Presentation is loading. Please wait.

Presentation is loading. Please wait.

This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in.

Published byBrent Barrett Modified over 9 years ago

Similar presentations

Presentation on theme: "This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in."— Presentation transcript:

1 This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in file: SMS_searchinput_motifs.xls

2 Smk-box

3 Smk analysis Fuchs et al. Nat. Struct. Mol. Biol. 2006 13:226 N(x) S MK -box (metK) complement Distance varies considerably from 50-350! nucleotides

4 S. agalactiae S. dysgalactiae S. equi S. gallolyticus S. gordoni S. mitis S. mutans S. oralis S. parasanguinis S. parauberis S. pasteurianis S. pneumoniae S. pyogenes S. salivarius S. sanguinis S. suis S thermophilus CNRZ S thermophilus S. uberis

5 E. faecalis L. acidophilus L. brevis L. casei L. crispatus L. delbrueckii L. fermentum l. gasseri L. helveticus L. johnsonii L. plantarum L. reuteri L. rhamnosus L. sakei L. salivarius L. lactis L. mesenteroides P. pentosaceus S. agalactiae S. dysgalactiae

6 MetK upstream (streptococci) stArt

7 Smk boxlysR-fam Streptococcus gordoni, sanguinis, parasanguinis, agalactiae, oralis, pneumoniae Streptococcus Streptococcus pasteurianis, suis, pyogenes, gallolyticus, mitis, mutans, dysgalactiae >300 bp Streptococcus parauberis, uberis, thermophilus, equi, Lactococcus lactis 50-100 100-250

8 Lactobacillus crispatus, helveticus, acidophilus, delbrueckii, johnsonii, gasseri Smk box Rest of the upstream region highly conserved and almost palindromic Lactobacillus

9 Smk box Lactobacillus fermentum, pediococcus pentosaceus, L. salivarius, casei, rhamnosus, sakei Smk box Lactobacillus brevis, reuteri, acidophilus, Enterococcus faecalis, L. plantarum

10 CmbR

11 Motif definition Earlier analysis in Sperandio et al. 2010 J. Bacteriol. 192:3464- 3473 and Kovaleva and Gelfand 2007 FEMS Microbiol Lett. 276:207-215

12 ATA-N9-TAT N6 ATA-N9-TATstart >SMU.496_cysK_/106-127 GTGATATGATTTCCTTATCACG >SUB1379_cysM_/97-122 ATGATAAGCCTTTCCTATCACG >GALLO_0500_cysK_/98-119 GTGATAGTATTTTTTTATCACC >SPs0499/86-111 GTGATATGGCTTTATTATCAGA >SEQ_1768/89-114 GTGATAGCGTCTCTTTATCACT >SDEG_1685_cysM_/94-119 GTGATAGAACTTTATTATCAGA >SGO_0606_cysK_/105-127 GATATAAAAAAAAGCTATGATA >SSA_1839_cysK_/102-124 GACATAAAGAAAAGCTATGGCT >SAG0334_cysK_/100-125 CCGATAAATAATAGCTATCACT >SSU0391_cysM_/106-129 TCTATTAAAAAAAGCTATCGGC >str0366_cysM1_/97-121 CTGATAGTCAAACATTATCACA >spr2015_cycK_/106-128 GATATATAGAAATCCTATCGCT >smi_2060_cysK_/106-128 GATATAAAAAAATCCTATCACT >SMU.496_cysK_/128-148 GTGATAAATAATTTATATTTT >SUB1379_cysM_/123-143 CCAATAAGATTAAACTATTTT >GALLO_0500_cysK_/120-140 TTGATAAGAAATATGTATTTT >SPs0499/112-132 GTGATAGTAAATCTGTATTTT >SEQ_1768/115-135 ACGATAGTAAATGGCTATTTT >SDEG_1685_cysM_/120-140 GTGATAGTAAATCTGTATTTT >SGO_0606_cysK_/128-148 GCCATAGCTTTTTTATATTTT >SSA_1839_cysK_/125-145 CTCATAGCTTTTTTATATTTT >SAG0334_cysK_/126-145 -TGATAAAGAATTGATATTTT >SSU0391_cysM_/130-150 GAGATAGTTTTTTTATATTAT >str0366_cysM1_/122-142 GTGATAAAGAAGATGTATTTT >spr2015_cycK_/129-149 TCGATAGGATTTCTATATTTT >smi_2060_cysK_/129-149 TCGATAGGATTTCTATATTTT CysK upstream

13 cysK upstream

14 HomR

15 HomR motif >1 GTCATAAATAAAATTTATAGC >2 CTTATAGTTTCTTTTTATAGC >3 GATATAGTTTTTTCTTATAGC >4 GTTATAGAAATAAACTATAAC >5 GTTATAGTAATAAACTATATC First palindrome of set taken from Sperandio et al. 2010 J. Bacteriol. 192:3464-3473

16 metBC upstream HomR

17 MetR/MtaR

18 metE and metH motif 2 in MEME search >SP_0585 ATAGTTTCAAACTAT >SOR_1524 ATAGTTTCAAACTAT >gbs2005 ATAGTTTAAAACTAT >stu0785 ATAGTTTAAAACTAT >SMU.873 ATAGCTTAAAACTAT >SSA_0416 ATAGTTTTAGACTAT >SGGBAA2069_c13050 ATAGTTAAAAACTAT >GALLO_1316 ATAGCTAAAAACTAT >L0100 ATAGTTTAAAACTAT >llmg_1225 ATAGTTAAAAACTAT >SSU1814 ATAGTTTGAAGCTAT >stu0583_1 ATAGTTTCAACCTAT >GALLO_1253_1 ATAGTTTTTAACTAA >SMU.951_1 ATAGTCTCTAACTAA metE metH Earlier definition in Rodionov et al. 2004 Nucleic Acid Res. 32:3342-3353

19 metE upstream metH upstream L.lactis S. suis S. agalactiae mmuP not in Streptococcus_s anguinis_SK36 metEyitJ

20 metE upstream

21 mmuP upstream

22 Upstream CysK in Lactobacilli

23 Cbs, cbl Structure forming? No additional hits found using motif: AAGGGCGCGAA Plasmid encoded highly conserved

24 Structure forming? No additional hits found using motif: AAGGGCGCGAA

25 Upstream Thr divergon in Lactobacilli

26 Thr divergon in Lactobacilli Analyzed region

27

Download ppt "This file provides the visual data that relates to the analysis of the upstream regions that were used to define the regulator specific motifs given in."

Similar presentations

Anmol Kaur 1, Sanu Arora 2 and Ravinder Nagpal 1 1 Department of Biotechnology, Lovely Professional University, Phagwara (Punjab), India. 2 Department.

Anmol Kaur 1, Sanu Arora 2 and Ravinder Nagpal 1 1 Department of Biotechnology, Lovely Professional University, Phagwara (Punjab), India. 2 Department.
GlnR. Schreier et al. 1991 J. Mol. Biol. 220:241 Gutowski and Schreier 1992 J. Bacteriol 174:671 Brown and Sonenshein 1996 J. Bacteriol 178:2450 Zalieckas.

GlnR. Schreier et al J. Mol. Biol. 220:241 Gutowski and Schreier 1992 J. Bacteriol 174:671 Brown and Sonenshein 1996 J. Bacteriol 178:2450 Zalieckas.
PROBIOTICS Jayanti Tokas1, Deepika Gupta1, Shalini Jain2 and Hariom Yadav2* 1Department of Biochemistry, CCS-HAU, Hisar, Haryana, India 2NIDDK, National.

PROBIOTICS Jayanti Tokas1, Deepika Gupta1, Shalini Jain2 and Hariom Yadav2* 1Department of Biochemistry, CCS-HAU, Hisar, Haryana, India 2NIDDK, National.
FERMENTATION Classical Biotechnology Humans have been using this technology for centuries Involves harnessing the wastes of bacteria and/or yeast for.

FERMENTATION Classical Biotechnology Humans have been using this technology for centuries Involves harnessing the wastes of bacteria and/or yeast for.
1 Chapter 19 Bacteria & Viruses. 2 19–1 Bacteria Prokaryote = single-celled organism lacking a nucleusProkaryote = single-celled organism lacking a nucleus.

1 Chapter 19 Bacteria & Viruses. 2 19–1 Bacteria Prokaryote = single-celled organism lacking a nucleusProkaryote = single-celled organism lacking a nucleus.
Yogurt And Other Products. Yogurt Semi-solid fermented milk product which originated centuries ago in Bulgaria Consistency, flavor and aroma may vary.

Yogurt And Other Products. Yogurt Semi-solid fermented milk product which originated centuries ago in Bulgaria Consistency, flavor and aroma may vary.
Milk microbiology standards for milk and milk product Shivnam Rana Msc. Microbiology (PAU) L -2011- BS -251 – M.

Milk microbiology standards for milk and milk product Shivnam Rana Msc. Microbiology (PAU) L BS -251 – M.
Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS.

Short Dispersed Repeats KALEIGH, MARIAM, MICHAEL AND NICHOLAS.
Finding Eukaryotic Open reading frames.

Finding Eukaryotic Open reading frames.
MOPAC: Motif-finding by Preprocessing and Agglomerative Clustering from Microarrays Thomas R. Ioerger 1 Ganesh Rajagopalan 1 Debby Siegele 2 1 Department.

MOPAC: Motif-finding by Preprocessing and Agglomerative Clustering from Microarrays Thomas R. Ioerger 1 Ganesh Rajagopalan 1 Debby Siegele 2 1 Department.
Modularity as an Organizing Principle in Protein Structure.

Modularity as an Organizing Principle in Protein Structure.
Www.cmmt.ubc.ca MOTIF ENRICHMENT ANALYSIS IN CO- EXPRESSED GENE SETS AND HIGH- THROUGHPUT SEQUENCE SETS Wyeth Wasserman Jan. 18, 2012 opossum.cisreg.ca/oPOSSUM3.

MOTIF ENRICHMENT ANALYSIS IN CO- EXPRESSED GENE SETS AND HIGH- THROUGHPUT SEQUENCE SETS Wyeth Wasserman Jan. 18, 2012 opossum.cisreg.ca/oPOSSUM3.
The Lactobacillus acidophilus complex is a clade of homologous Gram-positive, lactic acid bacteria including L. acidophilus, L. helveticus, L. crispatus,

The Lactobacillus acidophilus complex is a clade of homologous Gram-positive, lactic acid bacteria including L. acidophilus, L. helveticus, L. crispatus,
Staphylococcus. Staphylococcus Classification Family Genus Species Micrococcaceae Micrococcus and Staphylococcus S. aureus S. saprophyticus S. epidermidis.

Staphylococcus. Staphylococcus Classification Family Genus Species Micrococcaceae Micrococcus and Staphylococcus S. aureus S. saprophyticus S. epidermidis.
1. 2 3 4 5 6 7 Cervical cancer Aim of The Present Study Lactobacilli Cervical cancer 8.

Cervical cancer Aim of The Present Study Lactobacilli Cervical cancer 8.
益生菌与牙周健康 Probiotics and periodontal health. 益生菌（ Probiotics ） 定义 (definition) 通过摄取适当的量, 对食用者的身体健康能发挥有效作 用的活菌 (FAO & WHO, 2001) 。 living microbes, or as.

益生菌与牙周健康 Probiotics and periodontal health. 益生菌（ Probiotics ） 定义 (definition) 通过摄取适当的量, 对食用者的身体健康能发挥有效作 用的活菌 (FAO & WHO, 2001) 。 living microbes, or as.
or

or
Introduction to the CGE servers

Introduction to the CGE servers
Staph and Strep.

Staph and Strep.
Streptococcus.  Low G+C  Cocci pairs/chains  FA  Non motile, NSF  Capnophiles  Catalase (-)  Peroxidase  Hemolysins  Lancefield Groups 18 antigens.

Streptococcus.  Low G+C  Cocci pairs/chains  FA  Non motile, NSF  Capnophiles  Catalase (-)  Peroxidase  Hemolysins  Lancefield Groups 18 antigens.

Similar presentations

Ads by Google