GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Rhodobacter johrii JA192

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 (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
frcA mannose ABC transporter, ATPase component FrcA C8J29_RS11815 C8J29_RS17290
frcB mannose ABC transporter, substrate-binding component FrcB C8J29_RS11825
frcC mannose ABC transporter, permease component FrcC C8J29_RS11820 C8J29_RS17225
man-isomerase D-mannose isomerase C8J29_RS16415
scrK fructokinase C8J29_RS02915 C8J29_RS15765
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)
glcV mannose ABC transporter, ATPase component GlcV C8J29_RS07090 C8J29_RS18660
gluP mannose:Na+ symporter
HSERO_RS03635 mannose ABC transporter, substrate-binding component C8J29_RS03425
HSERO_RS03640 mannose ABC transporter, ATPase component C8J29_RS16570 C8J29_RS15005
HSERO_RS03645 mannose ABC transporter, permease component C8J29_RS17225 C8J29_RS16565
manA mannose-6-phosphate isomerase C8J29_RS10990
manMFS mannose transporter, MFS superfamily
mannokinase D-mannose kinase C8J29_RS15765
manP mannose PTS system, EII-CBA components C8J29_RS00715
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 C8J29_RS19500
TM1747 mannose ABC transporter, permease component 1 C8J29_RS19495 C8J29_RS21175
TM1748 mannose ABC transporter, permease component 2 C8J29_RS19490 C8J29_RS13935
TM1749 mannose ABC transporter, ATPase component 1 C8J29_RS21135 C8J29_RS18795
TM1750 mannose ABC transporter, ATPase component 2 C8J29_RS21130 C8J29_RS18800
TT_C0211 mannose ABC transporter, ATPase component MalK1 C8J29_RS14155 C8J29_RS18660
TT_C0326 mannose ABC transporter, permease component 2 C8J29_RS05980
TT_C0327 mannose ABC transporter, permease component 1
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