
                                 pepstats 



Function

   Protein statistics

Description

   pepstats outputs a report of simple protein sequence information
   including:

     * Molecular weight
     * Number of residues
     * Average residue weight
     * Charge
     * Isoelectric point
     * For each type of amino acid: number, molar percent, DayhoffStat
     * For each physico-chemical class of amino acid: number, molar
       percent
     * Probability of protein expression in E. coli inclusion bodies
     * Molar extinction coefficient (A280)
     * Extinction coefficient at 1 mg/ml (A280)

   DayhoffStat is the amino acid's molar percentage divided by the
   Dayhoff statistic. The Dayhoff statistic is the amino acid's relative
   occurence per 1000 aa normalised to 100 by rls@ebi.ac.uk (original
   work from 1993)

   The probability of expression in inclusion bodies is sometimes
   referred to as a type of solubility measure. If, however, a
   recombinant protein is expressed in Escherichia coli, it can be
   expressed as soluble in the cytosol or insoluble in inclusion bodies.
   If the Harrison model predicts a given protein to be probably
   expressed in includion bodies, this doesn't mean that it is not
   possible to get it soluble in the cytosol. One example: Thermatoga
   maritima cell divison protein FtsA with a C-terminal His-Tag has a 58%
   Harrison probability of being expressed in inclusion bodies. However,
   there was plenty of soluble protein in the E. coli cytosol (F. van den
   Ent and J. Lowe, EMBO J. 19, 5300-5307 2000). If the protein is
   expressed in inclusion bodies or not is not only dependent on the
   sequence, but also on many other factors, such as E. coli strain,
   incubation temperature, type of expression vector, strength of
   promoter and medium.

Usage

   Here is a sample session with pepstats


% pepstats 
Protein statistics
Input sequence(s): tsw:laci_ecoli
Output file [laci_ecoli.pepstats]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -aadata             datafile   Molecular weight data for amino acids
   -[no]termini        boolean    Include charge at N and C terminus

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -odirectory2         string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.pepstats
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -aadata Molecular weight data for amino acids Data file Eamino.dat
   -[no]termini Include charge at N and C terminus Boolean value Yes/No
   Yes

Input file format

   pepstats reads a normal protein sequence USA.

  Input files for usage example

   'tsw:laci_ecoli' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:laci_ecoli

ID   LACI_ECOLI     STANDARD;      PRT;   360 AA.
AC   P03023; P71309; Q47338; O09196;
DT   21-JUL-1986 (Rel. 01, Created)
DT   01-NOV-1997 (Rel. 35, Last sequence update)
DT   15-DEC-1998 (Rel. 37, Last annotation update)
DE   LACTOSE OPERON REPRESSOR.
GN   LACI.
OS   Escherichia coli.
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
RN   [1]
RP   SEQUENCE FROM N.A.
RX   MEDLINE; 78246991.
RA   FARABAUGH P.J.;
RT   "Sequence of the lacI gene.";
RL   Nature 274:765-769(1978).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   STRAIN=K12 / MG1655;
RX   MEDLINE; 97426617.
RA   BLATTNER F.R., PLUNKETT G. III, BLOCH C.A., PERNA N.T., BURLAND V.,
RA   RILEY M., COLLADO-VIDES J., GLASNER F.D., RODE C.K., MAYHEW G.F.,
RA   GREGOR J., DAVIS N.W., KIRKPATRICK H.A., GOEDEN M.A., ROSE D.J.,
RA   MAU B., SHAO Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1474(1997).
RN   [3]
RP   SEQUENCE FROM N.A.
RC   STRAIN=K12 / MG1655;
RA   DUNCAN M., ALLEN E., ARAUJO R., APARICIO A.M., CHUNG E., DAVIS K.,
RA   FEDERSPIEL N., HYMAN R., KALMAN S., KOMP C., KURDI O., LEW H.,
RA   LIN D., NAMATH A., OEFNER P., ROBERTS D., SCHRAMM S., DAVIS R.W.;
RL   Submitted (NOV-1996) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   SEQUENCE FROM N.A.
RA   CHEN J., MATTHEWS K.K.S.M.;
RL   Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   SEQUENCE FROM N.A.
RA   MARSH S.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   SEQUENCE OF 1-147; 159-230 AND 233-360.
RX   MEDLINE; 76091932.
RA   BEYREUTHER K., ADLER K., FANNING E., MURRAY C., KLEMM A., GEISLER N.;
RT   "Amino-acid sequence of lac repressor from Escherichia coli.
RT   Isolation, sequence analysis and sequence assembly of tryptic
RT   peptides and cyanogen-bromide fragments.";
RL   Eur. J. Biochem. 59:491-509(1975).
RN   [7]


  [Part of this file has been deleted for brevity]

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CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to license@isb-sib.ch).
CC   --------------------------------------------------------------------------
DR   EMBL; V00294; CAA23569.1; -.
DR   EMBL; J01636; AAA24052.1; -.
DR   EMBL; AE000141; AAC73448.1; -.
DR   EMBL; U73857; AAB18069.1; ALT_INIT.
DR   EMBL; X58469; CAA41383.1; -.
DR   EMBL; U86347; AAB47270.1; ALT_INIT.
DR   EMBL; U72488; AAB36549.1; -.
DR   EMBL; U78872; AAB37348.1; -.
DR   EMBL; U78873; AAB37351.1; -.
DR   EMBL; U78874; AAB37354.1; -.
DR   PIR; A03558; RPECL.
DR   PIR; S02540; S02540.
DR   PDB; 1LCC; 31-JAN-94.
DR   PDB; 1LCD; 31-JAN-94.
DR   PDB; 1LTP; 31-OCT-93.
DR   PDB; 1TLF; 31-JUL-95.
DR   PDB; 1LBG; 11-JUL-96.
DR   PDB; 1LBH; 11-JUL-96.
DR   PDB; 1LBI; 11-JUL-96.
DR   PDB; 1LQC; 12-FEB-97.
DR   ECO2DBASE; H039.0; 6TH EDITION.
DR   ECOGENE; EG10525; LACI.
DR   PFAM; PF00356; lacI; 1.
DR   PFAM; PF00532; Peripla_BP_like; 1.
DR   PROSITE; PS00356; HTH_LACI_FAMILY; 1.
KW   Transcription regulation; DNA-binding; Repressor; 3D-structure.
FT   DNA_BIND      6     25       H-T-H MOTIF.
FT   MUTAGEN      17     17       Y->H: BROADENING OF SPECIFICITY.
FT   MUTAGEN      22     22       R->N: RECOGNIZE AN OPERATOR VARIANT.
FT   VARIANT     282    282       Y -> D (IN T41 MUTANT).
FT   CONFLICT    286    286       S -> L (IN AAA24052, REF. 2, 4 AND 5).
FT   HELIX         6     13
FT   TURN         14     14
FT   HELIX        17     24
FT   HELIX        32     44
FT   TURN         49     50
SQ   SEQUENCE   360 AA;  38564 MW;  4CA5A1D6 CRC32;
     MKPVTLYDVA EYAGVSYQTV SRVVNQASHV SAKTREKVEA AMAELNYIPN RVAQQLAGKQ
     SLLIGVATSS LALHAPSQIV AAIKSRADQL GASVVVSMVE RSGVEACKAA VHNLLAQRVS
     GLIINYPLDD QDAIAVEAAC TNVPALFLDV SDQTPINSII FSHEDGTRLG VEHLVALGHQ
     QIALLAGPLS SVSARLRLAG WHKYLTRNQI QPIAEREGDW SAMSGFQQTM QMLNEGIVPT
     AMLVANDQMA LGAMRAITES GLRVGADISV VGYDDTEDSS CYIPPSTTIK QDFRLLGQTS
     VDRLLQLSQG QAVKGNQLLP VSLVKRKTTL APNTQTASPR ALADSLMQLA RQVSRLESGQ
//

Output file format

  Output files for usage example

  File: laci_ecoli.pepstats

PEPSTATS of LACI_ECOLI from 1 to 360

Molecular weight = 38563.97             Residues = 360
Average Residue Weight  = 107.122       Charge   = 1.5
Isoelectric Point = 6.8820
A280 Molar Extinction Coefficient  = 21620
A280 Extinction Coefficient 1mg/ml = 0.56
Improbability of expression in inclusion bodies = 0.670

Residue         Number          Mole%           DayhoffStat
A = Ala         44              12.222          1.421
B = Asx         0               0.000           0.000
C = Cys         3               0.833           0.287
D = Asp         17              4.722           0.859
E = Glu         15              4.167           0.694
F = Phe         4               1.111           0.309
G = Gly         22              6.111           0.728
H = His         7               1.944           0.972
I = Ile         18              5.000           1.111
K = Lys         11              3.056           0.463
L = Leu         40              11.111          1.502
M = Met         10              2.778           1.634
N = Asn         12              3.333           0.775
P = Pro         14              3.889           0.748
Q = Gln         28              7.778           1.994
R = Arg         19              5.278           1.077
S = Ser         33              9.167           1.310
T = Thr         19              5.278           0.865
V = Val         34              9.444           1.431
W = Trp         2               0.556           0.427
X = Xaa         0               0.000           0.000
Y = Tyr         8               2.222           0.654
Z = Glx         0               0.000           0.000

Property        Residues                Number          Mole%
Tiny            (A+C+G+S+T)             121             33.611
Small           (A+B+C+D+G+N+P+S+T+V)   198             55.000
Aliphatic       (I+L+V)                 92              25.556
Aromatic        (F+H+W+Y)               21               5.833
Non-polar       (A+C+F+G+I+L+M+P+V+W+Y) 199             55.278
Polar           (D+E+H+K+N+Q+R+S+T+Z)   161             44.722
Charged         (B+D+E+H+K+R+Z)         69              19.167
Basic           (H+K+R)                 37              10.278
Acidic          (B+D+E+Z)               32               8.889

Data files

   The Dayhoff statistic is read from the EMBOSS data file
   'Edayhoff.freq'. You can inspect and modify this file by copying it
   into your current directory with the command: 'embossdata -fetch'.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by the EMBOSS
   environment variable EMBOSS_DATA.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata".
   Files for all EMBOSS runs can be put in the user's home directory, or
   again in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   None.

References

    1. Roger G. Harrison "Expression of soluble heterologous proteins via
       fusion with NusA protein" in inNovations 11, June 2000, p 4 - 7.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                          Description
   backtranseq  Back translate a protein sequence
   charge       Protein charge plot
   checktrans   Reports STOP codons and ORF statistics of a protein
   compseq      Counts the composition of dimer/trimer/etc words in a sequence
   emowse       Protein identification by mass spectrometry
   freak        Residue/base frequency table or plot
   iep          Calculates the isoelectric point of a protein
   mwcontam     Shows molwts that match across a set of files
   mwfilter     Filter noisy molwts from mass spec output
   octanol      Displays protein hydropathy
   pepinfo      Plots simple amino acid properties in parallel
   pepwindow    Displays protein hydropathy
   pepwindowall Displays protein hydropathy of a set of sequences

Author(s)

   Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written (1999) - Alan Bleasby

Target users

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

Comments

   None
