GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Tatumella morbirosei LMG 23360

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 (21 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
manX mannose PTS system, EII-AB component ManX/ManL HA49_RS13125
manY mannose PTS system, EII-C component ManY/ManM HA49_RS13130
manZ mannose PTS system, EII-D component ManZ/ManN HA49_RS13135
manA mannose-6-phosphate isomerase HA49_RS13095 HA49_RS13120
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA HA49_RS16050 HA49_RS18545
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC HA49_RS18540 HA49_RS07340
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 HA49_RS01440 HA49_RS19415
gluP mannose:Na+ symporter HA49_RS00365
HSERO_RS03635 mannose ABC transporter, substrate-binding component
HSERO_RS03640 mannose ABC transporter, ATPase component HA49_RS18545 HA49_RS16030
HSERO_RS03645 mannose ABC transporter, permease component HA49_RS18540 HA49_RS07340
man-isomerase D-mannose isomerase HA49_RS17305
manMFS mannose transporter, MFS superfamily HA49_RS18965 HA49_RS08115
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components HA49_RS02720 HA49_RS07395
MST1 mannose:H+ symporter
scrK fructokinase HA49_RS02700 HA49_RS05790
STP6 mannose:H+ symporter HA49_RS12775 HA49_RS00475
TM1746 mannose ABC transporter, substrate-binding component
TM1747 mannose ABC transporter, permease component 1 HA49_RS11450 HA49_RS17725
TM1748 mannose ABC transporter, permease component 2 HA49_RS11445 HA49_RS17190
TM1749 mannose ABC transporter, ATPase component 1 HA49_RS17185 HA49_RS00965
TM1750 mannose ABC transporter, ATPase component 2 HA49_RS17180 HA49_RS11460
TT_C0211 mannose ABC transporter, ATPase component MalK1 HA49_RS19415 HA49_RS11785
TT_C0326 mannose ABC transporter, permease component 2 HA49_RS11805
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