EMBOSS: pepstats

| pepstats

## Function

Calculates 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
    Calculates 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

## Command line arguments

       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
       -[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
       -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 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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-outfile] (Parameter 2) | Pepstats program output file | Output file | <*>.pepstats
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
-aadata | Amino acid properties | Data file | Eamino.dat
-mwdata | Molecular weight data for amino acids | Data file | Emolwt.dat
-[no]termini | Include charge at N and C terminus | Boolean value Yes/No | Yes
-mono | Use monoisotopic weights | Boolean value Yes/No | No

## 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              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   20-MAR-2007, entry version 87.
    DE   Lactose operon repressor.
    GN   Name=lacI; OrderedLocusNames=b0345, JW0336;
    OS   Escherichia coli.
    OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
    OC   Enterobacteriaceae; Escherichia.
    OX   NCBI_TaxID=562;
    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]

    DR   Pfam; PF00532; Peripla_BP_1; 1.
    DR   PRINTS; PR00036; HTHLACI.
    DR   SMART; SM00354; HTH_LACI; 1.
    DR   PROSITE; PS00356; HTH_LACI_1; 1.
    DR   PROSITE; PS50932; HTH_LACI_2; 1.
    KW   3D-structure; Complete proteome; Direct protein sequencing;
    KW   DNA-binding; Repressor; Transcription; Transcription regulation.
    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   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   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 = 38590.06  		Residues = 360
    Average Residue Weight  = 107.195 	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 = 0.660

    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'.

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
checktrans | Reports STOP codons and ORF statistics of a protein
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
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
pepinfo | Plot amino acid properties of a protein sequence in parallel
pepwindow | Draw a Kyte-Doolittle hydropathy plot for a protein sequence
pepwindowall | Draw Kyte-Doolittle hydropathy plot for a protein alignment
wordcount | Count and extract unique words in DNA sequence(s)

## Author(s)

Alan Bleasby (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 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