSP_RS10595
scrK fructokinase RHSP_RS18860 RHSP_RS13800
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) RHSP_RS16125 RHSP_RS04035
glcV mannose ABC transporter, ATPase component GlcV RHSP_RS20460 RHSP_RS07740
gluP mannose:Na+ symporter RHSP_RS10145
HSERO_RS03635 mannose ABC transporter, substrate-binding component RHSP_RS08735 RHSP_RS07040
HSERO_RS03640 mannose ABC transporter, ATPase component RHSP_RS13515 RHSP_RS28505
HSERO_RS03645 mannose ABC transporter, permease component RHSP_RS32465 RHSP_RS23330
manA mannose-6-phosphate isomerase RHSP_RS13210
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase RHSP_RS16295 RHSP_RS13800
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 RHSP_RS11595
TM1747 mannose ABC transporter, permease component 1 RHSP_RS11600 RHSP_RS23785
TM1748 mannose ABC transporter, permease component 2 RHSP_RS11605 RHSP_RS23780
TM1749 mannose ABC transporter, ATPase component 1 RHSP_RS04235 RHSP_RS05585
TM1750 mannose ABC transporter, ATPase component 2 RHSP_RS11615 RHSP_RS08895
TT_C0211 mannose ABC transporter, ATPase component MalK1 RHSP_RS28065 RHSP_RS17890
TT_C0326 mannose ABC transporter, permease component 2 RHSP_RS07980 RHSP_RS03465
TT_C0327 mannose ABC transporter, permease component 1 RHSP_RS07975 RHSP_RS16130
TT_C0328 mannose ABC transporter, substrate-binding component RHSP_RS31990

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