**************************************** PROGRAM PARAMETERS TargetRNA version: 2.01 Replicon: Escherichia coli str. K-12 substr. MG1655 NTs before start codon: 80 NTs after start codon: 20 Seed length: 7 sRNA conservation and accessibility: true sRNA window size: 13 mRNA structural accessibility: true Interaction region: 20 Filter size: 400 Single target: - File of candidate targets: - p-value: 0.05 **************************************** Rank Gene Synonym Energy Pvalue sRNA_start sRNA_stop mRNA_start mRNA_stop 1 sdhD b0722 -12.98 0.004 28 42 -34 -20 2 ascG b2714 -12.65 0.005 52 65 8 20 3 ygjH b3074 -12.24 0.006 45 59 -8 6 4 sodB b1656 -11.43 0.011 37 50 -7 6 5 acnA b1276 -11.14 0.013 33 48 -6 9 6 gutQ b2708 -10.79 0.015 34 48 -6 8 7 cirA b2155 -10.71 0.016 40 57 -58 -40 8 nirB b3365 -10.51 0.018 37 55 -6 13 9 djlB b0646 -10.41 0.019 53 63 9 19 10 shiA b1981 -9.96 0.024 43 58 -63 -47 11 yhhN b3468 -9.78 0.026 50 62 -61 -49 12 ybbP b0496 -9.45 0.030 48 59 -7 4 13 ssuD b0935 -9.43 0.031 50 62 -19 -7 14 cysE b3607 -8.99 0.037 33 49 -8 10 15 insH1 b2030 -8.86 0.039 29 39 -75 -65 16 hscA b2526 -8.82 0.040 52 66 -20 -5 17 yciS b1279 -8.69 0.043 45 59 -10 5 18 dhaL b1199 -8.63 0.044 37 50 -8 6 19 nuoA b2288 -8.6 0.044 42 59 -8 8 20 narG b1224 -8.47 0.047 36 47 -51 -40 21 yraK b3145 -8.37 0.049 27 41 -80 -68 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% sdhD 1 RyhB 42 3' UACAGCACGAAAGUC 5' 28 ||||||||||||| sdhD -34 5' CUGUCGUGCUUUCAC 3' -20 Energy: -12.98 p-value: 0.004 16128697 gene product: succinate dehydrogenase, membrane subunit, binds cytochrome b556 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ascG 2 RyhB 65 3' AUUAUGACCUUCGU 5' 52 :||:|||||||: ascG 8 5' CGAUGCUGGAAGU- 3' 20 Energy: -12.65 p-value: 0.005 345452722 gene product: DNA-binding transcriptional repressor %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ygjH 3 RyhB 59 3' ACCUUCGUUACACUC 5' 45 |||||||||| || ygjH -8 5' AGGAAGCAAUG-GAA 3' 6 Energy: -12.24 p-value: 0.006 16130969 gene product: probable tRNA binding protein; putative tRNA corner chaperone %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% sodB 4 RyhB 50 3' ACACUCGUUACAGC 5' 37 || ||||||||| sodB -7 5' AGU-AGCAAUGUCA 3' 6 Energy: -11.43 p-value: 0.011 16129614 gene product: superoxide dismutase, Fe %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% acnA 5 RyhB 48 3' ACUCGUUACAGCACGA 5' 33 |||| ||||||| | acnA -6 5' GGAGCUAUGUCGU-CA 3' 9 Energy: -11.14 p-value: 0.013 16129237 gene product: aconitate hydratase 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% gutQ 6 RyhB 48 3' ACUCGUUACAGCACG 5' 34 |||||||| ||| gutQ -6 5' AGAGCAAUG-AGUGA 3' 8 Energy: -10.79 p-value: 0.015 90111480 gene product: D-arabinose 5-phosphate isomerase %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cirA 7 RyhB 57 3' CUUCGU-UACACUCGUUAC 5' 40 |||| | ||||||||:|| cirA -58 5' GAAGAAGAUGUGAGCGAUA 3' -40 Energy: -10.71 p-value: 0.016 16130093 gene product: catecholate siderophore receptor CirA %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nirB 8 RyhB 55 3' CG-UUACACUCGUUACAGC 5' 37 || || ||||||| ||| nirB -6 5' GCAAAAAUGAGCAAAGUCA 3' 13 Energy: -10.51 p-value: 0.018 16131244 gene product: nitrite reductase, large subunit, NAD(P)H-binding %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% djlB 9 RyhB 63 3' UAUGACCUUCG 5' 53 |:||||||| djlB 9 5' UUGCUGGAAGA 3' 19 Energy: -10.41 p-value: 0.019 16128629 gene product: predicted co-chaperone %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% shiA 10 RyhB 58 3' CCU-UCGUUACACUCGU 5' 43 || :||||||||||: shiA -63 5' CGACGGCAAUGUGAGUU 3' -47 Energy: -9.96 p-value: 0.024 16129925 gene product: shikimate transporter %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% yhhN 11 RyhB 62 3' AUGACCUUCGUUA 5' 50 ||||||||||| yhhN -61 5' AACUGGAAGCAAG 3' -49 Energy: -9.78 p-value: 0.026 16131340 gene product: predicted inner membrane protein, TMEM86 family %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ybbP 12 RyhB 59 3' ACCUUCGUUACA 5' 48 |||||| ||| ybbP -7 5' AGGAAGC-AUGA 3' 4 Energy: -9.45 p-value: 0.030 16128480 gene product: predicted ABC transporter permease %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ssuD 13 RyhB 62 3' AUGACCUUCGUUA 5' 50 |||||||| || ssuD -19 5' AACUGGAAGGAAA 3' -7 Energy: -9.43 p-value: 0.031 16128902 gene product: alkanesulfonate monooxygenase, FMNH(2)-dependent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cysE 14 RyhB 49 3' CACUCGUUACAGCACGA 5' 33 || ||||||||||||: cysE -8 5' GUAAGCAAUGUCGUGUG 3' 10 Energy: -8.99 p-value: 0.037 16131478 gene product: serine acetyltransferase %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% insH1 15 RyhB 39 3' AGCACGAAAGU 5' 29 :|||||||| insH1 -75 5' CUGUGCUUUCU 3' -65 Energy: -8.86 p-value: 0.039 16129971 gene product: IS5 transposase and trans-activator %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% hscA 16 RyhB 66 3' CAUU-AUGACCUUCGU 5' 52 ||| | |||||||| hscA -20 5' UUAAUUUCUGGAAGCU 3' -5 Energy: -8.82 p-value: 0.040 16130451 gene product: DnaK-like molecular chaperone specific for IscU %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% yciS 17 RyhB 59 3' ACCUUCGUUACACUC 5' 45 |||||:||||||| yciS -10 5' GGGAAGUAAUGUGAA 3' 5 Energy: -8.69 p-value: 0.043 16129240 gene product: DUF1049 family inner membrane protein, function unknown %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% dhaL 18 RyhB 50 3' ACACUCGUUACAGC 5' 37 | ||||||||| dhaL -8 5' AGAAAGCAAUGUCA 3' 6 Energy: -8.63 p-value: 0.044 16129162 gene product: dihydroxyacetone kinase, C-terminal domain %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% nuoA 19 RyhB 59 3' ACCUUCGUUACACUCGUU 5' 42 | |||||| ||||:| nuoA -8 5' AGUAAGCAA--UGAGUAU 3' 8 Energy: -8.6 p-value: 0.044 49176207 gene product: NADH:ubiquinone oxidoreductase, membrane subunit A %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% narG 20 RyhB 47 3' CUCGUUACAGCA 5' 36 |||||||||| narG -51 5' UAGCAAUGUCGA 3' -40 Energy: -8.47 p-value: 0.047 16129187 gene product: nitrate reductase 1, alpha subunit %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% yraK 21 RyhB 41 3' CAGCACGAAAGUCC 5' 27 ||: ||||||||| yraK -80 5' GUU-UGCUUUCAGU 3' -68 Energy: -8.37 p-value: 0.049 16131037 gene product: predicted fimbrial-like adhesin protein