-
Notifications
You must be signed in to change notification settings - Fork 0
/
epestfind.html
810 lines (651 loc) · 25.6 KB
/
epestfind.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
<HTML>
<HEAD>
<TITLE>
EMBOSS: epestfind
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
epestfind
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Finds PEST motifs as potential proteolytic cleavage sites
<H2>
Description
</H2>
<b>epestfind</b> allows rapid and objective identification of PEST motifs
in protein target sequences. Briefly, the PEST hypothesis was based on
a literature survey that combined both information on protein stability
as well as protein primary sequence information. Initially, the study
relied on 12 short-lived proteins with well-known properties [1], but
was continually extended later [2,3]. The initial group of proteins
included E1A, c-myc, p53, c-fos, v-myb, P730 phytochrome, heat shock
protein 70 (HSP 70), HMG-CoA reductase, tyrosine aminotransferase (TAT),
ornithine decarboxylase (ODC), alpha-Casein and beta-Casein. Although
all these proteins exerted various different cellular functions it
became apparent that they shared high local concentrations of amino
acids proline (P), glutamic acid (E), serine (S), threonine (T) and to a
lesser extent aspartic acid (D). From that it was concluded that PEST
motifs reduce the half-lives of proteins dramatically and hence, that
they target proteins for proteolytic degradation.
<p>
PEST means Black Death in German, so that the name of this programme
sounds a bit strange, at least in our ears.
<H2>
Algorithm
</H2>
PEST motifs were defined as hydrophilic stretches of at least 12 amino
acids length with a high local concentration of critical amino acids.
Remarkably, negatively charged amino acids are clustered within these
motifs while positively charged amino acids, arginine (R), histidine (H)
and lysine (K) are generally forbidden.
<p>
The <b>epestfind</b> algorithm defines the last criterion even more
stringently in that PEST motifs are required to be flanked by positively
charged amino acids. Though this implication greatly facilitates
computer scanning, a few PEST sequences might be missed. Especially
sequences with a high local concentration of critical amino acids but
with a long distance between positively charged amino acids are error
prone. Due to their length, these PEST motifs might become diluted,
which results in scores apparently lower than initially expected.
Another side effect of scanning for positively charged amino acids is
that very long PEST motifs are sub-divided into adjacent smaller ones.
However, identification of PEST motifs is achieved by an initial scan
for positively charged amino acids arginine (R), histidine (H) and
lysine (K) within the specified protein sequence. All amino acids
between the positively charged flanks are counted and only those motifs
are considered further, which contain a number of amino acids equal to
or higher than the window-size parameter. Additionally, all 'valid'
PEST regions are required to contain at least one proline (P), one
aspartate (D) or glutamate (E) and at least one serine (S) or
threonine(T). Sequences that do not meet the above criteria are
classified as 'invalid' PEST motifs and excluded from further analysis.
<p>
The quality of 'valid' PEST motifs is refined by means of a scoring
parameter based on the local enrichment of critical amino acids as well
as the motif's hydrophobicity. Enrichment of D, E, P, S and T is
expressed in mass percent (w/w) and corrected for one equivalent of D or
E, one of P and one of S or T. Calculation of hydrophobicity follows in
principle the method of J. Kyte and R.F. Doolittle [4]. For
simplified calculations, Kyte-Doolittle hydropathy indices, which
originally ranged from -4.5 for arginine to +4.5 for isoleucine, were
converted to positive integers. This was achieved by the following
linear transformation, which yielded values from 0 for arginine to 90
for isoleucine.
<p>
<center>Hydropathy index = 10 * Kyte-Doolittle hydropathy index + 45</center>
<p>
The motif's hydrophobicity is calculated as the sum over the products of
mole percent and hydrophobicity index for each amino acid species. The
desired PEST score is obtained as combination of local enrichment term
and hydrophobicity term as expressed by the following equation:
<p>
<center>PEST score = 0.55 * DEPST - 0.5 * hydrophobicity index.</center>
<p>
Although, the formula above differs from the publication [1], it is in
fact the correct one, which was also implemented in the original BASIC
programme (personal communication). In addition, the programme includes
a correction for the hydropathy index of tyrosine, introduced by Robert
H. Stellwagen from the University of Southern California. However,
PEST scores can range from -45 for poly-isoleucine to about +50 for
poly-aspartate plus one proline and one serine. 'Valid' PEST motifs
below the threshold score (5.0) are considered as 'poor', while PEST
scores above the threshold score are of real biological interest. The
higher the PEST score, the more likely is degradation of proteins
mediated via 'potential' PEST motifs in eukaryotic cells.
<p>
Presently, all modified Kyte-Doolittle hydropathy indices are
hard-coded into the programme, which might change in future.
<p>
The array of linear transformed Kyte-Doolittle hydropathy
indices (ltkdhi) is listed in alphabetical order below.
(A-M and N-Z as well as N-terminus and C-terminus)
<p>
63, 10, 70, 10, 10, 72, 41, 13, 90, 0, 6, 82, 64,
10, 0, 29, 10, 0, 36, 38, 0, 87, 36, 45, 58, 10,
0, 0
<p>
The linear transformation was ltkdhi = 10 * kdhi + 45
<br>
All values range from Argine R = 0 to Isoleucine I = 90
<br>
B=(N|D)=10 since N=10 and D=10
<br>
Z=(Q|E)=10 since Q=10 and E=10
<br>
X=10*0+45=45
<H2>
Usage
</H2>
<b>Here is a sample session with epestfind</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>epestfind -graph cps -invalid </b>
Finds PEST motifs as potential proteolytic cleavage sites
Input protein sequence: <b>exu2_drops.embl</b>
Window length [10]: <b></b>
Sort order of results
1 : length
2 : position
3 : score
Sort order of results [score]: <b></b>
Output file [exu2_drops.epestfind]: <b></b>
Created epestfind.ps
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Standard (Mandatory) qualifiers:
[-sequence] sequence Protein sequence USA to be analysed.
-window integer [10] Minimal distance between positively
charged amino acids. (Integer 2 or more)
-order selection [score] Name of the output file which holds
the results of the analysis. Results may be
sorted by length, position and score.
[-outfile] outfile [*.epestfind] Name of file to which results
will be written.
-graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
Additional (Optional) qualifiers:
-aadata datafile [Eamino.dat] Amino acids properties and
molecular weight data file
-threshold float [+5.0] Threshold value to discriminate weak
from potential PEST motifs. Valid PEST
motifs are discriminated into 'poor' and
'potential' motifs depending on this
threshold score. By default, the default
value is set to +5.0 based on experimental
data. Alterations are not recommended since
significance is a matter of biology, not
mathematics. (Number from -55.00 to 55.00)
Advanced (Unprompted) qualifiers:
-[no]potential boolean [Y] Decide whether potential PEST motifs
should be printed.
-[no]poor boolean [Y] Decide whether poor PEST motifs should
be printed.
-invalid boolean [N] Decide whether invalid PEST motifs
should be printed.
-[no]map boolean [Y] Decide whether PEST motifs should be
mapped to sequence.
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the 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
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence USA to be analysed.</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>-window</td>
<td>Minimal distance between positively charged amino acids.</td>
<td>Integer 2 or more</td>
<td>10</td>
</tr>
<tr>
<td>-order</td>
<td>Name of the output file which holds the results of the analysis. Results may be sorted by length, position and score.</td>
<td>Choose from selection list of values</td>
<td>score</td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Name of file to which results will be written.</td>
<td>Output file</td>
<td><i><*></i>.epestfind</td>
</tr>
<tr>
<td>-graph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-aadata</td>
<td>Amino acids properties and molecular weight data file</td>
<td>Data file</td>
<td>Eamino.dat</td>
</tr>
<tr>
<td>-threshold</td>
<td>Threshold value to discriminate weak from potential PEST motifs. Valid PEST motifs are discriminated into 'poor' and 'potential' motifs depending on this threshold score. By default, the default value is set to +5.0 based on experimental data. Alterations are not recommended since significance is a matter of biology, not mathematics.</td>
<td>Number from -55.00 to 55.00</td>
<td>+5.0</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>-[no]potential</td>
<td>Decide whether potential PEST motifs should be printed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-[no]poor</td>
<td>Decide whether poor PEST motifs should be printed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
<tr>
<td>-invalid</td>
<td>Decide whether invalid PEST motifs should be printed.</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr>
<td>-[no]map</td>
<td>Decide whether PEST motifs should be mapped to sequence.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>epestfind</b> reads any normal protein sequence USA.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: exu2_drops.embl</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID EXU2_DROPS STANDARD; PRT; 477 AA.
AC Q24617;
DT 01-NOV-1997 (Rel. 35, Created)
DT 01-NOV-1997 (Rel. 35, Last sequence update)
DT 01-NOV-1997 (Rel. 35, Last annotation update)
DE Maternal exuperantia 2 protein.
GN EXU2.
OS Drosophila pseudoobscura (Fruit fly).
OC Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
OC Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC Ephydroidea; Drosophilidae; Drosophila.
OX NCBI_TaxID=7237;
RN [1]
RP SEQUENCE FROM N.A.
RX MEDLINE=94350208; PubMed=8070663;
RA Luk S.K.-S., Kilpatrick M., Kerr K., Macdonald P.M.;
RT "Components acting in localization of bicoid mRNA are conserved among
RT Drosophila species.";
RL Genetics 137:521-530(1994).
CC -!- FUNCTION: ENSURES THE PROPER LOCALIZATION OF THE MRNA OF THE
CC BICOID GENE TO THE ANTERIOR REGIONS OF THE OOCYTE THUS PLAYING
CC A FUNDAMENTAL ROLE IN THE ESTABLISHMENT OF THE POLARITY OF THE
CC OOCYTE. MAY BIND THE BCD MRNA (BY SIMILARITY).
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use by non-profit institutions as long as its content is in no way
CC modified and this statement is not removed. Usage by and for commercial
CC entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC or send an email to [email protected]).
CC --------------------------------------------------------------------------
DR EMBL; L22553; AAA28523.1; -.
DR FlyBase; FBgn0014783; Dpse\exu2.
KW Developmental protein; RNA-binding.
FT DOMAIN 249 271 GLU/SER/PRO/THR-RICH (PEST REGION).
SQ SEQUENCE 477 AA; 53194 MW; 8B5334A77DB9467B CRC64;
MVSAISEDSA SATASGQCEV VKEELPAGNY ILVAVEIDTT GRRLIDEIVQ LAGYTSKGNF
QQYIMPYMNL NQAARQRHQI RVISIGFYRM LKSMQTYKII KSKSEVAALM DFLNWLETLL
AKQPNKEGIV MLYHDDRKFI PYMILEALKK YSLIDRFNRS VKAFANTCPM AKTFLGKHGI
KNCGLRKLSM LLAKSKDGNS TKEDEHENPE GNSSITDNSG HKNQKQGAFE GSANVRAKMV
YEMALQLIES ESTESPESFE SPESSESSEA EVKLLNAVRP FSQLLSSTIL ELKDQNHSLG
RQNSFRPVFL NYFRTTLNYR VRAVKYRIGL AEHGFTLKSL KAIWSDKRKP GLELVLTAID
SLKTEETAEL LDLLDSYYDP SKTTIKPRCK RSGNGTRRRN RAKGAASSKN GAIGAGGDNS
VPDSATKPGG RPRRKRNNIR NNILGPQNTE KGSPKAEMKT STPKSMSIKP PSEFADI
//
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<b>epestfind</b>
outputs a graph to the specified graphics device.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: exu2_drops.epestfind</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
PEST-find: Finds PEST motifs as potential proteolytic cleavage sites.
14 PEST motifs were identified in EXU2_DROPS
from positions 1 to 477 and sorted by score.
Potential PEST motif with 34 amino acids between position 238 and 273.
238 KMVYEMALQLIESESTESPESFESPESSESSEAEVK 273
DEPST: 54.46 % (w/w)
Hydrophobicity index: 38.31
PEST score: 10.80
Potential PEST motif with 14 amino acids between position 206 and 221.
206 HENPEGNSSITDNSGH 221
DEPST: 36.04 % (w/w)
Hydrophobicity index: 27.16
PEST score: 6.25
Poor PEST motif with 18 amino acids between position 363 and 382.
363 KTEETAELLDLLDSYYDPSK 382
PEST score: 2.93
Poor PEST motif with 17 amino acids between position 409 and 427.
409 KNGAIGAGGDNSVPDSATK 427
PEST score: -9.71
Poor PEST motif with 19 amino acids between position 22 and 42.
22 KEELPAGNYILVAVEIDTTGR 42
PEST score: -11.01
Poor PEST motif with 10 amino acids between position 440 and 451.
440 RNNILGPQNTEK 451
PEST score: -15.94
Poor PEST motif with 13 amino acids between position 279 and 293.
279 RPFSQLLSSTILELK 293
PEST score: -16.72
Poor PEST motif with 13 amino acids between position 349 and 363.
349 KPGLELVLTAIDSLK 363
PEST score: -19.94
Invalid PEST motif with 20 amino acids between position 1 and 22.
1 MVSAISEDSASATASGQCEVVK 22
Invalid PEST motif with 13 amino acids between position 43 and 57.
43 RLIDEIVQLAGYTSK 57
Invalid PEST motif with 17 amino acids between position 57 and 75.
57 KGNFQQYIMPYMNLNQAAR 75
Invalid PEST motif with 18 amino acids between position 103 and 122.
103 KSEVAALMDFLNWLETLLAK 122
Invalid PEST motif with 10 amino acids between position 138 and 149.
138 KFIPYMILEALK 149
Invalid PEST motif with 10 amino acids between position 225 and 236.
225 KQGAFEGSANVR 236
---------+---------+---------+---------+---------+---------+
1 MVSAISEDSASATASGQCEVVKEELPAGNYILVAVEIDTTGRRLIDEIVQLAGYTSKGNF 60
-------------------- OOOOOOOOOOOOOOOOOOO ------------- ---
61 QQYIMPYMNLNQAARQRHQIRVISIGFYRMLKSMQTYKIIKSKSEVAALMDFLNWLETLL 120
-------------- -----------------
121 AKQPNKEGIVMLYHDDRKFIPYMILEALKKYSLIDRFNRSVKAFANTCPMAKTFLGKHGI 180
- ----------
181 KNCGLRKLSMLLAKSKDGNSTKEDEHENPEGNSSITDNSGHKNQKQGAFEGSANVRAKMV 240
++++++++++++++ ---------- ++
241 YEMALQLIESESTESPESFESPESSESSEAEVKLLNAVRPFSQLLSSTILELKDQNHSLG 300
++++++++++++++++++++++++++++++++ OOOOOOOOOOOOO
301 RQNSFRPVFLNYFRTTLNYRVRAVKYRIGLAEHGFTLKSLKAIWSDKRKPGLELVLTAID 360
OOOOOOOOOOO
361 SLKTEETAELLDLLDSYYDPSKTTIKPRCKRSGNGTRRRNRAKGAASSKNGAIGAGGDNS 420
OO OOOOOOOOOOOOOOOOOO OOOOOOOOOOO
421 VPDSATKPGGRPRRKRNNIRNNILGPQNTEKGSPKAEMKTSTPKSMSIKPPSEFADI 477
OOOOOO OOOOOOOOOO
Symbols PEST motifs
+++++++ potential
OOOOOOO poor
------- invalid
</pre>
</td></tr></table><p>
<p><h3>Graphics File: epestfind.ps</h3>
<p><img src="epestfind.1.epestfind.gif" alt="[epestfind results]">
<p>
The output from <b>epestfind</b> is a simple text one. It reports poor
and potential PEST motifs together with their PEST score, mass percent
of DEPST and their hydrophobicity index.
<p>
'Valid' PEST motifs below the threshold score (5.0) are considered as
'poor', while PEST scores above the threshold score are of real
biological interest. The higher the PEST score, the more likely is
degradation of proteins mediated via 'potential' PEST motifs in
eukaryotic cells.
<p>
<H2>
Data files
</H2>
The physico-chemical properties of the residues are read from the EMBOSS
data file 'Eamino.dat'. This file can be copied into your current
directory and inspected or altered by using the application 'embossdata
-fetch'. Another file can be specified using the qualifier '-aadata'.
<p>
<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<p>
Here is the default Eamino.dat file:
<p>
<pre>
# Molecular weights of amino acids
# Also classified as:
# Tiny, Small, Aliphatic, Aromatic, Non-polar, Polar, Charge, +ve, -ve
#
A 71.0786 1 1 0 0 1 0 0 0 0
B 114.5960 0 1 0 0 0 0 -.5 0 1
C 103.1386 1 1 0 0 1 0 0 0 0
D 115.0884 0 1 0 0 0 1 -1 0 1
E 129.1152 0 0 0 0 0 1 -1 0 1
F 147.1762 0 0 0 1 1 0 0 0 0
G 57.0518 1 1 0 0 1 0 0 0 0
H 137.1408 0 0 0 1 0 1 .5 1 0
I 113.1590 0 0 1 0 1 0 0 0 0
J 0.0 0 0 0 0 0 0 0 0 0
K 128.1736 0 0 0 0 0 1 1 1 0
L 113.1590 0 0 1 0 1 0 0 0 0
# If met gets oxidised to the sulphoxide replace by 147.1926
M 131.1926 0 0 0 0 1 0 0 0 0
N 114.1036 0 1 0 0 0 1 0 0 0
O 0.0 0 0 0 0 0 0 0 0 0
P 97.1164 0 1 0 0 1 0 0 0 0
Q 128.1304 0 0 0 0 0 1 0 0 0
R 156.1870 0 0 0 0 0 1 1 1 0
S 87.0780 1 1 0 0 0 1 0 0 0
T 101.1048 1 1 0 0 0 1 0 0 0
U 0.0 0 0 0 0 0 0 0 0 0
V 99.1322 0 1 1 0 1 0 0 0 0
W 186.2128 0 0 0 1 1 0 0 0 0
X 144.0000 0 0 0 0 0 0 0 0 0
Y 163.1756 0 0 0 1 1 0 0 0 0
Z 128.6228 0 0 0 0 0 1 -.5 0 1
</pre>
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>Rogers S.W., Wells R., Rechsteiner M.
Amino acid sequences common to rapidly degraded proteins:
The PEST hypothesis
Science 234, 364-368 (1986)
<li>Rechsteiner M., Rogers S., Rote K.
Protein structure and intracellular stability
Trends Biochem. Sci. 12, 390-394 (1987)
<li>Rechsteiner M. and Rogers S.W.
PEST sequences and regulation by proteolysis
Trends Biochem. Sci. 21, 267-271 (1996)
<li>J. Kyte and R.F. Dootlittle
A simple method for displaying the hydropathic character of a protein
J. Mol. Biol. 157, 105 (1982)
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0.
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>Finds antigenic sites in proteins</td>
</tr>
<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>
<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>Search a protein sequence with a motif</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>Search a PROSITE motif database with a protein sequence</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>
<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>Reports protein signal cleavage sites</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Michael K. Schuster and Martin Grabner (martin.grabner © univie.ac.at)
<br>
from the Austrian National EMBnet node.
<p>
Original program 'epestfind' by Scott Rogers and Martin Rechsteiner
(C)1986.
<H2>
History
</H2>
This is based on the algorithm used in the QuickBasic program by Rodgers et al.
<p>
Written (March 2002).
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
</BODY>
</HTML>