eyinoyang |
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% eyinoyang Reports O-(beta)-GlcNAc attachment sites Input (aligned) protein sequence set: CBG_HUMAN.fsa Output file [cbg_human.eyinoyang]: |
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Example 2
% eyinoyang Reports O-(beta)-GlcNAc attachment sites Input (aligned) protein sequence set: LEUK_RAT.fsa Output file [leuk_rat.eyinoyang]: |
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Reports O-(beta)-GlcNAc attachment sites 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 [*.eyinoyang] Output file name Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -plot boolean [N] Produce graphics -format menu [short] Format (Values: short (short); long (long)) -netphos boolean [N] Run netphos and predict Yin-Yang sites -threshold float [0.5] Report netphos only scores above this value (Number from 0.000 to 1.000) 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 | <*>.eyinoyang | ||||
Additional (Optional) qualifiers | ||||||||
(none) | ||||||||
Advanced (Unprompted) qualifiers | ||||||||
-plot | boolean | Produce graphics | Boolean value Yes/No | No | ||||
-format | list | Format |
|
short | ||||
-netphos | boolean | Run netphos and predict Yin-Yang sites | Boolean value Yes/No | No | ||||
-threshold | float | Report netphos only scores above this value | Number from 0.000 to 1.000 | 0.5 | ||||
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 |
>CBG_HUMAN MPLLLYTCLLWLPTSGLWTVQAMDPNAAYVNMSNHHRGLASANVDFAFSLYKHLVALSPK KNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSD TSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQG KIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTI SYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLY IPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDT AGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV |
>LEUK_RAT P13838 LEUKOSIALIN PRECURSOR (LEUCOCYTE SIALOGLYCOPROTEIN) (SIALOPHORIN) (CD43) (W3/13 ANTIGEN) (FRAGMENT). - RATTUS NORVEGICUS (RAT). WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAP ASSIPLGTPELSSFFFTSAGASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTIT NPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATTVSSETSGPPVTMATGSLGPS KETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGN KSSGAPETDGSGQRPTLTTFFSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVE TPTSDGPQAKDGAAPQSL |
The predictions for O-GlcNAc sites in 1 sequence ############################################################################### Warning: This sequence seems to contain a signal peptide !! Proteins with signal peptides are most probably secreted and are unlikely to contain an O-(beta)-GlcNAc site # SignalP-NN ver. 3.0 euk predictions # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? CBG_HUMAN 0.645 23 Y 0.717 23 Y 0.981 13 Y 0.886 Y 0.801 Y ############################################################################### Name: CBG_HUMAN Length: 405 MPLLLYTCLLWLPTSGLWTVQAMDPNAAYVNMSNHHRGLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLG 80 TCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNF 160 QDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTI 240 SYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMG 320 IADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLAR 400 VMNPV 480 ..............G.....................................................G........... 80 ................................................................................ 160 ....G........................................................................... 240 ................................................................G............... 320 .....................GG......................................................... 400 ..... 480 ---------------------------------------------------------- SeqName Residue O-GlcNAc Potential Thresh. Thresh. result (1) (2) ---------------------------------------------------------- CBG_HUMAN 15 S + 0.4952 0.4560 0.5650 CBG_HUMAN 69 S + 0.5330 0.5116 0.6400 CBG_HUMAN 165 T + 0.5099 0.4381 0.5409 CBG_HUMAN 305 T ++ 0.5937 0.4585 0.5684 CBG_HUMAN 342 S ++ 0.4782 0.3860 0.4707 CBG_HUMAN 343 S + 0.4153 0.4096 0.5025 ---------------------------------------------------------- |
The predictions for O-GlcNAc sites in 1 sequence Name: LEUK_RAT Length: 378 WAQVVSQENLPNTMTMLPFTPNSESPSTSEALSTYSSIATVPVTEDPKESISPWGQTTAPASSIPLGTPELSSFFFTSAG 80 ASGNTPVPELTTSQEVSTEASLVLFPKSSGVASDPPVTITNPATSSAVASTSLETFKGTSAPPVTVTSSTMTSGPFVATT 160 VSSETSGPPVTMATGSLGPSKETHGLSATIATSSGESSSVAGGTPVFSTKISTTSTPNPITTVPPRPGSSGMLLVSMLIA 240 LTVVLVLVALLLLWRQRQKRRTGALTLSRGGKRNGTVDAWAGPARVPDEEATTASGSGGNKSSGAPETDGSGQRPTLTTF 320 FSRRKSRQGSVALEELKPGTGPNLKGEEEPLVGSEDEAVETPTSDGPQAKDGAAPQSL 400 .....G.............G..G....GG...G..........G.....G......GG...GG................. 80 ..........GGG...GG.........GG........G.G...GGG....G.............G.GGG...G.....G. 160 .GG..G....G...........G........GGG...G.........G.....G......GG......G........... 240 .....................G.............................GG.G............G.........G.. 320 ...........................................G............G. 400 ---------------------------------------------------------- SeqName Residue O-GlcNAc Potential Thresh. Thresh. result (1) (2) ---------------------------------------------------------- LEUK_RAT 6 S ++ 0.5334 0.4196 0.5159 LEUK_RAT 20 T + 0.4550 0.4247 0.5229 LEUK_RAT 23 S +++ 0.6551 0.3665 0.4444 LEUK_RAT 28 T + 0.3938 0.3852 0.4697 LEUK_RAT 29 S +++ 0.6920 0.4029 0.4935 LEUK_RAT 33 S + 0.4933 0.4381 0.5409 LEUK_RAT 44 T +++ 0.6693 0.4165 0.5118 LEUK_RAT 50 S + 0.3897 0.3747 0.4554 LEUK_RAT 57 T ++ 0.5390 0.4111 0.5046 LEUK_RAT 58 T +++ 0.6271 0.4053 0.4967 LEUK_RAT 62 S + 0.4869 0.4238 0.5217 LEUK_RAT 63 S ++ 0.6100 0.4194 0.5157 LEUK_RAT 91 T + 0.4330 0.4060 0.4977 LEUK_RAT 92 T ++ 0.4961 0.3934 0.4807 LEUK_RAT 93 S + 0.4557 0.4124 0.5063 LEUK_RAT 97 S + 0.4692 0.4066 0.4985 LEUK_RAT 98 T + 0.5114 0.4222 0.5195 LEUK_RAT 108 S + 0.4984 0.4119 0.5056 LEUK_RAT 109 S +++ 0.6209 0.3978 0.4866 LEUK_RAT 118 T ++++ 0.7542 0.4267 0.5256 LEUK_RAT 120 T ++ 0.5358 0.4281 0.5274 LEUK_RAT 124 T +++ 0.6470 0.4087 0.5013 LEUK_RAT 125 S +++ 0.7343 0.4145 0.5091 LEUK_RAT 126 S ++ 0.6243 0.4313 0.5318 LEUK_RAT 131 T + 0.4973 0.4487 0.5552 LEUK_RAT 145 T ++++ 0.7629 0.4440 0.5489 LEUK_RAT 147 T +++ 0.6993 0.4525 0.5603 LEUK_RAT 148 S ++ 0.5850 0.4536 0.5618 LEUK_RAT 149 S + 0.5067 0.4533 0.5614 LEUK_RAT 153 S + 0.4848 0.4352 0.5370 LEUK_RAT 159 T ++ 0.6054 0.4765 0.5927 LEUK_RAT 162 S ++++ 0.7702 0.4242 0.5221 LEUK_RAT 163 S + 0.4354 0.4092 0.5019 LEUK_RAT 166 S + 0.4314 0.3751 0.4560 LEUK_RAT 171 T +++ 0.7201 0.4458 0.5513 LEUK_RAT 183 T + 0.4774 0.4040 0.4950 LEUK_RAT 192 T ++ 0.5797 0.4320 0.5327 LEUK_RAT 193 S +++ 0.6347 0.4159 0.5110 LEUK_RAT 194 S + 0.4443 0.3990 0.4883 LEUK_RAT 198 S + 0.4110 0.4073 0.4994 LEUK_RAT 208 S ++ 0.5823 0.4501 0.5571 LEUK_RAT 214 T + 0.4242 0.4092 0.5020 LEUK_RAT 221 T ++ 0.5461 0.4168 0.5122 LEUK_RAT 222 T ++ 0.6041 0.4159 0.5110 LEUK_RAT 229 S + 0.4820 0.4089 0.5016 LEUK_RAT 262 T ++ 0.4988 0.3886 0.4742 LEUK_RAT 292 T + 0.3937 0.3877 0.4730 LEUK_RAT 293 T ++ 0.5152 0.3967 0.4851 LEUK_RAT 295 S + 0.4397 0.3839 0.4678 LEUK_RAT 308 T ++ 0.5271 0.3720 0.4518 LEUK_RAT 318 T + 0.4814 0.4671 0.5800 LEUK_RAT 364 S ++ 0.5089 0.3646 0.4419 LEUK_RAT 377 S +++ 0.6489 0.3408 0.4097 ---------------------------------------------------------- |
Program name | Description |
---|---|
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 |
eprop | Reports propeptide cleavage sites in proteins |
esignalp | Reports protein signal cleavage 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.