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
|
********************************************************************************
MAST - Motif Alignment and Search Tool
********************************************************************************
MAST version 3.0 (Release date: 2004/08/18 09:07:01)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
********************************************************************************
********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
********************************************************************************
********************************************************************************
DATABASE AND MOTIFS
********************************************************************************
DATABASE farntrans5.s (peptide)
Last updated on Mon Aug 16 21:19:59 2004
Database contains 5 sequences, 1900 residues
MOTIFS meme.farntrans5.tcm.txt (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 30 GGFQGRPNKEVHTCYTYWALAALAILNKLH
2 14 INKEKLIQWIKSCQ
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.22
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033
********************************************************************************
********************************************************************************
SECTION I: HIGH-SCORING SEQUENCES
********************************************************************************
- Each of the following 5 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
o finding the score of the single best match of each motif
to the sequence (best matches may overlap),
o calculating the sequence p-value of each score,
o forming the product of the p-values,
o taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
********************************************************************************
SEQUENCE NAME DESCRIPTION E-VALUE LENGTH
------------- ----------- -------- ------
BET2_YEAST YPT1/SEC4 PROTEINS GERANY... 2.9e-27 325
RATRABGERB Rat rab geranylgeranyl tr... 1.4e-25 331
CAL1_YEAST RAS PROTEINS GERANYLGERAN... 9.7e-22 376
PFTB_RAT PROTEIN FARNESYLTRANSFERA... 7.6e-21 437
RAM1_YEAST PROTEIN FARNESYLTRANSFERA... 6.2e-20 431
********************************************************************************
********************************************************************************
SECTION II: MOTIF DIAGRAMS
********************************************************************************
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
o -d- `d' residues separate the end of the preceding motif
occurrence and the start of the following motif occurrence
o [n] occurrence of motif `n' with p-value less than 0.0001.
********************************************************************************
SEQUENCE NAME E-VALUE MOTIF DIAGRAM
------------- -------- -------------
BET2_YEAST 2.9e-27 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_
3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_
4_[1]_24
RATRABGERB 1.4e-25 65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_
3_[1]_18_[1]_1_[2]_4_[1]_26
CAL1_YEAST 9.7e-22 125_[2]_50_[2]_1_[1]_4_[2]_22_
[1]_22_[1]_5_[2]_1
PFTB_RAT 7.6e-21 120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_
3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60
RAM1_YEAST 6.2e-20 144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_
1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4
********************************************************************************
********************************************************************************
SECTION III: ANNOTATED SEQUENCES
********************************************************************************
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
o the motif number of the occurrence,
o the position p-value of the occurrence,
o the best possible match to the motif, and
o columns whose match to the motif has a positive score (indicated
by a plus sign).
********************************************************************************
BET2_YEAST
YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
LENGTH = 325 COMBINED P-VALUE = 5.77e-28 E-VALUE = 2.9e-27
DIAGRAM: 6_[2]_3_[1]_1_[2]_4_[1]_4_[2]_3_[1]_1_[2]_3_[1]_21_[1]_1_[2]_4_[1]_24
[2] [1] [2] [1]
5.2e-05 2.7e-10 6.6e-10 5.9
INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGF
+++ +++++++ ++ + +++ +++ +++++ +++++++ + ++++++++++++++ + +
1 MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF
[2] [1]
e-14 4.8e-07 2.3e-17
QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN
+ +++++++ + ++++++ +++++ +++ +++++++ ++ + ++++ +++++++ +++++++++++
76 APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG
[2] [1] [1]
5.1e-07 1.4e-18 4.6
KLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH GGF
+++ ++++ ++++++++ ++++ ++++++++++++++++++++++++ +++
151 ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL
[2] [1]
e-22 2.0e-13 3.8e-17
QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKL
++++ ++++++++++++++++++++++ ++ +++++++++++ ++++++++++++++++ ++++++++++ +
226 NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD
H
+
301 NLVPIDPIYCMPKSVTSKFKKYPYK
RATRABGERB
Rat rab geranylgeranyl transferase beta-subunit
LENGTH = 331 COMBINED P-VALUE = 2.83e-26 E-VALUE = 1.4e-25
DIAGRAM: 65_[2]_3_[1]_1_[2]_3_[1]_1_[2]_3_[1]_18_[1]_1_[2]_4_[1]_26
[2]
1.0e-11
INKEKLIQWI
+++++++ ++
1 MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI
[1] [2] [1]
1.6e-14 1.4e-09 5.4e-19
KSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWAL
++++ ++ + +++++++ ++ ++++++++++++ +++++++ ++++++ + ++++++++++++++++++
76 KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV
[2] [1]
3.8e-12 4.8e-19
AALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH
++++++++++ ++++++++++++++ ++++++++ ++++++++++++ ++++++++
151 ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP
[1] [2] [1]
3.9e-21 1.2e-12 9.6e-18
GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAI
+++++++++++++++++++++++ ++++++ ++++++++++++++ ++++++++++++ +++ ++++++++
226 SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL
LNKLH
+++++
301 LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS
CAL1_YEAST
RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
LENGTH = 376 COMBINED P-VALUE = 1.94e-22 E-VALUE = 9.7e-22
DIAGRAM: 125_[2]_50_[2]_1_[1]_4_[2]_22_[1]_22_[1]_5_[2]_1
[2]
1.8e-08
INKEKLIQWIKSCQ
+++++++++++++
76 LDDTENTVISGFVGSLVMNIPHATTINLPNTLFALLSMIMLRDYEYFETILDKRSLARFVSKCQRPDRGSFVSCL
[2] [1]
4.8e-10 8.7e-14
INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALA
+++++++ ++++++ + + + +++++ +++ ++++
151 DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS
[2] [1]
5.9e-08 5.9e-20
ALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAIL
+++++++++ ++++++++++++ +++++++++ +++++++++++++ ++
226 TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL
[1] [2]
4.0e-13 2.1e-07
NKLH GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ
++++ ++++ + ++++++++++ + +++++++ + ++ +++++++++
301 TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC
PFTB_RAT
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
LENGTH = 437 COMBINED P-VALUE = 1.53e-21 E-VALUE = 7.6e-21
DIAGRAM: 120_[2]_3_[1]_4_[2]_3_[1]_1_[2]_3_[1]_1_[2]_4_[1]_14_[2]_4_[1]_60
[2] [1]
1.3e-07 2.8e-19
INKEKLIQWIKSCQ GGFQGRPNKEVHT
++ ++++++++ ++ +++++++++ +++
76 EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL
[2] [1] [2]
2.3e-09 2.1e-14 1.8e-0
CYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKL
+ +++++++++++++++ ++++++++++ +++ + + ++ +++++++ +++++++++++++++ + +++
151 APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT
[1] [2] [1]
8 7.4e-20 1.8e-08 2.2e-16
IQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCY
++++ +++ +++++ +++++++++++++++++ ++++++ + +++++++++++ ++++++ ++++++++
226 AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY
[2] [1]
5.0e-08 3.1e-15
TYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK
++++++ + ++++ ++++++++++++++ +++ +++++ +++++++++++++++++
301 SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH
LH
+
376 FGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPGFEECEDAVTSDPATD
RAM1_YEAST
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
LENGTH = 431 COMBINED P-VALUE = 1.24e-20 E-VALUE = 6.2e-20
DIAGRAM: 144_[1]_5_[2]_4_[1]_1_[2]_4_[1]_1_[2]_4_[1]_4_[2]_5_[1]_35_[2]_4
[1]
8.8e-1
GGFQGR
+ ++++
76 PALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVVKLFTISPSGGPFGGG
[2] [1]
7 6.4e-07 1.0e-13
PNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK
++++++++ ++++++++++ ++++ ++++++++++ +++ + ++ ++++++++ +++++++++++++
151 PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI
[2] [1] [2] [1]
2.5e-08 3.1e-17 4.7e-11 2.4e-
LH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQG
++ + ++++++++++++ + ++ +++++++++++++++++++++++ ++++++++++++++ ++ +
226 LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG
[2] [1]
16 4.9e-09 2.7e-13
RPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN
+ ++++++++++++ +++++++++ +++++++++++ ++ +++++++++++++++ +++ ++++++
301 RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE
[2]
9.8e-05
KLH INKEKLIQWIKSCQ
+ +++++++ + +++
376 SSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS
********************************************************************************
CPU: pmgm2
Time 0.130000 secs.
mast meme.farntrans5.tcm.txt -text -stdout
|
