MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2004/07/16 05:53:30)
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 /home/meme/meme.3.0.6/tests/farntrans5.s (peptide)
Last updated on Fri Jul 16 15:53:55 2004
Database contains 5 sequences, 1900 residues
MOTIFS meme.farntrans5.zoops.4.Linuxx86_64.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 32 QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
2 50 GEVDTRFVYCALSVASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.30
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
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- 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.
Links | Sequence Name | Description | E-value | Length
|
---|
| BET2_YEAST
| YPT1/SEC4 PROTEINS GERANY...
| 2.1e-70
| 325
|
| RATRABGERB
| Rat rab geranylgeranyl tr...
| 1.7e-67
| 331
|
| PFTB_RAT
| PROTEIN FARNESYLTRANSFERA...
| 9.8e-65
| 437
|
| RAM1_YEAST
| PROTEIN FARNESYLTRANSFERA...
| 1.1e-63
| 431
|
| CAL1_YEAST
| RAS PROTEINS GERANYLGERAN...
| 7.3e-25
| 376
|
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
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
Links | Name | Expect | Motifs
|
---|
| BET2_YEAST
| 2.1e-70
|
|
| RATRABGERB
| 1.7e-67
|
|
| PFTB_RAT
| 9.8e-65
|
|
| RAM1_YEAST
| 1.1e-63
|
|
| CAL1_YEAST
| 7.3e-25
|
|
SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
1 |
25 |
50 |
75 |
100 |
125 |
150 |
175 |
200 |
225 |
250 |
275 |
300 |
325 |
350 |
375 |
400 |
425 |
|
---|
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
- the motif number of the occurrence,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- 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 = 4.14e-71 E-VALUE = 2.1e-70
DIAGRAM: 31-[2]-50-[2]-37-[1]-17-[1]-26
[2]
2.3e-05
GEVDTRFVYCALSVASLLNILTPELVEGAIEFVLRCQNFDGGFG
+++ ++++ + + + ++ +++++ +
1 MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF
[2]
8.6e-45
CCPGAE GEVDTRFVYCALSVASLLN
+ +++++++++ +++++++++
76 APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG
[1]
3.5e-34
ILTPELVEGAIEFVLRCQNFDGGFGCCPGAE QQPEGGF
+++++++ +++++++++++++++++++++++ +++++++
151 ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL
[1]
1.0e-06
NGRPNKLPDVCYSWWVLGSLPIIGR QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
+++++++++++++++++++++++++ ++ +++ +++ + + + +++
226 NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD
RATRABGERB
Rat rab geranylgeranyl transferase beta-subunit
LENGTH = 331 COMBINED P-VALUE = 3.40e-68 E-VALUE = 1.7e-67
DIAGRAM: 42-[2]-46-[2]-34-[1]-17-[1]-28
[2]
4.7e-09
GEVDTRFVYCALSVASLLNILTPELVEGAIEFV
+++ +++ +++ + + + + ++
1 MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI
[2]
3.3e-43
LRCQNFDGGFGCCPGAE GEVDTRFVYCAL
++++ ++ + + ++++++++++++
76 KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV
[1]
7.6
SVASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE QQP
++++++++++++++++++++++++++++++++++++++ +++
151 ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP
[1]
e-33 2.1e-07
EGGFNGRPNKLPDVCYSWWVLGSLPIIGR QQPEGGFNGRPNKLPDVCYSWWVLGSLPI
+++++++++++++++++++++++++++++ + +++ ++ +++ + + + +
226 SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL
IGR
++
301 LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS
PFTB_RAT
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
LENGTH = 437 COMBINED P-VALUE = 1.95e-65 E-VALUE = 9.8e-65
DIAGRAM: 133-[1]-31-[2]-35-[1]-30-[1]-62
[1]
5.4e-09
QQPEGGFNGRPNKLPDV
+++++++ + + +
76 EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL
[2]
4.2e-44
CYSWWVLGSLPIIGR GEVDTRFVYCALSVASLLNILTPELVEGA
++ + + +++ +++++++++++++++++++++++++++++
151 APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT
[1]
1.9e-29
IEFVLRCQNFDGGFGCCPGAE QQPEGGFNGRPNKLPDVCY
+++++++++++++++++++++ +++++++++++++++++++
226 AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY
[1]
6.3e-07
SWWVLGSLPIIGR QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
++++++ ++++++ + + +++ + + + + +++ + +
301 SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH
RAM1_YEAST
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
LENGTH = 431 COMBINED P-VALUE = 2.14e-64 E-VALUE = 1.1e-63
DIAGRAM: 205-[2]-36-[1]-108
[2]
3.3e-45
GEVDTRFVYCALSVASLLNI
++++++++++++++++++++
151 PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI
[1]
2.8e-27
LTPELVEGAIEFVLRCQNFDGGFGCCPGAE QQPEGGFNG
+++++++++++++++++++++++++++++ ++++++++
226 LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG
RPNKLPDVCYSWWVLGSLPIIGR
++++++++++++++++++++++
301 RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE
CAL1_YEAST
RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
LENGTH = 376 COMBINED P-VALUE = 1.46e-25 E-VALUE = 7.3e-25
DIAGRAM: 212-[2]-8-[1]-20-[1]-22
[2]
7.4e-06
GEVDTRFVYCALS
+ ++++
151 DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS
[1]
2.8e-27
VASLLNILTPELVEGAIEFVLRCQNFDGGFGCCPGAE QQPEGGFNGRPNKLPDVCYSWWVLGSLPII
+++++ + + + ++ + ++++++++++++++++++++++++++++++
226 TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL
[1]
6.4e-05
GR QQPEGGFNGRPNKLPDVCYSWWVLGSLPIIGR
++ +++ + ++ + + +++++
301 TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC
Debugging Information
CPU: chromo
Time 0.090000 secs.
mast meme.farntrans5.zoops.4.Linuxx86_64.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information