MAST - Motif Alignment and Search Tool
MAST version 4.1.1 (Release date: Tue Apr 21 15:00:06 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 19 03:01:45 2010
Database contains 11 sequences, 2649 residues
MOTIFS ./memeout.txt (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 50 DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
2 50 NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
3 50 AINELRNETNNSSYQFIAVRLPYGVQADEDDCQDAIAFIQPDHVWTVNIK
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.10
3 0.07 0.08
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 11 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
|
|---|
|
| NADE_ECOLI/22-265
|
| 1.3e-157
| 244
|
|
| NADE_BACSU/22-263
|
| 2.8e-131
| 242
|
|
| NADE_PYRHO/9-245
|
| 5.9e-16
| 237
|
|
| NADE_MYCGE/7-237
|
| 1.8e-14
| 231
|
|
| NADE_MYCPN/8-237
|
| 1.2e-13
| 230
|
|
| NADE_METTH/11-253
|
| 6.4e-13
| 243
|
|
| NADE_ARCFU/6-238
|
| 1.3e-10
| 233
|
|
| NADE_METJA/10-254
|
| 7.9e-10
| 245
|
|
| NADE_HELPY/8-251
|
| 1.7e-06
| 244
|
|
| NADE_AQUAE/293-542
|
| 0.00076
| 250
|
|
| NADE_SYNY3/281-530
|
| 0.03
| 250
|
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
|
|---|
|
| NADE_ECOLI/22-265
| 1.3e-157
|
|
|
| NADE_BACSU/22-263
| 2.8e-131
|
|
|
| NADE_PYRHO/9-245
| 5.9e-16
|
|
|
| NADE_MYCGE/7-237
| 1.8e-14
|
|
|
| NADE_MYCPN/8-237
| 1.2e-13
|
|
|
| NADE_METTH/11-253
| 6.4e-13
|
|
|
| NADE_ARCFU/6-238
| 1.3e-10
|
|
|
| NADE_METJA/10-254
| 7.9e-10
|
|
|
| NADE_HELPY/8-251
| 1.7e-06
|
|
|
| NADE_AQUAE/293-542
| 0.00076
|
|
|
| NADE_SYNY3/281-530
| 0.03
|
|
| SCALE
|
| | |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 1 |
25 |
50 |
75 |
100 |
125 |
150 |
175 |
200 |
225 |
|
|---|
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).
NADE_ECOLI/22-265
LENGTH = 244 COMBINED P-VALUE = 1.17e-158 E-VALUE = 1.3e-157
DIAGRAM: 41-[3]-18-[1]-7-[2]-28
[3]
2.6e-56
AINELRNETNNSSYQFIAVRLPYGVQADEDDCQD
++++++++++++++++++++++++++++++++++
1 EIRRSVDFLKSYLQTYPFIKSLVLGISGGQDSTLAGKLCQMAINELRLETGNESLQFIAVRLPYGVQADEQDCQD
[1]
3.4e-59
AIAFIQPDHVWTVNIK DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFF
++++++++++++++++ +++++++++++++++++++++++++++++++++++++++++
76 AIAFIQPDRVLTVNIKGAVLASEQALREAGIELSDFVRGNEKARERMKAQYSIAGMTSGVVVGTDHAAEAITGFF
[2]
2.5e-56
TKYGDGGCD NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++
151 TKYGDGGTDINPLYRLNKRQGKQLLAALACPEHLYKKAPTADLEDDRPSLPDEVALGVTYDNIDDYLEGKNVPQQ
NADE_BACSU/22-263
LENGTH = 242 COMBINED P-VALUE = 2.58e-132 E-VALUE = 2.8e-131
DIAGRAM: 38-[3]-19-[1]-7-[2]-28
[3]
1.0e-44
AINELRNETNNSSYQFIAVRLPYGVQADEDDCQDAIA
+++++++++++++++++++++++++++++++++++++
1 EIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALK
[1]
6.4e-54
FIQPDHVWTVNIK DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTK
+++++++++++++ +++++++++++++++++++++++++++++++++++++++++++
76 FIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTK
[2]
1.1e-46
YGDGGCD NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++
151 YGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVS
NADE_PYRHO/9-245
LENGTH = 237 COMBINED P-VALUE = 5.36e-17 E-VALUE = 5.9e-16
DIAGRAM: 26-[2]-15-[1]-7-[2]-39
[2]
7.7e-05
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDD
+ + ++++ + + + + + + +++ + +
1 VIERILEFIREKGNNGVVIGISGGVDSATVAYLATKALGKEKVLGLIMPYFENKDVEDAKLVAEKLGIGYKVINI
[1] [2
2.6e-18 1.
Y DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD NK
+++ +++++ ++ + + +++++ + +++ +++ ++++ + +
76 KPIVDSFVENLELNLDRKGLGNIMSRTRMIMLYAHANSLGRIVLGTSNRSEFLTGYFTKWGDGASDYAPIINLYK
]
4e-06
RQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+ ++ + +++++++ + + + + +++
151 TEVWEIAKRIGVPERIVKKKPSAGLWEGQTDEDELGISYNLLDEILWRMIDLKIGKEEIAKDLGIPLSLVERVEE
NADE_MYCGE/7-237
LENGTH = 231 COMBINED P-VALUE = 1.68e-15 E-VALUE = 1.8e-14
DIAGRAM: 98-[1]-4-[2]-29
[1]
5.5e-18
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
++++++ +++ ++ + +++++ + + +++ ++++++
76 INIELEESFNLLVKTLGIDPKKDFLTAGNIKARLRMITLYAYAQKHNFLVLGTGNFVEYTLGYFTKWGDGACDIA
[2]
6.1e-05
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
++ + + + + ++++ ++++ + + +
151 PLAWLLKEDVYKLAKHFNIPEIVITRAPTASLFEGQTDETEMGITYKELDQYLKGDLILSSEKQKIVLDLKAKAE
NADE_MYCPN/8-237
LENGTH = 230 COMBINED P-VALUE = 1.12e-14 E-VALUE = 1.2e-13
DIAGRAM: 97-[1]-4-[2]-29
[1]
3.2e-16
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
+ ++ +++ ++ + + +++++ + + +++ ++++++
76 QVDLEPPYRAMLQALTIDPQKELMVAGNLKARLRMACLYTHAQKHNYLVLGTGNFIEYSLGYFTKWGDGACDVAP
[2]
2.6e-05
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
++ + + + + + ++++ ++++ + + +
151 LAFLLKSDVYALSQHFNVPELVIERAPTASLFAGQTDEAEMGLTYKELDQYFQGHLQLSATKQQRVDHLRQSSQH
NADE_METTH/11-253
LENGTH = 243 COMBINED P-VALUE = 5.82e-14 E-VALUE = 6.4e-13
DIAGRAM: 32-[2]-15-[1]-7-[2]-39
[2]
8.7e-05
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVT
+ + + + + +++ + +++++
1 VVSVIEDFIRQKVAESGASGVVLGLSGGVDSSTVAYLAVNALGPDRVLGLIMPSSTTPRDDLRHARTVADELGIE
[1]
1.1e-14
YDNIDDY DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
+ ++ + + +++++ + + ++ ++ + + + ++++++++ +
76 SETIDIDPIIESLTGLCSHNANELALANLKPRARMVILYYHANSLNRLVAGTGNRTELLLGYFTKYGDGGVDMLP
[2]
3.9e-06
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+ +++ ++ ++ + + ++ +++ + ++
151 IGGLYKGQVRELAGRLGVPPEIIKKPPTAGLWHGQTDEEELGMKYDLLDELLCLLVDRKLPVEEVASTLSLPPSE
NADE_ARCFU/6-238
LENGTH = 233 COMBINED P-VALUE = 1.23e-11 E-VALUE = 1.3e-10
DIAGRAM: 97-[1]-7-[2]-29
[1]
4.9e-13
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
+ + + +++ + + ++ ++ + + ++++++++ +
76 EYKLIEINDIVRVFKEKAGEGSKIAEANLKPRIRMVLNYYHANSMNRLVAGTGNKSELMVGYFTKYGDGGVDFLP
[2]
7.4e-06
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+ + ++++ ++ + ++ + + + + +++
151 IGDLYKTEVFQLAAYLGVPRRIIEKKPSARLWPGQTDEEEMGISYAELDEILKLIEKGERRDDEKFRRVVQMVER
NADE_METJA/10-254
LENGTH = 245 COMBINED P-VALUE = 7.18e-11 E-VALUE = 7.9e-10
DIAGRAM: 100-[1]-7-[2]-38
[1]
9.0e-13
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
++ +++ ++ + + +++ ++ + + ++ ++ +++
76 YIISDITDILKAFGAGGYVPTREFDKIADGNLKARIRMCILYYFANKYNLLVAGTSNKSEIYVGYGTKHGDIACD
[2]
5.7e-06
NKRQGRQLLRELGCPEHLYMKAPTADLEEDRPSLPDEVALGVTYDNIDDY
+ ++ +++ + + + + + + + + + + + +
151 IRPIGNLFKTEVKKLAKYIGVPKEIIEKPPSAGLWEGQTDEEELDIKYETLDTILKLYEKGKTPEEIHKETNIPL
NADE_HELPY/8-251
LENGTH = 244 COMBINED P-VALUE = 1.54e-07 E-VALUE = 1.7e-06
DIAGRAM: 95-[1]-99
[1]
8.9e-11
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGCD
+++ ++ ++ + +++++ + + + +++ ++
76 TEYSIAPYDAIFSSHFKDASLTRKGNFCARLRMAFLYDYSLKSDSLVIGTSNKSERMLGYGTLFGDLACAINPIG
NADE_AQUAE/293-542
LENGTH = 250 COMBINED P-VALUE = 6.89e-05 E-VALUE = 0.00076
DIAGRAM: 101-[1]-99
[1]
1.2e-07
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGC
+ ++ ++ + + +++ + + + + +++ +
76 FHVIPIKEIYRAYFNEFEKEICEITFDVADENIQARIRANILFYFSNKFRYLVLSTSNKSETAVGYTTIYGDMAG
D
151 GFAPIKDVYKTWVYKLARYRNSISPDIPERVFKKPPSAELRPNQTDQDVLPPYEILDQILMLYIEENLSPEEIIR
NADE_SYNY3/281-530
LENGTH = 250 COMBINED P-VALUE = 2.69e-03 E-VALUE = 0.03
DIAGRAM: 101-[1]-99
[1]
2.9e-06
DFVKGNEKARERMKAQYSIAGMNSGLVVGTDHAAENITGFFTKYGDGGC
+ + + +++ + + + + + + + +++
76 TQTIPIGPIMATYDQALVPLFQDAPFGLAEENLQSRIRGNLLMAIANKFGHLLLSTGNKSELAVGYCTLYGDMNG
D
151 GLAAIADVPKTQVFELCRWLNREQTIIPPSVLTKPPSAELKPGQVDTDSLPPYDVLDGILGRLVEKHQSPQEIIN
Debugging Information
CPU: kodomo-count
Time 0.060004 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