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IntaRNA 6244847

Input and runtime details for job 6244847 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? 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 6244847 (server version trunk)

?Job Submitted & Queued@ Fri Jan 07 21:36:19 CET 2022
?Pre-Processing Started@ Fri Jan 07 21:36:23 CET 2022
?IntaRNA Started@ Fri Jan 07 21:38:06 CET 2022
?IntaRNA Finished & Post-Processing@ Fri Jan 07 21:38:48 CET 2022
?Post-Processing Finished@ Fri Jan 07 21:39:11 CET 2022
?Job Completed@ Fri Jan 07 21:39:12 CET 2022
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6244847&toolName=IntaRNA ( 30 days expiry )

Description of the job

ChiX - E. coli

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b1737 -67 -49 ChiX 38 56 -19.2 0.0002604 0.7067256 chbC NN'-diacetylchitobiose-specific PTS enzyme IIC component
b0847 24 53 ChiX 26 55 -10.7 0.0125842 0.8602904 ybjL putative transport protein YbjL
b1831 -42 2 ChiX 38 75 -8.05 0.0459779 0.8602904 proQ RNA chaperone ProQ
b4337 -48 -37 ChiX 35 46 -8.23 0.042069 0.8602904 mdtM multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
b4342 -41 -28 ChiX 34 47 -9.34 0.024375 0.8602904 yjiT putative uncharacterized protein YjiT
b1040 -16 -2 ChiX 38 52 -9.19 0.0262335 0.8602904 csgD DNA-binding transcriptional dual regulator CsgD
b3186 -14 -1 ChiX 38 51 -8.73 0.0328826 0.8602904 rplU 50S ribosomal subunit protein L21
b0141 -22 -12 ChiX 37 47 -8.49 0.0370071 0.8602904 yadN putative fimbrial protein YadN
b2216 -75 -60 ChiX 39 52 -8.35 0.0396511 0.8602904 rcsD RcsD phosphotransferase
b2779 -37 -29 ChiX 39 47 -8.24 0.041862 0.8602904 eno enolase
b1182 -50 -32 ChiX 37 55 -9.77 0.0197568 0.8602904 hlyE hemolysin E
b2098 -19 -6 ChiX 42 55 -9.74 0.0200479 0.8602904 yegT putative transporter YegT
b3141 41 51 ChiX 38 48 -8.7 0.0333715 0.8602904 agaI putative deaminase AgaI
b1175 -10 -2 ChiX 40 48 -8.33 0.0400441 0.8602904 minD Z-ring positioning protein MinD
b0336 -13 -1 ChiX 40 52 -10.94 0.0112102 0.8602904 codB cytosine transporter
b3287 -68 -55 ChiX 41 54 -10.56 0.0134642 0.8602904 def peptide deformylase
b4175 -16 -5 ChiX 43 55 -10.44 0.0142687 0.8602904 hflC regulator of FtsH protease
b2851 -15 -4 ChiX 43 54 -10.38 0.0146892 0.8602904 ygeG TPR repeat-containing putative chaperone YgeG
b1345 -62 -50 ChiX 42 53 -10.35 0.0149041 0.8602904 intR Rac prophage putative integrase
b4255 -14 -6 ChiX 43 51 -10.02 0.0174928 0.8602904 rraB ribonuclease E inhibitor protein B
b2545 -15 -1 ChiX 41 55 -10 0.0176637 0.8602904 yphC putative zinc-binding dehydrogenase YphC
b0129 -75 -66 ChiX 41 50 -9.83 0.0191875 0.8602904 yadI putative PTS enzyme IIA component YadI
b3413 53 67 ChiX 41 55 -9.41 0.0235542 0.8602904 yhgH DNA utilization protein YhgH
b3909 -51 -40 ChiX 42 53 -9.37 0.0240197 0.8602904 kdgT 2-dehydro-3-deoxy-D-gluconate:H(+) symporter
b3801 -75 -58 ChiX 40 55 -8.71 0.0332077 0.8602904 aslA putative sulfatase AslA
b2241 -12 -5 ChiX 43 50 -8.7 0.0333715 0.8602904 glpA anaerobic glycerol-3-phosphate dehydrogenase subunit A
b1308 -75 -65 ChiX 40 50 -8.69 0.0335361 0.8602904 pspE thiosulfate sulfurtransferase PspE
b2014 -73 -61 ChiX 43 55 -8.57 0.035577 0.8602904 plaP putrescine:H(+) symporter PlaP
b2231 -17 -10 ChiX 43 50 -8.35 0.0396511 0.8602904 gyrA DNA gyrase subunit A
b1071 -17 -6 ChiX 43 54 -8.34 0.0398471 0.8602904 flgM anti-sigma factor for FliA (sigma(28))
b0755 -13 -7 ChiX 43 49 -8.2 0.0426964 0.8602904 gpmA 23-bisphosphoglycerate-dependent phosphoglycerate mutase
b4322 -17 2 ChiX 38 55 -10.82 0.0118768 0.8602904 uxuA D-mannonate dehydratase
b2461 65 73 ChiX 42 50 -9.88 0.0187259 0.8602904 eutP putative ethanolamine utilization acetate kinase EutP
b4040 -14 -7 ChiX 44 51 -8.77 0.0322419 0.8602904 ubiA 4-hydroxybenzoate octaprenyltransferase
b0094 -45 -38 ChiX 43 50 -8.44 0.0379302 0.8602904 ftsA cell division protein FtsA
b0537 -12 -6 ChiX 44 50 -8.09 0.0450788 0.8602904 intD DLP12 prophage putative integrase
b0924 -15 -6 ChiX 44 53 -8.09 0.0450788 0.8602904 mukB chromosome partitioning protein MukB
b0681 -19 -8 ChiX 45 56 -15.8 0.0011645 0.8602904 chiP chitobiose outer membrane channel
b3133 -16 -7 ChiX 44 53 -12.48 0.0053828 0.8602904 agaV N-acetyl-D-galactosamine specific PTS enzyme IIB component
b2688 54 64 ChiX 45 55 -12 0.0067551 0.8602904 gshA glutamate--cysteine ligase
b0549 -12 -2 ChiX 43 53 -11.99 0.0067873 0.8602904 ybcO DLP12 prophage putative nuclease YbcO
b4357 -13 -4 ChiX 44 53 -11.89 0.0071174 0.8602904 lgoR putative DNA-binding transcriptional regulator LgoR
b1363 -74 -59 ChiX 36 51 -11.89 0.0071174 0.8602904 trkG Rac prophage K(+) transporter TrkG
b1093 -13 2 ChiX 38 52 -11.48 0.0086532 0.8602904 fabG 3-oxoacyl-[acyl-carrier-protein] reductase FabG
b2835 36 46 ChiX 45 55 -11.4 0.0089906 0.8602904 lplT lysophospholipid transporter
b2019 -18 -7 ChiX 43 54 -10.86 0.0116502 0.8602904 hisG ATP phosphoribosyltransferase
b2448 -17 -5 ChiX 45 57 -10.66 0.0128294 0.8602904 yffQ CPZ-55 prophage uncharacterized protein YffQ
b1162 -14 -1 ChiX 42 56 -10.31 0.0151958 0.8602904 bluR DNA-binding transcriptional repressor BluR
b0526 34 45 ChiX 41 52 -9.83 0.0191875 0.8602904 cysS cysteine--tRNA ligase
b2204 -49 -39 ChiX 42 52 -9.73 0.0201459 0.8602904 napH ferredoxin-type protein NapH
b1003 -71 -56 ChiX 43 56 -9.72 0.0202444 0.8602904 yccJ PF13993 family protein YccJ
b3441 -16 -8 ChiX 45 53 -9.63 0.0211532 0.8602904 yhhY N-acetyltransferase YhhY
b3514 -12 2 ChiX 38 51 -9.59 0.0215704 0.8602904 mdtF multidrug efflux pump RND permease MdtF
b0886 -18 -8 ChiX 45 56 -9.48 0.0227615 0.8602904 cydC glutathione/L-cysteine ABC exporter subunit CydC
b1466 63 71 ChiX 45 53 -9.39 0.0237858 0.8602904 narW NarW putative private chaperone for NarZ nitrate reductase subunit
b0440 -16 -8 ChiX 44 52 -9.36 0.0241376 0.8602904 hupB DNA-binding protein HU-beta
b1474 -13 -5 ChiX 44 52 -9.28 0.0251018 0.8602904 fdnG formate dehydrogenase N subunit alpha
b1304 -16 -1 ChiX 37 54 -9.22 0.0258506 0.8602904 pspA phage shock protein A
b1444 42 51 ChiX 44 53 -9.1 0.0274172 0.8602904 patD gamma-aminobutyraldehyde dehydrogenase
b1740 59 72 ChiX 38 51 -8.84 0.031151 0.8602904 nadE NH3-dependent NAD(+) synthetase
b2457 -15 -7 ChiX 44 52 -8.82 0.0314588 0.8602904 eutM putative ethanolamine catabolic microcompartment shell protein EutM
b2962 -14 -7 ChiX 45 52 -8.71 0.0332077 0.8602904 yggX putative Fe(2(+))-trafficking protein
b0283 -13 -3 ChiX 44 54 -8.65 0.0342029 0.8602904 paoD molybdenum cofactor insertion chaperone PaoD
b3938 -20 -12 ChiX 45 53 -8.56 0.0357527 0.8602904 metJ DNA-binding transcriptional repressor MetJ
b4299 -15 -7 ChiX 45 53 -8.51 0.0366442 0.8602904 yjhI KpLE2 phage-like element putative DNA-binding transcriptional regulator YjhI
b0321 -18 -10 ChiX 45 53 -8.26 0.0414509 0.8602904 yahG DUF1116 domain-containing protein YahG
b1257 -15 2 ChiX 38 52 -8.11 0.0446359 0.8602904 yciE DUF892 domain-containing protein YciE
b2420 60 68 ChiX 45 53 -8.11 0.0446359 0.8602904 yfeS PF05406 family protein YfeS
b1048 -42 -33 ChiX 44 53 -11.91 0.0070501 0.8602904 opgG osmoregulated periplasmic glucans (OPGs) biosynthesis protein G
b0846 -14 -6 ChiX 44 52 -10.43 0.0143379 0.8602904 rcdA DNA-binding transcriptional regulator RcdA
b0545 -13 2 ChiX 38 53 -9.44 0.0232111 0.8602904 ybcL DLP12 prophage periplasmic protein YbcL
b1550 -12 -4 ChiX 44 52 -8.87 0.0306951 0.8602904 gnsB Qin prophage protein GnsB
b4047 -37 -30 ChiX 45 52 -8.42 0.038306 0.8602904 yjbL uncharacterized protein YjbL
b1736 -15 -7 ChiX 44 52 -8.33 0.0400441 0.8602904 chbA NN'-diacetylchitobiose-specific PTS enzyme IIA component
b0542 9 27 ChiX 38 53 -8.3 0.040641 0.8602904 renD DLP12 prophage protein RenD
b1872 -14 -4 ChiX 44 54 -8.18 0.0431199 0.8602904 torZ trimethylamine N-oxide reductase 2
b0317 -14 -5 ChiX 44 53 -8.12 0.0444161 0.8602904 yahC uncharacterized protein YahC
b1957 31 40 ChiX 46 55 -8.08 0.0453019 0.8602904 yodC protein YodC
b1486 -74 -67 ChiX 46 53 -8.9 0.0302459 0.8602904 ddpB putative DD-dipeptide ABC transporter membrane subunit DdpB
b1314 65 72 ChiX 47 54 -8.3 0.040641 0.8602904 ycjR 3-dehydro-D-guloside 4-epimerase
b0228 26 36 ChiX 44 54 -8.24 0.041862 0.8602904 rayT REP-associated tyrosine transposase
b3304 -31 -24 ChiX 46 53 -8.16 0.0435477 0.8602904 rplR 50S ribosomal subunit protein L18
b0619 -37 -26 ChiX 46 57 -16.12 0.0010084 0.8602904 dpiB sensor histidine kinase DpiB
b4199 -17 -6 ChiX 46 57 -12.36 0.0056965 0.8602904 yjfY DUF1471 domain-containing protein YjfY
b3657 20 30 ChiX 47 57 -11.21 0.0098469 0.8602904 yicJ putative xyloside transporter YicJ
b2513 -22 -11 ChiX 45 55 -10.11 0.0167442 0.8602904 yfgM ancillary SecYEG translocon subunit
b3176 -68 -60 ChiX 48 56 -9.42 0.0234392 0.8602904 glmM phosphoglucosamine mutase
b1114 10 40 ChiX 46 73 -8.98 0.0290804 0.8602904 mfd transcription-repair coupling factor
b1418 -18 -7 ChiX 45 55 -8.95 0.029512 0.8602904 cybB superoxide oxidase
b1732 -62 -54 ChiX 47 55 -8.82 0.0314588 0.8602904 katE catalase HPII
b2768 44 53 ChiX 48 57 -8.45 0.0377438 0.8602904 ygcP putative anti-terminator regulatory protein
b2705 -15 -7 ChiX 47 55 -8.4 0.0386856 0.8602904 srlD sorbitol-6-phosphate 2-dehydrogenase
b0793 45 54 ChiX 47 56 -8.36 0.0394561 0.8602904 ybhS ABC exporter membrane subunit YbhS
b1571 -23 -12 ChiX 44 56 -8.29 0.040842 0.8602904 ydfA Qin prophage DUF1391 domain-containing protein YdfA
b0115 64 73 ChiX 46 55 -8.26 0.0414509 0.8602904 aceF pyruvate dehydrogenase E2 subunit
b1561 38 73 ChiX 44 81 -8.75 0.0325606 0.8602904 rem Qin prophage protein Rem
b0517 -18 -7 ChiX 45 56 -8.66 0.034035 0.8602904 allD ureidoglycolate dehydrogenase
b3118 -30 -14 ChiX 42 57 -8.84 0.031151 0.8602904 tdcA DNA-binding transcriptional activator TdcA
b1476 -49 -27 ChiX 45 69 -11.4 0.0089906 0.8602904 fdnI formate dehydrogenase N subunit gamma
b2483 -32 -8 ChiX 45 75 -8.27 0.0412469 0.8602904 hyfC hydrogenase 4 component C

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
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