MAST - Motif Alignment and Search Tool
MAST version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.nbcr.net.
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 ./seed.fasta (peptide)
Last updated on Wed May 4 23:49:13 2011
Database contains 72 sequences, 8887 residues
MOTIFS ./memeout.txt (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 49 KGKNVFIVDDIISTGGTMCQACQWLKEQGAKSVYVCCTHCQFVNGAMMR
2 40 DALQDYGAKKITLMAPYMGYARQDRRFHPGEPISSQTVMH
3 18 PLCMPEFKRFPDGEKYVR
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.15
3 0.16 0.19
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 25 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
|
---|
| Q5JJD9_PYRKO/87-214
|
| 0.13
| 128
|
| Q2YAL8_NITMU/17-176
|
| 0.93
| 160
|
| Q64CX6_9ARCH/6-130
|
| 1.1
| 125
|
| Q3SMI9_THIDA/9-141
|
| 2.2
| 133
|
| PYREL_THEAC/57-173
|
| 2.2
| 117
|
| Q72L93_THET2/2-119
|
| 2.4
| 118
|
| Q8XK54_CLOPE/177-285
|
| 2.8
| 109
|
| UPP_AQUAE/45-158
|
| 3
| 114
|
| APT_TRIEI/24-148
|
| 3.3
| 125
|
| A2BJL0_HYPBU/91-207
|
| 3.4
| 117
|
| Q1BD39_MYCSS/177-335
|
| 3.8
| 159
|
| PYRE_DEIRA/36-152
|
| 4.1
| 117
|
| A6QAE7_SULNB/1-117
|
| 5.5
| 117
|
| A8LJR1_DINSH/152-260
|
| 5.8
| 109
|
| A3U7I6_9FLAO/9-129
|
| 6.3
| 121
|
| O83317_TREPA/215-333
|
| 6.8
| 119
|
| Q2RSZ0_RHORT/12-136
|
| 7.4
| 125
|
| A3MXE2_PYRCJ/188-316
|
| 7.8
| 129
|
| A7E5A9_SCLS1/59-194
|
| 7.9
| 136
|
| PYRE_HYPNA/36-146
|
| 8.2
| 111
|
| Q6XYT5_SPIKU/6-127
|
| 8.2
| 122
|
| PYRE_PROAC/45-157
|
| 8.3
| 113
|
| PYREL_METB6/62-178
|
| 8.4
| 117
|
| A3DN49_STAMF/119-244
|
| 8.7
| 126
|
| A5TS89_FUSNP/29-157
|
| 9.2
| 129
|
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
- Spacers and motif occurences are indicated by
- 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
|
---|
| Q5JJD9_PYRKO/87-214
| 0.13
|
|
| Q2YAL8_NITMU/17-176
| 0.93
|
|
| Q64CX6_9ARCH/6-130
| 1.1
|
|
| Q3SMI9_THIDA/9-141
| 2.2
|
|
| PYREL_THEAC/57-173
| 2.2
|
|
| Q72L93_THET2/2-119
| 2.4
|
|
| Q8XK54_CLOPE/177-285
| 2.8
|
|
| UPP_AQUAE/45-158
| 3
|
|
| APT_TRIEI/24-148
| 3.3
|
|
| A2BJL0_HYPBU/91-207
| 3.4
|
|
| Q1BD39_MYCSS/177-335
| 3.8
|
|
| PYRE_DEIRA/36-152
| 4.1
|
|
| A6QAE7_SULNB/1-117
| 5.5
|
|
| A8LJR1_DINSH/152-260
| 5.8
|
|
| A3U7I6_9FLAO/9-129
| 6.3
|
|
| O83317_TREPA/215-333
| 6.8
|
|
| Q2RSZ0_RHORT/12-136
| 7.4
|
|
| A3MXE2_PYRCJ/188-316
| 7.8
|
|
| A7E5A9_SCLS1/59-194
| 7.9
|
|
| PYRE_HYPNA/36-146
| 8.2
|
|
| Q6XYT5_SPIKU/6-127
| 8.2
|
|
| PYRE_PROAC/45-157
| 8.3
|
|
| PYREL_METB6/62-178
| 8.4
|
|
| A3DN49_STAMF/119-244
| 8.7
|
|
| A5TS89_FUSNP/29-157
| 9.2
|
|
SCALE
|
| |
| |
| |
| |
| |
| |
1 |
25 |
50 |
75 |
100 |
125 |
|
---|
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).
Q5JJD9_PYRKO/87-214
LENGTH = 128 COMBINED P-VALUE = 1.83e-03 E-VALUE = 0.13
DIAGRAM: 19-[1]-60
[1]
1.6e-06
KGKNVFIVDDIISTGGTMCQACQWLKEQGAKSVYVCCTHCQFVNGAMMR
+ + + + +++ + +++++++ +++ ++++ +
1 MPALSDTALMSLIAEEVASKYMDKDIDKVLTAETDGIVLGAHIARELGADLIYAKKKKEVGVEKFYEVNYVPSAS
Q2YAL8_NITMU/17-176
LENGTH = 160 COMBINED P-VALUE = 1.29e-02 E-VALUE = 0.93
DIAGRAM: 160
Q64CX6_9ARCH/6-130
LENGTH = 125 COMBINED P-VALUE = 1.58e-02 E-VALUE = 1.1
DIAGRAM: 18-[2]-67
[2]
4.5e-05
DALQDYGAKKITLMAPYMGYARQDRRFHPGEPISSQTVMH
+ +++++++ +++ + ++ + ++
1 SCILVDWNYAYDLCKDVRDEIKEAGFKPEVIVGVARGGWYLARVLCDFFLLKDLLSLKMEHWGVTATITGTAELK
Q3SMI9_THIDA/9-141
LENGTH = 133 COMBINED P-VALUE = 3.09e-02 E-VALUE = 2.2
DIAGRAM: 133
PYREL_THEAC/57-173
LENGTH = 117 COMBINED P-VALUE = 3.12e-02 E-VALUE = 2.2
DIAGRAM: 117
Q72L93_THET2/2-119
LENGTH = 118 COMBINED P-VALUE = 3.29e-02 E-VALUE = 2.4
DIAGRAM: 118
Q8XK54_CLOPE/177-285
LENGTH = 109 COMBINED P-VALUE = 3.85e-02 E-VALUE = 2.8
DIAGRAM: 109
UPP_AQUAE/45-158
LENGTH = 114 COMBINED P-VALUE = 4.22e-02 E-VALUE = 3
DIAGRAM: 114
APT_TRIEI/24-148
LENGTH = 125 COMBINED P-VALUE = 4.52e-02 E-VALUE = 3.3
DIAGRAM: 125
A2BJL0_HYPBU/91-207
LENGTH = 117 COMBINED P-VALUE = 4.68e-02 E-VALUE = 3.4
DIAGRAM: 117
Q1BD39_MYCSS/177-335
LENGTH = 159 COMBINED P-VALUE = 5.30e-02 E-VALUE = 3.8
DIAGRAM: 21-[1]-89
[1]
6.4e-05
KGKNVFIVDDIISTGGTMCQACQWLKEQGAKSVYVCCTHCQFVNGAMMR
++++ +++ + ++ + +++ + ++ + + + +
1 RRVFRDRREAGRVLADLLTAYRGRDDVIVLGLARGGVPVAWEVAAALGAPLDAFIVRKLGAPGHEEFAMGALATG
PYRE_DEIRA/36-152
LENGTH = 117 COMBINED P-VALUE = 5.75e-02 E-VALUE = 4.1
DIAGRAM: 117
A6QAE7_SULNB/1-117
LENGTH = 117 COMBINED P-VALUE = 7.62e-02 E-VALUE = 5.5
DIAGRAM: 117
A8LJR1_DINSH/152-260
LENGTH = 109 COMBINED P-VALUE = 8.02e-02 E-VALUE = 5.8
DIAGRAM: 109
A3U7I6_9FLAO/9-129
LENGTH = 121 COMBINED P-VALUE = 8.80e-02 E-VALUE = 6.3
DIAGRAM: 121
O83317_TREPA/215-333
LENGTH = 119 COMBINED P-VALUE = 9.42e-02 E-VALUE = 6.8
DIAGRAM: 119
Q2RSZ0_RHORT/12-136
LENGTH = 125 COMBINED P-VALUE = 1.02e-01 E-VALUE = 7.4
DIAGRAM: 125
A3MXE2_PYRCJ/188-316
LENGTH = 129 COMBINED P-VALUE = 1.08e-01 E-VALUE = 7.8
DIAGRAM: 129
A7E5A9_SCLS1/59-194
LENGTH = 136 COMBINED P-VALUE = 1.09e-01 E-VALUE = 7.9
DIAGRAM: 136
PYRE_HYPNA/36-146
LENGTH = 111 COMBINED P-VALUE = 1.13e-01 E-VALUE = 8.2
DIAGRAM: 111
Q6XYT5_SPIKU/6-127
LENGTH = 122 COMBINED P-VALUE = 1.14e-01 E-VALUE = 8.2
DIAGRAM: 122
PYRE_PROAC/45-157
LENGTH = 113 COMBINED P-VALUE = 1.16e-01 E-VALUE = 8.3
DIAGRAM: 113
PYREL_METB6/62-178
LENGTH = 117 COMBINED P-VALUE = 1.17e-01 E-VALUE = 8.4
DIAGRAM: 117
A3DN49_STAMF/119-244
LENGTH = 126 COMBINED P-VALUE = 1.21e-01 E-VALUE = 8.7
DIAGRAM: 126
A5TS89_FUSNP/29-157
LENGTH = 129 COMBINED P-VALUE = 1.28e-01 E-VALUE = 9.2
DIAGRAM: 129
Debugging Information
CPU: kodomo
Time 0.016001 secs.
mast ./memeout.txt -d ./seed.fasta -ev 10.000000 -mt 0.000100
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