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IntaRNA 4627738

Input and runtime details for job 4627738 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003210
? 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 4627738 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:20:43 CET 2020
?IntaRNA Started@ Mon Jan 27 14:22:37 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:24:00 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:24:55 CET 2020
?Job Completed@ Mon Jan 27 14:25:04 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4627738&toolName=IntaRNA ( 30 days expiry )

Description of the job

LhrA2 - Listeria monocytogenes

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003210 Listeria monocytogenes EGD-e

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
lmo1883 -5 28 LhrA2 139 173 -25.95 9.7e-06 0.0277905 chitinase
lmo1187 -62 -29 LhrA2 153 183 -19.53 0.0010984 0.863511 ethanolamine utilization protein EutQ
lmo1835 -25 28 LhrA2 154 207 -18.61 0.0019491 0.863511 carB carbamoyl-phosphate synthetase
lmo0397 -23 37 LhrA2 160 211 -18.55 0.0020219 0.863511
lmo0383 24 64 LhrA2 151 186 -18.44 0.002162 0.863511 methylmalonate-semialdehyde dehydrogenase
lmo2074 -69 -43 LhrA2 147 173 -18.23 0.0024551 0.863511
lmo0835 -20 29 LhrA2 146 186 -18.17 0.0025454 0.863511 peptidoglycan binding protein
lmo1147 -65 10 LhrA2 158 211 -18.08 0.0026867 0.863511 cobalamin biosynthesis protein CopB
lmo0851 -12 20 LhrA2 172 200 -17.88 0.0030274 0.863511 lmo0851
lmo2446 -22 16 LhrA2 154 187 -17.3 0.0042577 0.863511 glycosidase
lmo1229 -3 28 LhrA2 147 182 -17.22 0.0044601 0.863511
lmo1572 1 26 LhrA2 157 179 -17.19 0.0045383 0.863511 accA acetyl-CoA carboxylase carboxyltransferase subunit alpha
lmo2615 -18 25 LhrA2 155 202 -17.05 0.0049203 0.863511 rpsE 30S ribosomal protein S5
lmo1161 -12 36 LhrA2 158 204 -16.94 0.0052414 0.863511 ethanolamine utilization protein EutJ
lmo1507 -25 4 LhrA2 147 173 -16.85 0.0055185 0.863511 response regulator
lmo1403 -17 22 LhrA2 169 208 -16.71 0.0059768 0.863511 mutS DNA mismatch repair protein MutS
lmo2308 -14 7 LhrA2 147 170 -16.63 0.0062544 0.863511 single-stranded DNA-binding protein
lmo0233 38 73 LhrA2 157 198 -16.51 0.0066934 0.863511 DNA repair protein RadA
lmo0129 -14 15 LhrA2 176 203 -16.42 0.0070414 0.863511 N-acetylmuramoyl-L-alanine amidase
lmo1666 -46 7 LhrA2 157 204 -16.3 0.0075316 0.863511 peptidoglycan-linked protein
lmo0057 -22 7 LhrA2 157 181 -16.2 0.0079642 0.863511
lmo2768 30 51 LhrA2 161 179 -16.16 0.0081436 0.863511 hypothetical membrane protein
lmo1828 11 21 LhrA2 201 211 -16.11 0.0083732 0.863511
lmo0197 -23 48 LhrA2 99 173 -16.05 0.0086566 0.863511 regulatory protein SpoVG
lmo0139 52 72 LhrA2 166 186 -16.03 0.0087531 0.863511 lmo0139
lmo0482 44 69 LhrA2 172 210 -15.99 0.008949 0.863511 ribosomal RNA large subunit methyltransferase N
lmo1203 -27 -2 LhrA2 155 181 -15.88 0.0095091 0.863511 cbiL cobalt-precorrin-2 C(20)-methyltransferase
lmo2765 -13 18 LhrA2 155 199 -15.86 0.0096143 0.863511 PTS cellbiose transporter subunit IIA
lmo1952 -9 31 LhrA2 161 204 -15.84 0.0097207 0.863511 lysA diaminopimelate decarboxylase
lmo2486 -27 32 LhrA2 159 195 -15.82 0.0098281 0.863511 lmo2486
lmo0131 -8 31 LhrA2 165 204 -15.78 0.0100463 0.863511
lmo1875 -25 4 LhrA2 150 179 -15.67 0.0106699 0.863511 ABC transporter ATP-binding protein
lmo0551 -68 -3 LhrA2 154 204 -15.63 0.0109054 0.863511 lmo0551
lmo1984 -14 29 LhrA2 157 201 -15.62 0.0109651 0.863511 ilvB acetolactate synthase
lmo1258 24 74 LhrA2 157 207 -15.61 0.011025 0.863511 lmo1258
lmo0191 -75 -47 LhrA2 154 182 -15.56 0.0113293 0.863511 phospho-beta-glucosidase
lmo1584 -2 11 LhrA2 169 181 -15.55 0.0113911 0.863511
lmo2299 37 63 LhrA2 155 181 -15.54 0.0114532 0.863511 portal protein
lmo0196 -2 56 LhrA2 156 208 -15.48 0.0118324 0.8692263 regulatory protein SpoVG
lmo0205 -28 -2 LhrA2 160 186 -15.42 0.0122233 0.8754939 plcB phospholipase C
lmo1717 -6 17 LhrA2 147 170 -15.35 0.0126946 0.8870739
lmo1941 23 69 LhrA2 156 207 -15.29 0.0131118 0.8878302
lmo2282 -21 35 LhrA2 157 205 -15.26 0.0133252 0.8878302 protein gp21
lmo1689 -16 16 LhrA2 157 186 -15.11 0.0144414 0.9011628 A/G-specific adenine glycosylase
lmo0194 -20 42 LhrA2 155 212 -15.09 0.0145966 0.9011628 ABC transporter ATP-binding protein
lmo0926 56 74 LhrA2 155 175 -15.07 0.0147533 0.9011628 TetR family transcriptional regulator
lmo1481 1 24 LhrA2 151 181 -15.05 0.0149116 0.9011628 holA DNA polymerase III subunit delta
lmo0181 -54 -34 LhrA2 158 179 -15.02 0.0151521 0.9011628 sugar ABC transporter substrate-binding protein
lmo2327 -39 14 LhrA2 155 208 -14.96 0.0156437 0.9011628 lmo2327
lmo0922 -24 14 LhrA2 154 188 -14.95 0.0157271 0.9011628 pantothenate kinase
lmo0850 -49 -18 LhrA2 148 170 -14.84 0.0166718 0.9082262
lmo2121 32 72 LhrA2 153 189 -14.83 0.0167603 0.9082262 maltose phosphorylase
lmo0142a 37 73 LhrA2 119 157 -14.8 0.0170282 0.9082262
lmo2807 -29 7 LhrA2 157 186 -14.79 0.0171184 0.9082262 hypothetical secreted protein
lmo2759 -28 4 LhrA2 141 173 -14.73 0.0176689 0.9128702
lmo0649 -9 5 LhrA2 190 204 -14.7 0.0179502 0.9128702 transcriptional regulator
lmo0184 -42 10 LhrA2 158 203 -14.64 0.0185255 0.9128702 oligo-16-glucosidase
lmo1709 21 41 LhrA2 163 181 -14.62 0.0187209 0.9128702 methionine aminopeptidase
lmo2811 -50 -8 LhrA2 160 203 -14.59 0.0190178 0.9128702 trmE tRNA modification GTPase TrmE
lmo0302 -15 26 LhrA2 167 204 -14.58 0.0191177 0.9128702 lmo0302
lmo0788 -23 -4 LhrA2 197 212 -14.54 0.0195222 0.9163749 lmo0788
lmo0661 46 71 LhrA2 156 186 -14.51 0.0198308 0.9163749
lmo2654 -5 11 LhrA2 167 184 -14.34 0.0216662 0.9474659 fus elongation factor G
lmo0292 3 49 LhrA2 155 203 -14.32 0.0218921 0.9474659 heat-shock protein htrA serine protease
lmo0066 -22 6 LhrA2 158 199 -14.3 0.0221203 0.9474659 toxin
lmo2106 -29 22 LhrA2 159 207 -14.28 0.0223506 0.9474659
lmo2445 -67 -36 LhrA2 157 177 -14.24 0.0228179 0.9474659 internalin
lmo0200 -10 14 LhrA2 175 204 -14.21 0.0231743 0.9474659 prfA listeriolysin positive regulatory protein
lmo2566 -22 16 LhrA2 155 186 -14.16 0.0237797 0.9474659 lmo2566
lmo1454 -29 16 LhrA2 154 211 -14.13 0.02415 0.9474659 rpoD RNA polymerase sigma factor RpoD
lmo0022 -2 42 LhrA2 160 208 -14.13 0.02415 0.9474659 PTS fructose transporter subunit IIB
lmo2314 -15 17 LhrA2 171 207 -14.04 0.0252928 0.9474659 lmo2314
lmo1517 -59 -32 LhrA2 172 198 -14 0.0258166 0.9474659 nitrogen regulatory PII protein
lmo2146 -8 30 LhrA2 172 211 -13.99 0.0259491 0.9474659 LysR family transcriptional regulator
lmo0143 -75 -5 LhrA2 92 157 -13.99 0.0259491 0.9474659 lmo0143
lmo0444 5 27 LhrA2 157 181 -13.98 0.0260822 0.9474659
lmo1767 11 63 LhrA2 158 213 -13.96 0.0263503 0.9474659 purM phosphoribosylaminoimidazole synthetase
lmo1278 -16 16 LhrA2 173 203 -13.95 0.0264853 0.9474659 clpQ ATP-dependent protease peptidase subunit
lmo1327 11 40 LhrA2 157 186 -13.94 0.026621 0.9474659 rbfA ribosome-binding factor A
lmo2251 -12 5 LhrA2 149 165 -13.92 0.0268942 0.9474659 amino acid ABC transporter ATP-binding protein
lmo1575 -14 28 LhrA2 150 181 -13.9 0.02717 0.9474659
lmo0888 -1 37 LhrA2 174 211 -13.9 0.02717 0.9474659
lmo1109 -23 11 LhrA2 141 172 -13.88 0.0274484 0.9474659
lmo1631 -59 -38 LhrA2 148 170 -13.79 0.0287341 0.9493467 trpD anthranilate phosphoribosyltransferase
lmo1018 51 72 LhrA2 158 181 -13.69 0.0302275 0.9493467 copper homeostasis protein CutC
lmo2793 -2 47 LhrA2 115 174 -13.69 0.0302275 0.9493467 lmo2793
lmo2809 -46 -2 LhrA2 161 211 -13.64 0.0310006 0.9493467 hypothetical secreted protein
lmo2613 -16 13 LhrA2 177 203 -13.6 0.0316321 0.9493467 rplO 50S ribosomal protein L15
lmo1724 -57 12 LhrA2 156 211 -13.58 0.0319523 0.9493467 ABC transporter ATP-binding protein
lmo0198 29 59 LhrA2 153 183 -13.57 0.0321135 0.9493467 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase
lmo1217 28 75 LhrA2 167 211 -13.51 0.0330966 0.9493467 endo-14-beta-glucanase and to aminopeptidase
lmo1246 -20 5 LhrA2 184 206 -13.51 0.0330966 0.9493467 ATP-dependent RNA helicase
lmo2681 -27 4 LhrA2 154 182 -13.49 0.0334303 0.9493467 kdpB potassium-transporting ATPase subunit B
lmo0137 -20 28 LhrA2 154 207 -13.49 0.0334303 0.9493467 peptide ABC transporter permease
lmo1659 23 35 LhrA2 169 181 -13.48 0.0335984 0.9493467 lmo1659
lmo2797 -16 53 LhrA2 153 209 -13.46 0.0339368 0.9493467 PTS mannitol transporter subunit IIA
lmo0390 -50 -8 LhrA2 167 211 -13.46 0.0339368 0.9493467 uracil-DNA glycosylase
lmo2596 -36 -21 LhrA2 171 186 -13.45 0.0341071 0.9493467 rpsI 30S ribosomal protein S9
lmo1401 -52 9 LhrA2 155 204 -13.43 0.0344502 0.9493467
lmo1798 21 65 LhrA2 129 169 -13.42 0.034623 0.9493467

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
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Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14



		 
	

			





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