GapMind for catabolism of small carbon sources

 

D-mannose catabolism in Pseudomonas simiae WCS417

Best path

HSERO_RS03635, HSERO_RS03640, HSERO_RS03645, man-isomerase, scrK

Also see fitness data for the top candidates

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
HSERO_RS03635 mannose ABC transporter, substrate-binding component PS417_13645 PS417_17735
HSERO_RS03640 mannose ABC transporter, ATPase component PS417_13635 PS417_11890
HSERO_RS03645 mannose ABC transporter, permease component PS417_13640 PS417_12060
man-isomerase D-mannose isomerase PS417_22150
scrK fructokinase PS417_12685 PS417_12565
Alternative steps:
frcA mannose ABC transporter, ATPase component FrcA PS417_13635 PS417_11890
frcB mannose ABC transporter, substrate-binding component FrcB
frcC mannose ABC transporter, permease component FrcC PS417_12060 PS417_13640
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 PS417_27115 PS417_25760
gluP mannose:Na+ symporter
manA mannose-6-phosphate isomerase PS417_04790 PS417_09635
manMFS mannose transporter, MFS superfamily PS417_00170
mannokinase D-mannose kinase
manP mannose PTS system, EII-CBA components PS417_03975
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 PS417_11135 PS417_12175
TM1748 mannose ABC transporter, permease component 2 PS417_04055 PS417_11140
TM1749 mannose ABC transporter, ATPase component 1 PS417_04050 PS417_08075
TM1750 mannose ABC transporter, ATPase component 2 PS417_04045 PS417_08080
TT_C0211 mannose ABC transporter, ATPase component MalK1 PS417_22130 PS417_12700
TT_C0326 mannose ABC transporter, permease component 2 PS417_22135
TT_C0327 mannose ABC transporter, permease component 1 PS417_22140
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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