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enetphos |
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% 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
Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins
Version: EMBOSS:6.3.0
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
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| Qualifier | Type | Description | Allowed values | Default | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||
| [-sequence] (Parameter 1) |
seqset | (Aligned) 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 | ||||||||
| -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 | ||||||||
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |||||||||
| -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 | ||||||||
>EFTU_HUMAN P49411 Elongation factor Tu, mitochondrial precursor (EF-Tu) (P43). - Homo sapiens (Human). MAAATLLRATPHFSGLAAGRTFLLQGLLRLLKAPALPLLCRGLAVEAKKTYVRDKPHVNV GTIGHVDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAAR HYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYV NKADAVQDSEMVELVELEIRELLTEFGYKGEETPVIVGSALCALEGRDPELGLKSVQKLL DAVDTYIPVPARDLEKPFLLPVEAVYSVPGRGTVVTGTLERGILKKGDECELLGHSKNIR TVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMVKPGSIKPHQKVEAQVYILS KEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPEKELAMPGEDLKFNLILRQPMILEKGQ RFTLRDGNRTIGTGLVTNTLAMTEEEKNIKWG |
>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 ..
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| 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 |
The original CBS group application must be licensed and installed to use this wrapper.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.