                                  enetphos



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Function

   Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins

Description

   The NetPhos 2.0 server produces neural network predictions for serine,
   threonine and tyrosine phosphorylation sites in eukaryotic proteins.

Usage

   Here is a sample session with enetphos


% enetphos
Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
Input (aligned) sequence set: EFTU_HUMAN.fsa
Output file [eftu_human.enetphos]:


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

Command line arguments

Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.enetphos] Output file name

   Additional (Optional) qualifiers:
   -cutoff             float      [0.0] Report only scores above this value
                                  (Any numeric value)

   Advanced (Unprompted) qualifiers:
   -plot               boolean    [N] Produce graphics
   -two                boolean    [N] Run generic predictions only
   -kinase             boolean    [N] Run kinase-specific only
   -residue            menu       [all] Residues to predict with (Values: all
                                  (all); serine (serine); threonine
                                  (threonine); tyrosine (tyrosine))
   -gff                boolean    [N] Produce gff output
   -best               boolean    [N] Report only the highest score for each
                                  residue
   -addseq             boolean    [N] Add sequence to gff output

   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 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

   enetphos reads any normal sequence USAs.

  Input files for usage example

  File: EFTU_HUMAN.fsa

>EFTU_HUMAN  P49411 Elongation factor Tu, mitochondrial precursor (EF-Tu) (P43).
 - Homo sapiens (Human).
MAAATLLRATPHFSGLAAGRTFLLQGLLRLLKAPALPLLCRGLAVEAKKTYVRDKPHVNV
GTIGHVDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAAR
HYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYV
NKADAVQDSEMVELVELEIRELLTEFGYKGEETPVIVGSALCALEGRDPELGLKSVQKLL
DAVDTYIPVPARDLEKPFLLPVEAVYSVPGRGTVVTGTLERGILKKGDECELLGHSKNIR
TVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIKPHQKVEAQVYILS
KEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPEKELAMPGEDLKFNLILRQPMILEKGQ
RFTLRDGNRTIGTGLVTNTLAMTEEEKNIKWG

Output file format

  Output files for usage example

  File: eftu_human.enetphos

>EFTU_HUMAN     452 amino acids
#
# netphos-3.1b prediction results
#
# Sequence                 # x   Context     Score   Kinase    Answer
# -------------------------------------------------------------------
# EFTU_HUMAN               5 T   MAAATLLRA   0.776   PKC        YES
# EFTU_HUMAN               5 T   MAAATLLRA   0.520   cdc2       YES
# EFTU_HUMAN               5 T   MAAATLLRA   0.442   CaM-II      .
# EFTU_HUMAN               5 T   MAAATLLRA   0.428   GSK3        .
# EFTU_HUMAN               5 T   MAAATLLRA   0.382   CKI         .
# EFTU_HUMAN               5 T   MAAATLLRA   0.350   DNAPK       .
# EFTU_HUMAN               5 T   MAAATLLRA   0.345   p38MAPK     .
# EFTU_HUMAN               5 T   MAAATLLRA   0.285   CKII        .
# EFTU_HUMAN               5 T   MAAATLLRA   0.226   ATM         .
# EFTU_HUMAN               5 T   MAAATLLRA   0.221   PKG         .
# EFTU_HUMAN               5 T   MAAATLLRA   0.204   RSK         .
# EFTU_HUMAN               5 T   MAAATLLRA   0.187   cdk5        .
# EFTU_HUMAN               5 T   MAAATLLRA   0.172   unsp        .
# EFTU_HUMAN               5 T   MAAATLLRA   0.125   PKA         .
# EFTU_HUMAN               5 T   MAAATLLRA   0.073   PKB         .
#
# EFTU_HUMAN              10 T   LLRATPHFS   0.555   cdk5       YES
# EFTU_HUMAN              10 T   LLRATPHFS   0.531   p38MAPK    YES
# EFTU_HUMAN              10 T   LLRATPHFS   0.490   GSK3        .
# EFTU_HUMAN              10 T   LLRATPHFS   0.440   CaM-II      .
# EFTU_HUMAN              10 T   LLRATPHFS   0.369   CKI         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.343   DNAPK       .
# EFTU_HUMAN              10 T   LLRATPHFS   0.341   PKG         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.322   cdc2        .
# EFTU_HUMAN              10 T   LLRATPHFS   0.303   unsp        .
# EFTU_HUMAN              10 T   LLRATPHFS   0.275   RSK         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.266   ATM         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.249   CKII        .
# EFTU_HUMAN              10 T   LLRATPHFS   0.190   PKA         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.099   PKC         .
# EFTU_HUMAN              10 T   LLRATPHFS   0.093   PKB         .
#
# EFTU_HUMAN              14 S   TPHFSGLAA   0.547   cdc2       YES
# EFTU_HUMAN              14 S   TPHFSGLAA   0.468   CaM-II      .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.444   GSK3        .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.371   CKI         .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.342   DNAPK       .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.332   CKII        .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.306   PKG         .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.304   PKC         .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.290   p38MAPK     .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.270   ATM         .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.248   RSK         .
# EFTU_HUMAN              14 S   TPHFSGLAA   0.199   cdk5        .


  [Part of this file has been deleted for brevity]

# EFTU_HUMAN             439 T   LVTNTLAMT   0.446   CKII        .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.441   CaM-II      .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.425   CKI         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.424   GSK3        .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.420   cdc2        .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.364   PKA         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.279   p38MAPK     .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.275   ATM         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.264   PKG         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.192   RSK         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.160   cdk5        .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.160   unsp        .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.138   PKC         .
# EFTU_HUMAN             439 T   LVTNTLAMT   0.078   PKB         .
#
# EFTU_HUMAN             443 T   TLAMTEEEK   0.678   CKII       YES
# EFTU_HUMAN             443 T   TLAMTEEEK   0.480   CKI         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.447   unsp        .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.443   GSK3        .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.425   CaM-II      .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.376   cdc2        .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.348   DNAPK       .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.315   PKG         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.277   ATM         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.251   p38MAPK     .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.249   RSK         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.157   cdk5        .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.132   PKC         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.081   PKB         .
# EFTU_HUMAN             443 T   TLAMTEEEK   0.066   PKA         .
#
    MAAATLLRATPHFSGLAAGRTFLLQGLLRLLKAPALPLLCRGLAVEAKKT   #     50
    YVRDKPHVNVGTIGHVDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAPE   #    100
    ERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITGTAPLDGCILV   #    150
    VAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIR   #    200
    ELLTEFGYKGEETPVIVGSALCALEGRDPELGLKSVQKLLDAVDTYIPVP   #    250
    ARDLEKPFLLPVEAVYSVPGRGTVVTGTLERGILKKGDECELLGHSKNIR   #    300
    TVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIKPHQ   #    350
    KVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPEKELAMP   #    400
    GEDLKFNLILRQPMILEKGQRFTLRDGNRTIGTGLVTNTLAMTEEEKNIK   #    450
    WG                                                   #    500
%1  ....T....T...S...................................T   #     50
%1  Y....................T.T.................Y........   #    100
%1  ......T........S................Y.......T.........   #    150
%1  ..........T.................Y.........S...........   #    200
%1  .......Y....T...............................TY....   #    250
%1  ...............Y......T....T.................S....   #    300
%1  ...T.......S................................S.....   #    350
%1  .........S........................................   #    400
%1  ......................T.........T.....T...T.......   #    450
%1  ..

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   antigenic        Finds antigenic sites in proteins
   digest           Reports on protein proteolytic enzyme or reagent cleavage sites
   echlorop         Reports presence of chloroplast transit peptides
   eiprscan         Motif detection
   elipop           Prediction of lipoproteins
   emast            Motif detection
   ememe            Multiple EM for Motif Elicitation
   ememetext        Multiple EM for Motif Elicitation. Text file only
   enetnglyc        Reports N-glycosylation sites in human proteins
   enetoglyc        Reports mucin type GalNAc O-glycosylation sites in mammalian
                    proteins
   epestfind        Finds PEST motifs as potential proteolytic cleavage sites
   eprop            Reports propeptide cleavage sites in proteins
   esignalp         Reports protein signal cleavage sites
   etmhmm           Reports transmembrane helices
   eyinoyang        Reports O-(beta)-GlcNAc attachment sites
   fuzzpro          Search for patterns in protein sequences
   fuzztran         Search for patterns in protein sequences (translated)
   helixturnhelix   Identify nucleic acid-binding motifs in protein
                    sequences
   oddcomp          Identify proteins with specified sequence word composition
   omeme            Motif detection
   patmatdb         Searches protein sequences with a sequence motif
   patmatmotifs     Scan a protein sequence with motifs from the PROSITE
                    database
   pepcoil          Predicts coiled coil regions in protein sequences
   preg             Regular expression search of protein sequence(s)
   pscan            Scans protein sequence(s) with fingerprints from the PRINTS
                    database
   sigcleave        Reports on signal cleavage sites in a protein sequence

Author(s)

   This program is an EMBOSS wrapper for a program written by the CBS
   group http://www.cbs.dtu.dk/index.shtml

   The original CBS group application must be licensed and installed to
   use this wrapper.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

Target users

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

Comments

   None
