GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Phyllobacterium leguminum ORS 1419

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 (17 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA C7477_RS05175 C7477_RS15690
frcB mannose ABC transporter, substrate-binding component FrcB C7477_RS05185
frcC mannose ABC transporter, permease component FrcC C7477_RS05180 C7477_RS09410
man-isomerase D-mannose isomerase
scrK fructokinase C7477_RS05290 C7477_RS02345
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) C7477_RS15035
glcV mannose ABC transporter, ATPase component GlcV C7477_RS13775 C7477_RS10760
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component C7477_RS16720 C7477_RS09400
HSERO_RS03645 mannose ABC transporter, permease component C7477_RS09405 C7477_RS05180
manA mannose-6-phosphate isomerase C7477_RS14960
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase C7477_RS02345
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 C7477_RS10110 C7477_RS00880
TM1748 mannose ABC transporter, permease component 2 C7477_RS10115 C7477_RS00885
TM1749 mannose ABC transporter, ATPase component 1 C7477_RS16100 C7477_RS10290
TM1750 mannose ABC transporter, ATPase component 2 C7477_RS16095 C7477_RS00890
TT_C0211 mannose ABC transporter, ATPase component MalK1 C7477_RS15040 C7477_RS00240
TT_C0326 mannose ABC transporter, permease component 2 C7477_RS00555 C7477_RS15005
TT_C0327 mannose ABC transporter, permease component 1
TT_C0328 mannose ABC transporter, substrate-binding component C7477_RS00540 C7477_RS15020

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