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 zoops -protein -nmotifs 2 

model:  mod=         zoops    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=       33    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 = 27     sites = 33     llr = 1084     E-value = 2.8e-167

SimplifiedA:162:56112:1:215:::4::::11:
pos.-specificC:1:::::::::::::::::::::::::
probabilityD::::::::1:::1::::2:::::::::
matrixE::::::::1:::21:::5::11:::::
F:::::21:::3:::::1::::::::::
G:2:::12::4:::1:1::111:5:1:1
H:::::::::1::1:::1::::1:::::
I:::::::11:::::::::1::::5:2:
K::::a:::1:::2:::1::121::1::
L:::::::31:6:::4:215::1::1::
M::1::::1:1:1::2:1:1::::::::
N:::::::::1:::1::::::::2:1:4
P::::::::::::::::::::4::::::
Q::::::::::::1::11:::11:::::
R::::::::2:::3::22::2111:4:1
S:426::1:11:213:::1:1:1::::2
T:1:2::::1::4:21:::::11::1:1
V:::::::41::2:1::1:1::::3161
W:::::1:::::::::::::::::::::
Y9:::::::::::::::::2::2:::::
bits 6.7
6.0
5.4
4.7 
Information 4.0  
content 3.4  
(47.4 bits)2.7    
2.0             
1.3                       
0.7                           
0.0
Multilevel YSASKAAVxGLTRSLAxELAPxGIRVN
consensus FGLFSEMRDV
sequence V
NAME   START P-VALUE    SITES 
YRTP_BACSU1552.53e-22 GQRGAAVTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASD
BUDC_KLETE1524.81e-22 GHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTP
AP27_MOUSE1495.51e-21 AHVTFPNLITYSSTKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTD
NODG_RHIME1524.01e-20 GAIGNPGQTNYCASKAGMIGFSKSLAQEIATRNITVNCVAPGFIESA
FIXR_BRAJA1891.18e-19 SRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPGEIRTD
HMTR_LEIMA1935.57e-19 TNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLV
DHGB_BACME1609.19e-19 WKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTP
GUTD_ECOLI1542.44e-18 GKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLGNLLKS
HDHA_ECOLI1597.97e-18 AENKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGIAPGAILTD
2BHD_STREX1528.95e-18 GLMGLALTSSYGASKWGVRGLSKLAAVELGTDRIRVNSVHPGMTYTP
HDE_CANTR4671.59e-17 GIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPHAETAM
FVT1_HUMAN1861.78e-17 GQLGLFGFTAYSASKFAIRGLAEALQMEVKPYNVYITVAYPPDTDTP
DHB2_HUMAN2323.12e-17 GGAPMERLASYGSSKAAVTMFSSVMRLELSKWGIKVASIQPGGFLTN
YURA_MYXXA1604.34e-17 AGFRGLPATRYSASKAFLSTFMESLRVDLRGTGVRVTCIYPGFVKSE
DHMA_FLAS11654.34e-17 SFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPGPVDVT
RIDH_KLEAE1606.03e-17 GVVPVIWEPVYTASKFAVQAFVHTTRRQVAQYGVRVGAVLPGPVVTA
DHES_HUMAN1557.44e-16 GLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTA
BA72_EUBSP1571.11e-15 GIFGSLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTD
DHII_HUMAN1831.23e-15 GKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLID
BDH_HUMAN2081.35e-15 GRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAA
3BHD_COMTE1513.58e-15 SWLPIEQYAGYSASKAAVSALTRAAALSCRKQGYAIRVNSIHPDGIY
LIGD_PSEPA1571.11e-14 GFMGSALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPANIKSN
YINL_LISMO1542.10e-14 GLKAYPGGAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIYPAAIN
DHB3_HUMAN1983.60e-14 ALFPWPLYSMYSASKAFVCAFSKALQEEYKAKEVIIQVLTPYAVSTA
RFBB_NEIGO1655.61e-14 ETTPYAPSSPYSASKAAADHLVRAWQRTYRLPSIVSNCSNNYGPRQF
ENTA_ECOLI1448.67e-14 AHTPRIGMSAYGASKAALKSLALSVGLELAGSGVRCNVVSPGSTDTD
BPHB_PSEPS1538.96e-13 GFYPNGGGPLYTAAKQAIVGLVRELAFELAPYVRVNGVGPGGMNSDM
CSGA_MYXXA883.97e-12 AANTDGGAYAYRMSKAALNMAVRSMSTDLRPEGFVTVLLHPGWVQTD
FABI_ECOLI1591.06e-11 AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTL
ADH_DROME1521.42e-11 GFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTT
MAS1_AGRRA3923.27e-10 GQRVLNPLVGYNMTKHALGGLTKTTQHVGWDRRCAAIDICLGFVATD
DHCA_HUMAN1939.23e-10 HQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGW
PCR_PEA1441.27e-08 AKENYTIMHLDLASLDSVRQFVDNFRRSEMPLDVLINNAAVYFPTAK

Motif 1 block diagrams

NameLowest
p-value
   Motifs
YRTP_BACSU 2.5e-22

1
BUDC_KLETE 4.8e-22

1
AP27_MOUSE 5.5e-21

1
NODG_RHIME 4e-20

1
FIXR_BRAJA 1.2e-19

1
HMTR_LEIMA 5.6e-19

1
DHGB_BACME 9.2e-19

1
GUTD_ECOLI 2.4e-18

1
HDHA_ECOLI 8e-18

1
2BHD_STREX 9e-18

1
HDE_CANTR 1.6e-17

1
FVT1_HUMAN 1.8e-17

1
DHB2_HUMAN 3.1e-17

1
YURA_MYXXA 4.3e-17

1
DHMA_FLAS1 4.3e-17

1
RIDH_KLEAE 6e-17

1
DHES_HUMAN 7.4e-16

1
BA72_EUBSP 1.1e-15

1
DHII_HUMAN 1.2e-15

1
BDH_HUMAN 1.4e-15

1
3BHD_COMTE 3.6e-15

1
LIGD_PSEPA 1.1e-14

1
YINL_LISMO 2.1e-14

1
DHB3_HUMAN 3.6e-14

1
RFBB_NEIGO 5.6e-14

1
ENTA_ECOLI 8.7e-14

1
BPHB_PSEPS 9e-13

1
CSGA_MYXXA 4e-12

1
FABI_ECOLI 1.1e-11

1
ADH_DROME 1.4e-11

1
MAS1_AGRRA 3.3e-10

1
DHCA_HUMAN 9.2e-10

1
PCR_PEA 1.3e-08

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  8.37 secs.


P N
MOTIF 2     width = 25     sites = 30     llr = 962     E-value = 1.4e-139

SimplifiedA1::14::::531:::1517:2:322
pos.-specificC:::::::::1::::::::1::::::
probabilityD11::::::::1:::::1:::1:::1
matrixE1:::::::::::::::2::11::22
F:::::::::::::::1:::::3:::
G14::::::a4319:a:::::1::1:
H:::::::::::::::1::::1:1::
I::::124::::::6:::2:1::1::
K1161:::::::2:::3:::3:::21
L:::::5:::::::3:2:2:1161:1
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 QGKVALVTGAASGIGKATAKxLAAE
consensus VIIGGLLEIVFKA
sequence SR
NAME   START P-VALUE    SITES 
BUDC_KLETE18.42e-20 MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYN
YRTP_BACSU51.15e-19 MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRT
DHII_HUMAN333.75e-19 ANEEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARS
YINL_LISMO44.33e-19 MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARR
HDE_CANTR3214.91e-18 DASGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFK
ENTA_ECOLI42.42e-17 MDFSGKNVWVTGAGKGIGYATALAFVEAGAKVTGFDQA
HDHA_ECOLI101.85e-16 MFNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDIN
3BHD_COMTE52.84e-16 TNRLQGKVALVTGGASGVGLEVVKLLLGEGAKVAFSDIN
DHGB_BACME66.54e-16 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRS
RIDH_KLEAE137.24e-16 HSVSSMNTSLSGKVAAITGAASGIGLECARTLLGAGAKVVLIDRE
DHB3_HUMAN478.87e-16 KVLPKSFLRSMGQWAVITGAGDGIGKAYSFELAKRGLNVVLISRT
FIXR_BRAJA358.87e-16 DAVNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQ
BA72_EUBSP51.61e-15 MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGET
BDH_HUMAN541.78e-15 RTYASAAEPVGSKAVLVTGCDSGFGFSLAKHLHSKGFLVFAGCLM
FVT1_HUMAN313.50e-15 PLISPKPLALPGAHVVVTGGSSGIGKCIAIECYKQGAFITLVARN
AP27_MOUSE63.85e-15 MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRT
PCR_PEA854.24e-15 KSSSEGKKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACR
BPHB_PSEPS44.24e-15 MKLKGEAVLITGGASGLGRALVDRFVAEAKVAVLDKSA
DHB2_HUMAN814.66e-15 YLSGQELLPVDQKAVLVTGGDCGLGHALCKYLDELGFTVFAGVLN
DHCA_HUMAN35.62e-15 SSGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTAR
DHMA_FLAS1136.77e-15 AGVSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLA
DHES_HUMAN11.69e-14 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYAT
MAS1_AGRRA2446.23e-14 GFSHWTVEIHQSPVILVSGSNRGVGKAIAEDLIAHGYRLSLGARK
HMTR_LEIMA58.04e-14 MTAPTVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHR
NODG_RHIME58.74e-14 MFELTGRKALVTGASGAIGGAIARVLHAQGAIVGLHGTQ
2BHD_STREX52.35e-13 MNDLSGKTVIITGGARGLGAEAARQAVAAGARVVLADVL
LIGD_PSEPA54.80e-13 MKDFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVR
RFBB_NEIGO58.93e-13 MQTEGKKNILVTGGAGFIGSAVVRHIIQNTRDSVVNLDK
GUTD_ECOLI11.63e-11 MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQ
ADH_DROME55.11e-11 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDR

Motif 2 block diagrams

NameLowest
p-value
   Motifs
BUDC_KLETE 8.4e-20
2
YRTP_BACSU 1.1e-19

2
DHII_HUMAN 3.8e-19

2
YINL_LISMO 4.3e-19

2
HDE_CANTR 4.9e-18

2
ENTA_ECOLI 2.4e-17

2
HDHA_ECOLI 1.9e-16

2
3BHD_COMTE 2.8e-16

2
DHGB_BACME 6.5e-16

2
RIDH_KLEAE 7.2e-16

2
DHB3_HUMAN 8.9e-16

2
FIXR_BRAJA 8.9e-16

2
BA72_EUBSP 1.6e-15

2
BDH_HUMAN 1.8e-15

2
FVT1_HUMAN 3.5e-15

2
AP27_MOUSE 3.9e-15

2
PCR_PEA 4.2e-15

2
BPHB_PSEPS 4.2e-15

2
DHB2_HUMAN 4.7e-15

2
DHCA_HUMAN 5.6e-15

2
DHMA_FLAS1 6.8e-15

2
DHES_HUMAN 1.7e-14
2
MAS1_AGRRA 6.2e-14

2
HMTR_LEIMA 8e-14

2
NODG_RHIME 8.7e-14

2
2BHD_STREX 2.3e-13

2
LIGD_PSEPA 4.8e-13

2
RFBB_NEIGO 8.9e-13

2
GUTD_ECOLI 1.6e-11
2
ADH_DROME 5.1e-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 15.47 secs.


P N
SUMMARY OF MOTIFS


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

NameCombined
p-value
   Motifs
2BHD_STREX 6.49e-24

2
1
3BHD_COMTE 3.13e-24

2
1
1
ADH_DROME 1.49e-15

2
1
AP27_MOUSE 7.13e-29

2
1
BA72_EUBSP 5.27e-24

2
1
1
BDH_HUMAN 1.41e-23

2
1
BPHB_PSEPS 1.21e-20

2
1
BUDC_KLETE 1.57e-34
2
1
DHES_HUMAN 6.42e-23
2
1
DHGB_BACME 2.24e-27

2
1
DHII_HUMAN 2.18e-27

2
1
DHMA_FLAS1 1.06e-24

2
1
ENTA_ECOLI 6.10e-24

2
1
FIXR_BRAJA 4.56e-28

2
1
GUTD_ECOLI 1.21e-22
2
1
HDE_CANTR 3.99e-27

2
1
2
1
HDHA_ECOLI 5.13e-27

2
1
1
LIGD_PSEPA 2.09e-20

2
1
NODG_RHIME 1.10e-26

2
1
RIDH_KLEAE 1.37e-25

2
1
YINL_LISMO 2.89e-26

2
1
YRTP_BACSU 1.10e-34

2
1
CSGA_MYXXA 4.90e-09

1
DHB2_HUMAN 1.15e-24

2
1
DHB3_HUMAN 1.43e-22

2
1
DHCA_HUMAN 1.42e-17

2
1
1
FABI_ECOLI 1.17e-10

2
1
FVT1_HUMAN 3.61e-25

2
1
HMTR_LEIMA 1.91e-25

2
1
MAS1_AGRRA 1.70e-16

2
1
PCR_PEA 3.04e-16

2
1
RFBB_NEIGO 2.46e-19

2
1
YURA_MYXXA 1.82e-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

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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