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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
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequence] (Parameter 1) |
(Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||
| [-outfile] (Parameter 2) |
Output file name | Output file | <*>.enetphos | ||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||
| -cutoff | Report only scores above this value | Any numeric value | 0.0 | ||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||
| -plot | Produce graphics | Boolean value Yes/No | No | ||||||||
| -two | Run generic predictions only | Boolean value Yes/No | No | ||||||||
| -kinase | Run kinase-specific only | Boolean value Yes/No | No | ||||||||
| -residue | Residues to predict with |
|
all | ||||||||
| -gff | Produce gff output | Boolean value Yes/No | No | ||||||||
| -best | Report only the highest score for each residue | Boolean value Yes/No | No | ||||||||
| -addseq | Add sequence to gff output | Boolean value Yes/No | No | ||||||||
>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 | Motif detection |
| 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.
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.