Freiburg RNA Tools
CopraRNA - Results
BIF
IFF

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching

CopraRNA 3429477

Input and runtime details for job 3429477 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 3429477 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:26:36 CET 2018
?CopraRNA Started@ Fri Feb 16 15:27:01 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:15:20 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:15:27 CET 2018
?Job Completed@ Fri Feb 16 20:15:52 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
1 0 0 b3961 oxyR -149.65 0.000000 1 -- 105 1 -- 105 oxidative and nitrosative stress transcriptional regulator  
2 0.0001834 0.3 b2729 hypD -13.53 0.025234 75 -- 91 71 -- 87 hydrogenase maturation protein  
3 0.0006202 0.5173 b3310 rplN -11.54 0.056896 6 -- 16 77 -- 87 50S ribosomal subunit protein L14  
4 0.0006326 0.5173 b3230 rpsI -11.95 0.048152 221 -- 251 74 -- 108 30S ribosomal subunit protein S9  
5 0.0009313 0.5385 b3829 metE -12.51 0.038445 233 -- 242 75 -- 84 5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase  
6 0.001078 0.5385 b0849 grxA -11.19 0.065759 209 -- 232 58 -- 81 glutaredoxin 1 redox coenzyme for ribonucleotide reductase (RNR1a)  
7 0.001275 0.5385 b2175 mepS -13.85 0.022182 178 -- 188 25 -- 35 murein DD-endopeptidase space-maker hydrolase mutational suppressor of prc thermosensitivity outer membrane lipoprotein weak murein LD-carboxypeptidase  
8 0.001355 0.5385 b3915 fieF -13.87 0.021962 2 -- 39 50 -- 90 ferrous iron and zinc transporter  
9 0.0016 0.5385 b1709 btuD -9.25 0.141890 185 -- 194 75 -- 84 vitamin B12 ABC transporter ATPase  
10 0.001846 0.5385 b2099 yegU -13.29 0.027829 185 -- 270 5 -- 83 ADP-ribosylglycohydrolase family protein  
11 0.002269 0.5385 b1205 ychH -11.36 0.061344 181 -- 195 75 -- 90 DUF2583 family putative inner membrane protein  
12 0.002293 0.5385 b1823 cspC -13.69 0.023618 13 -- 32 14 -- 35 stress protein member of the CspA-family  
13 0.002299 0.5385 b3663 yicN -11.49 0.058154 241 -- 256 60 -- 78 DUF1198 family protein  
14 0.002739 0.5385 b0903 pflB -11.82 0.050867 80 -- 105 57 -- 81 formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1  
15 0.002894 0.5385 b2780 pyrG -11.46 0.058961 111 -- 140 60 -- 90 CTP synthetase  
16 0.002981 0.5385 b3428 glgP -10.45 0.088230 278 -- 289 76 -- 86 glycogen phosphorylase  
17 0.003067 0.5385 b1628 rsxB -11.62 0.055094 175 -- 198 58 -- 77 SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein  
18 0.003137 0.5385 b1824 yobF -13.30 0.027752 169 -- 188 14 -- 35 DUF2527 family heat-induced protein  
19 0.003195 0.5385 b3739 atpI -12.12 0.045044 59 -- 85 62 -- 85 ATP synthase membrane-bound accessory factor  
20 0.003438 0.5385 b3093 exuT -11.51 0.057623 213 -- 228 75 -- 90 hexuronate transporter  
21 0.003546 0.5385 b0820 ybiT -11.98 0.047670 3 -- 23 55 -- 78 ABC-F family putative regulatory ATPase  
22 0.004141 0.5385 b0462 acrB -13.08 0.030428 256 -- 265 75 -- 84 multidrug efflux system protein  
23 0.004272 0.5385 b3315 rplV -10.64 0.081808 245 -- 278 60 -- 90 50S ribosomal subunit protein L22  
24 0.00428 0.5385 b0090 murG -10.85 0.075280 191 -- 203 77 -- 89 N-acetylglucosaminyl transferase  
25 0.004715 0.5385 b0009 mog -11.66 0.054310 209 -- 227 68 -- 85 molybdochelatase incorporating molybdenum into molybdopterin  
26 0.00484 0.5385 b3033 yqiB -11.20 0.065436 106 -- 117 15 -- 27 DUF1249 protein YqiB  
27 0.005053 0.5385 b2058 wcaB -11.44 0.059229 168 -- 190 61 -- 82 putative acyl transferase  
28 0.005203 0.5385 b3308 rplE -12.95 0.031988 121 -- 134 62 -- 77 50S ribosomal subunit protein L5  
29 0.005218 0.5385 b3433 asd -11.22 0.064904 208 -- 219 71 -- 82 aspartate-semialdehyde dehydrogenase NAD(P)-binding  
30 0.005373 0.5385 b1624 ydgJ -10.76 0.078067 229 -- 247 61 -- 79 putative oxidoreductase  
31 0.005384 0.5385 b0159 mtn -14.65 0.015942 9 -- 52 71 -- 108 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase  
32 0.005403 0.5385 b0951 pqiB -10.24 0.095947 95 -- 108 69 -- 82 paraquat-inducible SoxRS-regulated MCE domain protein  
33 0.006009 0.5385 b1264 trpE -12.63 0.036478 39 -- 48 79 -- 88 component I of anthranilate synthase  
34 0.00612 0.5385 b1837 yebW -12.39 0.040382 203 -- 226 63 -- 86 uncharacterized protein  
35 0.006586 0.5385 b2351 gtrB -12.36 0.040837 174 -- 213 48 -- 89 CPS-53 (KpLE1) prophage; bactoprenol glucosyl transferase  
36 0.006672 0.5385 b3956 ppc -10.31 0.093393 270 -- 282 76 -- 88 phosphoenolpyruvate carboxylase  
37 0.006912 0.5385 b3693 dgoK -11.15 0.066742 227 -- 259 71 -- 102 2-oxo-3-deoxygalactonate kinase  
38 0.006978 0.5385 b3738 atpB -10.53 0.085759 128 -- 143 69 -- 84 F0 sector of membrane-bound ATP synthase subunit a  
39 0.007274 0.5385 b1636 pdxY -13.08 0.030384 230 -- 254 60 -- 84 pyridoxamine kinase  
40 0.008109 0.5385 b0784 moaD -13.26 0.028244 179 -- 200 15 -- 38 molybdopterin synthase small subunit  
41 0.00828 0.5385 b2246 rhmT -13.65 0.023999 257 -- 273 69 -- 86 putative L-rhamnonate transporter  
42 0.008798 0.5385 b0087 mraY -9.88 0.111048 142 -- 153 79 -- 90 phospho-N-acetylmuramoyl-pentapeptide transferase  
43 0.009109 0.5385 b2531 iscR -9.39 0.134324 275 -- 298 62 -- 87 isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor  
44 0.009138 0.5385 b4148 sugE -12.73 0.035076 273 -- 288 62 -- 77 multidrug efflux system protein  
45 0.009513 0.5385 b2513 yfgM -9.58 0.124672 177 -- 189 15 -- 27 ancillary SecYEG translocon subunit; putative anti-RcsB factor  
46 0.009803 0.5385 b1418 cybB -9.32 0.138160 281 -- 295 73 -- 89 cytochrome b561  
47 0.009854 0.5385 b3408 feoA -10.27 0.095129 159 -- 188 52 -- 83 ferrous iron transporter protein A  
48 0.009918 0.5385 b0641 lptE -9.88 0.110832 177 -- 184 74 -- 81 LPS assembly OM complex LptDE lipoprotein component  
49 0.01016 0.5385 b3354 yheU -13.31 0.027656 105 -- 118 71 -- 84 UPF0270 family protein  
50 0.0104 0.5385 b0661 miaB -10.15 0.099644 35 -- 45 74 -- 85 tRNA-i(6)A37 methylthiotransferase  
51 0.01052 0.5385 b0751 pnuC -11.84 0.050492 77 -- 89 77 -- 89 nicotinamide riboside transporter  
52 0.01055 0.5385 b2963 mltC -16.80 0.006570 83 -- 101 12 -- 32 membrane-bound lytic murein transglycosylase C  
53 0.01075 0.5385 b2215 ompC -12.88 0.032936 67 -- 90 57 -- 76 outer membrane porin protein C  
54 0.01077 0.5385 b1820 yobD -10.70 0.079862 85 -- 97 73 -- 84 UPF0266 family inner membrane protein  
55 0.01095 0.5385 b1220 ychO -5.56 0.517016 132 -- 175 64 -- 91 putative invasin  
56 0.01109 0.5385 b0425 panE -9.95 0.107741 273 -- 289 74 -- 89 2-dehydropantoate reductase NADPH-specific  
57 0.01133 0.5385 b0026 ileS -8.45 0.192830 289 -- 299 74 -- 83 isoleucyl-tRNA synthetase  
58 0.01138 0.5385 b2595 bamD -7.85 0.240744 21 -- 29 72 -- 80 BamABCDE complex OM biogenesis lipoprotein  
59 0.01163 0.5385 b1279 yciS -7.12 0.313424 44 -- 60 74 -- 90 DUF1049 family inner membrane protein function unknown  
60 0.01169 0.5385 b2441 eutB -14.17 0.019414 238 -- 261 12 -- 34 ethanolamine ammonia-lyase large subunit heavy chain  
61 0.01179 0.5385 b3748 rbsD -10.58 0.083988 129 -- 141 72 -- 84 D-ribose pyranase  
62 0.01254 0.5385 b0027 lspA -10.68 0.080768 51 -- 66 75 -- 90 prolipoprotein signal peptidase (signal peptidase II)  
63 0.01271 0.5385 b3306 rpsH -10.49 0.086924 89 -- 100 56 -- 67 30S ribosomal subunit protein S8  
64 0.01278 0.5385 b1718 infC -10.82 0.076139 1 -- 9 71 -- 79 translation initiation factor IF-3  
65 0.01282 0.5385 b0589 fepG -12.08 0.045738 8 -- 17 74 -- 83 iron-enterobactin ABC transporter permease  
66 0.01284 0.5385 b1645 ydhK -10.57 0.084210 155 -- 164 75 -- 84 putative efflux protein (PET) component of YdhJK efflux pump  
67 0.01284 0.5385 b1294 sapA -9.42 0.132690 25 -- 48 61 -- 86 antimicrobial peptide transport ABC transporter periplasmic binding protein  
68 0.013 0.5385 b2823 ppdC -12.74 0.034901 243 -- 262 69 -- 89 putative prepilin peptidase-dependent protein  
69 0.01301 0.5385 b0174 ispU -11.35 0.061456 97 -- 106 71 -- 80 undecaprenyl pyrophosphate synthase  
70 0.01301 0.5385 b1424 opgD -12.13 0.044753 222 -- 240 70 -- 90 OPG biosynthetic periplasmic protein  
71 0.01305 0.5385 b3843 ubiD -10.23 0.096580 123 -- 132 80 -- 89 3-octaprenyl-4-hydroxybenzoate decarboxylase  
72 0.0135 0.5385 b1117 lolD -8.66 0.177865 184 -- 202 66 -- 83 outer membrane-specific lipoprotein transporter subunit  
73 0.0135 0.5385 b3362 yhfG -12.23 0.043008 184 -- 212 50 -- 86 putative antitoxin for Fic  
74 0.01362 0.5385 b0946 zapC -12.02 0.046851 175 -- 197 15 -- 35 FtsZ stabilizer  
75 0.01364 0.5385 b0107 hofB -15.68 0.010425 272 -- 289 69 -- 87 T2SE secretion family protein; P-loop ATPase superfamily protein  
76 0.01392 0.5385 b0066 thiQ -9.74 0.117374 220 -- 232 71 -- 84 thiamine/thiamine pyrophosphate ABC transporter ATPase  
77 0.01396 0.5385 b3644 yicC -11.79 0.051421 238 -- 254 15 -- 31 UPF0701 family protein  
78 0.01399 0.5385 b3526 kdgK -7.99 0.228654 189 -- 197 80 -- 88 2-dehydro-3-deoxygluconokinase  
79 0.01412 0.5385 b2830 rppH -5.99 0.454649 93 -- 100 64 -- 71 RNA pyrophosphohydrolase  
80 0.01445 0.5385 b4257 yjgN -10.51 0.086376 202 -- 215 65 -- 78 DUF898 family inner membrane protein  
81 0.01462 0.5385 b3296 rpsD -10.19 0.098165 202 -- 218 60 -- 78 30S ribosomal subunit protein S4  
82 0.01477 0.5385 b3527 yhjJ -9.01 0.155560 190 -- 221 62 -- 91 putative periplasmic M16 family chaperone  
83 0.01501 0.5385 b2114 metG -6.55 0.379655 47 -- 64 63 -- 79 methionyl-tRNA synthetase  
84 0.01516 0.5385 b1871 cmoB -9.91 0.109770 166 -- 183 71 -- 87 tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent  
85 0.01519 0.5385 b0094 ftsA -12.00 0.047343 234 -- 271 69 -- 107 ATP-binding cell division FtsK recruitment protein  
86 0.01521 0.5385 b0605 ahpC -11.47 0.058587 74 -- 93 73 -- 89 alkyl hydroperoxide reductase C22 subunit  
87 0.01529 0.5385 b3636 rpmG -10.80 0.076825 199 -- 224 53 -- 84 50S ribosomal subunit protein L33  
88 0.01545 0.5385 b3009 yghB -9.13 0.148475 202 -- 216 61 -- 78 general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter  
89 0.01549 0.5385 b3147 lpoA -11.44 0.059349 235 -- 255 64 -- 83 OM lipoprotein stimulator of MrcA transpeptidase  
90 0.01553 0.5385 b1043 csgC -15.92 0.009464 100 -- 115 69 -- 84 curli assembly protein  
91 0.0156 0.5385 b0881 clpS -13.09 0.030255 248 -- 265 74 -- 90 regulatory protein for ClpA substrate specificity  
92 0.01569 0.5385 b1246 oppD -11.32 0.062179 266 -- 290 69 -- 90 oligopeptide ABC transporter ATPase  
93 0.01594 0.5385 b3430 glgC -8.76 0.171477 231 -- 238 75 -- 82 glucose-1-phosphate adenylyltransferase  
94 0.01616 0.5385 b4217 ytfK -8.94 0.160287 283 -- 290 75 -- 82 DUF1107 family protein  
95 0.01635 0.5385 b2287 nuoB -8.27 0.206762 33 -- 42 71 -- 80 NADH:ubiquinone oxidoreductase chain B  
96 0.0164 0.5385 b2670 alaE -9.59 0.124335 245 -- 257 74 -- 86 alanine exporter alanine-inducible stress-responsive  
97 0.01643 0.5385 b2704 srlB -9.20 0.144516 91 -- 103 75 -- 87 glucitol/sorbitol-specific enzyme IIA component of PTS  
98 0.0165 0.5385 b0151 fhuC -12.15 0.044517 184 -- 202 66 -- 85 iron(3+)-hydroxamate import ABC transporter ATPase  
99 0.01653 0.5385 b0004 thrC -7.16 0.308279 183 -- 210 49 -- 64 L-threonine synthase  
100 0.01671 0.5385 b3211 yhcC -9.80 0.114390 283 -- 295 70 -- 82 putative Fe-S oxidoreductase Radical SAM superfamily protein  
101 0.01678 0.5385 b0452 tesB -11.66 0.054224 159 -- 170 73 -- 84 acyl-CoA thioesterase 2  
102 0.01732 0.5385 b3442 yhhZ -11.63 0.054951 288 -- 294 75 -- 81 putative Hcp1 family polymorphic toxin protein; putative colicin-like DNase/tRNase activity  
103 0.01739 0.5385 b0945 pyrD -8.62 0.180746 193 -- 204 79 -- 90 dihydro-orotate oxidase FMN-linked  
104 0.0176 0.5385 b2788 gudX -9.05 0.153387 171 -- 179 57 -- 65 glucarate dehydratase-related protein substrate unknown  
105 0.01788 0.5385 b0619 citA -6.78 0.351941 4 -- 24 64 -- 89 sensory histidine kinase in two-component regulatory system with CitB  
106 0.01861 0.5385 b2754 ygbF -9.88 0.110684 283 -- 300 13 -- 30 CRISPR adaptation ssRNA endonuclease  
107 0.01867 0.5385 b1478 adhP -13.80 0.022588 200 -- 222 62 -- 83 ethanol-active dehydrogenase/acetaldehyde-active reductase  
108 0.0187 0.5385 b1210 hemA -9.14 0.148366 174 -- 184 75 -- 84 glutamyl tRNA reductase  
109 0.0187 0.5385 b2616 recN -10.46 0.088138 200 -- 208 75 -- 83 recombination and repair protein  
110 0.0189 0.5385 b3175 secG -9.72 0.118042 86 -- 106 67 -- 90 preprotein translocase membrane subunit  
111 0.01894 0.5385 b2600 tyrA -7.88 0.238290 191 -- 206 74 -- 89 fused chorismate mutase T/prephenate dehydrogenase  
112 0.0191 0.5385 b0854 potF -9.27 0.140763 36 -- 50 64 -- 78 putrescine ABC transporter periplasmic binding protein  
113 0.0192 0.5385 b2573 rpoE -9.32 0.137991 165 -- 193 49 -- 83 RNA polymerase sigma E factor  
114 0.01931 0.5385 b1951 rcsA -10.71 0.079523 269 -- 285 16 -- 29 transcriptional regulator of colanic acid capsular biosynthesis  
115 0.01932 0.5385 b3475 acpT -9.48 0.130030 187 -- 194 75 -- 82 4'-phosphopantetheinyl transferase  
116 0.01945 0.5385 b1175 minD -9.10 0.150484 222 -- 240 13 -- 34 inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system  
117 0.01966 0.5385 b1203 ychF -10.24 0.095997 26 -- 41 73 -- 87 catalase inhibitor protein; ATPase K+-dependent ribosome-associated  
118 0.01985 0.5385 b2318 truA -10.16 0.099312 131 -- 143 70 -- 82 tRNA pseudouridine(38-40) synthase  
119 0.02023 0.5385 b3579 yiaO -11.14 0.066893 104 -- 124 64 -- 84 2 3-diketo-L-gulonate-binding periplasmic protein  
120 0.02045 0.5385 b0979 cbdB -12.05 0.046235 177 -- 194 16 -- 34 cytochrome bd-II oxidase subunit II  
121 0.02058 0.5385 b0796 ybiH -9.41 0.133616 217 -- 230 24 -- 36 DUF1956 domain-containing tetR family putative transcriptional regulator  
122 0.02068 0.5385 b4529 ydbJ -12.93 0.032363 174 -- 233 8 -- 79 DUF333 family putative lipoprotein  
123 0.02095 0.5385 b2562 yfhL -10.74 0.078719 174 -- 195 59 -- 77 putative 4Fe-4S cluster-containing protein  
124 0.02124 0.5385 b0198 metI -9.85 0.112177 270 -- 285 71 -- 87 DL-methionine transporter subunit  
125 0.02168 0.5385 b3380 yhfW -9.99 0.106098 159 -- 190 48 -- 81 phosphopentomutase-related metalloenzyme superfamily protein  
126 0.02177 0.5385 b4162 orn -9.93 0.108535 62 -- 89 61 -- 86 oligoribonuclease  
127 0.02181 0.5385 b3057 bacA -7.57 0.267037 62 -- 69 75 -- 82 undecaprenyl pyrophosphate phosphatase  
128 0.02183 0.5385 b0874 ybjE -9.13 0.148469 198 -- 230 59 -- 85 putative transporter  
129 0.02219 0.5385 b4034 malE -15.67 0.010476 105 -- 137 9 -- 40 maltose transporter subunit  
130 0.02238 0.5385 b4365 yjjQ -17.31 0.005324 260 -- 274 14 -- 28 putative transcriptional regulator  
131 0.02244 0.5385 b1713 pheT -10.81 0.076409 64 -- 80 73 -- 89 phenylalanine tRNA synthetase beta subunit  
132 0.0226 0.5385 b2721 hycE -8.05 0.224194 140 -- 148 71 -- 79 hydrogenase 3 large subunit  
133 0.02275 0.5385 b0177 bamA -6.79 0.350358 265 -- 271 23 -- 29 BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor  
134 0.0229 0.5385 b3729 glmS -8.05 0.223933 255 -- 266 79 -- 90 L-glutamine:D-fructose-6-phosphate aminotransferase  
135 0.02294 0.5385 b4254 argI -11.70 0.053356 4 -- 33 59 -- 85 ornithine carbamoyltransferase 1 b0273
136 0.02309 0.5385 b3223 nanE -8.63 0.180292 34 -- 47 74 -- 86 putative N-acetylmannosamine-6-P epimerase  
137 0.02312 0.5385 b2153 folE -12.97 0.031813 230 -- 265 52 -- 87 GTP cyclohydrolase I  
138 0.02324 0.5385 b1826 mgrB -8.64 0.179438 205 -- 238 60 -- 90 regulatory peptide for PhoPQ feedback inhibition  
139 0.02326 0.5385 b1651 gloA -10.25 0.095619 225 -- 233 75 -- 83 glyoxalase I Ni-dependent  
140 0.02329 0.5385 b3026 qseC -7.47 0.277092 174 -- 202 52 -- 78 quorum sensing sensory histidine kinase in two-component regulatory system with QseB  
141 0.02331 0.5385 b1844 exoX -7.22 0.302733 200 -- 217 62 -- 83 exodeoxyribonuclease 10; DNA exonuclease X  
142 0.02338 0.5385 b1126 potA -10.56 0.084569 277 -- 295 14 -- 34 spermidine/putrescine ABC transporter ATPase  
143 0.02402 0.5467 b4029 yjbH -10.20 0.097639 107 -- 117 75 -- 85 DUF940 family extracellular polysaccharide protein  
144 0.02429 0.5467 b3156 yhbS -10.71 0.079718 207 -- 222 50 -- 67 GNAT family putative N-acetyltransferase  
145 0.02443 0.5467 b2569 lepA -12.53 0.038132 5 -- 17 71 -- 85 back-translocating elongation factor EF4 GTPase  
146 0.0246 0.5467 b2813 mltA -8.67 0.177423 203 -- 222 69 -- 90 membrane-bound lytic murein transglycosylase A  
147 0.02477 0.5467 b3259 prmA -10.37 0.091190 111 -- 125 72 -- 88 methyltransferase for 50S ribosomal subunit protein L11  
148 0.0249 0.5467 b2131 osmF -10.26 0.095288 236 -- 244 75 -- 83 putative ABC transporter periplasmic binding protein  
149 0.0249 0.5467 b0737 tolQ -11.44 0.059241 123 -- 143 57 -- 77 membrane spanning protein in TolA-TolQ-TolR complex  
150 0.02548 0.5485 b0180 fabZ -10.02 0.104939 240 -- 263 1 -- 24 (3R)-hydroxymyristol acyl carrier protein dehydratase  
151 0.02561 0.5485 b4041 plsB -9.39 0.134646 197 -- 210 74 -- 86 glycerol-3-phosphate O-acyltransferase  
152 0.02564 0.5485 b0887 cydD -10.22 0.096853 263 -- 271 74 -- 82 glutathione/cysteine ABC transporter export permease/ATPase  
153 0.02565 0.5485 b2764 cysJ -8.62 0.180864 16 -- 26 74 -- 84 sulfite reductase alpha subunit flavoprotein  
154 0.02609 0.5541 b4195 ulaC -15.85 0.009707 6 -- 31 56 -- 80 L-ascorbate-specific enzyme IIA component of PTS  
155 0.02668 0.5559 b1625 cnu -8.12 0.218326 240 -- 246 81 -- 87 nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor  
156 0.02672 0.5559 b0957 ompA -9.60 0.124024 22 -- 30 81 -- 89 outer membrane protein A (3a;II*;G;d)  
157 0.02703 0.5559 b3221 yhcH -9.14 0.148013 119 -- 127 77 -- 85 DUF386 family protein cupin superfamily  
158 0.02721 0.5559 b1724 ydiZ -8.58 0.183444 272 -- 279 57 -- 64 uncharacterized protein  
159 0.02757 0.5559 b2701 mltB -11.73 0.052671 73 -- 129 32 -- 90 membrane-bound lytic murein transglycosylase B  
160 0.02795 0.5559 b1475 fdnH -7.98 0.230122 69 -- 80 24 -- 35 formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible  
161 0.02817 0.5559 b0852 rimK -8.21 0.210781 44 -- 79 81 -- 107 ribosomal protein S6 modification protein  
162 0.02861 0.5559 b0564 appY -9.53 0.127084 148 -- 162 62 -- 79 global transcriptional activator; DLP12 prophage b1499 b3515 b4116 b0566 b3516
163 0.02879 0.5559 b4244 pyrI -5.82 0.477897 276 -- 293 60 -- 77 aspartate carbamoyltransferase regulatory subunit  
164 0.02889 0.5559 b1512 lsrR -7.59 0.264791 265 -- 277 71 -- 84 lsr operon transcriptional repressor  
165 0.02909 0.5559 b3283 yrdD -9.69 0.119373 265 -- 285 52 -- 72 ssDNA-binding protein function unknown  
166 0.02918 0.5559 b3518 yhjA -9.21 0.144312 113 -- 127 71 -- 85 putative cytochrome C peroxidase  
167 0.02971 0.5559 b3062 ttdB -9.65 0.121251 224 -- 260 75 -- 106 L-tartrate dehydratase beta subunit  
168 0.0298 0.5559 b0161 degP -8.84 0.166335 239 -- 253 75 -- 88 serine endoprotease (protease Do) membrane-associated  
169 0.03038 0.5559 b2912 fau -9.38 0.135051 85 -- 98 22 -- 35 5-formyltetrahydrofolate cyclo-ligase family protein  
170 0.03041 0.5559 b1629 rsxC -10.04 0.103937 197 -- 215 64 -- 83 SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex  
171 0.03054 0.5559 b0045 yaaU -10.82 0.076059 142 -- 153 73 -- 84 putative MFS sugar transporter; membrane protein  
172 0.03064 0.5559 b1542 ydfI -13.08 0.030437 273 -- 290 69 -- 86 putative NAD-dependent D-mannonate oxidoreductase  
173 0.03066 0.5559 b2928 yggC -11.87 0.049837 290 -- 298 75 -- 83 putative PanK family P-loop kinase  
174 0.03067 0.5559 b4005 purD -11.17 0.066076 4 -- 22 73 -- 90 phosphoribosylglycinamide synthetase phosphoribosylamine-glycine ligase  
175 0.03099 0.5559 b2149 mglA -9.34 0.136967 92 -- 105 70 -- 84 methyl-galactoside ABC transporter ATPase  
176 0.03112 0.5559 b2536 hcaT -7.63 0.261550 240 -- 259 67 -- 85 putative 3-phenylpropionic transporter  
177 0.03112 0.5559 b0080 cra -12.94 0.032158 57 -- 78 62 -- 84 transcriptional repressor-activator for carbon metabolism  
178 0.03115 0.5559 b2528 iscA -9.66 0.120899 187 -- 207 62 -- 80 FeS cluster assembly protein  
179 0.03159 0.5559 b0790 ybhP -12.03 0.046743 250 -- 264 71 -- 85 endo/exonuclease/phosphatase family protein  
180 0.03162 0.5559 b1941 fliI -9.97 0.106944 57 -- 70 74 -- 88 flagellum-specific ATP synthase  
181 0.03179 0.5559 b3240 aaeB -9.50 0.128739 275 -- 287 72 -- 86 p-hydroxybenzoic acid efflux system component  
182 0.03197 0.5559 b0212 gloB -7.96 0.231442 50 -- 71 56 -- 75 hydroxyacylglutathione hydrolase  
183 0.03203 0.5559 b4484 cpxP -9.38 0.135070 107 -- 120 71 -- 85 inhibitor of the cpx response; periplasmic adaptor protein  
184 0.03259 0.5559 b0811 glnH -9.61 0.123139 215 -- 230 74 -- 90 glutamine transporter subunit  
185 0.03283 0.5559 b1937 fliE -12.05 0.046361 209 -- 229 14 -- 35 flagellar basal-body component  
186 0.03285 0.5559 b1003 yccJ -7.53 0.270746 41 -- 54 75 -- 88 uncharacterized protein  
187 0.03332 0.5559 b2019 hisG -10.76 0.077976 170 -- 191 15 -- 34 ATP phosphoribosyltransferase  
188 0.03339 0.5559 b3232 zapE -6.91 0.336884 267 -- 282 15 -- 35 divisome ATPase  
189 0.03342 0.5559 b2172 yeiQ -17.65 0.004645 282 -- 298 70 -- 86 putative NAD-dependent D-mannonate oxidoreductase  
190 0.03345 0.5559 b4090 rpiB -6.75 0.355761 259 -- 286 57 -- 78 ribose 5-phosphate isomerase B/allose 6-phosphate isomerase  
191 0.03353 0.5559 b2129 yehX -7.36 0.287226 59 -- 67 69 -- 77 putative ABC transporter ATPase  
192 0.03364 0.5559 b2333 yfcP -8.48 0.190877 22 -- 36 61 -- 77 putative fimbrial-like adhesin protein  
193 0.03391 0.5559 b3642 pyrE -10.20 0.097546 70 -- 90 57 -- 80 orotate phosphoribosyltransferase  
194 0.03409 0.5559 b1836 yebV -7.98 0.229830 12 -- 23 77 -- 87 uncharacterized protein  
195 0.03428 0.5559 b0434 yajG -10.30 0.093744 131 -- 149 66 -- 84 putative lipoprotein  
196 0.0344 0.5559 b0954 fabA -7.50 0.274211 100 -- 110 74 -- 84 beta-hydroxydecanoyl thioester dehydrase  
197 0.0346 0.5559 b2829 ptsP -9.94 0.108120 103 -- 113 80 -- 90 PEP-protein phosphotransferase enzyme I; GAF domain containing protein  
198 0.03475 0.5559 b1249 clsA -8.08 0.221640 216 -- 230 57 -- 82 cardiolipin synthase 1  
199 0.03481 0.5559 b0407 yajC -8.41 0.195839 88 -- 104 15 -- 30 SecYEG protein translocase auxillary subunit  
200 0.03481 0.5559 b1058 yceO -9.40 0.133707 85 -- 100 70 -- 85 uncharacterized protein  

Details of Selected Interaction Download Interaction Details 

mRNA

sRNA


		

		

		

		
		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		
		
		
Evolutionary conservation of mRNA targets
			(alignment generated with
			Jalview)

		
		
		
Evolutionary conservation of sRNA
			(alignment generated with
			Jalview)

		
		
		

		
	

	
	
	

	
	
	




			 
	





	
Job resubmission

	

		

			Use the following button if you want to resubmit the job with
			altered input or parameterization:
		

		

			
			Feeds the job parameters to the input page to resubmit the job.
			
		

	


	





	
de.NBI 
		usability assessment

	

		

			
				
				
			 
		

		

			Please 
			support us 
			by filling this 
			short quality survey 
			for evaluating this
			de.NBI
			service.
		

	





	





	
	
		 
		
When using CopraRNA please cite :







		 
	
	
	
		 
		



Results are computed with CopraRNA version 2.1.2



		 
	

			





	About this web server
	  | 
	version 5.0.9
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer