Command line Training Set First Motif Summary of Motifs Termination Explanation


Search sequence databases for the best combined matches with these motifs using MAST.
Search sequence databases for all matches with these motifs using FIMO.
Submit these motifs to BLOCKS multiple alignment processor.

MEME - Motif discovery tool

MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009)

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= memeout/meme.fasta
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name Weight Length Sequence name Weight Length
_[Methanobacterium_formicicum_DSM_3637] 1.0000 651 _[Methanobrevibacter_smithii_DSM_2374] 1.0000 655
_[Methanolobus_psychrophilus_R15] 1.0000 660 _[Granulicella_tundricola_MP5ACTX9] 1.0000 662
_[Arthrobacter_gangotriensis_Lz1y] 1.0000 700 _[Collinsella_intestinalis_DSM_13280] 1.0000 749
_[Saccharomonospora_viridis_DSM_43017] 1.0000 719 _[Slackia_piriformis_YIT_12062] 1.0000 719
_[Streptomyces_bottropensis_ATCC_25435] 1.0000 709 _[Streptomyces_somaliensis_DSM_40738] 1.0000 714
_[Parachlamydia_acanthamoebae_UV-7] 1.0000 669 _[Arthrospira_maxima_CS-328] 1.0000 665
_[Chroococcidiopsis_thermalis_PCC_7203] 1.0000 665 _[Microcystis_aeruginosa_PCC_9701] 1.0000 667
_[Nostoc_punctiforme_PCC_73102] 1.0000 683 _[Synechococcus_elongatus_PCC_6301] 1.0000 666
_[Denitrovibrio_acetiphilus_DSM_12809] 1.0000 658 _[Dictyoglomus_thermophilum_H-6-12] 1.0000 662
_[Ignavibacterium_album_JCM_16511] 1.0000 670 _[Planctomyces_limnophilus_DSM_3776] 1.0000 707
_[Cupriavidus_metallidurans_CH34] 1.0000 697 _[Desulfovibrio_desulfuricans_ND132] 1.0000 667
_[Escherichia_coli_DEC7B] 1.0000 673 _[Geobacter_sulfurreducens_PCA] 1.0000 664
_[Marinobacter_adhaerens_HP15] 1.0000 686 _[Pseudomonas_fluorescens_A506] 1.0000 671
_[Leptospira_interrogans_str._2002000624] 1.0000 666 _[Leptospira_weilii_str._2006001853] 1.0000 666
_[Thermodesulfatator_indicus_DSM_15286] 1.0000 666 _[Bacillus_subtilis_subsp._subtilis_str._168] 1.0000 661
COMMAND LINE SUMMARY 
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme memeout/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -oc memeout/
model: mod= zoops nmotifs= 3 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= 30 wnsites= 0.8
theta: prob= 1 spmap= pam spfuzz= 120
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 20367 N= 30
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.072 C 0.005 D 0.068 E 0.096 F 0.034 G 0.057 H 0.018 I 0.069 K 0.049 L 0.097 M 0.022 N 0.031 P 0.041 Q 0.042 R 0.082 S 0.050 T 0.054 V 0.070 W 0.002 Y 0.039
Background letter frequencies (from dataset with add-one prior applied):
A 0.072 C 0.005 D 0.068 E 0.096 F 0.034 G 0.057 H 0.018 I 0.069 K 0.049 L 0.097 M 0.022 N 0.031 P 0.041 Q 0.042 R 0.082 S 0.050 T 0.054 V 0.070 W 0.002 Y 0.039
P N
MOTIF 1 width = 50 sites = 30 llr = 3885 E-value = 1.9e-1223
SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
190.6 (bits)
Relative Entropy
186.8 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME START P-VALUE SITES
_[Marinobacter_adhaerens_HP15] 74 6.55e-61 QVQRPTIIMA HNKTLAAQLYGEFKEFFPDNAVEYFVSYYDYYQPEAYVPSSDTFIEKDAS INEHIEQMRL
_[Bacillus_subtilis_subsp._subtilis_str._168] 64 1.27e-60 EVNKPTLVIA HNKTLAGQLYSEFKEFFPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDAS INDEIDKLRH
_[Saccharomonospora_viridis_DSM_43017] 87 2.07e-60 RLQRPTLVMA HNKTLAAQLANELREFFPHNAVEYFVSYYDYYQPEAYVPQTDTYIEKDSS INDDVERLRH
_[Denitrovibrio_acetiphilus_DSM_12809] 62 3.86e-60 QLNVPTLVIA HNKTLAAQLYGEFKKFFPNNAVEYFVSYYDYYQPEAYKPQTDTFIEKDSS INEDIDKLRH
_[Pseudomonas_fluorescens_A506] 63 1.09e-59 QTNRPTLVLA PNKTLAAQLYGEFKAFFPNNAVEYFVSYYDYYQPEAYVPSSDTFIEKDAS INDHIEQMRL
_[Chroococcidiopsis_thermalis_PCC_7203] 63 1.09e-59 KIGKPTLVLA HNKTLAAQLCNELREFFPNNAVEYFVSYYDYYQPEAYIPVTDTFIEKSAS INDEIDMLRH
_[Methanolobus_psychrophilus_R15] 63 1.66e-59 NVQMPTLVIA HNKTLAAQLYSEFREFFPDNAVEYFVSYYDYYQPEAYIPTTDTYIEKDAS INEEIDRLRL
_[Leptospira_weilii_str._2006001853] 64 4.98e-59 NLGLPTLVLS HNKTLAAQLFREFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTFIEKDSS INEEIDKLRL
_[Leptospira_interrogans_str._2002000624] 64 4.98e-59 NLGLPTLVLS HNKTLAAQLFREFKEFFPENAVEYFVSYYDYYQPEAYVPSSDTFIEKDSS INEEIDKLRL
_[Arthrospira_maxima_CS-328] 63 6.48e-59 QLGRPTLVLA HNKTLAAQLCNELREFFPNNAVEYFISYYDYYQPEAYIPVSDTYIEKTAS INDEIDMLRH
_[Thermodesulfatator_indicus_DSM_15286] 67 1.58e-58 RLNRPTLIIA PNKTLAAQLYNEFKKLFPYNAVEYFVSYYDYYQPEAYIPSTDTYIEKDAS INELIDRLRH
_[Collinsella_intestinalis_DSM_13280] 88 1.79e-58 ALGKPTLVMA PNKTLAAQLASELKEFFPNNAVVYFVSYYDYYQPEAYVPSSDTYIEKDSS INEEVEMLRH
_[Escherichia_coli_DEC7B] 64 2.02e-58 DLQRPTMVLA PNKTLAAQLYGEMKEFFPENAVEYFVSYYDYYQPEAYVPSSDTFIEKDAS VNEHIEQMRL
_[Dictyoglomus_thermophilum_H-6-12] 63 2.28e-58 NVQKPTLVIA PNKTLAAQLYSEFKEFFPYNAVEYFVSYYDYYQPEAYIPQTDTYIEKDAD INDRIDRLRH
_[Microcystis_aeruginosa_PCC_9701] 63 2.58e-58 KIGRPTLVLA HNKTLAAQLCNELRQFFPNNAVEYFISYYDYYQPEAYIPVSDTYIEKSSS INDEIDMLRH
_[Streptomyces_somaliensis_DSM_40738] 73 3.69e-58 RLQRPTLVMA PNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQSDTYIEKDSS INEEVERLRH
_[Streptomyces_bottropensis_ATCC_25435] 73 3.69e-58 KLQRPTLVMA PNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQSDTYIEKDSS INEEVERLRH
_[Methanobacterium_formicicum_DSM_3637] 63 4.68e-58 EVQKPTLVIS HNKTLAAQLYEEFKELFPNNAVEYFVSYYDYYQPEAYVPQSDTYIDKESS INEEIDMMRH
_[Geobacter_sulfurreducens_PCA] 63 6.62e-58 AVNRPALVLA PNKTLAAQLYGEFRELFPDNAVEYFVSYYDYYQPEAYIPTTDTFIEKDSS INDEIDKLRH
_[Synechococcus_elongatus_PCC_6301] 63 1.45e-57 QVGRPALVLA HNKTLAAQLCNELREFFPNNAVEYFISYYDYYQPEAYIPVTDTYIAKTAS INEEIDMLRH
_[Slackia_piriformis_YIT_12062] 86 2.01e-57 AVQKPTLVMA PNKTLAAQLAAELKEFFPHNAVVYFVSYYDYYQPEAYVPSTDTFIEKDAS INEEVEKLRH
_[Planctomyces_limnophilus_DSM_3776] 63 2.24e-57 QLQRPALVLS HNKTLAAQLYAEFKEFFPHNAVTYFVSYYDYYQPEAYIPQRDIYIEKDSS INEEIDRLRL
_[Cupriavidus_metallidurans_CH34] 83 2.49e-57 RMGRPAIVFA PNKTLAAQLYSEFREFFPRNAVEYFVSYYDYYQPEAYVPQRDLFIEKDSS INEHIEQMRL
_[Nostoc_punctiforme_PCC_73102] 81 3.08e-57 KIGKPTLVLA HNKTLAAQLCNELRDFFPNNAVEYFVSYYDYYQPEAYIPVTDTYIEKTAA INDEIDMLRH
_[Arthrobacter_gangotriensis_Lz1y] 73 3.42e-57 QVQRPTLVMV QNKTLAAQLANEFRELLPNNAVEYFVSYYDYYQPEAYVPQTDTFIEKDSS INEEVERLRH
_[Methanobrevibacter_smithii_DSM_2374] 63 3.79e-57 KVQKPTLVIS HNKTLAAQLYEEFKEFFPDNAVEYFVSYYDYYQPEAYVPRTDTFIDKESS VNEEIDIMRH
_[Granulicella_tundricola_MP5ACTX9] 62 6.60e-56 EVQRPALILA HNKTLAAQLYHEFKQFFPNNAVEYFVSYYDYYQPEAYIPSGDLFIEKEAT INEELDKLRL
_[Desulfovibrio_desulfuricans_ND132] 63 5.62e-55 TLNRPALVLA PNKTLAAQLYTEFRGLFPHNAVEYFVSYYDYYQPEAYLPHSDVYIEKDSS INDDIDKLRH
_[Ignavibacterium_album_JCM_16511] 63 1.12e-54 QVNKPTLVIS HNKTLAAQLYSEFKSFFPHNAVEFFISYYDYYQPEAYVVSRDLYIEKDFS INEEIDRLRL
_[Parachlamydia_acanthamoebae_UV-7] 64 1.12e-54 QVQRPTLVIA HNKTLAAQLYQEFKSFFPHNAIEYFVSYYDYYQPEAYIARTDTYIEKDMA INDRIDKMRL
Motif 1 block diagrams

Name		 Lowest
p-value		 Motifs
_[Marinobacter_adhaerens_HP15] 6.55e-61
1
_[Bacillus_subtilis_subsp._subtilis_str._168] 1.27e-60
1
_[Saccharomonospora_viridis_DSM_43017] 2.07e-60
1
_[Denitrovibrio_acetiphilus_DSM_12809] 3.86e-60
1
_[Pseudomonas_fluorescens_A506] 1.09e-59
1
_[Chroococcidiopsis_thermalis_PCC_7203] 1.09e-59
1
_[Methanolobus_psychrophilus_R15] 1.66e-59
1
_[Leptospira_weilii_str._2006001853] 4.98e-59
1
_[Leptospira_interrogans_str._2002000624] 4.98e-59
1
_[Arthrospira_maxima_CS-328] 6.48e-59
1
_[Thermodesulfatator_indicus_DSM_15286] 1.58e-58
1
_[Collinsella_intestinalis_DSM_13280] 1.79e-58
1
_[Escherichia_coli_DEC7B] 2.02e-58
1
_[Dictyoglomus_thermophilum_H-6-12] 2.28e-58
1
_[Microcystis_aeruginosa_PCC_9701] 2.58e-58
1
_[Streptomyces_somaliensis_DSM_40738] 3.69e-58
1
_[Streptomyces_bottropensis_ATCC_25435] 3.69e-58
1
_[Methanobacterium_formicicum_DSM_3637] 4.68e-58
1
_[Geobacter_sulfurreducens_PCA] 6.62e-58
1
_[Synechococcus_elongatus_PCC_6301] 1.45e-57
1
_[Slackia_piriformis_YIT_12062] 2.01e-57
1
_[Planctomyces_limnophilus_DSM_3776] 2.24e-57
1
_[Cupriavidus_metallidurans_CH34] 2.49e-57
1
_[Nostoc_punctiforme_PCC_73102] 3.08e-57
1
_[Arthrobacter_gangotriensis_Lz1y] 3.42e-57
1
_[Methanobrevibacter_smithii_DSM_2374] 3.79e-57
1
_[Granulicella_tundricola_MP5ACTX9] 6.60e-56
1
_[Desulfovibrio_desulfuricans_ND132] 5.62e-55
1
_[Ignavibacterium_album_JCM_16511] 1.12e-54
1
_[Parachlamydia_acanthamoebae_UV-7] 1.12e-54
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
Motif 1 in BLOCKS format

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

Scan sequence databases for the best match in each sequence using MAST.
Motif 1 position-specific probability matrix

Scan sequence databases for all matches with this motif using FIMO.
Motif 1 regular-expression
[HP]NKTLAAQL[YA][NS]E[FL][KR]E[FL]FP[NH]NAVEYFVSYYDYYQPEAY[VI]P[QS][TS]DT[YF]IEKD[SA]S
Time 27.48 secs.
P N
MOTIF 2 width = 50 sites = 30 llr = 3694 E-value = 1.3e-1133
SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
197.5 (bits)
Relative Entropy
177.6 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME START P-VALUE SITES
_[Escherichia_coli_DEC7B] 496 8.00e-59 EIIRDLRLGE FDVLVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNV NGKAILYGDK
_[Geobacter_sulfurreducens_PCA] 495 4.62e-58 QIIRDLRMGE FDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSARSLIQTCGRAARNV NGRVIMYADT
_[Marinobacter_adhaerens_HP15] 505 7.99e-58 EIIRDLRRGE FDVLVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTMGRAARNV HGKAILYGDR
_[Cupriavidus_metallidurans_CH34] 514 2.57e-57 EIIRDLRLGT FDVLVGINLLREGLDIPEVSLVAILDADKEGFLRAERSLIQTIGRAARNV NGTAILYGDR
_[Pseudomonas_fluorescens_A506] 494 5.99e-57 EIIRDLRLGT FDVLVGINLLREGLDMPEVSLVAILDADKEGFLRSERSLIQTIGRAARNL NGRAILYADR
_[Bacillus_subtilis_subsp._subtilis_str._168] 495 6.87e-57 EIIRDLRLGK YDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNA EGRVIMYADK
_[Parachlamydia_acanthamoebae_UV-7] 496 6.87e-57 QIIQDLRAGT FDVLVGINLLREGLDIPEVSLVAILDADKEGFLRSETSLIQTCGRAARNS EGRVIMYANK
_[Chroococcidiopsis_thermalis_PCC_7203] 494 8.08e-57 EILQDLREGS FDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRAERSLIQTIGRAARNV RGQAILYADN
_[Streptomyces_bottropensis_ATCC_25435] 503 1.08e-56 ELLRELRAGE YDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSGTSLIQTIGRAARNV SGQVHMYADR
_[Slackia_piriformis_YIT_12062] 516 1.73e-56 EILSALRKGE FDVLVGINLLREGLDLPEVSLVAILDADKEGFLRNHRSLIQTIGRAARNA SGQVIMYADK
_[Arthrobacter_gangotriensis_Lz1y] 503 1.73e-56 ELLRELRMGL FDVLVGINLLREGLDLPEVSLVAILDADKQGFLRSATSLIQTIGRAARNV DGQVHMYGDK
_[Methanobrevibacter_smithii_DSM_2374] 493 3.05e-56 DIVDDLRRGT FDVLVGVNLLREGLDLPEVSLVAILDADKEGFLRNETSLIQTIGRAARNI NGQVIMYVDE
_[Denitrovibrio_acetiphilus_DSM_12809] 494 6.76e-56 RILKQLRLGE FDVLVGINLLREGLDIPEVSLVAVLDADKEGFLRSEKSLIQTIGRAARNV NGRAIFYAEK
_[Streptomyces_somaliensis_DSM_40738] 503 1.00e-55 ELLRELRAGE YDVLVGINLLREGLDLPEVSLVAILDADKQGFLRSGTSLIQTIGRAARNV SGQVHMYADT
_[Saccharomonospora_viridis_DSM_43017] 518 1.62e-55 ELLRQLRSGD FDVLVGINLLREGLDLPEVSLVSILDADKEGFLRSSTSLIQTIGRAARNV SGQVHMYADT
_[Nostoc_punctiforme_PCC_73102] 512 1.83e-55 EILQNLREGK FDVLVGVNLLREGLDLPEVSLVAIMDADKEGFLRTERSLIQTIGRAARHV QGQAILYADN
_[Leptospira_interrogans_str._2002000624] 494 2.96e-55 GIIRDLRKGI YDVLIGINLLREGLDIPEVSLVAILDADKEGFLRNYKSLIQTIGRAARNV NGTAILYADK
_[Synechococcus_elongatus_PCC_6301] 494 7.20e-55 EILQDLRNGD FDVLIGVNLLREGLDLPEVSLVAILDADKEGFLRTERSLIQTIGRAARHI NGQAILYADR
_[Planctomyces_limnophilus_DSM_3776] 494 3.03e-54 EIIRELREGK YDTLVGVNLLREGLDIPEVSLVAILDADKEGFLRSETSLIQTIGRSARNV NAEVYLYADS
_[Dictyoglomus_thermophilum_H-6-12] 493 3.34e-54 GILQSLRLGK FDVLVGINLLREGLDLPEVSLVAILDADREGFLRSERSLIQVMGRAARNV NGKVIMYADV
_[Microcystis_aeruginosa_PCC_9701] 494 3.34e-54 EIIQDLREGV FDVLIGVNLLREGLDLPEVSLVAILDADKEGFLRATRSLIQTIGRAARHI RGQAILYGDN
_[Collinsella_intestinalis_DSM_13280] 518 3.67e-54 EILRSLRQGK IDVLVGINLLREGLDLPEVSLVAILDADKEGFLRNRRSLIQTIGRAARNA EGEVVMYADS
_[Methanolobus_psychrophilus_R15] 496 4.44e-54 EIVRDLRKGE FDVLVGINLLREGLDIPEVAFVAILDADKEGFLRSERSLIQTIGRASRNV NGHVILYADK
_[Leptospira_weilii_str._2006001853] 494 4.87e-54 AIIRDLRKGI YDVLIGINLLREGLDIPEVSLVAILDADKEGFLRNYKSLIQTVGRAARNV NGTAILYADK
_[Thermodesulfatator_indicus_DSM_15286] 499 6.43e-54 KLIRDLRLGV FEVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQIAGRAARNV NGTVILYADN
_[Arthrospira_maxima_CS-328] 494 9.24e-54 EILQSLQEGE FDVLIGVNLLREGLDLPQVSLVAIFDADKEGFLRTERSLIQTIGRAARHV RGQAILYADN
_[Granulicella_tundricola_MP5ACTX9] 493 9.24e-54 RLLRDLRKGE YDVLIGINLLREGLDLPEVSLVAILDADKEGFLRSQGSLIQTIGRAARHL EGRAILYADK
_[Ignavibacterium_album_JCM_16511] 496 6.81e-53 EILRDLRLGA FDVLVGVNLLREGLDLPEVSLVAIIDADKEGFLRSARSLMQTAGRTARNV NGKVIMYADI
_[Desulfovibrio_desulfuricans_ND132] 495 2.29e-52 AIIQALREGE FFVLVGINLLREGLDIPEVSLVAILDGDKEGFLRSTRSLVQTFGRAARNA DGRVILYADK
_[Methanobacterium_formicicum_DSM_3637] 493 1.22e-51 DIIDDLRRGE FHCLVGVNLLREGLDLPEVGLVGILDADKEGFLRSQPALIQTIGRAARNV EGQVIIYADK
Motif 2 block diagrams

Name		 Lowest
p-value		 Motifs
_[Escherichia_coli_DEC7B] 8.00e-59
2
_[Geobacter_sulfurreducens_PCA] 4.62e-58
2
_[Marinobacter_adhaerens_HP15] 7.99e-58
2
_[Cupriavidus_metallidurans_CH34] 2.57e-57
2
_[Pseudomonas_fluorescens_A506] 5.99e-57
2
_[Bacillus_subtilis_subsp._subtilis_str._168] 6.87e-57
2
_[Parachlamydia_acanthamoebae_UV-7] 6.87e-57
2
_[Chroococcidiopsis_thermalis_PCC_7203] 8.08e-57
2
_[Streptomyces_bottropensis_ATCC_25435] 1.08e-56
2
_[Slackia_piriformis_YIT_12062] 1.73e-56
2
_[Arthrobacter_gangotriensis_Lz1y] 1.73e-56
2
_[Methanobrevibacter_smithii_DSM_2374] 3.05e-56
2
_[Denitrovibrio_acetiphilus_DSM_12809] 6.76e-56
2
_[Streptomyces_somaliensis_DSM_40738] 1.00e-55
2
_[Saccharomonospora_viridis_DSM_43017] 1.62e-55
2
_[Nostoc_punctiforme_PCC_73102] 1.83e-55
2
_[Leptospira_interrogans_str._2002000624] 2.96e-55
2
_[Synechococcus_elongatus_PCC_6301] 7.20e-55
2
_[Planctomyces_limnophilus_DSM_3776] 3.03e-54
2
_[Dictyoglomus_thermophilum_H-6-12] 3.34e-54
2
_[Microcystis_aeruginosa_PCC_9701] 3.34e-54
2
_[Collinsella_intestinalis_DSM_13280] 3.67e-54
2
_[Methanolobus_psychrophilus_R15] 4.44e-54
2
_[Leptospira_weilii_str._2006001853] 4.87e-54
2
_[Thermodesulfatator_indicus_DSM_15286] 6.43e-54
2
_[Arthrospira_maxima_CS-328] 9.24e-54
2
_[Granulicella_tundricola_MP5ACTX9] 9.24e-54
2
_[Ignavibacterium_album_JCM_16511] 6.81e-53
2
_[Desulfovibrio_desulfuricans_ND132] 2.29e-52
2
_[Methanobacterium_formicicum_DSM_3637] 1.22e-51
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
Motif 2 in BLOCKS format

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

Scan sequence databases for the best match in each sequence using MAST.
Motif 2 position-specific probability matrix

Scan sequence databases for all matches with this motif using FIMO.
Motif 2 regular-expression
[FY]DVL[VI]G[IV]NLLREGLD[LI]PEVSLVAILDADKEGFLRSE[RT]SLIQTIGRAARNV
Time 52.48 secs.
P N
MOTIF 3 width = 50 sites = 30 llr = 3570 E-value = 2.0e-1078
SEQUENCE LOGO PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide
Information Content
178.3 (bits)
Relative Entropy
171.7 (bits)
Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]
NAME START P-VALUE SITES
_[Ignavibacterium_album_JCM_16511] 326 5.75e-59 APGTRPFNLL DYFPDDFLMVIDESHVTIPQIRGMYNGDRSRKETLVEYGFRLPSALDNRP MKFEEFESML
_[Synechococcus_elongatus_PCC_6301] 324 8.41e-58 EPGSPPECLI DYFPKDWLLVVDESHVTVPQLRGMYNGDQSRKKVLVDHGFRLPSAADNRP LKSEEFWEKV
_[Nostoc_punctiforme_PCC_73102] 342 4.18e-57 QAGDPPECLI DYFPKDWLLIIDESHVTVPQIRGMYNGDQARKKVLIEHGFRLPSAADNRP LKAEEFWQKV
_[Arthrospira_maxima_CS-328] 324 6.12e-57 LPGSPPECLV DYFPDDWLLVVDESHVTVPQIRAMYNGDQARKKVLIEHGFRLPSAADNRP LKSEEFWQKV
_[Streptomyces_bottropensis_ATCC_25435] 334 1.07e-56 EPGSPPNTLL DYFPDDFLLVIDESHVTVPQIGAMYEGDASRKRTLVDHGFRLPSALDNRP LKWEEFQERV
_[Saccharomonospora_viridis_DSM_43017] 348 1.54e-56 EPGSAPATLL DYFPEDFLLVIDESHVTVPQIGGMYEGDASRKRTLVEHGFRLPSALDNRP LTWEEFSDRI
_[Chroococcidiopsis_thermalis_PCC_7203] 324 2.62e-56 QAGEPPECLI DYFPNDWLLVVDESHVTVPQIRGMYNGDRARKLVLIDHGFRLPSAADNRP LKSEEFWAKV
_[Arthrobacter_gangotriensis_Lz1y] 334 3.12e-56 ESGTSPHCLI DYFPDDFLLVIDESHVTVPQIGAMYEGDMSRKRTLVEHGFRLPSAMDNRP LKWDEFLERI
_[Streptomyces_somaliensis_DSM_40738] 334 6.18e-56 EPGSPPNTLL DYFPEDFLLVIDESHVTVPQIGAMYEGDASRKRTLVDHGFRLPSALDNRP LKWEEFQERI
_[Collinsella_intestinalis_DSM_13280] 349 1.20e-55 KPGEPPFTLI DYFPKDMLCIIDESHVTVPQIRGMHEGDRSRKVTLVEHGFRLPSALDNRP LRYDEFEARI
_[Microcystis_aeruginosa_PCC_9701] 324 1.94e-55 LAGEPPECLV DYFPQDWLLVVDESHVSVPQIRGMYNGDQSRKKVLIDHGFRLPSAADNRP LKSEEFWQKV
_[Slackia_piriformis_YIT_12062] 347 4.22e-55 EPGEPAYTLL DYFPDDFLCIIDESHVTVPQIRGMHEGDRSRKVTLAEHGFRLPSCLDNRP LRFDEFEERI
_[Bacillus_subtilis_subsp._subtilis_str._168] 326 1.03e-54 PPGSTPYTLL DYFPDDFMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLPSALDNRP LRFEEFEKHM
_[Thermodesulfatator_indicus_DSM_15286] 329 2.11e-54 APGEPPYTLL DYFPDDFLIFIDESHITVPQLHGMYRGDRSRKETLVEYGFRLPSALDNRP LTFEEFEERI
_[Granulicella_tundricola_MP5ACTX9] 323 4.82e-54 LPGEPPPTLL DYFPRDYLLFIDESHVTVPQLHGMWHGDRSRKQNLVDYGFRLPSAMDNRP LKFDEFEGRT
_[Planctomyces_limnophilus_DSM_3776] 324 4.17e-53 PPGEPPYTLL DFFPNDFLTFIDESHVTIPQIRAMFNGDHARKTTLVEHGFRLPMALDNRP LKFDEWETRR
_[Escherichia_coli_DEC7B] 326 6.70e-53 GPGEPPPTLF DYLPADGLLVVDESHVTIPQIGGMYRGDRARKETLVEYGFRLPSALDNRP LKFEEFEALA
_[Marinobacter_adhaerens_HP15] 336 9.48e-53 RPGEAPPTLF DYLPPNALLVVDESHVTIPQIGAMYKGDRSRKETLVEYGFRLPSALDNRP MKFEEWERIA
_[Pseudomonas_fluorescens_A506] 325 1.86e-52 DSGAPPPTLY DYLPPDALLVIDESHVSVPQVGAMYKGDRSRKETLVEYGFRLPSALDNRP MRFDEWEAIS
_[Leptospira_interrogans_str._2002000624] 325 3.56e-52 KPGERPACLI DYFQGEFLLIVDESHVTIPQIGGMFAGDRARKQTLVDFGFRLPSALDNRP LNFQEFETLT
_[Dictyoglomus_thermophilum_H-6-12] 324 6.66e-52 KPGEPPYTLL DYFPDDFLVFIDESHLTIPQLRAMYHGDKSRKDNLVEYGFRLPSAYDNRP LTFEEFWERV
_[Methanobrevibacter_smithii_DSM_2374] 324 7.38e-52 KWGEKPYSLL KYFPEDYLTIIDESHVTLPQIRGMYNGDRARKETLVEHGFRLPSAKENRP LRFDEFESSI
_[Leptospira_weilii_str._2006001853] 325 9.99e-52 KAGERPACLI DYFQGEFLLIVDESHVTIPQIGGMFAGDKARKQTLVDFGFRLPSALDNRP LNFEEFETLT
_[Desulfovibrio_desulfuricans_ND132] 325 9.99e-52 VEGQPPATLL DYFPDDFILFVDESHIALPQVGGMYRGDRSRKTTLVDFGFRLPSALDNRP LNYEEFQERI
_[Methanobacterium_formicicum_DSM_3637] 324 9.44e-51 KWGETPYSLL RYFPDDYLTIIDESHVTVPQIRGMYAGDRARKDVLVDYGFRLPSARENRP LNFEEFQSLQ
_[Geobacter_sulfurreducens_PCA] 325 1.23e-50 TPGEPPYTLL DYFPRDFILFVDESHITVSQVGGMYRGDRSRKETLVNYGFRLPAALDNRP LTFGEFTERL
_[Denitrovibrio_acetiphilus_DSM_12809] 324 1.34e-50 QPGDTPPTLL SYLPKDALVIVDESHMTIPQIKGMYNGDRSRKTTLVEYGFRLPAALDNRP LKFEEFRERV
_[Parachlamydia_acanthamoebae_UV-7] 326 1.88e-50 QPGDPPPCLI DYFPSDFLLIIDESHQTLPQMRAMYNGDKARKAALVDFGFRLPSAYDNRP LKFEESYSHF
_[Cupriavidus_metallidurans_CH34] 345 1.03e-49 KPGEPPPTLV DYLPPDALMFLDESHVLIGQLNGMYNGDRARKTTLVEYGFRLPSALDNRP LKFDEYERKM
_[Methanolobus_psychrophilus_R15] 327 1.03e-49 KPGEPPSSLL NFFPEDYMVVIDESHVTIPQVRGMHNGDRARKESLISYGFRLPSAYDNRP LRYDEFERQL
Motif 3 block diagrams

Name		 Lowest
p-value		 Motifs
_[Ignavibacterium_album_JCM_16511] 5.75e-59
3
_[Synechococcus_elongatus_PCC_6301] 8.41e-58
3
_[Nostoc_punctiforme_PCC_73102] 4.18e-57
3
_[Arthrospira_maxima_CS-328] 6.12e-57
3
_[Streptomyces_bottropensis_ATCC_25435] 1.07e-56
3
_[Saccharomonospora_viridis_DSM_43017] 1.54e-56
3
_[Chroococcidiopsis_thermalis_PCC_7203] 2.62e-56
3
_[Arthrobacter_gangotriensis_Lz1y] 3.12e-56
3
_[Streptomyces_somaliensis_DSM_40738] 6.18e-56
3
_[Collinsella_intestinalis_DSM_13280] 1.20e-55
3
_[Microcystis_aeruginosa_PCC_9701] 1.94e-55
3
_[Slackia_piriformis_YIT_12062] 4.22e-55
3
_[Bacillus_subtilis_subsp._subtilis_str._168] 1.03e-54
3
_[Thermodesulfatator_indicus_DSM_15286] 2.11e-54
3
_[Granulicella_tundricola_MP5ACTX9] 4.82e-54
3
_[Planctomyces_limnophilus_DSM_3776] 4.17e-53
3
_[Escherichia_coli_DEC7B] 6.70e-53
3
_[Marinobacter_adhaerens_HP15] 9.48e-53
3
_[Pseudomonas_fluorescens_A506] 1.86e-52
3
_[Leptospira_interrogans_str._2002000624] 3.56e-52
3
_[Dictyoglomus_thermophilum_H-6-12] 6.66e-52
3
_[Methanobrevibacter_smithii_DSM_2374] 7.38e-52
3
_[Leptospira_weilii_str._2006001853] 9.99e-52
3
_[Desulfovibrio_desulfuricans_ND132] 9.99e-52
3
_[Methanobacterium_formicicum_DSM_3637] 9.44e-51
3
_[Geobacter_sulfurreducens_PCA] 1.23e-50
3
_[Denitrovibrio_acetiphilus_DSM_12809] 1.34e-50
3
_[Parachlamydia_acanthamoebae_UV-7] 1.88e-50
3
_[Cupriavidus_metallidurans_CH34] 1.03e-49
3
_[Methanolobus_psychrophilus_R15] 1.03e-49
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
Motif 3 in BLOCKS format

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

Scan sequence databases for the best match in each sequence using MAST.
Motif 3 position-specific probability matrix

Scan sequence databases for all matches with this motif using FIMO.
Motif 3 regular-expression
DYFPDDFLL[VIF][IV]DESHVT[VI]PQI[RG][GA]MY[NE]GDR[SA]RKE[TV]LV[ED][HY]GFRLPSALDNRP
Time 75.10 secs.
P N
SUMMARY OF MOTIFS
Combined block diagrams: non-overlapping sites with p-value < 0.0001

Name		 Combined
p-value
Motifs
_[Methanobacterium_formicicum_DSM_3637] 7.04e-146
1
3
2
_[Methanobrevibacter_smithii_DSM_2374] 1.21e-150
1
3
2
_[Methanolobus_psychrophilus_R15] 1.08e-148
1
3
2
_[Granulicella_tundricola_MP5ACTX9] 4.23e-149
1
3
2
_[Arthrobacter_gangotriensis_Lz1y] 3.45e-155
1
3
2
_[Collinsella_intestinalis_DSM_13280] 1.78e-153
1
3
2
_[Saccharomonospora_viridis_DSM_43017] 1.08e-157
1
3
2
_[Slackia_piriformis_YIT_12062] 2.95e-154
1
3
2
_[Streptomyces_bottropensis_ATCC_25435] 8.45e-157
1
3
2
_[Streptomyces_somaliensis_DSM_40738] 4.54e-155
1
3
2
_[Parachlamydia_acanthamoebae_UV-7] 2.11e-147
1
3
2
_[Arthrospira_maxima_CS-328] 5.77e-155
1
3
2
_[Chroococcidiopsis_thermalis_PCC_7203] 3.78e-158
1
3
2
_[Microcystis_aeruginosa_PCC_9701] 2.60e-153
1
3
2
_[Nostoc_punctiforme_PCC_73102] 4.06e-155
1
3
2
_[Synechococcus_elongatus_PCC_6301] 1.40e-155
1
3
2
_[Denitrovibrio_acetiphilus_DSM_12809] 5.12e-152
1
3
2
_[Dictyoglomus_thermophilum_H-6-12] 7.38e-150
1
3
2
_[Ignavibacterium_album_JCM_16511] 6.81e-152
1
3
2
_[Planctomyces_limnophilus_DSM_3776] 5.10e-150
1
3
2
_[Cupriavidus_metallidurans_CH34] 1.14e-149
1
3
2
_[Desulfovibrio_desulfuricans_ND132] 1.79e-144
1
3
2
_[Escherichia_coli_DEC7B] 1.78e-155
1
3
2
_[Geobacter_sulfurreducens_PCA] 5.67e-152
1
3
2
_[Marinobacter_adhaerens_HP15] 8.83e-157
1
3
2
_[Pseudomonas_fluorescens_A506] 1.95e-154
1
3
2
_[Leptospira_interrogans_str._2002000624] 7.98e-152
1
3
2
_[Leptospira_weilii_str._2006001853] 3.61e-150
1
3
2
_[Thermodesulfatator_indicus_DSM_15286] 3.28e-152
1
3
2
_[Bacillus_subtilis_subsp._subtilis_str._168] 1.44e-157
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

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


CPU: kodomo.fbb.msu.ru

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: