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 3.0 (Release date: 2004/07/16 05:53:30)

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

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.sdsc.edu.


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= /home/meme/meme.3.0.6/tests/adh.s
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
2BHD_STREX               1.0000    255  3BHD_COMTE               1.0000    253  
ADH_DROME                1.0000    255  AP27_MOUSE               1.0000    244  
BA72_EUBSP               1.0000    249  BDH_HUMAN                1.0000    343  
BPHB_PSEPS               1.0000    275  BUDC_KLETE               1.0000    241  
DHES_HUMAN               1.0000    327  DHGB_BACME               1.0000    262  
DHII_HUMAN               1.0000    292  DHMA_FLAS1               1.0000    270  
ENTA_ECOLI               1.0000    248  FIXR_BRAJA               1.0000    278  
GUTD_ECOLI               1.0000    259  HDE_CANTR                1.0000    906  
HDHA_ECOLI               1.0000    255  LIGD_PSEPA               1.0000    305  
NODG_RHIME               1.0000    245  RIDH_KLEAE               1.0000    249  
YINL_LISMO               1.0000    248  YRTP_BACSU               1.0000    238  
CSGA_MYXXA               1.0000    166  DHB2_HUMAN               1.0000    387  
DHB3_HUMAN               1.0000    310  DHCA_HUMAN               1.0000    276  
FABI_ECOLI               1.0000    262  FVT1_HUMAN               1.0000    332  
HMTR_LEIMA               1.0000    287  MAS1_AGRRA               1.0000    476  
PCR_PEA                  1.0000    399  RFBB_NEIGO               1.0000    346  
YURA_MYXXA               1.0000    258  

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.3.0.6/tests/adh.s -mod tcm -protein -nmotifs 2 

model:  mod=           tcm    nmotifs=         2    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       50    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=       megap    b=           49980    maxiter=        50
        distance=    1e-05
data:   n=            9996    N=              33

sample: seed=            0    seqfrac=         1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
W 0.010 Y 0.027 
Background letter frequencies (from dataset with add-one prior applied):
A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 
L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 
W 0.010 Y 0.027 

P N
MOTIF 1     width = 22     sites = 31     llr = 890     E-value = 2.3e-120

SimplifiedA:162:56112:1:215:::4::
pos.-specificC:1::::::::::::::::::::
probabilityD::::::::1::::::::2::::
matrixE::::::::1:::31:::5::11
F:::::31:::3:::::1:::::
G:2:::12::4:::1:1::111:
H:::::::::1::1::::::::1
I:::::::11:::::::::1:::
K::::a:::1:::2:::1::121
L:::::::31:6:::5:215::1
M::1::::1:1:1::2:1:1:::
N:::::::::1::::::::::::
P::::::::::::::::::::4:
Q::::::::::::1::11:::1:
R::::::::1:::3::21::21:
S:426::1:11:213:::::1:1
T:1:1::::1::4:2::::::11
V:::::::41::2:1::1:1:::
W:::::1::::::::::::::::
Ya:::::::::::::::::2::2
bits 6.7
6.0
5.4
4.7 
Information 4.0  
content 3.4  
(41.4 bits)2.7    
2.0            
1.3                    
0.7                      
0.0
Multilevel YSASKAAVxGLTRSLAxELAPx
consensus AFGLFEMRD
sequence
NAME   START P-VALUE    SITES 
YRTP_BACSU1557.98e-19 GQRGAAVTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPS
FVT1_HUMAN1862.84e-17 GQLGLFGFTAYSASKFAIRGLAEALQMEVKPYNVYITVAYPP
BUDC_KLETE1525.90e-17 GHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPG
AP27_MOUSE1491.04e-16 AHVTFPNLITYSSTKGAMTMLTKAMAMELGPHKIRVNSVNPT
NODG_RHIME1524.04e-16 GAIGNPGQTNYCASKAGMIGFSKSLAQEIATRNITVNCVAPG
DHES_HUMAN1551.28e-15 GLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECG
BPHB_PSEPS1532.35e-15 GFYPNGGGPLYTAAKQAIVGLVRELAFELAPYVRVNGVGPGG
GUTD_ECOLI1542.66e-15 GKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLG
FIXR_BRAJA1897.64e-15 SRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPG
HMTR_LEIMA1938.56e-15 TNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPG
DHB2_HUMAN2329.59e-15 GGAPMERLASYGSSKAAVTMFSSVMRLELSKWGIKVASIQPG
DHGB_BACME1601.68e-14 WKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPG
3BHD_COMTE1511.68e-14 SWLPIEQYAGYSASKAAVSALTRAAALSCRKQGYAIRVNSIH
YURA_MYXXA1602.09e-14 AGFRGLPATRYSASKAFLSTFMESLRVDLRGTGVRVTCIYPG
DHB3_HUMAN1983.99e-14 ALFPWPLYSMYSASKAFVCAFSKALQEEYKAKEVIIQVLTPY
YINL_LISMO1544.43e-14 GLKAYPGGAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIY
RIDH_KLEAE1604.92e-14 GVVPVIWEPVYTASKFAVQAFVHTTRRQVAQYGVRVGAVLPG
HDE_CANTR4676.07e-14 GIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPH
DHMA_FLAS11657.46e-14 SFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPG
DHII_HUMAN1839.16e-14 GKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCV
2BHD_STREX1522.74e-13 GLMGLALTSSYGASKWGVRGLSKLAAVELGTDRIRVNSVHPG
HDHA_ECOLI1594.02e-13 AENKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGIAPG
HDE_CANTR1637.77e-13 GLYGNFGQANYASAKSALLGFAETLAKEGAKYNIKANAIAPL
BDH_HUMAN2089.34e-13 GRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPG
RFBB_NEIGO1651.02e-12 ETTPYAPSSPYSASKAAADHLVRAWQRTYRLPSIVSNCSNNY
BA72_EUBSP1571.76e-12 GIFGSLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPG
CSGA_MYXXA881.92e-12 AANTDGGAYAYRMSKAALNMAVRSMSTDLRPEGFVTVLLHPG
LIGD_PSEPA1572.74e-12 GFMGSALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPA
ENTA_ECOLI1441.73e-11 AHTPRIGMSAYGASKAALKSLALSVGLELAGSGVRCNVVSPG
ADH_DROME1527.59e-11 GFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPG
FABI_ECOLI1598.18e-09 AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAG

Motif 1 block diagrams

NameLowest
p-value
   Motifs
YRTP_BACSU 8e-19

1
FVT1_HUMAN 2.8e-17

1
BUDC_KLETE 5.9e-17

1
AP27_MOUSE 1e-16

1
NODG_RHIME 4e-16

1
DHES_HUMAN 1.3e-15

1
BPHB_PSEPS 2.4e-15

1
GUTD_ECOLI 2.7e-15

1
FIXR_BRAJA 7.6e-15

1
HMTR_LEIMA 8.6e-15

1
DHB2_HUMAN 9.6e-15

1
DHGB_BACME 1.7e-14

1
3BHD_COMTE 1.7e-14

1
YURA_MYXXA 2.1e-14

1
DHB3_HUMAN 4e-14

1
YINL_LISMO 4.4e-14

1
RIDH_KLEAE 4.9e-14

1
HDE_CANTR 7.8e-13

1
1
DHMA_FLAS1 7.5e-14

1
DHII_HUMAN 9.2e-14

1
2BHD_STREX 2.7e-13

1
HDHA_ECOLI 4e-13

1
BDH_HUMAN 9.3e-13

1
RFBB_NEIGO 1e-12

1
BA72_EUBSP 1.8e-12

1
CSGA_MYXXA 1.9e-12

1
LIGD_PSEPA 2.7e-12

1
ENTA_ECOLI 1.7e-11

1
ADH_DROME 7.6e-11

1
FABI_ECOLI 8.2e-09

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

Motif 1 in BLOCKS format


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


Motif 1 position-specific probability matrix






Time 11.03 secs.


P N
MOTIF 2     width = 25     sites = 31     llr = 995     E-value = 1.3e-139

SimplifiedA1::14::::531:::1516:2:422
pos.-specificC:::::::::1::::::::1::::::
probabilityD11::::::::1:::::1:::1:::1
matrixE1:::::::::::::::2::11::22
F:::::::::::::::1:::::3:::
G14::::::a4329:a:::::1::1:
H:::::::::::::::1::::1:1::
I::::135::::::6:::2:1::1::
K1161:::::::2:::3:::3:::31
L:::::5:::::::3:2:2:2161:1
M1::::::::::::::::1:::::::
N:1:1::::::1:::::::::::::1
P::1::::::::::::::::::::::
Q211::::::::1:::::::::::11
R:::::::::::2:::2:::21::11
S11:::::::133::::1:1::::11
T1::1:::9:::::::::3::1::1:
V:::5425::::::1:::12:1:1::
W:::::::::::::::::::::::::
Y:::::::::::::::::1:::::::
bits 6.7
6.0
5.4
4.7
Information 4.0
content 3.4   
(46.3 bits)2.7      
2.0            
1.3                       
0.7                         
0.0
Multilevel xGKVALVTGAGSGIGKATAKxLAKE
consensus VIIGALIFA
sequence S
NAME   START P-VALUE    SITES 
BUDC_KLETE18.34e-20 MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYN
YRTP_BACSU51.54e-19 MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRT
YINL_LISMO41.79e-19 MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARR
HDE_CANTR3213.75e-19 DASGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFK
DHII_HUMAN335.76e-19 ANEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARS
ENTA_ECOLI42.17e-17 MDFSGKNVWVTGAGKGIGYATALAFVEAGAKVTGFDQA
HDE_CANTR77.74e-17 MSPVDFKDKVVIITGAGGGLGKYYSLEFAKLGAKVVVNDLG
HDHA_ECOLI101.50e-16 MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDIN
DHB3_HUMAN473.54e-16 KVLPKSFLRSMGQWAVITGAGDGIGKAYSFELAKRGLNVVLISRT
DHGB_BACME64.36e-16 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRS
3BHD_COMTE56.59e-16 TNRLQGKVALVTGGASGVGLEVVKLLLGEGAKVAFSDIN
RIDH_KLEAE131.21e-15 HSVSSMNTSLSGKVAAITGAASGIGLECARTLLGAGAKVVLIDRE
FIXR_BRAJA351.21e-15 DAVNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQ
BA72_EUBSP51.33e-15 MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGET
BDH_HUMAN542.64e-15 RTYASAAEPVGSKAVLVTGCDSGFGFSLAKHLHSKGFLVFAGCLM
FVT1_HUMAN313.88e-15 PLISPKPLALPGAHVVVTGGSSGIGKCIAIECYKQGAFITLVARN
PCR_PEA854.26e-15 KSSSEGKKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACR
DHB2_HUMAN814.68e-15 YLSGQELLPVDQKAVLVTGGDCGLGHALCKYLDELGFTVFAGVLN
BPHB_PSEPS44.68e-15 MKLKGEAVLITGGASGLGRALVDRFVAEAKVAVLDKSA
AP27_MOUSE66.20e-15 MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRT
DHCA_HUMAN36.80e-15 SSGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTAR
DHMA_FLAS1137.46e-15 AGVSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLA
DHES_HUMAN12.20e-14 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYAT
MAS1_AGRRA2448.72e-14 GFSHWTVEIHQSPVILVSGSNRGVGKAIAEDLIAHGYRLSLGARK
HMTR_LEIMA51.03e-13 MTAPTVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHR
NODG_RHIME51.55e-13 MFELTGRKALVTGASGAIGGAIARVLHAQGAIVGLHGTQ
2BHD_STREX52.33e-13 MNDLSGKTVIITGGARGLGAEAARQAVAAGARVVLADVL
LIGD_PSEPA54.40e-13 MKDFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVR
RFBB_NEIGO51.62e-12 MQTEGKKNILVTGGAGFIGSAVVRHIIQNTRDSVVNLDK
GUTD_ECOLI11.96e-11 MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQ
ADH_DROME53.35e-11 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDR

Motif 2 block diagrams

NameLowest
p-value
   Motifs
BUDC_KLETE 8.3e-20
2
YRTP_BACSU 1.5e-19

2
YINL_LISMO 1.8e-19

2
HDE_CANTR 7.7e-17

2
2
DHII_HUMAN 5.8e-19

2
ENTA_ECOLI 2.2e-17

2
HDHA_ECOLI 1.5e-16

2
DHB3_HUMAN 3.5e-16

2
DHGB_BACME 4.4e-16

2
3BHD_COMTE 6.6e-16

2
RIDH_KLEAE 1.2e-15

2
FIXR_BRAJA 1.2e-15

2
BA72_EUBSP 1.3e-15

2
BDH_HUMAN 2.6e-15

2
FVT1_HUMAN 3.9e-15

2
PCR_PEA 4.3e-15

2
DHB2_HUMAN 4.7e-15

2
BPHB_PSEPS 4.7e-15

2
AP27_MOUSE 6.2e-15

2
DHCA_HUMAN 6.8e-15

2
DHMA_FLAS1 7.5e-15

2
DHES_HUMAN 2.2e-14
2
MAS1_AGRRA 8.7e-14

2
HMTR_LEIMA 1e-13

2
NODG_RHIME 1.6e-13

2
2BHD_STREX 2.3e-13

2
LIGD_PSEPA 4.4e-13

2
RFBB_NEIGO 1.6e-12

2
GUTD_ECOLI 2e-11
2
ADH_DROME 3.3e-11

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

Motif 2 in BLOCKS format


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


Motif 2 position-specific probability matrix






Time 20.26 secs.


P N
SUMMARY OF MOTIFS


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

NameCombined
p-value
   Motifs
2BHD_STREX 1.66e-19

2
1
3BHD_COMTE 3.34e-23

2
1
ADH_DROME 5.15e-15

2
1
AP27_MOUSE 1.89e-24

2
1
BA72_EUBSP 6.20e-21

2
1
BDH_HUMAN 1.29e-20

2
1
BPHB_PSEPS 3.98e-23

2
1
BUDC_KLETE 1.68e-29
2
1
DHES_HUMAN 1.44e-22
2
1
DHGB_BACME 2.40e-23

2
1
DHII_HUMAN 2.37e-25

2
1
DHMA_FLAS1 1.80e-21

2
1
ENTA_ECOLI 1.02e-21

2
1
FIXR_BRAJA 3.42e-23

2
1
GUTD_ECOLI 1.40e-19
2
1
HDE_CANTR 1.07e-24

2
1
2
1
HDHA_ECOLI 1.80e-22

2
1
LIGD_PSEPA 4.31e-18

2
1
NODG_RHIME 1.71e-22

2
1
RIDH_KLEAE 1.68e-22

2
1
YINL_LISMO 2.59e-26

2
1
YRTP_BACSU 4.30e-31

2
1
CSGA_MYXXA 2.54e-09

1
DHB2_HUMAN 3.25e-22

2
1
DHB3_HUMAN 6.54e-23

2
1
DHCA_HUMAN 2.23e-14

2
1
FABI_ECOLI 7.53e-08

2
1
FVT1_HUMAN 6.41e-25

2
1
HMTR_LEIMA 3.21e-21

2
1
MAS1_AGRRA 7.13e-12

2
1
PCR_PEA 1.64e-11

2
RFBB_NEIGO 7.66e-18

2
1
YURA_MYXXA 7.22e-11

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

Motif summary in machine readable format.
Stopped because nmotifs = 2 reached.


CPU: chromo


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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