GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Yersinia intermedia Y228

Best path

manX, manY, manZ, 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 (22 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX mannose PTS system, EII-AB component ManX/ManL CH53_RS21435 CH53_RS04320
manY mannose PTS system, EII-C component ManY/ManM CH53_RS21440 CH53_RS04325
manZ mannose PTS system, EII-D component ManZ/ManN CH53_RS21445 CH53_RS04330
manA mannose-6-phosphate isomerase CH53_RS19535 CH53_RS16325
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA CH53_RS09630 CH53_RS08865
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC CH53_RS08870 CH53_RS18480
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 CH53_RS01010 CH53_RS16980
gluP mannose:Na+ symporter CH53_RS04195 CH53_RS19800
HSERO_RS03635 mannose ABC transporter, substrate-binding component CH53_RS08875
HSERO_RS03640 mannose ABC transporter, ATPase component CH53_RS08865 CH53_RS18475
HSERO_RS03645 mannose ABC transporter, permease component CH53_RS08870 CH53_RS04140
man-isomerase D-mannose isomerase
manMFS mannose transporter, MFS superfamily CH53_RS06820 CH53_RS08490
mannokinase D-mannose kinase CH53_RS13920 CH53_RS21720
manP mannose PTS system, EII-CBA components CH53_RS01145
MST1 mannose:H+ symporter
scrK fructokinase CH53_RS13920 CH53_RS05635
STP6 mannose:H+ symporter
TM1746 mannose ABC transporter, substrate-binding component CH53_RS19110 CH53_RS19105
TM1747 mannose ABC transporter, permease component 1 CH53_RS19115 CH53_RS01285
TM1748 mannose ABC transporter, permease component 2 CH53_RS19120 CH53_RS04380
TM1749 mannose ABC transporter, ATPase component 1 CH53_RS19125 CH53_RS08150
TM1750 mannose ABC transporter, ATPase component 2 CH53_RS08145 CH53_RS19130
TT_C0211 mannose ABC transporter, ATPase component MalK1 CH53_RS10605 CH53_RS21020
TT_C0326 mannose ABC transporter, permease component 2 CH53_RS10590
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