enetphos |
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% enetphos Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins Input (aligned) protein sequence set: EFTU_HUMAN.fsa Output file [eftu_human.enetphos]: |
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Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins Version: EMBOSS:6.4.0.0 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 -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 |
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 | ||||||||
-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 .. |
Program name | Description |
---|---|
enetnglyc | Reports N-glycosylation sites in human proteins |
enetoglyc | Reports mucin type GalNAc O-glycosylation sites in mammalian proteins |
eprop | Reports propeptide cleavage sites in proteins |
esignalp | Reports protein signal cleavage sites |
eyinoyang | Reports O-(beta)-GlcNAc attachment sites |
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.