EMBASSY: CBSTOOLS: enetphos

enetphos

Wiki

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Function

Report 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 Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins Input (aligned) protein 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

Report Ser, Thr and Tyr phosphorylation sites in eukaryotic proteins
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) protein 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
   -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

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1) seqset (Aligned) protein sequence set filename and optional format, or reference (input USA) Readable set of sequences Required

[-outfile]
(Parameter 2) outfile Output file name Output file <*>.enetphos

Additional (Optional) qualifiers

-cutoff float Report only scores above this value Any numeric value 0.0

Advanced (Unprompted) qualifiers

-plot boolean Produce graphics Boolean value Yes/No No

-two boolean Run generic predictions only Boolean value Yes/No No

-kinase boolean Run kinase-specific only Boolean value Yes/No No

-residue list Residues to predict with
all (all)
serine (serine)
threonine (threonine)
tyrosine (tyrosine)
all

-gff boolean Produce gff output Boolean value Yes/No No

-best boolean Report only the highest score for each residue Boolean value Yes/No No

-addseq boolean Add sequence to gff output Boolean value Yes/No No

Associated qualifiers

"-sequence" associated seqset qualifiers

-sbegin1
-sbegin_sequence integer Start of each sequence to be used Any integer value 0

-send1
-send_sequence integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequence boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequence boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequence boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequence boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequence boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequence boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequence boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequence boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequence string Input sequence format Any string

-iquery1
-iquery_sequence string Input query fields or ID list Any string

-ioffset1
-ioffset_sequence integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequence string Database name Any string

-sid1
-sid_sequence string Entryname Any string

-ufo1
-ufo_sequence string UFO features Any string

-fformat1
-fformat_sequence string Features format Any string

-fopenfile1
-fopenfile_sequence string Features file name Any string

"-outfile" associated outfile qualifiers

-odirectory2
-odirectory_outfile string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

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.

Program name	Description
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esignalp	Report protein signal cleavage sites
eyinoyang	Report O-(beta)-GlcNAc attachment sites

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.

History

Target users

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

Comments

None

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

File: EFTU_HUMAN.fsa

Output file format

Output files for usage example

File: eftu_human.enetphos

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments