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 oops -protein -nmotifs 2 

model:  mod=          oops    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=       33    maxsites=       33    wnsites=       0.8
theta:  prob=            1    spmap=         pam    spfuzz=        120
em:     prior=        dmix    b=               0    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 = 29     sites = 33     llr = 1118     E-value = 3.6e-165

SimplifiedA:162:56112:1:215:::4:::::::11
pos.-specificC:1:::::::::::1:::::::::::1:1:
probabilityD::::::::1:::1::::2:::::::::::
matrixE::::::::1:::21:::5:111:::::::
F:::::31:::2:::::1::::::::::::
G:2:::13::4:::1:1:::11:5:1:11:
H:::::::::1::1:::1::::1:::::::
I:::::::11:::::::::1::::5:2:13
K::::9:::1:::2:::1::121::1:1::
L:::::::31:6:1:5:215::1:::::12
M::1::::1:2:1::2:1:1::::::::::
N:::::::::1::::::::::::2:1:41:
P::::::::::::::::::::3::::::::
Q::::::::::::1::11:::11:::::::
R::::::::2:::3::22::21:1:4:1::
S:426::1:11:213:::::1:11:::21:
T:1:2::::1::3:1::::::11::1:11:
V:::::::41::2:1::1:1::::316123
W:::::1:::::::::::::::::::::::
Y9:::::::::::::::::2::2:::::::
bits 6.7
6.0
5.4
4.7 
Information 4.0  
content 3.4  
(48.9 bits)2.7    
2.0          
1.3                        
0.7                             
0.0
Multilevel YSASKAAVxGLTRSLAxELAPxGIRVNVV
consensus FGLFSEMRDVI
sequence
NAME   START P-VALUE    SITES 
YRTP_BACSU1551.64e-22 GQRGAAVTSAYSASKFAVLGLTESLMQEVRKHNIRVSALTPSTVASDMS
AP27_MOUSE1496.32e-22 AHVTFPNLITYSSTKGAMTMLTKAMAMELGPHKIRVNSVNPTVVLTDMG
NODG_RHIME1521.13e-21 GAIGNPGQTNYCASKAGMIGFSKSLAQEIATRNITVNCVAPGFIESAMT
BUDC_KLETE1524.04e-21 GHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMW
FIXR_BRAJA1896.12e-21 SRVHPFAGSAYATSKAALASLTRELAHDYAPHGIRVNAIAPGEIRTDML
DHGB_BACME1607.52e-20 WKIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAINTPIN
HMTR_LEIMA1933.35e-19 TNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDD
YURA_MYXXA1604.82e-19 AGFRGLPATRYSASKAFLSTFMESLRVDLRGTGVRVTCIYPGFVKSELT
GUTD_ECOLI1544.82e-19 GKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLMLGNLLKSPM
2BHD_STREX1521.11e-18 GLMGLALTSSYGASKWGVRGLSKLAAVELGTDRIRVNSVHPGMTYTPMT
HDHA_ECOLI1591.25e-18 AENKNINMTSYASSKAAASHLVRNMAFDLGEKNIRVNGIAPGAILTDAL
DHB2_HUMAN2322.23e-18 GGAPMERLASYGSSKAAVTMFSSVMRLELSKWGIKVASIQPGGFLTNIA
DHMA_FLAS11655.53e-18 SFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPGPVDVTGN
HDE_CANTR4679.65e-18 GIYGNFGQANYSSSKAGILGLSKTMAIEGAKNNIKVNIVAPHAETAMTL
FVT1_HUMAN1862.86e-17 GQLGLFGFTAYSASKFAIRGLAEALQMEVKPYNVYITVAYPPDTDTPGF
BDH_HUMAN2088.20e-17 GRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATS
RIDH_KLEAE1609.09e-17 GVVPVIWEPVYTASKFAVQAFVHTTRRQVAQYGVRVGAVLPGPVVTALL
DHES_HUMAN1551.37e-16 GLMGLPFNDVYCASKFALEGLCESLAVLLLPFGVHLSLIECGPVHTAFM
BA72_EUBSP1572.52e-16 GIFGSLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTDMT
LIGD_PSEPA1571.21e-15 GFMGSALAGPYSAAKAASINLMEGYRQGLEKYGIGVSVCTPANIKSNIA
DHII_HUMAN1831.61e-15 GKVAYPMVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTE
ENTA_ECOLI1441.77e-15 AHTPRIGMSAYGASKAALKSLALSVGLELAGSGVRCNVVSPGSTDTDMQ
3BHD_COMTE1517.81e-15 SWLPIEQYAGYSASKAAVSALTRAAALSCRKQGYAIRVNSIHPDGIYTP
DHB3_HUMAN1988.55e-15 ALFPWPLYSMYSASKAFVCAFSKALQEEYKAKEVIIQVLTPYAVSTAMT
RFBB_NEIGO1651.47e-14 ETTPYAPSSPYSASKAAADHLVRAWQRTYRLPSIVSNCSNNYGPRQFPE
YINL_LISMO1543.24e-14 GLKAYPGGAVYGATKWAVRDLMEVLRMESAQEGTNIRTATIYPAAINTE
BPHB_PSEPS1531.80e-12 GFYPNGGGPLYTAAKQAIVGLVRELAFELAPYVRVNGVGPGGMNSDMRG
CSGA_MYXXA882.10e-12 AANTDGGAYAYRMSKAALNMAVRSMSTDLRPEGFVTVLLHPGWVQTDMG
FABI_ECOLI1594.15e-12 AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAA
ADH_DROME1525.20e-12 GFNAIYQVPVYSGTKAAVVNFTSSLAKLAPITGVTAYTVNPGITRTTLV
DHCA_HUMAN1934.80e-10 HQKEGWPSSAYGVTKIGVTVLSRIHARKLSEQRKGDKILLNACCPGWVR
PCR_PEA262.77e-08 PKEGKIGASLKDSTLFGVSSLSDSLKGDFTSSALRCKELRQKVGAVRAE
MAS1_AGRRA3495.72e-08 VDYQRFHLQWYINCVAPLRMTELCLPHLYETGSGRIVNINSMSGQRVLN

Motif 1 block diagrams

NameLowest
p-value
   Motifs
YRTP_BACSU 1.6e-22

1
AP27_MOUSE 6.3e-22

1
NODG_RHIME 1.1e-21

1
BUDC_KLETE 4e-21

1
FIXR_BRAJA 6.1e-21

1
DHGB_BACME 7.5e-20

1
HMTR_LEIMA 3.4e-19

1
YURA_MYXXA 4.8e-19

1
GUTD_ECOLI 4.8e-19

1
2BHD_STREX 1.1e-18

1
HDHA_ECOLI 1.2e-18

1
DHB2_HUMAN 2.2e-18

1
DHMA_FLAS1 5.5e-18

1
HDE_CANTR 9.7e-18

1
FVT1_HUMAN 2.9e-17

1
BDH_HUMAN 8.2e-17

1
RIDH_KLEAE 9.1e-17

1
DHES_HUMAN 1.4e-16

1
BA72_EUBSP 2.5e-16

1
LIGD_PSEPA 1.2e-15

1
DHII_HUMAN 1.6e-15

1
ENTA_ECOLI 1.8e-15

1
3BHD_COMTE 7.8e-15

1
DHB3_HUMAN 8.6e-15

1
RFBB_NEIGO 1.5e-14

1
YINL_LISMO 3.2e-14

1
BPHB_PSEPS 1.8e-12

1
CSGA_MYXXA 2.1e-12

1
FABI_ECOLI 4.2e-12

1
ADH_DROME 5.2e-12

1
DHCA_HUMAN 4.8e-10

1
PCR_PEA 2.8e-08

1
MAS1_AGRRA 5.7e-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  2.38 secs.


P N
MOTIF 2     width = 29     sites = 33     llr = 1106     E-value = 2.3e-159

SimplifiedA:14::::531:1:1516:2:322:51111
pos.-specificC:::::::1::::::::1::::::::::::
probabilityD::::::::1:::::1:::1:::1::::::
matrixE::::::::::::::2::11::22::::::
F:::::::::::::1:::::2::::1::1:
G::::::a4218:9:::::1::1:8:1:11
H:::::::::::::1:::11:1:1::1:::
I::124::::::5:::2:1::1:::::1:1
K61:::::::2:::2:::3:::21:13:::
L:::51::::::3:2:2:1151:1:111:3
M:::::::::::::::1::::::1::::::
N:1::::::1:::::::::::::1::1:::
P1::::::::::::::::::::::::::::
Q1::::::::1:::::::::::11::::::
R:1:::::::2:::2:::21::111:1:::
S:::::::123::1:1:1:::111:1111:
T111::9::::1::::2::1::1:::::1:
V:4425::::::1:::12:1:1:::::553
W:::::::::::::::::::::::::::::
Y:::::::::::::::1::::::::1::::
bits 6.7
6.0
5.4
4.7
Information 4.0
content 3.4  
(48.4 bits)2.7     
2.0             
1.3                         
0.7                             
0.0
Multilevel KVALVTGAASGIGKATAKxLAAEGAKVVL
consensus VIIGGLRIFKV
sequence S
NAME   START P-VALUE    SITES 
HDE_CANTR3232.44e-23 SGAPTVSLKDKVVLITGAGAGLGKEYAKWFAKYGAKVVVNDFKDATKTV
DHII_HUMAN355.50e-23 EEFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQK
YINL_LISMO65.38e-22 MTIKNKVIIITGASSGIGKATALLLAEKGAKLVLAARRVEKLEK
HDHA_ECOLI125.65e-20 FNSDNLRLDGKCAIITGAGAGIGKEIAITFATAGASVVVSDINADAANH
RIDH_KLEAE151.17e-19 VSSMNTSLSGKVAAITGAASGIGLECARTLLGAGAKVVLIDREGEKLNK
BUDC_KLETE31.17e-19 MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATA
ENTA_ECOLI64.74e-19 MDFSGKNVWVTGAGKGIGYATALAFVEAGAKVTGFDQAFTQEQY
AP27_MOUSE89.31e-19 MKLNFSGLRALVTGAGKGIGRDTVKALHASGAKVVAVTRTNSDLVS
DHMA_FLAS1152.50e-18 VSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLAPRLAAT
YRTP_BACSU73.45e-18 MQSLQHKTALITGGGRGIGRATALALAKEGVNIGLIGRTSANVEK
DHGB_BACME85.86e-18 MYKDLEGKVVVITGSSTGLGKSMAIRFATEKAKVVVNYRSKEDEAN
DHB3_HUMAN499.86e-18 LPKSFLRSMGQWAVITGAGDGIGKAYSFELAKRGLNVVLISRTLEKLEA
PCR_PEA872.47e-17 SSEGKKTLRKGNVVITGASSGLGLATAKALAESGKWHVIMACRDYLKAA
BDH_HUMAN563.01e-17 YASAAEPVGSKAVLVTGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHD
BA72_EUBSP73.33e-17 MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDT
FIXR_BRAJA374.06e-17 VNARVDRGEPKVMLLTGASRGIGHATAKLFSEAGWRIISCARQPFDGER
3BHD_COMTE74.06e-17 TNRLQGKVALVTGGASGVGLEVVKLLLGEGAKVAFSDINEAAGQQ
2BHD_STREX78.05e-17 MNDLSGKTVIITGGARGLGAEAARQAVAAGARVVLADVLDEEGAA
HMTR_LEIMA71.90e-16 MTAPTVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEAN
FVT1_HUMAN332.77e-16 ISPKPLALPGAHVVVTGGSSGIGKCIAIECYKQGAFITLVARNEDKLLQ
DHB2_HUMAN833.65e-16 SGQELLPVDQKAVLVTGGDCGLGHALCKYLDELGFTVFAGVLNENGPGA
LIGD_PSEPA78.31e-16 MKDFQDQVAFITGGASGAGFGQAKVFGQAGAKIVVADVRAEAVEK
NODG_RHIME74.05e-15 MFELTGRKALVTGASGAIGGAIARVLHAQGAIVGLHGTQIEKLET
DHCA_HUMAN55.24e-15 SSGIHVALVTGGNKGIGLAIVRDLCRLFSGDVVLTARDVTRGQ
MAS1_AGRRA2463.00e-14 SHWTVEIHQSPVILVSGSNRGVGKAIAEDLIAHGYRLSLGARKVKDLEV
BPHB_PSEPS68.47e-14 MKLKGEAVLITGGASGLGRALVDRFVAEAKVAVLDKSAERLAEL
GUTD_ECOLI31.46e-13 MNQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAAN
DHES_HUMAN31.46e-13 ARTVVLITGCSSGIGLHLAVRLASDPSQSFKVYATLRDLKT
RFBB_NEIGO71.59e-12 MQTEGKKNILVTGGAGFIGSAVVRHIIQNTRDSVVNLDKLTYAGN
ADH_DROME76.97e-10 SFTLTNKNVIFVAGLGGIGLDTSKELLKRDLKNLVILDRIENPAA
FABI_ECOLI73.15e-09 MGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLK
YURA_MYXXA1172.77e-07 RLPWERVRGIIDTNVTGAAATLSAVLPQMVERKRGHLVGVSSLAGFRGL
CSGA_MYXXA524.24e-07 TINALGPLRVTSAMLPGLRQGALRRVAHVTSRMGSLAANTDGGAYAYRM

Motif 2 block diagrams

NameLowest
p-value
   Motifs
HDE_CANTR 2.4e-23

2
DHII_HUMAN 5.5e-23

2
YINL_LISMO 5.4e-22

2
HDHA_ECOLI 5.7e-20

2
RIDH_KLEAE 1.2e-19

2
BUDC_KLETE 1.2e-19

2
ENTA_ECOLI 4.7e-19

2
AP27_MOUSE 9.3e-19

2
DHMA_FLAS1 2.5e-18

2
YRTP_BACSU 3.4e-18

2
DHGB_BACME 5.9e-18

2
DHB3_HUMAN 9.9e-18

2
PCR_PEA 2.5e-17

2
BDH_HUMAN 3e-17

2
BA72_EUBSP 3.3e-17

2
FIXR_BRAJA 4.1e-17

2
3BHD_COMTE 4.1e-17

2
2BHD_STREX 8e-17

2
HMTR_LEIMA 1.9e-16

2
FVT1_HUMAN 2.8e-16

2
DHB2_HUMAN 3.7e-16

2
LIGD_PSEPA 8.3e-16

2
NODG_RHIME 4.1e-15

2
DHCA_HUMAN 5.2e-15

2
MAS1_AGRRA 3e-14

2
BPHB_PSEPS 8.5e-14

2
GUTD_ECOLI 1.5e-13

2
DHES_HUMAN 1.5e-13

2
RFBB_NEIGO 1.6e-12

2
ADH_DROME 7e-10

2
FABI_ECOLI 3.1e-09

2
YURA_MYXXA 2.8e-07

2
CSGA_MYXXA 4.2e-07

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  4.27 secs.


P N
SUMMARY OF MOTIFS


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

NameCombined
p-value
   Motifs
2BHD_STREX 3.15e-28

2
1
3BHD_COMTE 9.69e-25

2
1
ADH_DROME 6.95e-15

2
1
AP27_MOUSE 2.21e-33

2
1
BA72_EUBSP 2.62e-26

2
1
BDH_HUMAN 1.58e-26

2
1
BPHB_PSEPS 4.38e-19

2
1
BUDC_KLETE 1.73e-33

2
1
DHES_HUMAN 9.98e-23

2
1
DHGB_BACME 1.78e-30

2
1
DHII_HUMAN 4.64e-31

2
1
DHMA_FLAS1 5.69e-29

2
1
ENTA_ECOLI 2.69e-27

2
1
FIXR_BRAJA 1.15e-30

2
1
GUTD_ECOLI 2.33e-25

2
1
HDE_CANTR 1.43e-32

2
1
2
1
HDHA_ECOLI 2.75e-31

2
1
1
LIGD_PSEPA 4.54e-24

2
1
NODG_RHIME 1.55e-29

2
1
RIDH_KLEAE 3.67e-29

2
1
YINL_LISMO 5.92e-29

2
1
YRTP_BACSU 2.01e-33

2
1
CSGA_MYXXA 5.53e-13

2
1
DHB2_HUMAN 6.87e-27

2
1
DHB3_HUMAN 4.11e-25

2
1
DHCA_HUMAN 6.86e-18

2
1
FABI_ECOLI 2.57e-14

2
1
FVT1_HUMAN 4.64e-26

2
1
HMTR_LEIMA 2.93e-28

2
1
MAS1_AGRRA 1.26e-14

2
1
PCR_PEA 4.22e-18

1
2
RFBB_NEIGO 1.14e-19

2
1
YURA_MYXXA 3.34e-19

2
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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