NetPhosBac 1.0 Output format

Output format

DESCRIPTION

For each input sequence the length and the name of the sequence are stated followed by a table with the prediction results. There is a table row for each serine or threonine residue in the sequence; the columns are:

sequence name, truncated to 20 characters;
residue position in the sequence;
residue: serine (S) or threonine (T);
score, a number between 0 and 1; when the score is above 0.5 the residue is a predicted phosphorylation site;
kinase: the current version of NetPhosBac does not make kinase specific predictions;
answer: either the word "YES" or a dot ("."), reflecting the score.

After the table, the whole sequence is printed alongside a summary of the predicted glycation sites and their positions.

Finally, if the 'Generate graphics' button has been checked, the server displays a figure in GIF showing a plot of the score for each serine or threonine residue against the sequence position of that residue. -->

EXAMPLE OUTPUT

The example below shows the output for the UniProt entry P0A6C7 --> Amino-acid acetyltransferase -->

>sp_P0A6C7_ARGA_ECO57 443 amino acids # # netphosbac-1.0a prediction results # # Sequence # x Context Score Kinase Answer # ------------------------------------------------------------------- # sp_P0A6C7_ARGA_ECO57 7 T KERKTELVE 0.319 main . # sp_P0A6C7_ARGA_ECO57 16 S GFRHSVPYI 0.591 main Y # sp_P0A6C7_ARGA_ECO57 22 T PYINTHRGK 0.482 main . # sp_P0A6C7_ARGA_ECO57 27 T HRGKTFVIM 0.474 main . # sp_P0A6C7_ARGA_ECO57 43 S HENFSSIVN 0.461 main . # sp_P0A6C7_ARGA_ECO57 44 S ENFSSIVND 0.498 main . # sp_P0A6C7_ARGA_ECO57 54 S GLLHSLGIR 0.673 main Y # sp_P0A6C7_ARGA_ECO57 89 T NIRVTDAKT 0.199 main . # sp_P0A6C7_ARGA_ECO57 93 T TDAKTLELV 0.420 main . # sp_P0A6C7_ARGA_ECO57 103 T QAAGTLQLD 0.171 main . # sp_P0A6C7_ARGA_ECO57 109 T QLDITARLS 0.452 main . # sp_P0A6C7_ARGA_ECO57 113 S TARLSMSLN 0.271 main . # sp_P0A6C7_ARGA_ECO57 115 S RLSMSLNNT 0.306 main . # sp_P0A6C7_ARGA_ECO57 119 T SLNNTPLQG 0.160 main . # sp_P0A6C7_ARGA_ECO57 130 S INVVSGNFI 0.439 main . # sp_P0A6C7_ARGA_ECO57 150 S DYCHSGRIR 0.839 main Y # sp_P0A6C7_ARGA_ECO57 167 S RQLDSGAIV 0.488 main . # sp_P0A6C7_ARGA_ECO57 179 S PVAVSVTGE 0.305 main . # sp_P0A6C7_ARGA_ECO57 181 T AVSVTGESF 0.285 main . # sp_P0A6C7_ARGA_ECO57 184 S VTGESFNLT 0.499 main . # sp_P0A6C7_ARGA_ECO57 188 T SFNLTSEEI 0.202 main . # sp_P0A6C7_ARGA_ECO57 189 S FNLTSEEIA 0.418 main . # sp_P0A6C7_ARGA_ECO57 194 T EEIATQLAI 0.228 main . # sp_P0A6C7_ARGA_ECO57 210 S IGFCSSQGV 0.476 main . # sp_P0A6C7_ARGA_ECO57 211 S GFCSSQGVT 0.413 main . # sp_P0A6C7_ARGA_ECO57 215 T SQGVTNDDG 0.184 main . # sp_P0A6C7_ARGA_ECO57 223 S GDIVSELFP 0.342 main . # sp_P0A6C7_ARGA_ECO57 245 S GDYNSGTVR 0.533 main Y # sp_P0A6C7_ARGA_ECO57 247 T YNSGTVRFL 0.359 main . # sp_P0A6C7_ARGA_ECO57 260 S KACRSGVRR 0.776 main Y # sp_P0A6C7_ARGA_ECO57 269 S CHLISYQED 0.312 main . # sp_P0A6C7_ARGA_ECO57 282 S QELFSRDGI 0.319 main . # sp_P0A6C7_ARGA_ECO57 288 T DGIGTQIVM 0.264 main . # sp_P0A6C7_ARGA_ECO57 294 S IVMESAEQI 0.516 main Y # sp_P0A6C7_ARGA_ECO57 302 T IRRATINDI 0.318 main . # sp_P0A6C7_ARGA_ECO57 326 S LVRRSREQL 0.456 main . # sp_P0A6C7_ARGA_ECO57 338 T IDKFTIIQR 0.451 main . # sp_P0A6C7_ARGA_ECO57 345 T QRDNTTIAC 0.442 main . # sp_P0A6C7_ARGA_ECO57 346 T RDNTTIACA 0.309 main . # sp_P0A6C7_ARGA_ECO57 374 S PDYRSSSRG 0.287 main . # sp_P0A6C7_ARGA_ECO57 375 S DYRSSSRGE 0.771 main Y # sp_P0A6C7_ARGA_ECO57 376 S YRSSSRGEV 0.701 main Y # sp_P0A6C7_ARGA_ECO57 392 S QAKQSGLSK 0.288 main . # sp_P0A6C7_ARGA_ECO57 395 S QSGLSKLFV 0.581 main Y # sp_P0A6C7_ARGA_ECO57 401 T LFVLTTRSI 0.432 main . # sp_P0A6C7_ARGA_ECO57 402 T FVLTTRSIH 0.362 main . # sp_P0A6C7_ARGA_ECO57 404 S LTTRSIHWF 0.729 main Y # sp_P0A6C7_ARGA_ECO57 414 T ERGFTPVDI 0.359 main . # sp_P0A6C7_ARGA_ECO57 424 S LLPESKKQL 0.294 main . # sp_P0A6C7_ARGA_ECO57 435 S YQRKSKVLM 0.548 main Y # MVKERKTELVEGFRHSVPYINTHRGKTFVIMLGGEAIEHENFSSIVNDIG # 50 LLHSLGIRLVVVYGARPQIDANLAAHHHEPLYHKNIRVTDAKTLELVKQA # 100 AGTLQLDITARLSMSLNNTPLQGAHINVVSGNFIIAQPLGVDDGVDYCHS # 150 GRIRRIDEDAIHRQLDSGAIVLMGPVAVSVTGESFNLTSEEIATQLAIKL # 200 KAEKMIGFCSSQGVTNDDGDIVSELFPNEAQARVEAQEEKGDYNSGTVRF # 250 LRGAVKACRSGVRRCHLISYQEDGALLQELFSRDGIGTQIVMESAEQIRR # 300 ATINDIGGILELIRPLEQQGILVRRSREQLEMEIDKFTIIQRDNTTIACA # 350 ALYPFPEEKIGEMACVAVHPDYRSSSRGEVLLERIAAQAKQSGLSKLFVL # 400 TTRSIHWFQERGFTPVDIDLLPESKKQLYNYQRKSKVLMADLG # 450 %1 ...............S.................................. # 50 %1 ...S.............................................. # 100 %1 .................................................S # 150 %1 .................................................. # 200 %1 ............................................S..... # 250 %1 .........S.................................S...... # 300 %1 .................................................. # 350 %1 ........................SS..................S..... # 400 %1 ...S..............................S........ .

GETTING HELP

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