Freiburg RNA Tools
IntaRNA - 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

IntaRNA 7814698

Input and runtime details for job 7814698 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_002516
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 7814698 (server version trunk)

?Job Submitted & Queued@ Fri Jan 07 21:23:03 CET 2022
?Pre-Processing Started@ Fri Jan 07 21:23:24 CET 2022
?IntaRNA Started@ Fri Jan 07 21:25:48 CET 2022
?IntaRNA Finished & Post-Processing@ Fri Jan 07 21:26:49 CET 2022
?Post-Processing Finished@ Fri Jan 07 21:27:12 CET 2022
?Job Completed@ Fri Jan 07 21:27:13 CET 2022
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7814698&toolName=IntaRNA ( 30 days expiry )

Description of the job

PrrF1 - Pseudomonas aeruginosa

? Output [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

? Identified Interactions for NC_002516 Pseudomonas aeruginosa PAO1

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
PA3621 44 55 PrrF1 71 82 -19.78 5.15e-05 0.1650844 fdxA ferredoxin I
PA0119 53 73 PrrF1 101 121 -19.45 6.97e-05 0.1650844 C4-dicarboxylate transporter DctA
PA2831 -26 -6 PrrF1 99 118 -18.5 0.0001603 0.246324 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1103 -16 54 PrrF1 38 102 -17.95 0.0002537 0.246324 flagellar assembly protein FliH
PA1571 -33 -7 PrrF1 96 121 -17.92 0.00026 0.246324 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA5300 -45 -27 PrrF1 99 116 -16.71 0.0006743 0.5323598 cycB cytochrome C5
PA2715 44 55 PrrF1 71 82 -16.49 0.000796 0.5386646 ferredoxin
PA5490 -20 41 PrrF1 67 120 -16.18 0.0010019 0.5771389 cc4 cytochrome C4
PA5351 -10 22 PrrF1 71 99 -15.79 0.0013306 0.5771389 rubA1 rubredoxin
PA3291 11 32 PrrF1 70 90 -15.78 0.0013402 0.5771389 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2659 -9 17 PrrF1 75 99 -15.78 0.0013402 0.5771389 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2264 -30 -9 PrrF1 99 121 -15.57 0.0015572 0.5837442 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0007 -4 13 PrrF1 104 120 -15.53 0.001602 0.5837442 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1464 28 51 PrrF1 68 89 -15.33 0.0018445 0.6240997 purine-binding chemotaxis protein
PA3767 -40 -23 PrrF1 98 121 -15.05 0.0022411 0.6680946 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3255 -74 -60 PrrF1 101 115 -15.04 0.0022566 0.6680946 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1432 25 50 PrrF1 70 89 -14.9 0.0024845 0.6765752 lasI acyl-homoserine-lactone synthase
PA0365 43 52 PrrF1 101 110 -14.85 0.0025709 0.6765752 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4756 52 64 PrrF1 107 119 -14.73 0.0027896 0.6954913 carB carbamoyl phosphate synthase large subunit
PA5164 -13 4 PrrF1 101 121 -14.59 0.0030663 0.7262532 rmlC dTDP-4-dehydrorhamnose 35-epimerase
PA1551 -15 5 PrrF1 100 118 -14.25 0.0038469 0.8677507 ferredoxin
PA3032 -5 4 PrrF1 101 109 -14.09 0.0042741 0.8860661 snr1 cytochrome C Snr1
PA0112 -40 -29 PrrF1 98 109 -14.08 0.0043022 0.8860661 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3618 -9 24 PrrF1 76 122 -13.93 0.0047445 0.9364457 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4812 -21 -7 PrrF1 96 109 -13.84 0.0050296 0.9377188 fdnG formate dehydrogenase-O major subunit
PA4156 -49 -33 PrrF1 99 117 -13.71 0.0054693 0.9377188 TonB-dependent receptor
PA0882 40 54 PrrF1 105 119 -13.68 0.0055756 0.9377188 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3402 25 45 PrrF1 40 57 -13.64 0.0057204 0.9377188 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2894 -39 -23 PrrF1 104 121 -13.63 0.0057571 0.9377188 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0916 -13 -1 PrrF1 107 119 -13.58 0.005944 0.9377188 ribosomal protein S12 methylthiotransferase RimO
PA1069 -21 22 PrrF1 71 109 -13.51 0.006215 0.9377188 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2953 -28 -6 PrrF1 95 119 -13.48 0.0063346 0.9377188 electron transfer flavoprotein-ubiquinone oxidoreductase
PA2689 -6 5 PrrF1 100 110 -13.41 0.0066218 0.9505293 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4155 -10 5 PrrF1 100 114 -13.27 0.0072326 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1216 -28 15 PrrF1 78 119 -13.13 0.0078947 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA5206 -43 62 PrrF1 35 118 -12.8 0.0096811 0.9556607 argE acetylornithine deacetylase
PA0898 -56 -29 PrrF1 99 122 -12.8 0.0096811 0.9556607 aruD N-succinylglutamate 5-semialdehyde dehydrogenase
PA0353 -26 -8 PrrF1 98 120 -12.74 0.0100432 0.9556607 ilvD dihydroxy-acid dehydratase
PA4017 36 45 PrrF1 37 46 -12.67 0.0104813 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0443 -44 4 PrrF1 75 113 -12.67 0.0104813 0.9556607 transporter
PA0981 53 67 PrrF1 99 117 -12.62 0.0108048 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4792 42 53 PrrF1 73 84 -12.61 0.0108706 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2147 -18 -9 PrrF1 96 105 -12.6 0.0109368 0.9556607 katE catalase HPII
PA2528 -24 -7 PrrF1 101 118 -12.57 0.0111375 0.9556607 resistance-nodulation-cell division (RND) efflux membrane fusion protein
PA1962 -75 -63 PrrF1 106 117 -12.5 0.011619 0.9556607 azoR2 FMN-dependent NADH-azoreductase
PA0596 -6 11 PrrF1 101 118 -12.42 0.0121926 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA5491 -16 -6 PrrF1 98 108 -12.38 0.012489 0.9556607 cytochrome
PA2173a -61 -51 PrrF1 107 118 -12.32 0.012946 0.9556607
PA5012 -11 5 PrrF1 100 118 -12.32 0.012946 0.9556607 waaF heptosyltransferase II
PA2593 -75 -60 PrrF1 40 56 -12.25 0.0134985 0.9556607 qteE quorum threshold expression protein QteE
PA4656 25 38 PrrF1 100 119 -12.22 0.0137418 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2669 -5 7 PrrF1 99 109 -12.21 0.0138238 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA0364 -26 -11 PrrF1 104 121 -12.21 0.0138238 0.9556607 oxidoreductase
PA0562 22 37 PrrF1 74 91 -12.19 0.0139891 0.9556607 hydrolase
PA1477 -23 7 PrrF1 98 123 -12.15 0.0143251 0.9556607 ccmC heme exporter protein CcmC
PA1283 25 36 PrrF1 35 46 -12.06 0.0151084 0.9556607 transcriptional regulator
PA3354 3 13 PrrF1 75 86 -11.95 0.0161188 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1602 -52 -34 PrrF1 101 117 -11.94 0.0162137 0.9556607 oxidoreductase
PA5070 13 29 PrrF1 104 121 -11.88 0.0167935 0.9556607 tatC transporter TatC
PA0008 -46 -35 PrrF1 72 82 -11.87 0.016892 0.9556607 glyS glycine--tRNA ligase subunit beta
PA4639 22 31 PrrF1 101 110 -11.85 0.0170905 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3974 -13 33 PrrF1 43 79 -11.84 0.0171905 0.9556607 ladS lost adherence sensor LadS
PA1329 -8 7 PrrF1 98 110 -11.84 0.0171905 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2056 -60 -44 PrrF1 106 119 -11.83 0.0172911 0.9556607 transcriptional regulator
PA1248 4 22 PrrF1 101 119 -11.83 0.0172911 0.9556607 aprF alkaline protease secretion protein AprF
PA1336 43 53 PrrF1 107 119 -11.82 0.0173922 0.9556607 two-component sensor
PA5043 -16 4 PrrF1 70 90 -11.77 0.0179059 0.9556607 pilN type 4 fimbrial biogenesis protein PilN
PA3737 38 47 PrrF1 100 109 -11.76 0.0180103 0.9556607 dsbC thiol:disulfide interchange protein DsbC
PA1196 36 55 PrrF1 103 121 -11.73 0.0183269 0.9556607 transcriptional regulator
PA0796 -5 10 PrrF1 104 118 -11.73 0.0183269 0.9556607 prpB 2-methylisocitrate lyase
PA4235 64 73 PrrF1 37 46 -11.73 0.0183269 0.9556607 bfrA bacterioferritin
PA0483 25 40 PrrF1 40 54 -11.7 0.0186484 0.9556607 acetyltransferase
PA2967 -13 21 PrrF1 68 101 -11.7 0.0186484 0.9556607 fabG 3-oxoacyl-[acyl-carrier-protein] reductase FabG
PA0613 -3 19 PrrF1 102 119 -11.69 0.0187568 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3785 -13 5 PrrF1 74 91 -11.68 0.0188657 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA1205 -16 -3 PrrF1 104 119 -11.66 0.0190852 0.9556607 quercetin 23-dioxygenase
PA3381 -74 -61 PrrF1 103 116 -11.64 0.0193071 0.9556607 transcriptional regulator
PA1389 -4 10 PrrF1 104 118 -11.6 0.0197578 0.9556607 glycosyl transferase family protein
PA3263 -66 -51 PrrF1 104 119 -11.58 0.0199868 0.9556607 recombination associated protein RdgC
PA4182 22 33 PrrF1 78 89 -11.56 0.0202182 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4968 6 14 PrrF1 38 46 -11.52 0.0206883 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4940 -60 -41 PrrF1 100 123 -11.51 0.0208073 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4430 -16 4 PrrF1 101 119 -11.46 0.0214121 0.9556607 cytochrome b
PA3504 -3 12 PrrF1 105 119 -11.44 0.0216584 0.9556607 aldehyde dehydrogenase
PA1838 -30 -7 PrrF1 98 121 -11.42 0.0219074 0.9556607 cysI sulfite reductase
PA1581 6 21 PrrF1 108 123 -11.38 0.022413 0.9556607 sdhC succinate dehydrogenase subunit C
PA4420 -36 -14 PrrF1 40 62 -11.37 0.0225411 0.9556607 S-adenosyl-methyltransferase MraW
PA3216 -2 20 PrrF1 98 118 -11.35 0.0227992 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3745 58 73 PrrF1 107 119 -11.31 0.0233235 0.9556607 rpsP 30S ribosomal protein S16
PA0502 4 16 PrrF1 34 46 -11.3 0.0234563 0.9556607 biotin biosynthesis protein BioH
PA4456 -16 5 PrrF1 100 119 -11.27 0.0238588 0.9556607 ABC transporter ATP-binding protein
PA0918 -10 10 PrrF1 104 123 -11.25 0.0241306 0.9556607 cytochrome b561
PA0059 -61 -42 PrrF1 73 91 -11.24 0.0242675 0.9556607 osmC osmotically inducible protein OsmC
PA4467 -12 3 PrrF1 102 118 -11.23 0.0244052 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA2509 8 29 PrrF1 104 121 -11.21 0.0246826 0.9556607 catB muconate cycloisomerase I
PA3086 -73 -61 PrrF1 98 109 -11.14 0.0256763 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA3988 -14 4 PrrF1 101 116 -11.14 0.0256763 0.9556607 'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'
PA4236 -22 -7 PrrF1 96 112 -11.12 0.0259669 0.9556607 katA catalase
PA5489 -23 26 PrrF1 6 53 -11.08 0.0265569 0.9556607 dsbA thiol:disulfide interchange protein DsbA
PA2741 -74 -54 PrrF1 74 91 -11.04 0.027159 0.9556607 rplT 50S ribosomal protein L20

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
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 IntaRNA please cite :







		 
	
	
	
		 
		



Results are computed with IntaRNA version 3.2.0 linking Vienna RNA package 2.4.14



		 
	

			





	About this web server
	  | 
	version 5.0.10
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer