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RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

History: Version 1.33 online

= Post Processing =

Post Processing of selected Interactions:

No GO-terms available for NC_009085, no GO analysis possible.

Detailed View for selected Interactions:

Interaction1 Energy [kJ/mol] -7.68 zInteraction [dot-bracket] Score 0.94 ((((((.((((&)))).)))))) mRNA [Start] -190 mRNA [End] -180 sRNA [Start] 115 sRNA [End] 125 Gene Annotation "benzoate dioxygenase large subunit A1S" Locus Tag A1S_1861 Genomic Coordinates c21653142164713 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G A U G G C C G U A G 3 ' Plot: Calculate (new | | | | | || | | | window) s R N A :3 ' -U U A C C G C C G U C 5 ' RNAup Webserver: Submit (new window) Interaction2 Energy [kJ/mol] -8.89 zInteraction [dot-bracket] Score 0.53 (((((((((......(((((. ((((&)))).))))).........))))))))) mRNA [Start] -178 mRNA [End] -154 sRNA [Start] 117 sRNA [End] 144 Gene Annotation "beta ketoadipyl CoA thiolase A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

2149442A1S_1849 2150499

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G C C G G U G A G A U A C C G U A A U G U3 ' Plot: Calculate (new | | | | | | | | | | || || window) s R N A :3 ' -C G G C U A U U C A U A A C U C C A A U U A C C5 ' RNAup Webserver: Submit (new window) Interaction3 Energy [kJ/mol] -8.87 zInteraction [dot-bracket] Score 0.54 (((((((((......(((((. ((((&)))).))))).........))))))))) mRNA [Start] -177 mRNA [End] -153 sRNA [Start] 117 sRNA [End] 144 Gene Annotation "beta ketoadipyl CoA thiolase A1S" Locus Tag A1S_1891 Genomic Coordinates c21935192192471 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G C C G G U G A G A U A C C G U A A U G U3 ' Plot: Calculate (new | | | | | | | | | | || || window) s R N A :3 ' -C G G C U A U U C A U A A C U C C A A U U A C C5 ' RNAup Webserver: Submit (new window) Interaction4

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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Energy [kJ/mol] -12.45

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

zInteraction [dot-bracket] Score -0.65 ((((((((((&)))))))))) mRNA [Start] -174 mRNA [End] -165 sRNA [Start] 169 sRNA [End] 178 Gene Annotation "23 dihydro 2;3 dihydroxybenzoate synthetase; isochorismatase A1S" Locus Tag A1S_2580 Genomic Coordinates c29847522984034 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -C A C G G C C A G A 3 ' Plot: Calculate (new | | | | | | | | | | window) s R N A :3 ' -G U G C C G G U C U 5 ' RNAup Webserver: Submit (new window) Interaction5 Energy [kJ/mol] -13.70 zInteraction [dot-bracket] Score -1.06 (((((((((..((&))..))))))))) mRNA [Start] -153 mRNA [End] -141 sRNA [Start] 105 sRNA [End] 117 Gene Annotation "p hydroxybenzoate hydroxylase transcriptional activator A1S" Locus Tag A1S_1355 Genomic Coordinates c15873501586476 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -C A G G A A U G A A A G G3 ' Plot: Calculate (new | | | | | | | | | | | window) s R N A :3 ' -G U C C U U A C U C G C C5 ' RNAup Webserver: Submit (new window) Interaction6 Energy [kJ/mol] -11.02 zInteraction [dot-bracket] Score -0.17 ((((((((((&)))))))))) mRNA [Start] -93 mRNA [End] -84 sRNA [Start] 264 sRNA [End] 273 Gene Annotation "porin for benzoate transport (BenP) A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

2170698A1S_1868 2171473

Associated GONo GO-terms available terms download: mRNA sequence Detailed Interaction(as ASCII): download: sRNA sequence Accessiblity m R N A :5 ' -A G U G C C G A G G 3 ' Plot: | | | | | | | | | | Calculate (new C G C G G U U C C window) s R N A :3 ' -U 5 ' RNAup Webserver: Submit (new window) Interaction7 Energy [kJ/mol] -7.83 zInteraction [dot-bracket] Score 0.89 mRNA [Start] mRNA [End] -70 sRNA [Start] 107 sRNA [End] 129 Gene Annotation "3 ketoacyl CoA thiolase A1S" Locus Tag A1S_0305 Genomic Coordinates c332884331587 Accession Replicon NC_009085 chromosome

((((((.(.(((.((.(((((((&)).))))).)).)))).)))))) -92

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G U U A A G G A G C G A C G U G A A U 3 ' Plot: Calculate (new | | | | | ||| | | | | | || | window) s R N A :3 ' -C C A A U U A C C G C C G U C C U U A C 5 ' RNAup Webserver: Submit (new window)

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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Interaction8 Energy [kJ/mol] -6.21

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

zInteraction [dot-bracket] Score 1.42 ((((....((.((((.((((((&)))))))))).))..)))) mRNA [Start] -60 mRNA [End] -39 sRNA [Start] 246 sRNA [End] 264 Locus Tag A1S_2596 Genomic Coordinates 30050583006034

Gene Annotation "fructose 1;6 bisphosphatase A1S"

Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G A A U U U U G G G U A G C G C A 3 ' Plot: Calculate (new | | | | || | | || | | window) s R N A :3 ' -C C U U C U U C A G U C G G U 5 ' RNAup Webserver: Submit (new window) Interaction9 Energy [kJ/mol] -16.12 zInteraction [dot-bracket] Score (((.(((((.(((((. -1.87 (((((((&))))))).)))))..))))).))) mRNA [Start] -43 mRNA [End] -21 sRNA [Start] 99 sRNA [End] 122 Gene Annotation "putative ferredoxin reductase subunit of phenylpropionate dioxygenase A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

1098146A1S_0950 1098690

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G C U G C A G G U U G G G C A G U U A G 3 ' Plot: Calculate (new | | || | | | | | | | | | | | | | | window) s R N A :3 ' -C C G C C G U C C U U A C U C G C C A G U C 5 ' RNAup Webserver: Submit (new window) Interaction10 Energy [kJ/mol] -15.02 zInteraction [dot-bracket] Score -1.5 (((((((((((.((((((&))).)))...))))))))))) mRNA [Start] -33 mRNA [End] -16 sRNA [Start] 142 sRNA [End] 162 Gene Annotation "LysR family transcriptional regulator A1S" Locus Tag A1S_1506 Genomic Coordinates 17521131752951 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G A G G G G G A G C G U C U G -3 ' Plot: Calculate (new | | | | | | | | | | | | | | window) s R N A :3 ' -C U C U C U C U C G C U U U G A U U5 ' RNAup Webserver: Submit (new window)

Interaction11 Energy [kJ/mol] -10.82 zInteraction [dot-bracket] Score -0.11 (((.(((.(.((((((..(((((((. ((&)).))))))))))))))))).))) mRNA [Start] -31 mRNA [End] -4 sRNA [Start] 253 sRNA [End] 276 Gene Annotation "Beta ketoadipyl CoA thiolase A1S" Locus Tag A1S_1848 Genomic Coordinates 21490802149471 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -U G A U G C G A C U C A A G G G U A A G G A A 3 ' Plot: Calculate (new | | || | ||| | | | | | | | || | window) s R N A :3 ' -A C U U C G C G G U U C C C U U C U U C 5 ' RNAup Webserver: Submit (new window)

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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Interaction12 Energy [kJ/mol] -10.82

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

zInteraction [dot-bracket] Score -0.11 (((.(((.(.((((((..(((((((. ((&)).))))))))))))))))).)))

mRNA [Start] -30

mRNA [End] -3

sRNA [Start] 253

sRNA [End] 276

Gene Annotation "Beta ketoadipyl CoA thiolase A1S"

Locus Tag A1S_1892

Genomic Coordinates c21938812193490

Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -U G A U G C G A C U C A A G G G U A A G G A A 3 ' Plot: Calculate (new | | || | ||| | | | | | | | || | window) s R N A :3 ' -A C U U C G C G G U U C C C U U C U U C 5 ' RNAup Webserver: Submit (new window) Interaction13 zEnergy [kJ/mol] Score Interaction [dot-bracket] -7.47 1.01 (((...(((((.(...(((((. (((((((&))))))))))))))))))...))) mRNA [Start] -21 mRNA [End] 7 sRNA [Start] 106 sRNA [End] 129 Gene Annotation "2;3 dihydroxybenzoate 2;3 dehydrogenase A1S" Locus Tag A1S_2579 Genomic Coordinates c29841072983206 Accession Replicon

NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G U G A C U G G C G U G A A U C A G G G C A U 3 ' Plot: Calculate (new | | | | | | | || | | | | || | window) s R N A :3 ' -C C A A U U A C C G C C G U C C U U A 5 ' RNAup Webserver: Submit (new window) Interaction14 Energy [kJ/mol] -13.86 zInteraction [dot-bracket] Score -1.12 (((((.(((((((((.(&).))))))))).))))) mRNA [Start] -19 mRNA [End] -3 sRNA [Start] 90 sRNA [End] 106 Gene Annotation "multidrug efflux MFS transporter putative A1S" Locus Tag A1S_1799 Genomic Coordinates 20953942097063 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G U C G A U A U U C G C G G U G 3 ' Plot: Calculate (new | | | | || | | | | | | | || window) s R N A :3 ' -C C A G U C G U A A G C G C C U C 5 ' RNAup Webserver: Submit (new window) Interaction15 Energy [kJ/mol] -15.91 zInteraction [dot-bracket] Score -1.8 mRNA [Start] mRNA [End] 11 sRNA [Start] 107 sRNA [End] 129 Gene Annotation "aldo/keto reductase A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

((((..(((.(((..(((((((((&)))))))))))).)))...)))) -12

A1S_3266 37565503757037

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G U U U A G G U U G C A U G G G A A U G 3 ' Plot: Calculate (new | | | | | | | | | | | | | | | | window) s R N A :3 ' -C C A A U U A C C G C C G U C C U U A C 5 ' RNAup Webserver:

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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Submit (new window) Interaction16 Energy [kJ/mol] -16.45

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

zInteraction [dot-bracket] Score -1.98

mRNA [Start]

mRNA [End] 18

sRNA [Start] 94

sRNA [End] 122

Gene Annotation "putative signal peptide A1S"

Locus Tag A1S_3139

Genomic Coordinates c36271233626405

Accession Replicon NC_009085 chromosome

((((....((((. -11 (((((((((((((((((&)))))))))))..)))))).)))).))))

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G C G A C U U U A G G C A U G G G U U C A G C A U 3 ' Plot: Calculate (new | | | | || || | | | | | | | | | | | | | window) s R N A :3 ' -C C G C C G U C C U U A C U C G C C A G U C G U A 5 ' RNAup Webserver: Submit (new window) Interaction17 Energy [kJ/mol] -11.22 zInteraction [dot-bracket] Score -0.24 ((((((.......(((((((((&)))))))))........)))))) mRNA [Start] -9 mRNA [End] 12 sRNA [Start] 251 sRNA [End] 273 Gene Annotation "LysR family transcriptional regulator A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

c3761052A1S_3271 3760010

Associated GONo GO-terms available terms download: mRNA sequence Detailed Interaction(as ASCII): download: sRNA sequence Accessiblity m R N A :5 ' -A G C G C U U A A A C A U G A G U C A G C 3 ' Plot: Calculate (new | | | | | | | | | | | | | | window) C G C G G U U C C C U U C U U C A G U C G s R N A :3 ' -U 5 ' RNAup Webserver: Submit (new window)

Interaction18 Energy [kJ/mol] -9.19 zInteraction [dot-bracket] Score 0.43 ((((.....(((((&)))))...)))) mRNA [Start] -9 mRNA [End] 4 sRNA [Start] 120 sRNA [End] 131 Gene Annotation "fructose 1;6 bisphosphate aldolase A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

1796550A1S_1544 1797787

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G A G G A U A U U A U G 3 ' Plot: Calculate (new | | | | | | | window) s R N A :3 ' -C U C C A A U U A C 5 ' RNAup Webserver: Submit (new window) Interaction19 Energy [kJ/mol] -7.68 zInteraction [dot-bracket] Score 0.94 (((((((...(((.((((.((&)).))))..)))....))))))) mRNA [Start] -3 mRNA [End] 17 sRNA [Start] 259 sRNA [End] 281 Gene Annotation "benzoate 12 dioxygenase beta subunit A1S" Locus Tag A1S_1214 Genomic Coordinates c14213491420775 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -C U G G A U G C C A G C U U G G G 3 ' Plot: Calculate (new | | | | | | | | | | || window)

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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RNAup Webserver: Submit (new window)

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

s R N A :3 ' -G A C C U A C U U C G C G G U U C C C 5 '

Interaction20 Energy [kJ/mol] -9.12 zInteraction [dot-bracket] Score 0.46 (((((((..(((&)))..))))))) mRNA [Start] -1 mRNA [End] 10 sRNA [Start] 220 sRNA [End] 231 Gene Annotation "phosphopyruvate hydratase A1S" Locus Tag A1S_1898 Genomic Coordinates c21992592197860 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G G U G G U U G G U C 3 ' Plot: Calculate (new | | | | | | | | | | window) s R N A :3 ' -C C C A C U A G U U A G 5 ' RNAup Webserver: Submit (new window) Interaction21 Energy [kJ/mol] -15.37 zInteraction [dot-bracket] Score -1.62 (((((((((((((((((((&))))))))).)))).)))))) mRNA [Start] 0 mRNA [End] 18 sRNA [Start] 117 sRNA [End] 137 Gene Annotation "alpha beta hydrolase family esterase A1S" Locus Tag A1S_2792 Genomic Coordinates c32360803235080 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -A G U G U U A G G U A G U G G U G 3 ' Plot: Calculate (new | | | | | || | | || | | | | | | window) s R N A :3 ' -U C A U A A C U C C A A U U A C C G C 5 ' RNAup Webserver: Submit (new window) Interaction22 Energy [kJ/mol] -13.74 zInteraction [dot-bracket] Score -1.08 (((((((((((&))))))))))) mRNA [Start] 0 mRNA [End] 10 sRNA [Start] 115 sRNA [End] 125 Gene Annotation "putative monooxygenase (DszA like) A1S" Locus Tag Genomic Coordinates Accession Replicon NC_009085 chromosome

c1732080A1S_1486 1730753

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -A A U G G C G G C A G 3 ' Plot: Calculate (new | | | | | | | | | | | window) s R N A :3 ' -U U A C C G C C G U C 5 ' RNAup Webserver: Submit (new window) Interaction23 Energy [kJ/mol] -10.47 zInteraction [dot-bracket] Score 0.01 (((((..((((((((&))))))))..))))) mRNA [Start] 7 mRNA [End] 21 sRNA [Start] 252 sRNA [End] 266 Gene Annotation "carbon storage regulator A1S" Locus Tag A1S_1141 Genomic Coordinates c13314541331036 Accession Replicon NC_009085 chromosome

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity m R N A :5 ' -G G G G A U C A A G U C A G U 3 ' Plot:

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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Calculate (new window) RNAup Webserver: Submit (new window) Interaction24 Energy [kJ/mol] -15.40

RNApredator bacterial sRNA target prediction Webserver - Postprocessing - http://www.tbi.univie.ac.at/

| | | | | | | | | | | | | s R N A :3 ' -U 5 ' C C C U U C U U C A G U C G

zInteraction [dot-bracket] Score -1.63 ((((.(((((.((((((((&)))))))))))))))))

mRNA [Start] 863

mRNA [End] 881

sRNA [Start] 258

sRNA [End] 274

Gene Annotation "putative benzoate transport porin (BenP) A1S"

Locus Tag

Genomic Coordinates

Accession Replicon NC_009085 chromosome

c1415736A1S_1209 1414496

Associated GONo GO-terms available terms download: mRNA sequence download: Detailed Interaction(as ASCII): sRNA sequence Accessiblity Plot: m R N A :5 ' -A A G C A G C C A A U G G G G A G 3 ' Calculate (new | | | | | | | | | | | | | | | window) s R N A :3 ' -U U C G C G G U U C C C U U C 5 ' RNAup Webserver: Submit (new window)

2010 - 2012 TBI - Contact - Publication

http://rna.tbi.univie.ac.at/RNApredator2/target_search.cgi?page=3&tempdir=eieAZ18dVl

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