TargetRNA2

A tool for identifying targets of small regulatory RNAs in bacteria

Predicted targets for RyhB

GCGATCAGGAAGACCCTCGCGGAGAACCTGAAAGCACGAC
ATTGCTCACATTGCTTCCAGTATTACTTAGCCAGCCGGGT
GCTGGCTTTT


Rank Gene Synonym Energy Pvalue
1
90
1 sdhD b0722 -12.98 0.004
2 ascG b2714 -12.65 0.005
3 ygjH b3074 -12.24 0.006
4 sodB b1656 -11.43 0.011
5 acnA b1276 -11.14 0.013
6 gutQ b2708 -10.79 0.015
7 cirA b2155 -10.71 0.016
8 nirB b3365 -10.51 0.018
9 djlB b0646 -10.41 0.019
10 shiA b1981 -9.96 0.024
11 yhhN b3468 -9.78 0.026
12 ybbP b0496 -9.45 0.030
13 ssuD b0935 -9.43 0.031
14 cysE b3607 -8.99 0.037
15 insH1 b2030 -8.86 0.039
16 hscA b2526 -8.82 0.040
17 yciS b1279 -8.69 0.043
18 dhaL b1199 -8.63 0.044
19 nuoA b2288 -8.6 0.044
20 narG b1224 -8.47 0.047
21 yraK b3145 -8.37 0.049


1
 sdhD succinate dehydrogenase, membrane subunit, binds cytochrome b556
Energy: -12.98 p-value: 0.004

sRNA 42 UACAGCACGAAAGUC 28
     |||||||||||||    
mRNA (sdhD) -34 CUGUCGUGCUUUCAC -20


2
 ascG DNA-binding transcriptional repressor
Energy: -12.65 p-value: 0.005

sRNA 65 AUUAUGACCUUCGU 52
     :||:|||||||:    
mRNA (ascG) 8 CGAUGCUGGAAGU- 20


3
 ygjH probable tRNA binding protein; putative tRNA corner chaperone
Energy: -12.24 p-value: 0.006

sRNA 59 ACCUUCGUUACACUC 45
     |||||||||| ||    
mRNA (ygjH) -8 AGGAAGCAAUG-GAA 6


4
 sodB superoxide dismutase, Fe
Energy: -11.43 p-value: 0.011

sRNA 50 ACACUCGUUACAGC 37
     || |||||||||    
mRNA (sodB) -7 AGU-AGCAAUGUCA 6


5
 acnA aconitate hydratase 1
Energy: -11.14 p-value: 0.013

sRNA 48 ACUCGUUACAGCACGA 33
     |||| ||||||| |    
mRNA (acnA) -6 GGAGCUAUGUCGU-CA 9


6
 gutQ D-arabinose 5-phosphate isomerase
Energy: -10.79 p-value: 0.015

sRNA 48 ACUCGUUACAGCACG 34
     ||||||||  |||    
mRNA (gutQ) -6 AGAGCAAUG-AGUGA 8


7
 cirA catecholate siderophore receptor CirA
Energy: -10.71 p-value: 0.016

sRNA 57 CUUCGU-UACACUCGUUAC 40
    |||| | ||||||||:||    
mRNA (cirA) -58 GAAGAAGAUGUGAGCGAUA -40


8
 nirB nitrite reductase, large subunit, NAD(P)H-binding
Energy: -10.51 p-value: 0.018

sRNA 55 CG-UUACACUCGUUACAGC 37
    || ||  ||||||| |||    
mRNA (nirB) -6 GCAAAAAUGAGCAAAGUCA 13


9
 djlB predicted co-chaperone
Energy: -10.41 p-value: 0.019

sRNA 63 UAUGACCUUCG 53
     |:|||||||    
mRNA (djlB) 9 UUGCUGGAAGA 19


10
 shiA shikimate transporter
Energy: -9.96 p-value: 0.024

sRNA 58 CCU-UCGUUACACUCGU 43
     || :||||||||||:    
mRNA (shiA) -63 CGACGGCAAUGUGAGUU -47


11
 yhhN predicted inner membrane protein, TMEM86 family
Energy: -9.78 p-value: 0.026

sRNA 62 AUGACCUUCGUUA 50
     |||||||||||    
mRNA (yhhN) -61 AACUGGAAGCAAG -49


12
 ybbP predicted ABC transporter permease
Energy: -9.45 p-value: 0.030

sRNA 59 ACCUUCGUUACA 48
     |||||| |||    
mRNA (ybbP) -7 AGGAAGC-AUGA 4


13
 ssuD alkanesulfonate monooxygenase, FMNH(2)-dependent
Energy: -9.43 p-value: 0.031

sRNA 62 AUGACCUUCGUUA 50
     |||||||| ||    
mRNA (ssuD) -19 AACUGGAAGGAAA -7


14
 cysE serine acetyltransferase
Energy: -8.99 p-value: 0.037

sRNA 49 CACUCGUUACAGCACGA 33
    || ||||||||||||:    
mRNA (cysE) -8 GUAAGCAAUGUCGUGUG 10


15
 insH1 IS5 transposase and trans-activator
Energy: -8.86 p-value: 0.039

sRNA 39 AGCACGAAAGU 29
     :||||||||    
mRNA (insH1) -75 CUGUGCUUUCU -65


16
 hscA DnaK-like molecular chaperone specific for IscU
Energy: -8.82 p-value: 0.040

sRNA 66 CAUU-AUGACCUUCGU 52
     ||| | ||||||||    
mRNA (hscA) -20 UUAAUUUCUGGAAGCU -5


17
 yciS DUF1049 family inner membrane protein, function unknown
Energy: -8.69 p-value: 0.043

sRNA 59 ACCUUCGUUACACUC 45
     |||||:|||||||    
mRNA (yciS) -10 GGGAAGUAAUGUGAA 5


18
 dhaL dihydroxyacetone kinase, C-terminal domain
Energy: -8.63 p-value: 0.044

sRNA 50 ACACUCGUUACAGC 37
     |  |||||||||    
mRNA (dhaL) -8 AGAAAGCAAUGUCA 6


19
 nuoA NADH:ubiquinone oxidoreductase, membrane subunit A
Energy: -8.6 p-value: 0.044

sRNA 59 ACCUUCGUUACACUCGUU 42
     | ||||||  ||||:|    
mRNA (nuoA) -8 AGUAAGCAA--UGAGUAU 8


20
 narG nitrate reductase 1, alpha subunit
Energy: -8.47 p-value: 0.047

sRNA 47 CUCGUUACAGCA 36
     ||||||||||    
mRNA (narG) -51 UAGCAAUGUCGA -40


21
 yraK predicted fimbrial-like adhesin protein
Energy: -8.37 p-value: 0.049

sRNA 41 CAGCACGAAAGUCC 27
    ||: |||||||||    
mRNA (yraK) -80 GUU-UGCUUUCAGU -68



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

(View results as text file)