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 7743500

Input and runtime details for job 7743500 (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 7743500 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:35:00 CET 2018
?CopraRNA Started@ Fri Feb 16 21:27:12 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 06:56:30 CET 2018
?Post-Processing Finished@ Sat Feb 17 06:56:38 CET 2018
?Job Completed@ Sat Feb 17 06:57:11 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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 pa3775 N/A -6.65 0.627514 32 -- 38 50 -- 56 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
2 9.847e-10 2.263e-06 pa5490 cc4 -23.49 0.000003 181 -- 254 56 -- 120 cytochrome C4  
3 1.464e-07 0.0002243 pa3814 iscS -11.38 0.090161 182 -- 237 39 -- 110 cysteine desulfurase  
4 5.154e-07 0.0005922 pa1581 sdhC -15.05 0.009907 206 -- 221 108 -- 123 succinate dehydrogenase subunit C  
5 7.253e-07 0.0006667 pa5351 rubA1 -17.51 0.001615 172 -- 222 71 -- 121 rubredoxin  
6 4.972e-06 0.003808 pa1336 N/A -12.31 0.054230 242 -- 253 107 -- 120 two-component sensor  
7 9.272e-06 0.004211 pa1571 N/A -18.24 0.000884 168 -- 194 96 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
8 1.007e-05 0.004211 pa3621 fdxA -18.47 0.000724 244 -- 255 71 -- 82 ferredoxin I  
9 1.098e-05 0.004211 pa0119 N/A -18.72 0.000584 256 -- 296 78 -- 118 C4-dicarboxylate transporter DctA pa5479 pa1183
10 1.1e-05 0.004211 pa5300 cycB -16.80 0.002828 155 -- 174 99 -- 117 cytochrome C5  
11 1.195e-05 0.004211 pa3638 N/A -14.67 0.012752 102 -- 115 100 -- 120 tRNA(Ile)-lysidine synthase  
12 1.22e-05 0.004211 pa3312 N/A -10.60 0.134070 231 -- 250 100 -- 119 3-hydroxyisobutyrate dehydrogenase  
13 1.26e-05 0.004211 pa3276 N/A -14.47 0.014594 182 -- 242 38 -- 108 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
14 1.283e-05 0.004211 pa2953 N/A -15.00 0.010274 173 -- 195 95 -- 119 electron transfer flavoprotein-ubiquinone oxidoreductase  
15 2.583e-05 0.007914 pa3049 rmf -22.33 0.000014 230 -- 282 40 -- 88 ribosome modulation factor  
16 3.003e-05 0.008352 pa2689 N/A -17.00 0.002414 189 -- 205 100 -- 117 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
17 3.089e-05 0.008352 pa5396 N/A -7.92 0.424136 180 -- 186 104 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
18 3.753e-05 0.009449 pa5036 gltB -9.24 0.251750 240 -- 259 103 -- 120 glutamate synthase subunit alpha  
19 3.906e-05 0.009449 pa0443 N/A -14.62 0.013168 152 -- 204 75 -- 119 transporter  
20 4.966e-05 0.01105 pa5388 N/A -18.86 0.000517 168 -- 251 37 -- 123 'Product name confidence: class 4:Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences.' pa3236 pa0030 pa5378
21 5.061e-05 0.01105 pa1778 cobA -17.87 0.001208 184 -- 227 69 -- 109 uroporphyrin-III C-methyltransferase  
22 5.562e-05 0.01105 pa2264 N/A -16.58 0.003334 170 -- 193 98 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
23 5.711e-05 0.01105 pa2967 fabG -15.49 0.007349 171 -- 236 53 -- 111 3-oxoacyl-[acyl-carrier-protein] reductase FabG  
24 5.771e-05 0.01105 pa5035 gltD -10.90 0.115442 181 -- 216 79 -- 110 glutamate synthase subunit beta  
25 6.377e-05 0.01172 pa4235 bfrA -17.70 0.001383 58 -- 83 99 -- 122 bacterioferritin  
26 6.892e-05 0.01177 pa0375 ftsX -18.23 0.000891 153 -- 205 100 -- 144 cell division protein FtsX  
27 6.94e-05 0.01177 pa5535 N/A -11.95 0.066023 197 -- 251 53 -- 120 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
28 7.532e-05 0.01177 pa2865 N/A -15.38 0.007930 179 -- 247 40 -- 110 glycosylase  
29 7.803e-05 0.01177 pa5491 N/A -19.34 0.000334 185 -- 216 75 -- 108 cytochrome  
30 8.033e-05 0.01177 pa3717 N/A -10.05 0.175331 209 -- 216 75 -- 82 FkbP-type peptidyl-prolyl cis-trans isomerase  
31 8.059e-05 0.01177 pa5164 rmlC -15.78 0.005968 187 -- 204 101 -- 122 dTDP-4-dehydrorhamnose 3 5-epimerase  
32 8.271e-05 0.01177 pa5176 N/A -17.77 0.001308 216 -- 255 75 -- 119 ADP-ribose diphosphatase NudE  
33 8.454e-05 0.01177 pa3481 N/A -18.00 0.001084 15 -- 90 50 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
34 0.0001037 0.01388 pa0494 N/A -14.76 0.012046 49 -- 92 75 -- 117 acetyl-CoA carboxylase biotin carboxylase subunit  
35 0.0001057 0.01388 pa1103 N/A -18.12 0.000977 185 -- 207 81 -- 102 flagellar assembly protein FliH  
36 0.0001485 0.01896 pa2147 katE -15.32 0.008256 177 -- 207 74 -- 109 catalase HPII  
37 0.0001556 0.01933 pa4880 N/A -12.85 0.039617 174 -- 244 39 -- 119 bacterioferritin  
38 0.0001678 0.02029 pa4131 N/A -10.32 0.153559 164 -- 172 74 -- 82 iron-sulfur protein  
39 0.0001834 0.02162 pa3120 leuD -14.73 0.012246 171 -- 252 39 -- 118 isopropylmalate isomerase small subunit  
40 0.0001908 0.02192 pa5015 aceE -12.88 0.038887 273 -- 297 101 -- 123 pyruvate dehydrogenase subunit E1  
41 0.000201 0.02253 pa1808 N/A -10.12 0.169236 14 -- 78 39 -- 99 ABC transporter permease  
42 0.000247 0.02703 pa4550 fimU -17.01 0.002407 39 -- 109 35 -- 119 type 4 fimbrial biogenesis protein FimU pa4549
43 0.0002634 0.02815 pa2831 N/A -19.04 0.000437 175 -- 195 99 -- 118 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
44 0.0002709 0.02829 pa1340 N/A -13.31 0.030188 17 -- 34 101 -- 117 amino acid ABC transporter permease  
45 0.0002969 0.02946 pa0151 N/A -17.56 0.001552 238 -- 273 39 -- 82 TonB-dependent receptor  
46 0.0003006 0.02946 pa4460 N/A -9.10 0.267813 234 -- 244 75 -- 85 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
47 0.0003012 0.02946 pa1776 sigX -11.73 0.074706 90 -- 102 103 -- 115 RNA polymerase sigma factor SigX  
48 0.0003226 0.03063 pa2507 catA -12.73 0.042466 203 -- 291 39 -- 120 catechol 1 2-dioxygenase  
49 0.0003265 0.03063 pa0541 N/A -11.15 0.101438 170 -- 235 53 -- 118 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
50 0.0003784 0.03426 pa2805 N/A -14.24 0.016920 210 -- 223 74 -- 88 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
51 0.0003802 0.03426 pa4431 N/A -18.94 0.000478 156 -- 218 72 -- 123 iron-sulfur protein  
52 0.0004019 0.03518 pa4012 N/A -10.34 0.152385 122 -- 132 100 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
53 0.0004056 0.03518 pa1750 N/A -9.05 0.272805 157 -- 194 32 -- 72 phospho-2-dehydro-3-deoxyheptonate aldolase  
54 0.000431 0.03637 pa5355 glcD -9.87 0.190611 164 -- 178 41 -- 54 glycolate oxidase subunit GlcD  
55 0.0004353 0.03637 pa0086 N/A -16.64 0.003171 21 -- 37 100 -- 117 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
56 0.0004529 0.03717 pa2678 N/A -16.50 0.003530 187 -- 235 44 -- 90 ABC transporter permease  
57 0.0004766 0.03843 pa1413 N/A -13.23 0.031643 209 -- 220 33 -- 44 transcriptional regulator pa0708 pa4203
58 0.0005047 0.0395 pa4066 N/A -14.62 0.013175 166 -- 238 44 -- 118 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
59 0.0005101 0.0395 pa2173a N/A -13.53 0.026409 139 -- 150 107 -- 119    
60 0.000522 0.0395 pa1477 ccmC -13.58 0.025601 178 -- 207 98 -- 123 heme exporter protein CcmC  
61 0.0005242 0.0395 pa4564 N/A -14.31 0.016198 190 -- 242 35 -- 89 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
62 0.0005356 0.0397 pa5012 waaF -13.04 0.035456 194 -- 235 70 -- 110 heptosyltransferase II  
63 0.0005567 0.04061 pa4538 ndh -15.78 0.005953 57 -- 71 102 -- 118 NADH dehydrogenase  
64 0.000634 0.04553 pa1832 N/A -15.82 0.005823 184 -- 249 39 -- 110 protease  
65 0.0006555 0.04603 pa0184 N/A -11.46 0.086208 64 -- 73 101 -- 110 ABC transporter ATP-binding protein pa2294
66 0.0006609 0.04603 pa1980 eraR -16.49 0.003558 189 -- 219 71 -- 102 response regulator EraR  
67 0.0007208 0.0493 pa0304 spuH -8.66 0.319981 266 -- 281 40 -- 54 polyamine transporter PotI  
68 0.0007335 0.0493 pa0794 N/A -9.72 0.203453 182 -- 194 107 -- 118 aconitate hydratase  
69 0.0007462 0.0493 pa0882 N/A -13.09 0.034380 240 -- 255 104 -- 119 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
70 0.0007568 0.0493 pa3767 N/A -16.77 0.002880 160 -- 178 98 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
71 0.000767 0.0493 pa3381 N/A -11.39 0.089379 127 -- 140 103 -- 116 transcriptional regulator  
72 0.0007723 0.0493 pa2659 N/A -15.67 0.006436 157 -- 217 75 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
73 0.0008061 0.04991 pa0112 N/A -16.64 0.003170 93 -- 149 38 -- 90 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
74 0.0008152 0.04991 pa3942 tesB -9.59 0.215645 1 -- 36 40 -- 80 acyl-CoA thioesterase II  
75 0.0008154 0.04991 pa4367 bifA -16.44 0.003694 124 -- 142 99 -- 118 protein BifA  
76 0.0008254 0.04991 pa0029 N/A -13.54 0.026240 35 -- 51 100 -- 123 sulfate transporter  
77 0.0008517 0.05078 pa4366 sodB -3.26 0.982782 263 -- 269 117 -- 123 superoxide dismutase  
78 0.000864 0.05078 pa4263 rplC -13.85 0.021626 50 -- 71 101 -- 122 50S ribosomal protein L3  
79 0.0008761 0.05078 pa2577 N/A -12.88 0.038908 242 -- 256 40 -- 55 transcriptional regulator  
80 0.0008839 0.05078 pa0353 ilvD -13.41 0.028361 174 -- 187 107 -- 121 dihydroxy-acid dehydratase  
81 0.0009408 0.05338 pa2962 tmk -12.93 0.037833 94 -- 116 34 -- 55 thymidylate kinase  
82 0.000993 0.05566 pa5549 glmS -14.85 0.011343 179 -- 208 71 -- 110 glucosamine--fructose-6-phosphate aminotransferase  
83 0.001018 0.05635 pa1553 ccoO1 -12.95 0.037511 176 -- 198 75 -- 98 cbb3-type cytochrome C oxidase subunit II pa1556
84 0.001042 0.05699 pa3121 leuC -8.58 0.330521 182 -- 193 98 -- 110 3-isopropylmalate dehydratase large subunit  
85 0.001072 0.05733 pa4430 N/A -13.41 0.028331 184 -- 204 101 -- 120 cytochrome b  
86 0.001073 0.05733 pa0916 N/A -12.39 0.051807 188 -- 200 107 -- 119 ribosomal protein S12 methylthiotransferase RimO  
87 0.001101 0.05816 pa1343 N/A -16.83 0.002748 192 -- 238 44 -- 87 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
88 0.001191 0.06151 pa1669 N/A -13.12 0.033789 66 -- 116 61 -- 119 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)' pa0077
89 0.001191 0.06151 pa1669 N/A -13.12 0.033789 66 -- 116 61 -- 119 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)' pa0077
90 0.001223 0.06177 pa1071 braF -14.34 0.015804 45 -- 124 40 -- 117 ABC transporter ATP-binding protein  
91 0.001223 0.06177 pa3618 N/A -14.35 0.015718 191 -- 224 76 -- 123 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
92 0.001266 0.06327 pa1307 N/A -13.15 0.033214 250 -- 278 41 -- 65 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
93 0.001289 0.06355 pa4454 N/A -9.11 0.266760 170 -- 178 75 -- 83 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
94 0.001308 0.06355 pa1587 lpdG -9.92 0.185926 282 -- 296 75 -- 91 2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase  
95 0.001333 0.06355 pa5380 gbdR -10.99 0.110367 154 -- 228 78 -- 123 protein GbdR  
96 0.00134 0.06355 pa1641 N/A -15.72 0.006244 223 -- 294 34 -- 118 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
97 0.001341 0.06355 pa3929 cioB -12.35 0.052798 141 -- 190 33 -- 89 cyanide insensitive terminal oxidase  
98 0.001381 0.06477 pa5040 pilQ -10.76 0.123916 69 -- 120 75 -- 117 type 4 fimbrial biogenesis outer membrane protein PilQ  
99 0.001467 0.06809 pa5206 argE -18.10 0.000993 157 -- 251 40 -- 119 acetylornithine deacetylase  
100 0.001607 0.07384 pa0607 rpe -12.76 0.041806 177 -- 194 99 -- 118 ribulose-phosphate 3-epimerase  
101 0.001673 0.07499 pa1787 acnB -10.32 0.154094 277 -- 296 100 -- 121 aconitate hydratase B  
102 0.001679 0.07499 pa2657 N/A -10.65 0.130856 243 -- 261 104 -- 121 two-component response regulator  
103 0.001681 0.07499 pa3587 metR -12.26 0.055812 244 -- 261 101 -- 121 transcriptional regulator MetR  
104 0.00171 0.07531 pa4333 N/A -8.52 0.338548 151 -- 157 40 -- 46 fumarase  
105 0.00174 0.07531 pa4182 N/A -13.56 0.025913 222 -- 265 39 -- 89 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
106 0.001743 0.07531 pa4019 N/A -13.63 0.024857 269 -- 289 98 -- 119 aromatic acid decarboxylase  
107 0.001753 0.07531 pa3707 N/A -15.86 0.005654 190 -- 241 38 -- 85 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
108 0.001802 0.07562 pa0365 N/A -14.54 0.013920 243 -- 252 101 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
109 0.001808 0.07562 pa0202 N/A -7.70 0.456423 178 -- 185 75 -- 82 amidase pa4342
110 0.00181 0.07562 pa2449 N/A -19.06 0.000430 48 -- 69 99 -- 122 transcriptional regulator  
111 0.001873 0.07755 pa4347 N/A -11.13 0.102611 35 -- 49 91 -- 105 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
112 0.001904 0.07812 pa5310 N/A -10.92 0.114175 276 -- 285 74 -- 83 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
113 0.001932 0.07857 pa1964 N/A -9.53 0.221537 258 -- 274 103 -- 120 ABC-F family ATPase  
114 0.001956 0.07883 pa1616 N/A -7.83 0.436748 16 -- 25 101 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
115 0.001984 0.07883 pa3002 mfd -15.72 0.006234 203 -- 232 53 -- 84 transcription-repair coupling factor  
116 0.00199 0.07883 pa4478 N/A -13.34 0.029660 177 -- 225 39 -- 82 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
117 0.002052 0.07999 pa0290 N/A -8.56 0.333144 143 -- 150 40 -- 47 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
118 0.002082 0.07999 pa5066 hisI -12.42 0.050876 194 -- 221 100 -- 123 phosphoribosyl-AMP cyclohydrolase  
119 0.002082 0.07999 pa4053 ribE -9.84 0.193218 284 -- 298 103 -- 117 6 7-dimethyl-8-ribityllumazine synthase  
120 0.002089 0.07999 pa3670 N/A -15.68 0.006401 170 -- 246 44 -- 120 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
121 0.002197 0.08331 pa2583 N/A -13.54 0.026172 146 -- 169 69 -- 89 sensor/response regulator hybrid protein pa3044 pa3946 pa4982 pa1611
122 0.002226 0.08331 pa4286 N/A -14.46 0.014621 171 -- 194 98 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
123 0.00223 0.08331 pa0552 pgk -10.33 0.153234 163 -- 259 42 -- 119 phosphoglycerate kinase  
124 0.002337 0.08662 pa3949 N/A -9.36 0.238904 5 -- 33 38 -- 61 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
125 0.002365 0.08694 pa4303 tadZ -11.60 0.080140 12 -- 30 101 -- 120 class 2: Function of highly similar gene experimentally demonstrated in another organism (and gene context consistent in terms of pathways its involved in (if known).  
126 0.002419 0.08825 pa0452 N/A -8.57 0.332234 172 -- 209 83 -- 122 'Product name confidence: class 3 (Function proposed based on presence of conserved amino acid motif structural feature or limited sequence similarity to an experimentally studied gene)'  
127 0.002525 0.0912 pa3976 thiE -9.31 0.244259 189 -- 204 101 -- 123 thiamine-phosphate pyrophosphorylase  
128 0.00255 0.0912 pa3463 N/A -7.51 0.486845 225 -- 240 104 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
129 0.002597 0.0912 pa2983 N/A -10.36 0.150975 196 -- 207 70 -- 82 translocation protein TolQ  
130 0.002619 0.0912 pa1320 cyoD -12.20 0.057664 172 -- 192 99 -- 119 cytochrome o ubiquinol oxidase subunit IV  
131 0.002644 0.0912 pa4772 N/A -11.20 0.098904 193 -- 209 105 -- 123 ferredoxin  
132 0.002652 0.0912 pa0364 N/A -15.84 0.005742 174 -- 193 100 -- 122 oxidoreductase  
133 0.002661 0.0912 pa2511 N/A -14.22 0.017134 181 -- 210 98 -- 119 transcriptional regulator  
134 0.002678 0.0912 pa1421 gbuA -12.45 0.050008 184 -- 195 107 -- 120 guanidinobutyrase  
135 0.002679 0.0912 pa0035 trpA -9.18 0.258333 240 -- 261 101 -- 123 tryptophan synthase subunit alpha  
136 0.00271 0.09122 pa0516 nirF -12.42 0.050980 176 -- 250 51 -- 109 heme d1 biosynthesis protein NirF pa0519 pa0509
137 0.002719 0.09122 pa5476 citA -9.77 0.199491 137 -- 148 71 -- 82 citrate transporter pa0703 pa4343
138 0.002776 0.09245 pa0440 N/A -11.93 0.067049 197 -- 216 104 -- 120 oxidoreductase  
139 0.002816 0.0931 pa1173 napB -8.92 0.288683 179 -- 194 100 -- 120 cytochrome C protein NapB  
140 0.002911 0.09555 pa4656 N/A -13.59 0.025440 215 -- 238 100 -- 120 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
141 0.002959 0.09644 pa5519 N/A -12.18 0.058415 260 -- 272 100 -- 118 acyl-CoA thioesterase pa2693
142 0.003054 0.09883 pa4939 N/A -10.79 0.122172 84 -- 99 39 -- 58 ATP phosphoribosyltransferase  
143 0.003113 0.1001 pa1811 N/A -11.02 0.108661 233 -- 245 105 -- 120 solute-binding protein  
144 0.003137 0.1001 pa1516 N/A -10.35 0.151671 51 -- 72 44 -- 62 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
145 0.003161 0.1002 pa4147 acoR -9.16 0.260996 230 -- 255 98 -- 121 transcriptional regulator AcoR pa4021
146 0.003267 0.1028 pa0918 N/A -13.83 0.021920 192 -- 207 107 -- 122 cytochrome b561  
147 0.003398 0.1053 pa4657 N/A -14.94 0.010704 152 -- 169 105 -- 123 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
148 0.003408 0.1053 pa1533 N/A -10.12 0.169364 218 -- 231 101 -- 120 nucleoid-associated protein  
149 0.003414 0.1053 pa3109 N/A -16.06 0.004890 59 -- 72 33 -- 46 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
150 0.003458 0.106 pa5558 atpF -11.25 0.096505 215 -- 228 107 -- 120 ATP synthase subunit B  
151 0.003549 0.1073 pa4443 cysD -8.92 0.288201 61 -- 67 74 -- 80 sulfate adenylyltransferase subunit 2  
152 0.003562 0.1073 pa3096 xcpY -9.37 0.238148 248 -- 259 98 -- 110 type II secretion system protein L  
153 0.003576 0.1073 pa5013 ilvE -11.20 0.098760 213 -- 229 103 -- 120 branched-chain amino acid aminotransferase  
154 0.003595 0.1073 pa3974 ladS -15.87 0.005612 181 -- 233 43 -- 89 lost adherence sensor LadS  
155 0.003654 0.1083 pa1551 N/A -14.46 0.014645 185 -- 205 100 -- 119 ferredoxin  
156 0.00379 0.1117 pa3495 nth -14.09 0.018638 94 -- 117 105 -- 123 endonuclease III  
157 0.003825 0.112 pa0687 N/A -10.29 0.156397 189 -- 203 102 -- 118 type II secretion system protein pa3102
158 0.003862 0.1123 pa4780 N/A -10.69 0.128339 184 -- 207 98 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
159 0.003984 0.115 pa2627 N/A -8.37 0.359084 22 -- 39 38 -- 59 high frequency lysogenization protein HflD  
160 0.004014 0.115 pa3736 hom -12.18 0.058138 179 -- 203 72 -- 98 homoserine dehydrogenase  
161 0.004027 0.115 pa0009 glyQ -13.96 0.020216 43 -- 68 95 -- 119 glycine--tRNA ligase subunit alpha  
162 0.00407 0.1155 pa4993 N/A -9.83 0.193366 13 -- 32 104 -- 121 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
163 0.004151 0.1159 pa3263 N/A -13.17 0.032863 133 -- 150 104 -- 121 recombination associated protein RdgC  
164 0.004161 0.1159 pa4420 N/A -11.64 0.078545 165 -- 187 40 -- 62 S-adenosyl-methyltransferase MraW  
165 0.004162 0.1159 pa1850 N/A -12.78 0.041348 242 -- 255 104 -- 117 transcriptional regulator  
166 0.004233 0.117 pa2585 uvrC -12.59 0.046141 89 -- 105 106 -- 123 excinuclease ABC subunit C  
167 0.004312 0.117 pa2583 N/A -13.54 0.026172 146 -- 169 69 -- 89 sensor/response regulator hybrid protein pa3044 pa3946 pa4982 pa1611
168 0.004312 0.117 pa2583 N/A -13.54 0.026172 146 -- 169 69 -- 89 sensor/response regulator hybrid protein pa3044 pa3946 pa4982 pa1611
169 0.004373 0.117 pa4102 bfmS -16.20 0.004411 15 -- 27 35 -- 47 protein BfmS  
170 0.004404 0.117 pa0562 N/A -14.73 0.012303 222 -- 237 74 -- 91 hydrolase pa2067
171 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
172 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
173 0.004404 0.117 pa3327 N/A -14.55 0.013827 159 -- 238 39 -- 118 non-ribosomal peptide synthetase  
174 0.00444 0.1171 pa4756 carB -14.46 0.014655 252 -- 264 107 -- 119 carbamoyl phosphate synthase large subunit  
175 0.004467 0.1171 pa2047 N/A -7.63 0.467709 171 -- 177 103 -- 109 transcriptional regulator  
176 0.004483 0.1171 pa1774 crfX -11.59 0.080592 153 -- 172 96 -- 117 Product name confidence: class 1: Function experimentally demonstrated in P. aeruginosa  
177 0.004514 0.1172 pa4639 N/A -11.28 0.094804 222 -- 231 101 -- 110 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
178 0.004573 0.1181 pa0900 N/A -12.48 0.049102 209 -- 242 75 -- 111 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
179 0.004617 0.1185 pa4812 fdnG -14.50 0.014314 180 -- 196 94 -- 109 formate dehydrogenase-O major subunit  
180 0.004705 0.1199 pa3616 N/A -16.34 0.003989 120 -- 132 35 -- 47 recombination regulator RecX  
181 0.004727 0.1199 pa2509 catB -12.44 0.050225 208 -- 226 106 -- 121 muconate cycloisomerase I  
182 0.004765 0.1199 pa1522 N/A -10.50 0.140829 28 -- 41 106 -- 119 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
183 0.004788 0.1199 pa0638 N/A -13.00 0.036234 1 -- 21 40 -- 62 bacteriophage protein  
184 0.004799 0.1199 pa1298 N/A -15.65 0.006528 2 -- 21 39 -- 58 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
185 0.004884 0.1213 pa2528 N/A -11.72 0.074904 177 -- 197 98 -- 118 resistance-nodulation-cell division (RND) efflux membrane fusion protein  
186 0.004909 0.1213 pa3889 N/A -13.61 0.025105 195 -- 204 101 -- 110 ABC transporter  
187 0.004933 0.1213 pa0613 N/A -16.40 0.003821 197 -- 220 101 -- 120 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
188 0.00503 0.1227 pa1766 N/A -13.35 0.029524 230 -- 250 100 -- 120 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
189 0.005044 0.1227 pa4284 recB -12.92 0.038081 40 -- 56 70 -- 89 exodeoxyribonuclease V subunit beta  
190 0.005086 0.123 pa0591 N/A -15.37 0.007942 156 -- 173 100 -- 120 protein ApaG  
191 0.005174 0.1243 pa4409 ftsQ -12.87 0.039132 188 -- 243 45 -- 102 cell division protein FtsQ  
192 0.005234 0.1243 pa1840 N/A -6.31 0.681723 125 -- 149 99 -- 122 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
193 0.005243 0.1243 pa3725 recJ -10.65 0.130688 184 -- 203 102 -- 119 single-stranded-DNA-specific exonuclease RecJ  
194 0.005258 0.1243 pa3808 N/A -13.66 0.024437 189 -- 216 98 -- 123 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
195 0.005273 0.1243 pa4698 N/A -10.50 0.140691 227 -- 236 35 -- 44 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
196 0.005339 0.1252 pa1085 flgJ -8.97 0.282317 179 -- 193 98 -- 119 peptidoglycan hydrolase FlgJ  
197 0.005405 0.1261 pa2580 N/A -16.79 0.002834 13 -- 30 70 -- 88 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
198 0.005468 0.1268 pa5463 N/A -11.00 0.109950 289 -- 298 38 -- 47 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  
199 0.005488 0.1268 pa1158 N/A -11.27 0.095596 213 -- 231 101 -- 120 two-component sensor  
200 0.005522 0.1269 pa1052 N/A -14.49 0.014391 203 -- 224 103 -- 123 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'  

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 5.0.10
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer