MEME

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
Methanocella_arvoryzae_MRE50	1.0000	172	Methanosarcina_barkeri_str._Fusaro	1.0000	178
Amsacta_moorei_entomopoxvirus_'L'	1.0000	152	Paramecium_bursaria_Chlorella_virus_1	1.0000	187
Paramecium_bursaria_Chlorella_virus_FR483	1.0000	169	Pieris_rapae_granulovirus	1.0000	156
Mamestra_configurata_nucleopolyhedrovirus_B	1.0000	151	Candidatus_Solibacter_usitatus_Ellin6076	1.0000	174
Thermocrinis_albus_DSM_14484	1.0000	173	Aquifex_aeolicus_VF5	1.0000	169
Parachlamydia_acanthamoebae_UV-7	1.0000	178	Candidatus_Protochlamydia_amoebophila_UWE25	1.0000	205
Granulicella_tundricola_MP5ACTX9	1.0000	180	Granulicella_mallensis_MP5ACTX8	1.0000	173
Rhodopirellula_sallentina_SM41	1.0000	214	Planctomyces_maris_DSM_8797	1.0000	196
Deinococcus_gobiensis_I-0	1.0000	145	Pseudanabaena_biceps_PCC_7429	1.0000	236
Synechococcus_sp._CC9605	1.0000	178	Lyngbya_sp._PCC_8106	1.0000	201
Rhodococcus_triatomae_BKS_15-14	1.0000	208	Streptosporangium_roseum_DSM_43021	1.0000	226
Fulvivirga_imtechensis_AK7	1.0000	205	Formosa_sp._AK20	1.0000	201
Campylobacter_showae_CSUNSWCD	1.0000	182	Cystobacter_fuscus_DSM_2262	1.0000	177
Azoarcus_sp._KH32C	1.0000	175	Sphingomonas_sp._MM-1	1.0000	183
Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2	1.0000	174	Vibrio_cholerae_O1_biovar_El_Tor_str._N16961	1.0000	171
Bacillus_subtilis_strain_168	1.0000	196	Anolis_carolinensis	1.0000	159
Xenopus_laevis	1.0000	274	Salmo_salar	1.0000	154
Sarcophilus_harrisii	1.0000	154	Rattus_norvegicus	1.0000	154
Otolemur_garnettii	1.0000	153	Branchiostoma_floridae	1.0000	156
Culex_quinquefasciatus	1.0000	153	Drosophila_melanogaster	1.0000	153
Bombus_impatiens	1.0000	168	Acyrthosiphon_pisum	1.0000	152
Ixodes_scapularis	1.0000	154	Caenorhabditis_elegans	1.0000	180
Aplysia_californica	1.0000	155	Physcomitrella_patens_subsp._patens	1.0000	170
Selaginella_moellendorffii	1.0000	210	Cucumis_sativus	1.0000	221
Penicillium_chrysogenum_Wisconsin_54-1255	1.0000	174	Cryptococcus_gattii_WM276	1.0000	153
Tetrahymena_thermophila	1.0000	184	Dictyostelium_discoideum_AX4	1.0000	152
Capsaspora_owczarzaki_ATCC_30864	1.0000	177	Perkinsus_marinus_ATCC_50983	1.0000	258
Acanthamoeba_castellanii_str._Neff	1.0000	157	Naegleria_gruberi	1.0000	135

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=	56	wnsites=	0.8
theta:	prob=	1	spmap=	pam	spfuzz=	120
em:	prior=	dirichlet	b=	0.01	maxiter=	50
	distance=	1e-05
data:	n=	9995	N=	56
sample:	seed=	0	seqfrac=	1
Letter frequencies in dataset:
A 0.088 C 0.019 D 0.063 E 0.046 F 0.032 G 0.135 H 0.050 I 0.055 K 0.055 L 0.070 M 0.017 N 0.055 P 0.048 Q 0.023 R 0.030 S 0.058 T 0.065 V 0.078 W 0.002 Y 0.011
Background letter frequencies (from dataset with add-one prior applied): A 0.088 C 0.019 D 0.063 E 0.046 F 0.032 G 0.135 H 0.050 I 0.055 K 0.055 L 0.070 M 0.017 N 0.055 P 0.048 Q 0.023 R 0.030 S 0.058 T 0.065 V 0.078 W 0.002 Y 0.011

MOTIF 1 width = 21 sites = 56 llr = 1925 E-value = 4.4e-496

SEQUENCE LOGO

PNG LOGOS require CONVERT from ImageMagick; see MEME installation guide

Information Content
55.3 (bits)

Relative Entropy
49.6 (bits)

Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]

NAME	START	P-VALUE	SITES
Selaginella_moellendorffii	93	7.90e-22	`GPTTVKVKIS`	`GLTPGKHGFHLHEFGDTTNGC`	`LSTGAHFNPE`
Physcomitrella_patens_subsp._patens	52	7.90e-22	`GPTKVNVKIT`	`GLTPGKHGFHLHEFGDTTNGC`	`MSTGPHFNPE`
Aplysia_californica	38	7.90e-22	`DSTIVTGEVK`	`GLAPGKHGFHIHQFGDYTNGC`	`MSAGGHFNPL`
Pieris_rapae_granulovirus	33	1.43e-21	`CPVHITGYLY`	`NLPYGYHGFHIHEFGDTTNGC`	`TSAGEHFNPF`
Cucumis_sativus	103	1.74e-21	`GPTSVNVRIT`	`GLTPGLHGFHLHEFGDTTNGC`	`ISTGAHFNPN`
Acanthamoeba_castellanii_str._Neff	40	2.56e-21	`EPTTIDVEIK`	`GLKPGPHGFHVHEFGDNTNGC`	`VSAGGHFNPF`
Ixodes_scapularis	37	3.73e-21	`QPVVVTGEIT`	`GLEQGLHGFHVHEFGDNTNGC`	`TSAGPHFNPL`
Branchiostoma_floridae	37	3.73e-21	`PVEVTGTISN`	`LTPPGKHGFHIHEFGDTTNGC`	`TSAGSHFNPA`
Dictyostelium_discoideum_AX4	34	6.50e-21	`SPVIISGVIS`	`GLKEGKHGFHVHEFGDTTNGC`	`LSAGAHFNPF`
Parachlamydia_acanthamoebae_UV-7	65	6.50e-21	`EGVQIVANVQ`	`GLPAGKHGFHIHEFGDCSAPD`	`ASSAGAHYDP`
Drosophila_melanogaster	35	7.79e-21	`TPVKVSGEVC`	`GLAKGLHGFHVHEFGDNTNGC`	`MSSGPHFNPY`
Salmo_salar	37	9.34e-21	`APVKLTGEIA`	`GLTPGEHGFHVHAFGDNTNGC`	`MSAGPHFNPH`
Anolis_carolinensis	41	9.34e-21	`GEVRVAGQLQ`	`GLTIGKHGFHVHEFGDNTNGC`	`TSAGAHFNPE`
Sarcophilus_harrisii	37	1.33e-20	`EPVELSGSIK`	`GLAEGYHGFHVHEFGDNTQGC`	`TSAGAHFNPH`
Caenorhabditis_elegans	58	2.26e-20	`DQAVIEGEIK`	`GLTPGLHGFHVHQYGDSTNGC`	`ISAGPHFNPF`
Acyrthosiphon_pisum	35	2.68e-20	`SPVEITGELT`	`GLSKGRHGFHIHEFGDNTNGC`	`MSSGPHFNPF`
Rattus_norvegicus	37	2.68e-20	`EPVVVSGQIT`	`GLTEGEHGFHVHQYGDNTQGC`	`TTAGPHFNPH`
Mamestra_configurata_nucleopolyhedrovirus_B	33	1.21e-19	`HLLHITGYIM`	`NLPKGLHGFHVHEFGDISNGC`	`TSAGEHFNPT`
Culex_quinquefasciatus	35	1.66e-19	`DAVKVTGEVT`	`GLKAGNHGFHIHEFGDNTNGC`	`TSAGPHFNPH`
Xenopus_laevis	119	4.96e-19	`NTCIIEGTLD`	`GLSPGLHGIHVHEFGDISNGC`	`ESCGEHYNPH`
Otolemur_garnettii	36	5.78e-19	`GPVMVKGRIT`	`GLAEGDHGFHVHQFGDNTQGC`	`TSAGPHFNPQ`
Azoarcus_sp._KH32C	62	1.63e-18	`GGVIVEARLG`	`GLAPGGHGFHIHEKGDCSAPD`	`ATSAGGHFNP`
Amsacta_moorei_entomopoxvirus_'L'	33	2.18e-18	`GSVHVKGKIV`	`GLSKGLHGFHVHEYGDVSNGC`	`TSAGEHFNPY`
Bombus_impatiens	52	8.79e-18	`NLIEITGKVY`	`GLTPGLHGIHVHEKGDLRDGC`	`MSTGPHFNPE`
Tetrahymena_thermophila	59	1.50e-17	`DKCKIRAEVK`	`GLAQGKHGFHIHEYGNLIDGC`	`KSAGAHFNPT`
Planctomyces_maris_DSM_8797	82	2.53e-17	`NKIHVEGEIT`	`GLKPGKHGFHVHEKGDLSDKE`	`TGKSAGGHFN`
Candidatus_Protochlamydia_amoebophila_UWE25	93	2.53e-17	`GGVKIIADVM`	`GLTPGKHGFHIHEFGDCGKNG`	`EAAGAHFNPM`
Rhodopirellula_sallentina_SM41	103	7.88e-17	`DTVKVTGEVR`	`GLSPGKHGFHVHEKGDLSDTE`	`TGKSAGGHFN`
Pseudanabaena_biceps_PCC_7429	100	1.14e-16	`LGLQVIVNVE`	`NLTQGEHMIHIHENGKCDAPD`	`FKTSGNHFNP`
Synechococcus_sp._CC9605	60	3.28e-16	`QGLVIYPDLA`	`GLTPGEHGFHLHSTGSCEAGQ`	`TAQGTAIAGL`
Cryptococcus_gattii_WM276	36	5.17e-16	`PVTVSGDIKN`	`LDANAERGFHVHEFGDNTNGC`	`TSAGPHFNPH`
Methanocella_arvoryzae_MRE50	58	5.78e-16	`GTVQINVSVD`	`GLPPGRHGIHIHAVGNCTPPF`	`TGAGDHYNPL`
Paramecium_bursaria_Chlorella_virus_1	66	6.47e-16	`KVKISVDISG`	`LKPNRKHGFHVHEAGDLTDGC`	`TSACAHFNPF`
Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2	57	1.12e-15	`YGLLFTPHLS`	`SLPAGIHGFHIHENGSCDAGM`	`KDGKPVAALA`
Formosa_sp._AK20	85	1.12e-15	`GKVTMVAVFD`	`GLTPGTHAIHLHEKSDCSAPD`	`GTSTGGHWNP`
Cystobacter_fuscus_DSM_2262	61	2.12e-15	`DKVTLDLEVA`	`GATPGLHGAHIHQTGDCTAAD`	`AASAGGHWNP`
Paramecium_bursaria_Chlorella_virus_FR483	48	3.20e-15	`KVKISVDMAG`	`LTPNKEHGFHVHEAGDMTDKC`	`TSACAHFNPY`
Penicillium_chrysogenum_Wisconsin_54-1255	59	7.12e-15	`DGLNIEDRLT`	`GVPFGKHGIHVHENGSTGNEC`	`LDAGGHYNPT`
Granulicella_tundricola_MP5ACTX9	59	1.05e-14	`GTLTVKLALK`	`NLPPGDHAVHIHQKPLCDAPD`	`FKSAGGHFNP`
Candidatus_Solibacter_usitatus_Ellin6076	58	1.15e-14	`KGVKIALNLK`	`GLPPGEHALHIHTNAKCEAPA`	`FTSAGGHFNP`
Streptosporangium_roseum_DSM_43021	95	1.39e-14	`GKSRIRVVVR`	`GLPPGYHGIHFHNKGVCDPKS`	`TDPATGSPFF`
Vibrio_cholerae_O1_biovar_El_Tor_str._N16961	54	1.53e-14	`YGTVFTPQLT`	`GLPAGLHGFHVHANGSCETSS`	`KDGKTVLGGA`
Perkinsus_marinus_ATCC_50983	135	1.68e-14	`RTKITYDVSN`	`LEPGSQHGVHVHEFADFSNGC`	`ASTGGHYNPF`
Fulvivirga_imtechensis_AK7	90	2.65e-14	`GKVKFELEVK`	`NAKPGQHAVHLHENGDCSAAD`	`ASSAGGHWNP`
Campylobacter_showae_CSUNSWCD	69	2.90e-14	`YGVALFPNLK`	`GLEGGAHGFHVHQNADCGANE`	`KGLGMKAGGH`
Lyngbya_sp._PCC_8106	84	3.79e-14	`TVEVKAEVSG`	`LPPNTKHGFHIHQTAKCEPDF`	`GAAGGHFDPG`
Aquifex_aeolicus_VF5	55	4.13e-14	`GVLIKLEASN`	`LPPNAELAFHIHELGKCDPPD`	`FKSAKGHFNP`
Granulicella_mallensis_MP5ACTX8	57	8.90e-14	`KGVKVKIDLK`	`NVPFGPHGVHIHQNASCEGPD`	`FKSAGGHFNP`
Rhodococcus_triatomae_BKS_15-14	92	1.05e-13	`ETVVVTVAAN`	`GLEPGFHGLHIHSVGSCEGDF`	`TSAGGHLQVA`
Sphingomonas_sp._MM-1	68	1.24e-13	`GGVRVAVEGQ`	`GLPPGAHGLHLHMVGLCEGPG`	`FVSAGTHWNP`
Thermocrinis_albus_DSM_14484	59	1.24e-13	`GVLIKLRASG`	`LPPNSELALHIHEVGKCDPPD`	`FMSAKGHFNP`
Methanosarcina_barkeri_str._Fusaro	63	1.57e-13	`GPVHINVNVR`	`GLKLGLHGIHIHNTGKCIGPS`	`FTSAGEHYNP`
Deinococcus_gobiensis_I-0	21	3.41e-13	`GGLEVTVSAR`	`GLTPGMHGMHVHTNPVCAPGP`	`DATTGEVVAF`
Bacillus_subtilis_strain_168	76	3.62e-12	`GLDIHISANS`	`LRPGASLGFHIYEKGSCVRPD`	`FESAGGPFNP`
Capsaspora_owczarzaki_ATCC_30864	62	5.17e-12	`LTRITANITG`	`LAANSVHGFHIHELGALDAQG`	`LASGGHYNPF`
Naegleria_gruberi	24	9.18e-12	`LTRVYGKICG`	`LTAQSTHGLHIHTYGELDLTD`	`GTRTGGHFNP`

Motif 1 block diagrams

Name

Lowest
p-value

Motifs

Selaginella_moellendorffii

7.90e-22

Physcomitrella_patens_subsp._patens

7.90e-22

Aplysia_californica

7.90e-22

Pieris_rapae_granulovirus

1.43e-21

Cucumis_sativus

1.74e-21

Acanthamoeba_castellanii_str._Neff

2.56e-21

Ixodes_scapularis

3.73e-21

Branchiostoma_floridae

3.73e-21

Dictyostelium_discoideum_AX4

6.50e-21

Parachlamydia_acanthamoebae_UV-7

6.50e-21

Drosophila_melanogaster

7.79e-21

Salmo_salar

9.34e-21

Anolis_carolinensis

9.34e-21

Sarcophilus_harrisii

1.33e-20

Caenorhabditis_elegans

2.26e-20

Acyrthosiphon_pisum

2.68e-20

Rattus_norvegicus

2.68e-20

Mamestra_configurata_nucleopolyhedrovirus_B

1.21e-19

Culex_quinquefasciatus

1.66e-19

Xenopus_laevis

4.96e-19

Otolemur_garnettii

5.78e-19

Azoarcus_sp._KH32C

1.63e-18

Amsacta_moorei_entomopoxvirus_'L'

2.18e-18

Bombus_impatiens

8.79e-18

Tetrahymena_thermophila

1.50e-17

Planctomyces_maris_DSM_8797

2.53e-17

Candidatus_Protochlamydia_amoebophila_UWE25

2.53e-17

Rhodopirellula_sallentina_SM41

7.88e-17

Pseudanabaena_biceps_PCC_7429

1.14e-16

Synechococcus_sp._CC9605

3.28e-16

Cryptococcus_gattii_WM276

5.17e-16

Methanocella_arvoryzae_MRE50

5.78e-16

Paramecium_bursaria_Chlorella_virus_1

6.47e-16

Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2

1.12e-15

Formosa_sp._AK20

1.12e-15

Cystobacter_fuscus_DSM_2262

2.12e-15

Paramecium_bursaria_Chlorella_virus_FR483

3.20e-15

Penicillium_chrysogenum_Wisconsin_54-1255

7.12e-15

Granulicella_tundricola_MP5ACTX9

1.05e-14

Candidatus_Solibacter_usitatus_Ellin6076

1.15e-14

Streptosporangium_roseum_DSM_43021

1.39e-14

Vibrio_cholerae_O1_biovar_El_Tor_str._N16961

1.53e-14

Perkinsus_marinus_ATCC_50983

1.68e-14

Fulvivirga_imtechensis_AK7

2.65e-14

Campylobacter_showae_CSUNSWCD

2.90e-14

Lyngbya_sp._PCC_8106

3.79e-14

Aquifex_aeolicus_VF5

4.13e-14

Granulicella_mallensis_MP5ACTX8

8.90e-14

Rhodococcus_triatomae_BKS_15-14

1.05e-13

Sphingomonas_sp._MM-1

1.24e-13

Thermocrinis_albus_DSM_14484

1.24e-13

Methanosarcina_barkeri_str._Fusaro

1.57e-13

Deinococcus_gobiensis_I-0

3.41e-13

Bacillus_subtilis_strain_168

3.62e-12

Capsaspora_owczarzaki_ATCC_30864

5.17e-12

Naegleria_gruberi

9.18e-12

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250

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

GL[PT]PGKHGFH[IV]HEFGDCT[NA][GP][CD]

Time 10.86 secs.

MOTIF 2 width = 21 sites = 56 llr = 1876 E-value = 8.0e-477

SEQUENCE LOGO

Information Content
56.2 (bits)

Relative Entropy
48.3 (bits)

Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]

NAME	START	P-VALUE	SITES
Culex_quinquefasciatus	127	2.98e-21	`VHADPDDLGV`	`GGHELSKTTGNAGARLACGVI`	`GICKA`
Azoarcus_sp._KH32C	151	5.97e-20	`VGRAVIVHAA`	`PDDFTTQPTGNSGARVACGVI`	`ASN`
Salmo_salar	129	7.33e-20	`IHEKADDLGK`	`GDNEESRKTGNAGSRLACGVI`	`GIAQ`
Anolis_carolinensis	133	7.33e-20	`VHAKPDDLGR`	`GGNDESLKTGNAGARLACGVI`	`GLAKA`
Acyrthosiphon_pisum	127	1.10e-19	`VHADQDDLGK`	`GGHELSATTGNAGARIACGVI`	`GITK`
Aplysia_californica	130	1.35e-19	`VHEKEDDLGK`	`GGNEESLKTGNAGPRVACGVI`	`GITK`
Granulicella_tundricola_MP5ACTX9	152	1.35e-19	`GGTSIMIHEK`	`ADDMKTDPTGNAGGRIACGVI`	`IEPAPGK`
Ixodes_scapularis	129	1.64e-19	`IHADPDDLGK`	`GGHELSKTTGNAGARLACGVV`	`GVTK`
Otolemur_garnettii	128	2.42e-19	`VHEKADDLGK`	`GGNEESTKTGNAGGRLACGVI`	`GIAQ`
Rattus_norvegicus	129	3.53e-19	`VHEKQDDLGK`	`GGNEESTKTGNAGSRLACGVI`	`GIAQ`
Methanosarcina_barkeri_str._Fusaro	154	4.25e-19	`NGTSLVIHAD`	`PDDQMTNPTGNSGARIVCGVI`	`EKK`
Sarcophilus_harrisii	129	6.14e-19	`VHEKPDDLGK`	`GGNEESEKTGNAGPRLACGVI`	`GIAK`
Drosophila_melanogaster	127	1.05e-18	`VHADADDLGQ`	`GGHELSKSTGNAGARIGCGVI`	`GIAKV`
Cucumis_sativus	195	1.25e-18	`VHELEDDLGK`	`GGHELSLTTGNAGGRLACGVV`	`GLTPV`
Xenopus_laevis	208	2.09e-18	`VDEREDDLGH`	`GGHQLSKTTGNSGRRLACGII`	`ARSAGLFENN`
Sphingomonas_sp._MM-1	159	2.09e-18	`DGAALVVHAS`	`PDDYRTDPTGNSGGRIACGVV`	`VPN`
Thermocrinis_albus_DSM_14484	151	2.47e-18	`GGTALIVHHH`	`RDDYKTDPAGNAGPRIACGVI`	`R`
Acanthamoeba_castellanii_str._Neff	132	2.91e-18	`VHADEDDFGK`	`GGFEDSLTTGHAGARLACGVI`	`GLSK`
Aquifex_aeolicus_VF5	147	3.43e-18	`GGTALVIHGG`	`PDDYKSDPAGNAGKRIACGVV`	`K`
Cryptococcus_gattii_WM276	128	4.75e-18	`VHAGTDDFGK`	`GGNAESLKTGNAGARAACGVI`	`GISN`
Selaginella_moellendorffii	185	5.58e-18	`IHELEDDLGK`	`GGHELSPTTGNAGGRLACGVV`	`GLTP`
Physcomitrella_patens_subsp._patens	144	7.65e-18	`IHEAEDDLGK`	`GGHELSSTTGNAGGRLACGVV`	`GLTPL`
Branchiostoma_floridae	129	8.93e-18	`VHAGEDDLGK`	`GGFEDSLTTGHAGGRLACGVI`	`GITKQA`
Granulicella_mallensis_MP5ACTX8	150	1.41e-17	`GGTSIVVHEK`	`ADDMKTDPSGNSGNRIACGVI`	`KN`
Methanocella_arvoryzae_MRE50	148	2.56e-17	`DGSAIIIHAG`	`SDDQMTDPSGGSGARIACGVI`	`EKA`
Paramecium_bursaria_Chlorella_virus_FR483	140	3.42e-17	`IHAETDDCGK`	`GGNNESLKTGNAGKRLSCGVI`	`GYAKENFC`
Streptosporangium_roseum_DSM_43021	202	4.54e-17	`KRYGLKDGRT`	`GPDADTLKTGDSGARIACGVI`	`TRG`
Candidatus_Solibacter_usitatus_Ellin6076	151	7.91e-17	`GGTALVIHAK`	`PDDLMSDPSGNAGDRIACGTI`	`TK`
Mamestra_configurata_nucleopolyhedrovirus_B	126	9.06e-17	`VHSDRDDLGL`	`TDHPLSKTTGNSGGRLGCGII`	`GITI`
Pieris_rapae_granulovirus	125	1.04e-16	`VHTMKDDYGK`	`GDNKSSKITGNAGGRLGCGVI`	`GVKHESQVAI`
Perkinsus_marinus_ATCC_50983	227	1.76e-16	`LHAGQDDLGQ`	`GGNAGSKTTGNSGARLACGPI`	`ALDKSVFRGN`
Tetrahymena_thermophila	153	1.76e-16	`IHADEDDLGL`	`GNFEDSKTTGHAGARVACGPI`	`GLCAKFSFDF`
Penicillium_chrysogenum_Wisconsin_54-1255	150	1.76e-16	`IHADEDDLGR`	`GNNPDSKINGNSGPRLACGVI`	`VSV`
Paramecium_bursaria_Chlorella_virus_1	158	2.00e-16	`VHADTDDLGL`	`GGNAESLKTGNAGKRIGCAVI`	`GYAKENFC`
Caenorhabditis_elegans	153	2.94e-16	`GQDDLGEGVG`	`DKAEESKKTGNAGARAACGVI`	`ALAAPQ`
Dictyostelium_discoideum_AX4	126	3.34e-16	`VHDKEDDLGR`	`GNSQDSKITGNAGSRLGCGII`	`ALSKI`
Parachlamydia_acanthamoebae_UV-7	152	3.34e-16	`VGKSIVIHED`	`EDDFKSQPAGNSGKRVACGLI`	`LPLEE`
Amsacta_moorei_entomopoxvirus_'L'	126	3.78e-16	`VHDSPDDLGK`	`TDHPLSKTSGNSGGRLGCGII`	`GIAKD`
Cystobacter_fuscus_DSM_2262	149	6.17e-16	`VGKALVIHAG`	`QDDLATDPAGNSGGRVACGVI`	`AEKTDKK`
Fulvivirga_imtechensis_AK7	179	1.12e-15	`LNKAVIVHAG`	`ADDFTSQPSGAAGAMIGCGVI`	`KQGVE`
Rhodococcus_triatomae_BKS_15-14	186	1.58e-15	`FANIPTRYAP`	`APDQATLDTGDAGARVACGVI`	`K`
Candidatus_Protochlamydia_amoebophila_UWE25	179	1.98e-15	`IGRSIMIHAD`	`EDDFKTQPSGASGARIGCGTI`	`EIENE`
Formosa_sp._AK20	176	2.76e-15	`LDKAVIVHQG`	`ADDFTSQPTGDAGGRVSCGGI`	`INLE`
Bacillus_subtilis_strain_168	168	5.26e-15	`DGSAFIIHEQ`	`ADDYLTNPSGNSGARIVCGAL`	`LGNNEKQ`
Bombus_impatiens	144	7.98e-15	`IHSGEDDLGR`	`GSSPLSASTGNSGDRWACGII`	`KAE`
Capsaspora_owczarzaki_ATCC_30864	150	8.84e-15	`IGRAFILHLN`	`PDDCVTQPVGNAGSRIAQGVI`	`GILIEN`
Rhodopirellula_sallentina_SM41	190	1.08e-14	`IIGRSLMIHE`	`GEDQFTQPTGDAGGRVAFGKI`	`EKN`
Deinococcus_gobiensis_I-0	120	4.14e-14	`LNRSVVLHAM`	`HDDYASDPAGKSGSREQCGVI`	`TPAG`
Planctomyces_maris_DSM_8797	169	6.49e-14	`IIGRSIVVHA`	`GEDQFTQPSGDAGDRVAFGDI`	`IEEKTD`
Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2	152	3.16e-13	`HAIMIHTGGD`	`NHEDHPNPLGGGGARIACGVI`	`K`
Vibrio_cholerae_O1_biovar_El_Tor_str._N16961	148	6.27e-13	`KALMVHAGGD`	`NHSDHPMPLGGGGARIVCGVI`	`GL`
Campylobacter_showae_CSUNSWCD	160	8.41e-13	`HSLMIHVGGD`	`NHSDHPKPLGGGGARMVCGVI`	`K`
Synechococcus_sp._CC9605	153	3.76e-12	`GKALIVHAGG`	`DTYRDEPPLGGGGARVACGVV`	`PDER`
Naegleria_gruberi	112	1.14e-11	`GRGLVLHTTR`	`DDGTSTSATGNAGGRIAVAAI`	`GI`
Pseudanabaena_biceps_PCC_7429	212	2.17e-11	`GGTSILIHAG`	`ANGNSTIPNVDYKTRIACGVI`	`KKF`
Lyngbya_sp._PCC_8106	176	2.48e-10	`GSAFIVHIDE`	`DQGTTGVQGGAGGGRLGCGII`	`EKQA`

Motif 2 block diagrams

Name

Lowest
p-value

Motifs

Culex_quinquefasciatus

2.98e-21

Azoarcus_sp._KH32C

5.97e-20

Salmo_salar

7.33e-20

Anolis_carolinensis

7.33e-20

Acyrthosiphon_pisum

1.10e-19

Aplysia_californica

1.35e-19

Granulicella_tundricola_MP5ACTX9

1.35e-19

Ixodes_scapularis

1.64e-19

Otolemur_garnettii

2.42e-19

Rattus_norvegicus

3.53e-19

Methanosarcina_barkeri_str._Fusaro

4.25e-19

Sarcophilus_harrisii

6.14e-19

Drosophila_melanogaster

1.05e-18

Cucumis_sativus

1.25e-18

Xenopus_laevis

2.09e-18

Sphingomonas_sp._MM-1

2.09e-18

Thermocrinis_albus_DSM_14484

2.47e-18

Acanthamoeba_castellanii_str._Neff

2.91e-18

Aquifex_aeolicus_VF5

3.43e-18

Cryptococcus_gattii_WM276

4.75e-18

Selaginella_moellendorffii

5.58e-18

Physcomitrella_patens_subsp._patens

7.65e-18

Branchiostoma_floridae

8.93e-18

Granulicella_mallensis_MP5ACTX8

1.41e-17

Methanocella_arvoryzae_MRE50

2.56e-17

Paramecium_bursaria_Chlorella_virus_FR483

3.42e-17

Streptosporangium_roseum_DSM_43021

4.54e-17

Candidatus_Solibacter_usitatus_Ellin6076

7.91e-17

Mamestra_configurata_nucleopolyhedrovirus_B

9.06e-17

Pieris_rapae_granulovirus

1.04e-16

Perkinsus_marinus_ATCC_50983

1.76e-16

Tetrahymena_thermophila

1.76e-16

Penicillium_chrysogenum_Wisconsin_54-1255

1.76e-16

Paramecium_bursaria_Chlorella_virus_1

2.00e-16

Caenorhabditis_elegans

2.94e-16

Dictyostelium_discoideum_AX4

3.34e-16

Parachlamydia_acanthamoebae_UV-7

3.34e-16

Amsacta_moorei_entomopoxvirus_'L'

3.78e-16

Cystobacter_fuscus_DSM_2262

6.17e-16

Fulvivirga_imtechensis_AK7

1.12e-15

Rhodococcus_triatomae_BKS_15-14

1.58e-15

Candidatus_Protochlamydia_amoebophila_UWE25

1.98e-15

Formosa_sp._AK20

2.76e-15

Bacillus_subtilis_strain_168

5.26e-15

Bombus_impatiens

7.98e-15

Capsaspora_owczarzaki_ATCC_30864

8.84e-15

Rhodopirellula_sallentina_SM41

1.08e-14

Deinococcus_gobiensis_I-0

4.14e-14

Planctomyces_maris_DSM_8797

6.49e-14

Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2

3.16e-13

Vibrio_cholerae_O1_biovar_El_Tor_str._N16961

6.27e-13

Campylobacter_showae_CSUNSWCD

8.41e-13

Synechococcus_sp._CC9605

3.76e-12

Naegleria_gruberi

1.14e-11

Pseudanabaena_biceps_PCC_7429

2.17e-11

Lyngbya_sp._PCC_8106

2.48e-10

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250

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

G[DG][DN]EL[ST]K[PT]TGN[AS]G[AG]R[LI]ACGVI

Time 18.68 secs.

MOTIF 3 width = 22 sites = 47 llr = 1761 E-value = 1.1e-441

SEQUENCE LOGO

Information Content
59.2 (bits)

Relative Entropy
54.1 (bits)

Download LOGO
Without SSC:[EPS][PNG]
With SSC:[EPS][PNG]

NAME	START	P-VALUE	SITES
Acanthamoeba_castellanii_str._Neff	67	3.44e-25	`TNGCVSAGGH`	`FNPFGKKHGGPDDEERHVGDLG`	`NVVADETGVA`
Acyrthosiphon_pisum	62	6.85e-23	`TNGCMSSGPH`	`FNPFGKTHGAPNDDVRHVGDLG`	`NIEAPGSSVT`
Sarcophilus_harrisii	64	8.61e-23	`TQGCTSAGAH`	`FNPHSKKHGGPDDDERHVGDLG`	`NVKADKDGVA`
Dictyostelium_discoideum_AX4	61	3.20e-22	`TNGCLSAGAH`	`FNPFKKEHGSPNDENRHVGDLG`	`NIESNKDKKS`
Naegleria_gruberi	52	7.25e-22	`LTDGTRTGGH`	`FNPFNKTHGYPGSTERHVGDLG`	`NVTADDSGIA`
Selaginella_moellendorffii	120	7.25e-22	`TNGCLSTGAH`	`FNPENKTHGGPNDSVRHAGDLG`	`NVVADDKGNV`
Rattus_norvegicus	64	7.25e-22	`TQGCTTAGPH`	`FNPHSKKHGGPADEERHVGDLG`	`NVAAGKDGVA`
Anolis_carolinensis	68	1.30e-21	`TNGCTSAGAH`	`FNPENQTHGGPQDEMRHVGDLG`	`NVEANGSGVA`
Tetrahymena_thermophila	86	1.57e-21	`IDGCKSAGAH`	`FNPTKQTHGAPDSKERHVGDLG`	`NIENKLSEEN`
Otolemur_garnettii	63	2.29e-21	`TQGCTSAGPH`	`FNPQSKKHGGPKDEERHVGDLG`	`NVTAGKNGEA`
Caenorhabditis_elegans	85	3.95e-21	`TNGCISAGPH`	`FNPFGKTHGGPKSEIRHVGDLG`	`NVEAGADGVA`
Pieris_rapae_granulovirus	60	5.62e-21	`TNGCTSAGEH`	`FNPFHKEHGGPHDEERHLGDLG`	`NIYSVGGNAT`
Cryptococcus_gattii_WM276	63	1.12e-20	`TNGCTSAGPH`	`FNPHGKNHGAPSDSERHVGDLG`	`NVKTDGNGVA`
Paramecium_bursaria_Chlorella_virus_FR483	75	1.56e-20	`TDKCTSACAH`	`FNPYKRYHGGPDSKERHVGDLG`	`NVKADKNGKA`
Physcomitrella_patens_subsp._patens	79	2.16e-20	`TNGCMSTGPH`	`FNPEGKTHGAPEDDNRHAGDLG`	`NVIAGNDGVV`
Ixodes_scapularis	64	4.06e-20	`TNGCTSAGPH`	`FNPLGKEHGAPTDTNRHVGDLG`	`NVIAGDDGVA`
Drosophila_melanogaster	62	4.06e-20	`TNGCMSSGPH`	`FNPYGKEHGAPVDENRHLGDLG`	`NIEATGDCPT`
Branchiostoma_floridae	64	7.50e-20	`TNGCTSAGSH`	`FNPAKKNHGGPQDAERHVGDLG`	`NVEVGDDGVA`
Salmo_salar	64	7.50e-20	`TNGCMSAGPH`	`FNPHNHTHGGPTDTVRHVGDLG`	`NVTAAADSVA`
Culex_quinquefasciatus	62	8.71e-20	`TNGCTSAGPH`	`FNPHGKEHGAPDASVRHAGDLG`	`NVVADAGGVA`
Candidatus_Protochlamydia_amoebophila_UWE25	120	1.01e-19	`GKNGEAAGAH`	`FNPMNQKHGGPDSLERHVGDFG`	`NLEADSHGHA`
Planctomyces_maris_DSM_8797	111	2.40e-19	`KETGKSAGGH`	`FNPTDKPHGKPTDSERHVGDLG`	`NIEANADGLA`
Rhodopirellula_sallentina_SM41	132	4.18e-19	`TETGKSAGGH`	`FNPTNQEHGKPSEEKRHVGDLG`	`NIEANEDGVA`
Aplysia_californica	65	1.06e-18	`TNGCMSAGGH`	`FNPLGATHGGPDDAVRHAGDLG`	`NIIAGDDGVA`
Paramecium_bursaria_Chlorella_virus_1	93	1.20e-18	`TDGCTSACAH`	`FNPFGTAHGGPDSKIRHVGDLG`	`NILADKNGKA`
Bombus_impatiens	79	1.76e-18	`RDGCMSTGPH`	`FNPENVTHGGQNSPVRHVGDLG`	`NILANESGVA`
Cucumis_sativus	130	2.56e-18	`TNGCISTGAH`	`FNPNKLTHGAPEDEIRHAGDLG`	`NITANADGVA`
Penicillium_chrysogenum_Wisconsin_54-1255	86	2.89e-18	`GNECLDAGGH`	`YNPTNVSHGGPNDAERHIGDWG`	`NFDVAGDPHL`
Aquifex_aeolicus_VF5	83	3.69e-18	`PPDFKSAKGH`	`FNPFKKKHGLLNPEGPHAGDMP`	`NIHTDDKGNV`
Mamestra_configurata_nucleopolyhedrovirus_B	60	4.16e-18	`SNGCTSAGEH`	`FNPTGSNHGAPNAAVRHVGDLG`	`NIEAKVSNSL`
Bacillus_subtilis_strain_168	104	5.94e-18	`RPDFESAGGP`	`FNPLNKEHGFNNPMGHHAGDLP`	`NLEVGADGKV`
Xenopus_laevis	146	8.41e-18	`SNGCESCGEH`	`YNPHRNSHGGPGEDNRHVGDLG`	`NIFAEDNGRA`
Thermocrinis_albus_DSM_14484	87	8.41e-18	`PPDFMSAKGH`	`FNPYKKKHGLLNPDGPHAGDMP`	`NVFTDSNGNL`
Parachlamydia_acanthamoebae_UV-7	93	3.17e-17	`APDASSAGAH`	`YDPTHHKHGGPDDLDRHVGDLG`	`NLEANENGHA`
Perkinsus_marinus_ATCC_50983	162	3.52e-17	`SNGCASTGGH`	`YNPFYNTHGDRNSRVRHVGDMG`	`NIKADRNGRA`
Methanosarcina_barkeri_str._Fusaro	91	4.81e-17	`GPSFTSAGEH`	`YNPLGKEHGLNNPKGPHAGDLP`	`NLKVGKDGTG`
Granulicella_mallensis_MP5ACTX8	85	6.55e-17	`GPDFKSAGGH`	`FNPDGKKHGFDNPMGHHNGDLP`	`QNVSVGEDHT`
Azoarcus_sp._KH32C	90	8.85e-17	`APDATSAGGH`	`FNPTGMPHGQPGKPEHHAGDLP`	`MLVADAAGNA`
Granulicella_tundricola_MP5ACTX9	87	8.85e-17	`APDFKSAGGH`	`FNPEMKQHGTLNPMGHHAGDLP`	`QNVTVGPDGT`
Methanocella_arvoryzae_MRE50	85	9.78e-17	`TPPFTGAGDH`	`YNPLGKQHGLDNPQGPHAGDLP`	`DIRVNRAGTG`
Sphingomonas_sp._MM-1	96	8.00e-15	`GPGFVSAGTH`	`WNPTHMVHGKDAQGGPHWGDLP`	`NLIVGTDGAG`
Fulvivirga_imtechensis_AK7	118	1.98e-14	`AADASSAGGH`	`WNPTNTKHGKRGEGEFHKGDIG`	`NMEVGNDGNG`
Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2	93	1.36e-13	`VAALAAGGHL`	`DPQHTNKHLGPYNPEGHLGDLP`	`ALYVNQAGNA`
Vibrio_cholerae_O1_biovar_El_Tor_str._N16961	90	2.04e-13	`VLGGAAGGHY`	`DPQNTGKHGYPWTNDNHLGDLP`	`ALYVDAQGQA`
Campylobacter_showae_CSUNSWCD	101	2.70e-13	`GLGMKAGGHW`	`DPSDTKKHSFAWDDNGHKGDLP`	`ALFVDAEGNA`
Capsaspora_owczarzaki_ATCC_30864	91	1.14e-11	`QGLASGGHYN`	`PFNVTHACPGTGAAVRHVGDLG`	`NIKADANGNA`
Amsacta_moorei_entomopoxvirus_'L'	61	3.52e-11	`NGCTSAGEHF`	`NPYNRQHGDISDKIHRHVGDFG`	`NVYADENGVA`

Motif 3 block diagrams

Name

Lowest
p-value

Motifs

Acanthamoeba_castellanii_str._Neff

3.44e-25

Acyrthosiphon_pisum

6.85e-23

Sarcophilus_harrisii

8.61e-23

Dictyostelium_discoideum_AX4

3.20e-22

Naegleria_gruberi

7.25e-22

Selaginella_moellendorffii

7.25e-22

Rattus_norvegicus

7.25e-22

Anolis_carolinensis

1.30e-21

Tetrahymena_thermophila

1.57e-21

Otolemur_garnettii

2.29e-21

Caenorhabditis_elegans

3.95e-21

Pieris_rapae_granulovirus

5.62e-21

Cryptococcus_gattii_WM276

1.12e-20

Paramecium_bursaria_Chlorella_virus_FR483

1.56e-20

Physcomitrella_patens_subsp._patens

2.16e-20

Ixodes_scapularis

4.06e-20

Drosophila_melanogaster

4.06e-20

Branchiostoma_floridae

7.50e-20

Salmo_salar

7.50e-20

Culex_quinquefasciatus

8.71e-20

Candidatus_Protochlamydia_amoebophila_UWE25

1.01e-19

Planctomyces_maris_DSM_8797

2.40e-19

Rhodopirellula_sallentina_SM41

4.18e-19

Aplysia_californica

1.06e-18

Paramecium_bursaria_Chlorella_virus_1

1.20e-18

Bombus_impatiens

1.76e-18

Cucumis_sativus

2.56e-18

Penicillium_chrysogenum_Wisconsin_54-1255

2.89e-18

Aquifex_aeolicus_VF5

3.69e-18

Mamestra_configurata_nucleopolyhedrovirus_B

4.16e-18

Bacillus_subtilis_strain_168

5.94e-18

Xenopus_laevis

8.41e-18

Thermocrinis_albus_DSM_14484

8.41e-18

Parachlamydia_acanthamoebae_UV-7

3.17e-17

Perkinsus_marinus_ATCC_50983

3.52e-17

Methanosarcina_barkeri_str._Fusaro

4.81e-17

Granulicella_mallensis_MP5ACTX8

6.55e-17

Azoarcus_sp._KH32C

8.85e-17

Granulicella_tundricola_MP5ACTX9

8.85e-17

Methanocella_arvoryzae_MRE50

9.78e-17

Sphingomonas_sp._MM-1

8.00e-15

Fulvivirga_imtechensis_AK7

1.98e-14

Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2

1.36e-13

Vibrio_cholerae_O1_biovar_El_Tor_str._N16961

2.04e-13

Campylobacter_showae_CSUNSWCD

2.70e-13

Capsaspora_owczarzaki_ATCC_30864

1.14e-11

Amsacta_moorei_entomopoxvirus_'L'

3.52e-11

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250

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

FNPx[GN]K[KT]HGGP[ND]DEERH[VA]GDL[GP]

Time 25.04 secs.

SUMMARY OF MOTIFS

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

Name

Combined
p-value

Motifs

Methanocella_arvoryzae_MRE50

2.33e-38

Methanosarcina_barkeri_str._Fusaro

5.72e-38

Amsacta_moorei_entomopoxvirus_'L'

2.49e-34

Paramecium_bursaria_Chlorella_virus_1

3.47e-39

Paramecium_bursaria_Chlorella_virus_FR483

2.96e-41

Pieris_rapae_granulovirus

1.45e-47

Mamestra_configurata_nucleopolyhedrovirus_B

5.80e-43

Candidatus_Solibacter_usitatus_Ellin6076

9.51e-26

Thermocrinis_albus_DSM_14484

4.16e-38

Aquifex_aeolicus_VF5

8.12e-39

Parachlamydia_acanthamoebae_UV-7

1.51e-42

Candidatus_Protochlamydia_amoebophila_UWE25

1.63e-40

Granulicella_tundricola_MP5ACTX9

2.46e-39

Granulicella_mallensis_MP5ACTX8

1.24e-36

Rhodopirellula_sallentina_SM41

1.21e-38

Planctomyces_maris_DSM_8797

1.01e-38

Deinococcus_gobiensis_I-0

1.21e-22

Pseudanabaena_biceps_PCC_7429

2.33e-20

Synechococcus_sp._CC9605

1.25e-20

Lyngbya_sp._PCC_8106

8.84e-17

Rhodococcus_triatomae_BKS_15-14

4.99e-21

Streptosporangium_roseum_DSM_43021

2.45e-23

Fulvivirga_imtechensis_AK7

1.26e-32

Formosa_sp._AK20

7.65e-23

Campylobacter_showae_CSUNSWCD

7.56e-29

Cystobacter_fuscus_DSM_2262

8.66e-25

Azoarcus_sp._KH32C

1.86e-43

Sphingomonas_sp._MM-1

3.49e-35

Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2

5.42e-31

Vibrio_cholerae_O1_biovar_El_Tor_str._N16961

1.89e-29

Bacillus_subtilis_strain_168

2.18e-33

Anolis_carolinensis

1.84e-50

Xenopus_laevis

8.07e-43

Salmo_salar

8.90e-49

Sarcophilus_harrisii

1.31e-50

Rattus_norvegicus

1.23e-49

Otolemur_garnettii

5.27e-48

Branchiostoma_floridae

4.24e-47

Culex_quinquefasciatus

7.35e-49

Drosophila_melanogaster

5.45e-48

Bombus_impatiens

1.94e-39

Acyrthosiphon_pisum

3.68e-51

Ixodes_scapularis

4.37e-49

Caenorhabditis_elegans

6.91e-46

Aplysia_californica

1.97e-48

Physcomitrella_patens_subsp._patens

3.11e-48

Selaginella_moellendorffii

1.63e-49

Cucumis_sativus

2.96e-46

Penicillium_chrysogenum_Wisconsin_54-1255

5.96e-38

Cryptococcus_gattii_WM276

3.69e-43

Tetrahymena_thermophila

1.08e-43

Dictyostelium_discoideum_AX4

1.10e-47

Capsaspora_owczarzaki_ATCC_30864

4.83e-27

Perkinsus_marinus_ATCC_50983

5.71e-36

Acanthamoeba_castellanii_str._Neff

5.56e-53

Naegleria_gruberi

4.24e-34

SCALE

\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|	\|
1	25	50	75	100	125	150	175	200	225	250

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:

The version of MEME and the date it was released.
The reference to cite if you use MEME in your research.
A description of the sequences you submitted (the "training set") showing the name, "weight" and length of each sequence.
The command line summary detailing the parameters with which you ran MEME.
Information on each of the motifs MEME discovered, including:
1. A summary line showing the width, number of occurrences, log likelihood ratio and statistical significance of the motif.
2. A sequence LOGO.
3. The information content of the motif.
4. The relative entropy of the motif.
5. Downloadable LOGO files suitable for publication.
6. The occurrences of the motif sorted by p-value and aligned with each other.
7. Block diagrams of the occurrences of the motif within each sequence in the training set.
8. The motif in BLOCKS or FASTA format.
9. A position-specific scoring matrix (PSSM) for use by the MAST database search program.
10. The position specific probability matrix (PSPM) describing the motif.
11. A regular expression describing the motif.
A summary of motifs showing an optimized (non-overlapping) tiling of all of the motifs onto each of the sequences in the training set.
The reason why MEME stopped and the name of the CPU on which it ran.
This explanation of how to interpret MEME results.

MOTIFS

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

Summary Line
This line gives the width ('width'), number of occurrences in the training set ('sites'), log likelihood ratio ('llr') and 'E-value' of the motif. Each motif describes a pattern of a fixed width--no gaps are allowed in MEME motifs. MEME numbers the motifs consecutively from one as it finds them. MEME usually finds the most statistically significant (low E-value) motifs first. The statistical significance of a motif is based on its log likelihood ratio, its width and number of occurrences, the background letter frequencies (given in the command line summary ), and the size of the training set. The E-value is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and number of occurrences, that one would find in a similarly sized set of random sequences. (In random sequences each position is independent with letters chosen according to the background letter frequencies.) The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.) Clicking on the buttons to the left of the motif summary line takes you to the previous motif (P) or next motif (N).

Sequence LOGO

MEME motifs are represented by position-specific probability matrices that specify the probability of each possible letter appearing at each possible position in an occurrence of the motif. These are displayed as "sequence LOGOS", containing stacks of letters at each position in the motif. The total height of the stack is the "information content" of that position in the motif in bits. The height of the individual letters in a stack is the probability of the letter at that position multiplied by the total information content of the stack.

Note: The MEME LOGO differs from those produced by the Weblogo program because a small-sample correction is NOT applied. However, MEME LOGOs in PNG and encapsulated postscript (EPS) formats with small-sample correction (SSC) are available by clicking on one of the links named "With SSC" (EPS or PNG) under Download LOGO. The MEME LOGOs without small sample correction are similarly available. Error bars are included in the LOGOs with small-sample correction.

The information content of each motif position is computed as described in the paper by Schneider and Stephens, "Sequence Logos: A New Way to Display Consensus Sequences" but the small-sample correction, e(n), is set to zero for the LOGO displayed in the MEME output. The corrected information content of position i is given by

           R(i) for amino acids   = log2(20) - (H(i) + e(n))   (1a) 
           R(i) for nucleic acids =    2    - (H(i) + e(n))    (1b)

where H(i) is the entropy of position i,

           H(l) = - (Sum f(a,i) * log2[ f(a,i) ]).             (2)

Here, f(a,i) is the frequency of base or amino acid a at position i, and e(n) is the small-sample correction for an alignment of n letters. The height of letter a in column i is given by

           height = f(a,i) * R(i)                              (3)

The approximation for the small-sample correction, e(n), is given by:

           e(n) = (s-1) / (2 * ln(2) * n),                     (4)

where s is 4 for nucleotides, 20 for amino acids, and n is the number of sequences in the alignment.

The letters in the logos are colored as follows. For DNA sequences, the letter categories contain one letter each. For proteins, the categories are based on the biochemical properties of the various amino acids. The categories and their colors are:

NUCLEIC ACIDS	COLOR
A	RED
C	BLUE
G	ORANGE
T	GREEN

AMINO ACIDS	COLOR	PROPERTIES
A, C, F, I, L, V, W and M	BLUE	Most hydrophobic[Kyte and Doolittle, 1982]
NQST	GREEN	Polar, non-charged, non-aliphatic residues
DE	MAGENTA	Acidic
KR	RED	Positively charged
H	PINK
G	ORANGE
P	YELLOW
Y	TURQUOISE

J. Kyte and R. Doolittle, 1982. "A Simple Method for Displaying the Hydropathic Character of a Protein", J. Mol Biol. 157, 105-132.

Note: the "text" output format of MEME preserves the historical MEME format where LOGOS are replaced by a simplified probability matrix, a relative entropy plot, and a multi-level consensus sequence.

Information Content
This is the information content of the motif in bits. It is equal to the sum of the uncorrected information content, R(), in the columns of the LOGO. This is equal relative entropy of the motif relative to a uniform background frequency model.
Relative Entropy
This is the relative entropy of the motif, computed in bits and relative to the background letter frequencies given in the command line summary. It is equal to the log-likelihood ratio (llr) divided by the number of occurrences (sites) of the motif times 1/ln(2),
```
               re = llr / (sites * ln(2)).
	    
```
Occurrences of the Motif
MEME displays the occurrences (sites) of the motif in the training set. The sites are shown aligned with each other, and the ten sequence positions preceding and following each site are also shown. Each site is identified by the name of the sequence where it occurs, the strand (if both strands of DNA sequences are being used), and the position in the sequence where the site begins. When the DNA strand is specified, '+' means the sequence in the training set, and '-' means the reverse complement of the training set sequence. (For '-' strands, the 'start' position is actually the position on the positive strand where the site ends.) The sites are listed in order of increasing statistical significance (p-value). The p-value of a site is computed from the the match score of the site with the position specific scoring matrix for the motif. The p-value gives the probability of a random string (generated from the background letter frequencies) having the same match score or higher. (This is referred to as the position p-value by the MAST algorithm.)
Block Diagrams of Motif Occurrences
The occurrences of the motif in the training set sequences are shown with MAST-style block diagrams. One diagram is printed for each sequence showing all the occurrences of the motif in that sequence. The sequences are sorted by the lowest p-value among all occurrences of the motif in a given sequence. (The p-value of an occurrence is the probability of a single random subsequence the length of the motif, generated according to the 0-order background model, having a score at least as high as the score of the occurrence.) When the DNA strand is specified, '+' means the motif appears from left to right on the sequence, and '-' means the motif appears from right to left on the complementary strand. A sequence position scale is shown at the end of each table of block diagrams. Very long sequences are shown with thick lines connecting the motifs and are not drawn to scale.
Motif in BLOCKS format or FASTA format>
For use with BLOCKS tools, MEME prints the occurrences of the motif in BLOCKS format.
You can convert these blocks to PSSMs (position-specific scoring matrices), LOGOS (color representations of the motifs), phylogeny trees and search them against a database of other blocks by pasting everything from the "BL" line to the "//" line (inclusive) into the Multiple Alignment Processor.
If you include the -print_fasta switch on the command line, MEME prints the motif sites in FASTA format instead of BLOCKS format.
Position-Specific Scoring Matrix
The position-specific scoring matrix corresponding to the motif is printed for use by database search programs such as MAST. This matrix is a log-odds matrix calculated by taking 100 times the log (base 2) of the ratio p/f at each position in the motif where p is the probability of a particular letter at that position in the motif, and f is the background frequency of the letter (given in the command line summary section.) This is the same matrix that is used above in computing the p-values of the occurrences of the motif in the Occurrences of the Motif and Block Diagrams of Motif Occurrences sections. The scoring matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The scoring matrix is preceded by a line starting with "log-odds matrix:" and containing the length of the alphabet, width of the motif, number of characters in the training set, the scoring threshold (obsolete) and the motif E-value.
Note: The probability p used to compute the PSSM is not exactly the same as the corresponding value in the Position Specific Probability Matrix (PSPM). The values of p used to compute the PSSM take into account the motif prior, whereas the values in the PSPM are just the observed frequencies of letters in the motif sites.
Position-Specific Probability Matrix
The motif itself is a position-specific probability matrix giving, for each position in the pattern, the observed frequency ("probability") of each possible letter. The probability matrix is printed "sideways"--columns correspond to the letters in the alphabet (in the same order as shown in the simplified motif) and rows corresponding to the positions of the motif, position one first. The motif is preceded by a line starting with "letter-probability matrix:" and containing the length of the alphabet, width of the motif, number of occurrences of the motif, and the E-value of the motif.
Note: Earlier versions of MEME gave the posterior probabilities--the probability after applying a prior on letter frequencies--rather than the observed frequencies. These versions of MEME also gave the number of possible positions for the motif rather than the actual number of occurrences. The output from these earlier versions of MEME can be distinguished by "n=" rather than "nsites=" in the line preceding the matrix.
Regular Expression
This is a regular expression (RE) describing the motif. In each column, all letters with observed frequencies greater than 0.2 are shown; less-frequent letters are not included in the RE. MEME regular expressions are interpreted as follows: single letters match that letter; groups of letters in square brackets match any of the letters in the group. Regular expressions can be used for searching for the motif in sequences (using, for example, PatMatch ) but the search accuracy will usually be better with the PSSM (using, for example MAST.)
Motif Summary Tiling
The motif summary tiling is done using the same algorithm as used by MAST. The motif occurrences shown in the motif summary may not be exactly the same as those reported in each motif section because only motifs with a position p-value of 0.0001 that don't overlap other, more significant motif occurrences are shown. The format of the machine readable motif-summary is:
```
        [sequence_name combined_p-value number_of_motif_occurrences [motif_number start_of_motif position_p-value]+]+
        
```
See the documentation for MAST output for the definition of position and combined p-values.