GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Chromobacterium vaccinii MWU205

Best path

manP, manA

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 (18 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manP mannose PTS system, EII-CBA components VL52_RS18010 VL52_RS07470
manA mannose-6-phosphate isomerase VL52_RS07485 VL52_RS08770
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA VL52_RS18715 VL52_RS09435
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC VL52_RS18720
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 VL52_RS09435 VL52_RS12740
gluP mannose:Na+ symporter VL52_RS04135
HSERO_RS03635 mannose ABC transporter, substrate-binding component VL52_RS16360
HSERO_RS03640 mannose ABC transporter, ATPase component VL52_RS18715 VL52_RS07675
HSERO_RS03645 mannose ABC transporter, permease component VL52_RS18720
man-isomerase D-mannose isomerase
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase VL52_RS08435
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
scrK fructokinase VL52_RS12005 VL52_RS18705
STP6 mannose:H+ symporter
TM1746 mannose ABC transporter, substrate-binding component
TM1747 mannose ABC transporter, permease component 1 VL52_RS00050 VL52_RS00990
TM1748 mannose ABC transporter, permease component 2 VL52_RS00045 VL52_RS00985
TM1749 mannose ABC transporter, ATPase component 1 VL52_RS00040 VL52_RS00980
TM1750 mannose ABC transporter, ATPase component 2 VL52_RS00035 VL52_RS00975
TT_C0211 mannose ABC transporter, ATPase component MalK1 VL52_RS12740 VL52_RS04920
TT_C0326 mannose ABC transporter, permease component 2 VL52_RS08415 VL52_RS04910
TT_C0327 mannose ABC transporter, permease component 1 VL52_RS08420
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 24 2021. The underlying query database was built on Sep 17 2021.

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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