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eprop |
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% eprop Reports propeptide cleavage sites in proteins Input (aligned) sequence set: EDA_HUMAN.fsa Output file [eda_human.eprop]: |
Go to the input files for this example
Go to the output files for this example
Reports propeptide cleavage sites in proteins
Version: EMBOSS:6.3.0
Standard (Mandatory) qualifiers:
[-sequence] seqset (Aligned) sequence set filename and optional
format, or reference (input USA)
[-outfile] outfile [*.eprop] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-plot boolean [N] Produce graphics
-pcprediction boolean [N] Perform proprotein convertase prediction
-signalp boolean [N] Include signal peptide cleavage site
prediction
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) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| [-outfile] (Parameter 2) |
outfile | Output file name | Output file | <*>.eprop |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -plot | boolean | Produce graphics | Boolean value Yes/No | No |
| -pcprediction | boolean | Perform proprotein convertase prediction | Boolean value Yes/No | No |
| -signalp | boolean | Include signal peptide cleavage site prediction | 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 |
>EDA_HUMAN Q92838 Ectodysplasin A (Ectodermal dysplasia protein) (EDA protein). - Homo sapiens (Human). MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCC YLELRSELRRERGAESRLGGSGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGE AALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRSKSNEGADGPVKNKKKGKKAG PPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGT YFIYSQVEVYYINFTDFASYEVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKI AVKMVHADISINMSKHTTFFGAIRLGEAPAS |
##### ProP v.1.0b ProPeptide Cleavage Site Prediction #####
##### Furin-type cleavage site prediction (Arginine/Lysine residues) #####
391 EDA_HUMAN
MGYPEVERRELLPAAAPRERGSQGCGCGGAPARAGEGNSCLLFLGFFGLSLALHLLTLCCYLELRSELRRERGAESRLGG 80
SGTPGTSGTLSSLGGLDPDSPITSHLGQPSPKQQPLEPGEAALHSDSQDGHQMALLNFFFPDEKPYSEEESRRVRRNKRS 160
KSNEGADGPVKNKKKGKKAGPPGPNGPPGPPGPPGPQGPPGIPGIPGIPGTTVMGPPGPPGPPGPQGPPGLQGPSGAADK 240
AGTRENQPAVVHLQGQGSAIQVKNDLSGGVLNDWSRITMNPKVFKLHPRSGELEVLVDGTYFIYSQVEVYYINFTDFASY 320
EVVVDEKPFLQCTRSIETGKTNYNTCYTAGVCLLKARQKIAVKMVHADISINMSKHTTFFGAIRLGEAPAS 400
................................................................................ 80
..............................................................................P. 160
................................................................................ 240
................................................................................ 320
....................................................................... 400
Propeptide cleavage sites predicted: Arg(R)/Lys(K): 1
Name Pos Context Score Pred
____________________________v_________________
EDA_HUMAN 8 GYPEVER|RE 0.057 .
EDA_HUMAN 9 YPEVERR|EL 0.128 .
EDA_HUMAN 18 LPAAAPR|ER 0.135 .
EDA_HUMAN 20 AAAPRER|GS 0.102 .
EDA_HUMAN 33 CGGAPAR|AG 0.090 .
EDA_HUMAN 65 CCYLELR|SE 0.089 .
EDA_HUMAN 69 ELRSELR|RE 0.081 .
EDA_HUMAN 70 LRSELRR|ER 0.195 .
EDA_HUMAN 72 SELRRER|GA 0.293 .
EDA_HUMAN 77 ERGAESR|LG 0.112 .
EDA_HUMAN 112 LGQPSPK|QQ 0.064 .
EDA_HUMAN 144 FFFPDEK|PY 0.060 .
EDA_HUMAN 152 YSEEESR|RV 0.096 .
EDA_HUMAN 153 SEEESRR|VR 0.114 .
EDA_HUMAN 155 EESRRVR|RN 0.204 .
EDA_HUMAN 156 ESRRVRR|NK 0.482 .
EDA_HUMAN 158 RRVRRNK|RS 0.182 .
EDA_HUMAN 159 RVRRNKR|SK 0.819 *ProP*
EDA_HUMAN 161 RRNKRSK|SN 0.131 .
EDA_HUMAN 171 GADGPVK|NK 0.060 .
EDA_HUMAN 173 DGPVKNK|KK 0.066 .
EDA_HUMAN 174 GPVKNKK|KG 0.119 .
EDA_HUMAN 175 PVKNKKK|GK 0.156 .
EDA_HUMAN 177 KNKKKGK|KA 0.116 .
EDA_HUMAN 178 NKKKGKK|AG 0.120 .
EDA_HUMAN 240 PSGAADK|AG 0.060 .
EDA_HUMAN 244 ADKAGTR|EN 0.082 .
EDA_HUMAN 263 GSAIQVK|ND 0.066 .
EDA_HUMAN 276 VLNDWSR|IT 0.077 .
EDA_HUMAN 282 RITMNPK|VF 0.057 .
EDA_HUMAN 285 MNPKVFK|LH 0.064 .
EDA_HUMAN 289 VFKLHPR|SG 0.116 .
EDA_HUMAN 327 EVVVDEK|PF 0.060 .
EDA_HUMAN 334 PFLQCTR|SI 0.152 .
EDA_HUMAN 340 RSIETGK|TN 0.061 .
EDA_HUMAN 355 AGVCLLK|AR 0.059 .
EDA_HUMAN 357 VCLLKAR|QK 0.099 .
EDA_HUMAN 359 LLKARQK|IA 0.073 .
EDA_HUMAN 363 RQKIAVK|MV 0.078 .
EDA_HUMAN 375 ISINMSK|HT 0.067 .
EDA_HUMAN 384 TFFGAIR|LG 0.076 .
____________________________^_________________
|
| 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 |
| enetphos | Reports ser, thr and tyr phosphorylation sites in eukaryotic proteins |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| 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.