EMBOSS: findkm

| ## EMBOSS: findkm

# Program findkm

## Function

Find Km and Vmax for an enzyme reaction by a Hanes/Woolf plot

## Description

Takes a file of enzymatic data and plots Michaelis Menten and Hanes Woolf plots of the data. From these ot calculates the Michaelis Menten constant (Km) and the maximum velocity (Vmax) of the reaction.

## Usage

Here is a sample session with findkm.

    %findkm
    Calculates Km and Vmax for an enzyme reaction.
    Enter name of file containing data: enztest.dat
    Display on device [xwin]:

## Command line arguments

       Mandatory qualifiers:
      [-infile]            infile     Enter name of file containing data
      [-outfile]           outfile    Output file name
       -graphlb            xygraph    Graph type

       Optional qualifiers: (none)
       Advanced qualifiers:
       -[no]plot           bool       S/V vs S

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | Enter name of file containing data | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | <sequence>.findkm
-graphlb | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
-[no]plot | S/V vs S | Yes/No | Yes

## Input file format

The input file is a file of enzymatic data, [S] against V, Substrate concentration against reaction velocity.

The data for the example run are shown below:

      0.10   2
      0.20   4
      0.50   9
      1.00  17
      2.00  29
      5.00  50
     10.00  67
     20.00  80
     50.00  91
    100.00  95

## Output file format

Here is a sample output from the example above, together with the plots:

    ---Hanes Woolf Plot Calculations---
    Slope of best fit line is a = 0.01
    Coefficient in Eqn of line y = ma +b is b = 0.05
    Where line cuts x axis = (-0.20, 0)
    Where line cuts y axis = (0, 0.05)
    Limit-point of graph for plot = (103.00, 1.08)

    Vmax = 99.70, Km = 4.894612

Click here for the graphical output

## Data files

See Input File Format

## Notes

## References

1. Voet & Voet (1993) 'Biochemistry'
2. Dawes 'Quantitative Problems in Biochemistry' 5th Edition.
3. Manuel G. Claros, Francisco M. Canovas 'Lines&Kinetics: a graphic tool to deal with linear regressions and enzyme kinetics.' EMBnet.news vol 5.1 http://www.uk.embnet.org/embnet.news/vol5_1/kinetics.html
4. Cornish-Bowden (1996) 'Fundamentals of Enzyme kinetics' Portland Press, London.

## Warnings

## Diagnostic Error Messages

## Exit status

## Known bugs

## See also

Program name | Description
--- | ---

## Author(s)

This application was written by Sinead O'Leary (soleary@hgmp.mrc.ac.uk)

This application was modified for inclusion in EMBOSS by David Martin (david.martin@biotek.uio.no) at the Norwegian EMBnet node.

## History

Completed November 1999

Modified May 2000

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments