                                  pepstats



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Function

   Calculate statistics of protein properties

Description

   pepstats reads one or more protein sequences and writes an output file
   with various statistics on the protein properties. This includes:
     * 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)

Usage

   Here is a sample session with pepstats


% pepstats -pkdata Epkexpasy.dat
Calculate statistics of protein properties
Input protein sequence(s): tsw:laci_ecoli
Pepstats program output file [laci_ecoli.pepstats]:


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

   Example 2


% pepstats
Calculate statistics of protein properties
Input protein sequence(s): tsw:laci_ecoli
Pepstats program output file [laci_ecoli.pepstats]:


   Go to the output files for this example

Command line arguments

Calculate statistics of protein properties
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Protein sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.pepstats] Pepstats program output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -aadata             datafile   [Eamino.dat] Amino acid properties
   -mwdata             datafile   [Emolwt.dat] Molecular weight data for amino
                                  acids
   -pkdata             datafile   [Epk.dat] Values of pKa for amino acids
   -[no]termini        boolean    [Y] Include charge at N and C terminus
   -mono               boolean    [N] Use monoisotopic weights

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


Input file format

   pepstats reads one or more protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  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              Reviewed;         360 AA.
AC   P03023; O09196; P71309; Q2MC79; Q47338;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   19-JUL-2003, sequence version 3.
DT   13-JUN-2012, entry version 136.
DE   RecName: Full=Lactose operon repressor;
GN   Name=lacI; OrderedLocusNames=b0345, JW0336;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0;
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene.";
RL   Nature 274:765-769(1978).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Chen J., Matthews K.K.S.M.;
RL   Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Marsh S.;
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RA   Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA   Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA   Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT   "Sequence of minutes 4-25 of Escherichia coli.";
RL   Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   MEDLINE=97426617; PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.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   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains


  [Part of this file has been deleted for brevity]

FT   CHAIN         1    360       Lactose operon repressor.
FT                                /FTId=PRO_0000107963.
FT   DOMAIN        1     58       HTH lacI-type.
FT   DNA_BIND      6     25       H-T-H motif.
FT   VARIANT     282    282       Y -> D (in T41 mutant).
FT   MUTAGEN      17     17       Y->H: Broadening of specificity.
FT   MUTAGEN      22     22       R->N: Recognizes an operator variant.
FT   CONFLICT    286    286       L -> S (in Ref. 1, 4 and 7).
FT   HELIX         6     11
FT   TURN         12     14
FT   HELIX        17     24
FT   HELIX        33     45
FT   HELIX        51     56
FT   STRAND       63     69
FT   HELIX        74     89
FT   STRAND       93     98
FT   STRAND      101    103
FT   HELIX       104    115
FT   TURN        116    118
FT   STRAND      122    126
FT   HELIX       130    139
FT   TURN        140    142
FT   STRAND      145    150
FT   STRAND      154    156
FT   STRAND      158    161
FT   HELIX       163    177
FT   STRAND      181    186
FT   HELIX       192    207
FT   STRAND      213    217
FT   HELIX       222    234
FT   STRAND      240    246
FT   HELIX       247    259
FT   TURN        265    267
FT   STRAND      268    271
FT   HELIX       277    281
FT   STRAND      282    284
FT   STRAND      287    290
FT   HELIX       293    308
FT   STRAND      314    319
FT   STRAND      322    324
FT   STRAND      334    338
FT   HELIX       343    353
FT   HELIX       354    356
SQ   SEQUENCE   360 AA;  38590 MW;  347A8DEE92D736CB CRC64;
     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 CYIPPLTTIK 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 = 38590.16             Residues = 360
Average Residue Weight  = 107.195       Charge   = 1.5
Isoelectric Point = 6.3901
A280 Molar Extinction Coefficients  = 22920 (reduced)   23045 (cystine bridges)
A280 Extinction Coefficients 1mg/ml = 0.594 (reduced)   0.597 (cystine bridges)
Improbability of expression in inclusion bodies = 0.660

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
J = ---         0               0.000           0.000
K = Lys         11              3.056           0.463
L = Leu         41              11.389          1.539
M = Met         10              2.778           1.634
N = Asn         12              3.333           0.775
O = ---         0               0.000           0.000
P = Pro         14              3.889           0.748
Q = Gln         28              7.778           1.994
R = Arg         19              5.278           1.077
S = Ser         32              8.889           1.270
T = Thr         19              5.278           0.865
U = ---         0               0.000           0.000
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)             120             33.333
Small           (A+B+C+D+G+N+P+S+T+V)   197             54.722
Aliphatic       (A+I+L+V)               137             38.056
Aromatic        (F+H+W+Y)               21               5.833
Non-polar       (A+C+F+G+I+L+M+P+V+W+Y) 200             55.556
Polar           (D+E+H+K+N+Q+R+S+T+Z)   160             44.444
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


  Output files for usage example 2

  File: laci_ecoli.pepstats

PEPSTATS of LACI_ECOLI from 1 to 360

Molecular weight = 38590.16             Residues = 360
Average Residue Weight  = 107.195       Charge   = 1.5
Isoelectric Point = 6.8385
A280 Molar Extinction Coefficients  = 22920 (reduced)   23045 (cystine bridges)
A280 Extinction Coefficients 1mg/ml = 0.594 (reduced)   0.597 (cystine bridges)
Improbability of expression in inclusion bodies = 0.660

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
J = ---         0               0.000           0.000
K = Lys         11              3.056           0.463
L = Leu         41              11.389          1.539
M = Met         10              2.778           1.634
N = Asn         12              3.333           0.775
O = ---         0               0.000           0.000
P = Pro         14              3.889           0.748
Q = Gln         28              7.778           1.994
R = Arg         19              5.278           1.077
S = Ser         32              8.889           1.270
T = Thr         19              5.278           0.865
U = ---         0               0.000           0.000
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)             120             33.333
Small           (A+B+C+D+G+N+P+S+T+V)   197             54.722
Aliphatic       (A+I+L+V)               137             38.056
Aromatic        (F+H+W+Y)               21               5.833
Non-polar       (A+C+F+G+I+L+M+P+V+W+Y) 200             55.556
Polar           (D+E+H+K+N+Q+R+S+T+Z)   160             44.444
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'.

   Absorption coefficients use values read from the EMBOSS data file
   'Eamino.dat'. Values in this file assume cysteines are reduced. If
   cysteines are in disulphide bridges the value should be adjusted as
   documented at the top of the file, and a local copy used to override
   the default values.

   Molecular weights are read from a local data file Emolwt.dat.

   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

   DayhoffStat is the amino acid's molar percentage divided by the Dayhoff
   statistic. The Dayhoff statistic is read from the EMBOSS data file
   Edayhoff.freq and is the amino acid's relative occurence per 1000 aa
   normalised to 100.

   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.

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
   backtranambig    Back-translate a protein sequence to ambiguous nucleotide
                    sequence
   backtranseq      Back-translate a protein sequence to a nucleotide sequence
   charge           Draw a protein charge plot
   compseq          Calculate the composition of unique words in sequences
   emowse           Search protein sequences by digest fragment molecular weight
   freak            Generate residue/base frequency table or plot
   hmoment          Calculate and plot hydrophobic moment for protein sequence(s)
   iep              Calculate the isoelectric point of proteins
   mwcontam         Find weights common to multiple molecular weights files
   mwfilter         Filter noisy data from molecular weights file
   octanol          Draw a White-Wimley protein hydropathy plot
   oddcomp          Identify proteins with specified sequence word composition
   pepdigest        Report on protein proteolytic enzyme or reagent cleavage
                    sites
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepwindow        Draw a hydropathy plot for a protein sequence
   pepwindowall     Draw Kyte-Doolittle hydropathy plot for a protein
                    alignment
   wordcount        Count and extract unique words in molecular sequence(s)

Author(s)

   Alan Bleasby
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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
