Command line Training Set First Motif Summary of Motifs Termination Explanation


Search sequence databases with these motifs using MAST.
Submit these motifs to BLOCKS multiple alignment processor.
Build and use a motif-based hidden Markov model (HMM) using Meta-MEME.


MEME - Motif discovery tool

MEME version 3.5.0 (Release date: 2005/07/29 20:02:31)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net.


REFERENCE

If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.


TRAINING SET

DATAFILE= C:\Documents_and_Settings\juhur\Desktop\ProtSeq.fas
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
At1g01140.1_4-2-4_SnRK3. 1.0000    447  At1g01140.2_SnRK3.12     1.0000    449  
At1g01140.3_SnRK3.12     1.0000    451  At1g01450.1_2-1-1        1.0000    470  
At1g01540.1_1-6-3        1.0000    386  At1g01540.2_Putative     1.0000    472  
At1g01560.1_4-5-1_MPK11  1.0000    275  At1g01740.1_1-16-1       1.0000    483  
At1g02970.1_4-3-1        1.0000    500  At1g03740.1_4-5-2        1.0000    542  
At1g03920.1_4-2-6        1.0000    569  At1g03930.1_3-1-1-1_ADK1 1.0000    471  
At1g04210.1_protein      1.0000   1112  At1g04440.1_3-1-1-1      1.0000    468  
At1g04700.1_2-1-4-1_Raf1 1.0000   1042  At1g05100.1_4-4-1_MAPKKK 1.0000    339  
At1g05700.1_1-8-1        1.0000    843  At1g06390.1_4-5-4_ASK-io 1.0000    407  
At1g06390.2_ASK-iota     1.0000    407  

COMMAND LINE SUMMARY

This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme /home/meme/meme-rocks/LOGS/meme.5659.data -protein -mod zoops -nmotifs 3 -minw 6 -maxw 20 -evt 1e100 -time 7200 -maxsize 60000 -nostatus -maxiter 20 

model:  mod=         zoops    nmotifs=         3    evt=        1e+100
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       19    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=       megap    b=           50665    maxiter=        20
        distance=    1e-05
data:   n=           10133    N=              19

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.053 C 0.017 D 0.055 E 0.071 F 0.041 G 0.066 H 0.024 I 0.051 K 0.065 
L 0.099 M 0.023 N 0.048 P 0.046 Q 0.034 R 0.061 S 0.091 T 0.050 V 0.062 
W 0.011 Y 0.032 
Background letter frequencies (from dataset with add-one prior applied):
A 0.053 C 0.017 D 0.055 E 0.071 F 0.041 G 0.065 H 0.024 I 0.051 K 0.065 
L 0.099 M 0.023 N 0.048 P 0.046 Q 0.034 R 0.061 S 0.091 T 0.050 V 0.062 
W 0.011 Y 0.032 

P N
MOTIF 1     width = 20     sites = 18     llr = 680     E-value = 1.7e-119

SimplifiedA::::1::1::::::::::::
pos.-specificC121::::1:1:::1::::::
probabilityD:::::1::::9:::3::::6
matrixE2::2::::::1:::2:::::
F1:::::1::1::::::1:::
G:2:::6:::1:::1:::::2
H127:::::a:::::::::::
I21::::31:::4::::322:
K:::131::::::9::::::1
L:21::::2:1:3::::584:
M:1:1::::::::::::::1:
N::11:2::::::1::a:::2
P::::31:::::::6::::::
Q::::::::::::::1:::::
R::::31:::8::::::::::
S1::4:::::::::24:::::
T::11:::::::::1::::::
V:1:2::52:::2::::1:3:
W::::::::::::::::::::
Y4:::::12:::::::::1::
bits 6.5
5.9
5.2 
4.6  
Information 3.9    
content 3.3     
(54.5 bits)2.6            
2.0                   
1.3                    
0.7                    
0.0
Multilevel YCHSKGVLHRDIKPSNLLLD
consensus RIVLDIV
sequence PYVE
NAME   START P-VALUE    SITES 
At1g01140.3_SnRK3.121324.45e-22 YFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDF
At1g01140.2_SnRK3.121324.45e-22 YFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDF
At1g01140.1_4-2-4_SnRK3.1324.45e-22 YFQQLINAVDYCHSRGVYHRDLKPENLILDANGVLKVSDF
At1g04440.1_3-1-1-11181.09e-19 LADQMINRVEYMHVKGFLHRDIKPDNFLMGLGRKANQVYI
At1g03740.1_4-5-23271.23e-19 YMRQLLSGLEHCHSRGVLHRDIKGSNLLIDSKGVLKIADF
At1g03930.1_3-1-1-1_ADK11181.25e-18 LADQLINRVEFMHTRGFLHRDIKPDNFLMGLGRKANQVYI
At1g01560.1_4-5-1_MPK111561.25e-18 FLYQLLRGLKYVHSANVLHRDLKPSNLLLNANCDLKIGDF
At1g06390.2_ASK-iota1852.75e-18 TYQIFRGLAYIHTVPGVCHRDVKPQNLLVDPLTHQVKLCD
At1g06390.1_4-5-4_ASK-io1852.75e-18 TYQIFRGLAYIHTVPGVCHRDVKPQNLLVDPLTHQVKLCD
At1g03920.1_4-2-62502.87e-17 YIAESVLAIESIHNRNYIHRDIKPDNLLLDRYGHLRLSDF
At1g04210.1_protein9171.15e-16 IARDISGALMELHSKDIIHRDIKSENVLIDLDNQSANGEP
At1g04700.1_2-1-4-1_Raf18851.86e-16 ITLDSAFGMEYLHMKNIVHFDLKCDNLLVNLRDPQRPICK
At1g01540.2_Putative2701.08e-15 GMAKGLAYLHEGLEPKVVHRDIKSSNILLDRQWNAKVSDF
At1g01540.1_1-6-32701.08e-15 GMAKGLAYLHEGLEPKVVHRDIKSSNILLDRQWNAKVSDF
At1g02970.1_4-3-13621.55e-15 IMHQIAKALHFVHEKGIAHLDVKPDNIYIKNGVCKLGDFG
At1g05100.1_4-4-1_MAPKKK1215.71e-15 TRQILLGLEYIHNSKGIAHCDIKGSNVLVGENGEAKIADF
At1g05700.1_1-8-16748.73e-15 DAAQGLEYLHCGCKPPIVHRDVKTSNILLNEKNRAKLADF
At1g01450.1_2-1-11391.36e-13 LMLQIALGMEYLHSKRIYHGELNPSNILVKPRSNQSGDGY

Motif 1 block diagrams

NameLowest
p-value
   Motifs
At1g01140.3_SnRK3.12 4.4e-22

1
At1g01140.2_SnRK3.12 4.4e-22

1
At1g01140.1_4-2-4_SnRK3. 4.4e-22

1
At1g04440.1_3-1-1-1 1.1e-19

1
At1g03740.1_4-5-2 1.2e-19

1
At1g03930.1_3-1-1-1_ADK1 1.2e-18

1
At1g01560.1_4-5-1_MPK11 1.2e-18

1
At1g06390.2_ASK-iota 2.8e-18

1
At1g06390.1_4-5-4_ASK-io 2.8e-18

1
At1g03920.1_4-2-6 2.9e-17

1
At1g04210.1_protein 1.2e-16

1
At1g04700.1_2-1-4-1_Raf1 1.9e-16

1
At1g01540.2_Putative 1.1e-15

1
At1g01540.1_1-6-3 1.1e-15

1
At1g02970.1_4-3-1 1.5e-15

1
At1g05100.1_4-4-1_MAPKKK 5.7e-15

1
At1g05700.1_1-8-1 8.7e-15

1
At1g01450.1_2-1-1 1.4e-13

1
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900 925 950 975

Motif 1 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 1 position-specific scoring matrix


Motif 1 position-specific probability matrix






Time  5.34 secs.


P N
MOTIF 2     width = 20     sites = 19     llr = 659     E-value = 7.1e-103

SimplifiedA2:::11:1::1:::2:::::
pos.-specificC1::::2:3::::::::::::
probabilityD19:::::::::1::::::::
matrixE:::1:::::::7::::11::
F:::1:4::::3:1::::::4
G::::::a:::1::::9::::
H:::::::::::::::::1::
I2:5::::2321:22::::11
K::::::::::::::1:2:::
L::2::2::361:5511:321
M:::::::1:12:22::::::
N:::::::::::::::::2::
P:::::::::::::::::361
Q::::::::::::::::21::
R::::::::::::::111:::
S3:::9::::1::::::2:::
T:::::1:11:::::5::1:1
V213::1:331:2:11::111
W::15::::::1::::::::2
Y:::3:::1::11:1::2::1
bits 6.5
5.9
5.2
4.6
Information 3.9   
content 3.3     
(50.0 bits)2.6         
2.0                  
1.3                    
0.7                    
0.0
Multilevel SDIWSFGCILFELLTGKPPF
consensus VVYLVVMIIASLL
sequence LMY
NAME   START P-VALUE    SITES 
At1g01140.3_SnRK3.122013.48e-19 LSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYK
At1g01140.2_SnRK3.122013.48e-19 LSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYK
At1g01140.1_4-2-4_SnRK3.2013.48e-19 LSDKGYDGAAADVWSCGVILFVLMAGYLPFDEPNLMTLYK
At1g06390.2_ASK-iota2522.15e-18 IFGATEYTASIDIWSAGCVLAELLLGQPLFPGENSVDQLV
At1g06390.1_4-5-4_ASK-io2522.15e-18 IFGATEYTASIDIWSAGCVLAELLLGQPLFPGENSVDQLV
At1g04210.1_protein10041.15e-17 MHEQNFYGLEVDIWSFGCLIFELLTLQNPYFDLSELQIHE
At1g01540.2_Putative3373.85e-17 YACTGMLNEKSDIYSFGILIMEIITGRNPVDYSRPQGETN
At1g01540.1_1-6-33373.85e-17 YACTGMLNEKSDIYSFGILIMEIITGRNPVDYSRPQGEVF
At1g01560.1_4-5-1_MPK112225.46e-17 LLNCSEYTAAIDIWSVGCILGEIMTREPLFPGRDYVQQLR
At1g03920.1_4-2-63566.13e-17 VLLKKGYGMECDWWSLGAIMYEMLVGYPPFYADDPMSTCR
At1g05100.1_4-4-1_MAPKKK1852.92e-16 AARGERQGKESDIWAVGCTVIEMVTGSQPWIGADFTDPVS
At1g01450.1_2-1-12263.26e-16 TAGSLKYSDKSDVYSFGMVSFELLTGKVPFEDSHLQGDKM
At1g04700.1_2-1-4-1_Raf19566.83e-16 NGSSNRVSEKVDVFSFGIVMWEILTGEEPYANLHCGAIIG
At1g05700.1_1-8-17427.58e-16 CFETNGLNEKSDIYSFGVVLLEMITGKTVIKESQTKRVHV
At1g03740.1_4-5-23953.12e-15 LLGASHYGVGVDLWSTGCILGELYAGKPILPGKTEVEQLH
At1g02970.1_4-3-14257.29e-14 LNEDYEHLDKVDIFSLGVTVYELIKGSPLTESRNQSLNIK
At1g04440.1_3-1-1-11941.03e-13 THLGIEQSRRDDLESLGYLLMYFLRGSLPWQGLRAGTKKQ
At1g03930.1_3-1-1-1_ADK11941.23e-13 THLGVEQSRRDDLEALGYVLMYFLKGSLPWQGLKAGTKKQ
At1g01740.1_1-16-12301.14e-12 YLRTGRITAESVIYSFGTLLLDLLTGKHIPPSHALDLIRD

Motif 2 block diagrams

NameLowest
p-value
   Motifs
At1g01140.3_SnRK3.12 3.5e-19

2
At1g01140.2_SnRK3.12 3.5e-19

2
At1g01140.1_4-2-4_SnRK3. 3.5e-19

2
At1g06390.2_ASK-iota 2.1e-18

2
At1g06390.1_4-5-4_ASK-io 2.1e-18

2
At1g04210.1_protein 1.1e-17

2
At1g01540.2_Putative 3.8e-17

2
At1g01540.1_1-6-3 3.8e-17

2
At1g01560.1_4-5-1_MPK11 5.5e-17

2
At1g03920.1_4-2-6 6.1e-17

2
At1g05100.1_4-4-1_MAPKKK 2.9e-16

2
At1g01450.1_2-1-1 3.3e-16

2
At1g04700.1_2-1-4-1_Raf1 6.8e-16

2
At1g05700.1_1-8-1 7.6e-16

2
At1g03740.1_4-5-2 3.1e-15

2
At1g02970.1_4-3-1 7.3e-14

2
At1g04440.1_3-1-1-1 1e-13

2
At1g03930.1_3-1-1-1_ADK1 1.2e-13

2
At1g01740.1_1-16-1 1.1e-12

2
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900 925 950 975

Motif 2 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 2 position-specific scoring matrix


Motif 2 position-specific probability matrix






Time 10.58 secs.


P N
MOTIF 3     width = 15     sites = 18     llr = 453     E-value = 1.3e-051

SimplifiedA::2::2::::62:::
pos.-specificC1:1::2:::11::::
probabilityD:1::::9:1:::::2
matrixE:1::::::::::::1
F:::::::9::::21:
G4::::2::9:1:::1
H11::::::::::::1
I:1::31::::::1::
K:::8:::::::511:
L::3:4::::7::14:
M::::::::::1::::
N22::::::::::1::
P1:1:::::::::1::
Q:2:::::::::::::
R:1:1:::::1:21:4
S:::::4:::13:121
T::::::1::::11::
V:33:3::::::1111
W1:::::::::::1::
Y:::1:::1:::::1:
bits 6.5
5.9
5.2
4.6 
Information 3.9   
content 3.3    
(36.3 bits)2.6       
2.0             
1.3               
0.7               
0.0
Multilevel GVLKLSDFGLAKFLR
consensus QVVSS
sequence AI
NAME   START P-VALUE    SITES 
At1g01540.2_Putative2923.89e-14 KSSNILLDRQWNAKVSDFGLAKLLGSESSYVTTRV
At1g01540.1_1-6-32923.89e-14 KSSNILLDRQWNAKVSDFGLAKLLGSESSYVTTRV
At1g03740.1_4-5-23491.00e-13 KGSNLLIDSKGVLKIADFGLATFFDPAKSVSLTSH
At1g01140.3_SnRK3.121543.37e-13 KPENLILDANGVLKVSDFGLSAFSRQVREDGLLHT
At1g01140.2_SnRK3.121543.37e-13 KPENLILDANGVLKVSDFGLSAFSRQVREDGLLHT
At1g01140.1_4-2-4_SnRK3.1543.37e-13 KPENLILDANGVLKVSDFGLSAFSRQVREDGLLHT
At1g06390.2_ASK-iota2084.72e-13 PQNLLVDPLTHQVKLCDFGSAKVLVKGEPNISYIC
At1g06390.1_4-5-4_ASK-io2084.72e-13 PQNLLVDPLTHQVKLCDFGSAKVLVKGEPNISYIC
At1g05100.1_4-4-1_MAPKKK1431.85e-12 KGSNVLVGENGEAKIADFGCAKWVEPEITEPVRGT
At1g02970.1_4-3-13832.05e-12 VKPDNIYIKNGVCKLGDFGCATRLDKSLPVEEGDA
At1g04700.1_2-1-4-1_Raf19111.32e-11 LLVNLRDPQRPICKVGDFGLSRIKRNTLVSGGVRG
At1g04440.1_3-1-1-11431.44e-11 NFLMGLGRKANQVYIIDYGLAKKYRDLQTHKHIPY
At1g03920.1_4-2-62721.72e-11 KPDNLLLDRYGHLRLSDFGLCKPLDCSVIDGEDFT
At1g03930.1_3-1-1-1_ADK11432.05e-11 NFLMGLGRKANQVYIIDFGLGKKYRDLQTHRHIPY
At1g01560.1_4-5-1_MPK111782.05e-11 KPSNLLLNANCDLKIGDFGLARTKSETDFMTEYVV
At1g05700.1_1-8-16968.48e-11 KTSNILLNEKNRAKLADFGLSRSFHTESRSHVSTL
At1g04210.1_protein9464.02e-10 DLDNQSANGEPIVKLCDFDRAVPLRSHLHGCCIAH
At1g01740.1_1-16-11903.20e-09 NAYRVLFDEECNPRLSTFGLMKNSRDGKSYSTNLA

Motif 3 block diagrams

NameLowest
p-value
   Motifs
At1g01540.2_Putative 3.9e-14

3
At1g01540.1_1-6-3 3.9e-14

3
At1g03740.1_4-5-2 1e-13

3
At1g01140.3_SnRK3.12 3.4e-13

3
At1g01140.2_SnRK3.12 3.4e-13

3
At1g01140.1_4-2-4_SnRK3. 3.4e-13

3
At1g06390.2_ASK-iota 4.7e-13

3
At1g06390.1_4-5-4_ASK-io 4.7e-13

3
At1g05100.1_4-4-1_MAPKKK 1.9e-12

3
At1g02970.1_4-3-1 2e-12

3
At1g04700.1_2-1-4-1_Raf1 1.3e-11

3
At1g04440.1_3-1-1-1 1.4e-11

3
At1g03920.1_4-2-6 1.7e-11

3
At1g03930.1_3-1-1-1_ADK1 2e-11

3
At1g01560.1_4-5-1_MPK11 2e-11

3
At1g05700.1_1-8-1 8.5e-11

3
At1g04210.1_protein 4e-10

3
At1g01740.1_1-16-1 3.2e-09

3
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900 925 950 975

Motif 3 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 3 position-specific scoring matrix


Motif 3 position-specific probability matrix






Time 15.71 secs.


P N
SUMMARY OF MOTIFS


Combined block diagrams: non-overlapping sites with p-value < 0.0001

NameCombined
p-value
   Motifs
At1g01140.1_4-2-4_SnRK3. 2.21e-41

1
3
2
At1g01140.2_SnRK3.12 2.24e-41

1
3
2
At1g01140.3_SnRK3.12 2.27e-41

1
3
2
At1g01450.1_2-1-1 1.04e-20

1
2
At1g01540.1_1-6-3 3.03e-34

1
3
2
At1g01540.2_Putative 5.60e-34

1
3
2
At1g01560.1_4-5-1_MPK11 9.15e-35

1
3
2
At1g01740.1_1-16-1 2.50e-13

3
2
At1g02970.1_4-3-1 7.05e-29

1
3
2
At1g03740.1_4-5-2 2.21e-35

1
1
3
2
At1g03920.1_4-2-6 1.72e-32

1
3
2
At1g03930.1_3-1-1-1_ADK1 8.93e-31

1
3
2
At1g04210.1_protein 2.09e-30

1
3
1
2
At1g04440.1_3-1-1-1 4.88e-32

1
3
2
At1g04700.1_2-1-4-1_Raf1 5.29e-30

1
3
2
At1g05100.1_4-4-1_MAPKKK 3.23e-31

1
3
2
At1g05700.1_1-8-1 8.01e-28

1
3
2
At1g06390.1_4-5-4_ASK-io 7.10e-37

1
3
2
At1g06390.2_ASK-iota 7.10e-37

1
3
2
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900 925 950 975

Motif summary in machine readable format.
Stopped because nmotifs = 3 reached.


CPU: compute-0-1.local


EXPLANATION OF MEME RESULTS

The MEME results consist of:

MOTIFS

For each motif that it discovers in the training set, MEME prints the following information:


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