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IntaRNA 8403881

Input and runtime details for job 8403881 (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 8403881 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:15:25 CET 2020
?IntaRNA Started@ Mon Jan 27 14:18:18 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:19:13 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:20:45 CET 2020
?Job Completed@ Mon Jan 27 14:20:57 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - 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
b1683 8 33 RyhB 38 66 -21.41 4.71e-05 0.1636725 sufB component of SufBCD Fe-S cluster assembly scaffold
b0894 -38 -18 RyhB 43 62 -19.93 0.0001337 0.1837117 dmsA dimethyl sulfoxide reductase anaerobic subunit A
b3743 40 66 RyhB 34 60 -19.68 0.0001586 0.1837117 asnC transcriptional activator of asnA autorepressor
b4255 -63 -43 RyhB 39 59 -18.09 0.0004554 0.3956288 rraB protein inhibitor of RNase E
b2170 -33 -7 RyhB 2 24 -17.18 0.0008131 0.5651045 setB lactose/glucose efflux system
b4019 -10 7 RyhB 43 58 -16.82 0.001018 0.5895917 metH homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent
b1181 49 69 RyhB 37 60 -16.27 0.0014284 0.7090986 ycgN UPF0153 family cysteine cluster protein
b4348 -73 -53 RyhB 40 66 -15.87 0.0018209 0.7909534 hsdS specificity determinant for hsdM and hsdR
b3885 56 75 RyhB 41 62 -15.48 0.0023007 0.8637808 yihX alpha-D-glucose-1-phosphate phosphatase anomer-specific
b0313 54 75 RyhB 40 61 -15.35 0.0024857 0.8637808 betI choline-inducible betIBA-betT divergent operon transcriptional repressor
b1120 -17 5 RyhB 46 68 -14.88 0.0032796 0.9291058 cobB deacetylase of acs and cheY chemotaxis regulator
b0722 -33 -15 RyhB 22 41 -14.16 0.0049771 0.9291058 sdhD succinate dehydrogenase membrane subunit binds cytochrome b556
b3080 -59 -34 RyhB 1 25 -14.07 0.0052402 0.9291058 ygjK alpha-glucosidase
b2823 42 60 RyhB 40 58 -14.06 0.0052703 0.9291058 ppdC putative prepilin peptidase-dependent protein
b0968 -11 6 RyhB 37 58 -13.79 0.0061458 0.9291058 yccX weak acylphosphatase
b0528 57 74 RyhB 42 61 -13.77 0.0062158 0.9291058 ybcJ ribosome-associated protein putative RNA-binding protein
b3084 -35 -25 RyhB 37 47 -13.75 0.0062866 0.9291058 rlmG 23S rRNA m(2)G1835 methyltransferase SAM-dependent
b4532 -9 18 RyhB 38 58 -13.67 0.0065776 0.9291058 hicA mRNA interferase toxin of the HicAB toxin-antitoxin system
b3110 57 75 RyhB 44 62 -13.55 0.0070381 0.9291058 yhaO putative transporter
b4469 -11 12 RyhB 38 60 -13.54 0.0070778 0.9291058 ygiQ Radical SAM superfamily protein
b1107 -41 18 RyhB 37 81 -13.54 0.0070778 0.9291058 nagZ beta N-acetyl-glucosaminidase
b4176 18 67 RyhB 31 86 -13.5 0.0072388 0.9291058 yjeT DUF2065 family protein
b2830 62 74 RyhB 44 56 -13.5 0.0072388 0.9291058 rppH RNA pyrophosphohydrolase
b1430 63 74 RyhB 53 64 -13.44 0.0074869 0.9291058 tehB tellurite selenium methyltransferase SAM-dependent tellurite selenium resistance protein
b2563 -20 16 RyhB 25 63 -13.42 0.0075713 0.9291058 acpS holo-[acyl-carrier-protein] synthase 1
b3991 -75 -66 RyhB 40 49 -13.4 0.0076567 0.9291058 thiG thiamine biosynthesis ThiGH complex subunit
b2789 55 75 RyhB 37 62 -13.26 0.0082802 0.9291058 gudP putative D-glucarate transporter
b3607 -11 7 RyhB 36 59 -13.23 0.0084199 0.9291058 cysE serine acetyltransferase
b1227 47 67 RyhB 2 22 -13.21 0.0085143 0.9291058 narI nitrate reductase 1 gamma (cytochrome b(NR)) subunit
b0613 -18 6 RyhB 37 59 -13.15 0.0088035 0.9291058 citG 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A synthase
b1423 9 56 RyhB 38 84 -13.15 0.0088035 0.9291058 ydcJ putative metalloenzyme
b2799 -75 -65 RyhB 56 66 -13.09 0.0091019 0.9291058 fucO L-12-propanediol oxidoreductase
b4355 -74 -65 RyhB 16 25 -13.09 0.0091019 0.9291058 tsr methyl-accepting chemotaxis protein I serine sensor receptor
b3928 30 40 RyhB 51 61 -13.08 0.0091526 0.9291058 zapB FtsZ stabilizer septal ring assembly factor cell division stimulator
b2283 -15 -6 RyhB 52 61 -13.04 0.0093579 0.9291058 nuoG NADH:ubiquinone oxidoreductase chain G
b0556 -10 11 RyhB 39 58 -12.89 0.0101674 0.9496255 rzpD DLP12 prophage putative murein endopeptidase
b2230 -27 3 RyhB 40 76 -12.71 0.0112262 0.9496255 yfaA DUF2138 family protein putative host defense protein
b0896 51 69 RyhB 36 54 -12.7 0.011288 0.9496255 dmsC dimethyl sulfoxide reductase anaerobic subunit C
b3248 19 35 RyhB 18 35 -12.53 0.0123886 0.9496255 yhdE dTTP/UTP pyrophosphatase m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase
b1044 63 73 RyhB 52 62 -12.49 0.012662 0.9496255 ymdA uncharacterized protein
b3219 -10 11 RyhB 39 59 -12.48 0.0127312 0.9496255 yhcF putative transcriptional regulator
b4547 -4 42 RyhB 38 88 -12.44 0.0130116 0.9496255 ypfN putative membrane protein UPF0370 family
b2819 20 33 RyhB 47 62 -12.43 0.0130826 0.9496255 recD exonuclease V (RecBCD complex) alpha chain
b4470 -72 -27 RyhB 4 61 -12.39 0.0133704 0.9496255 yhaM putative L-serine dehydratase alpha chain
b2820 2 13 RyhB 37 48 -12.36 0.0135901 0.9496255 recB exonuclease V (RecBCD complex) beta subunit
b1784 -16 -2 RyhB 52 66 -12.31 0.0139638 0.9496255 yeaH UPF0229 family protein
b1778 -35 -24 RyhB 43 54 -12.27 0.0142698 0.9496255 msrB methionine sulfoxide reductase B
b1013 -75 -34 RyhB 7 44 -12.26 0.0143473 0.9496255 rutR rut operon transcriptional repressor for
b1342 -10 11 RyhB 41 59 -12.25 0.0144251 0.9496255 ydaN putative Zn(II) transporter
b4633 -42 -17 RyhB 37 66 -12.21 0.0147406 0.9496255 xisD pseudogene exisionase in defective prophage DLP12Phage or Prophage Related
b1224 -50 -41 RyhB 37 46 -12.19 0.0149008 0.9496255 narG nitrate reductase 1 alpha subunit
b1156 -15 4 RyhB 1 21 -12.15 0.0152261 0.9496255 tfaE e14 prophage putative tail fiber assembly protein
b2120 43 58 RyhB 71 86 -12.11 0.0155581 0.9496255 yehM uncharacterized protein
b3543 -67 -48 RyhB 41 58 -12.11 0.0155581 0.9496255 dppB dipeptide/heme ABC transporter permease
b0943 -22 6 RyhB 37 60 -12.08 0.0158115 0.9496255 ycbV putative fimbrial-like adhesin protein
b2727 -7 4 RyhB 39 49 -12.05 0.0160688 0.9496255 hypB GTP hydrolase involved in nickel liganding into hydrogenases
b2253 -13 5 RyhB 38 58 -12.03 0.0162426 0.9496255 arnB uridine 5'-(beta-1-threo-pentapyranosyl-4-ulose diphosphate) aminotransferase PLP-dependent
b3902 43 75 RyhB 57 89 -11.97 0.0167745 0.9496255 rhaD rhamnulose-1-phosphate aldolase
b3010 -68 -29 RyhB 38 86 -11.97 0.0167745 0.9496255 yqhC transcriptional activator of yqhD
b1269 -46 8 RyhB 42 90 -11.89 0.0175092 0.9496255 rluB 23S rRNA pseudouridine(2605) synthase
b3573 47 75 RyhB 37 66 -11.77 0.0186683 0.9496255 ysaA putative hydrogenase 4Fe-4S ferredoxin-type component
b0005 -18 50 RyhB 1 65 -11.73 0.0190705 0.9496255 yaaX DUF2502 family putative periplasmic protein
b0624 35 48 RyhB 53 66 -11.71 0.0192746 0.9496255 flc fluoride efflux channel dual topology membrane protein
b1654 -12 7 RyhB 43 58 -11.69 0.0194808 0.9496255 grxD glutaredoxin-4
b2736 56 71 RyhB 38 59 -11.65 0.0198994 0.9496255 ygbJ putative dehydrogenase
b2007 -72 -61 RyhB 37 48 -11.62 0.0202189 0.9496255 yeeX UPF0265 family protein
b2264 43 51 RyhB 52 60 -11.61 0.0203264 0.9496255 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase SEPHCHC synthase
b4308 25 59 RyhB 53 90 -11.59 0.0205432 0.9496255 yjhR pseudogene helicase family putative frameshift suppressor
b1189 10 30 RyhB 47 66 -11.54 0.0210945 0.9496255 dadA D-amino acid dehydrogenase
b2239 58 75 RyhB 37 58 -11.5 0.0215456 0.9496255 glpQ periplasmic glycerophosphodiester phosphodiesterase
b0156 -11 13 RyhB 37 59 -11.5 0.0215456 0.9496255 erpA iron-sulfur cluster insertion protein
b3391 -11 13 RyhB 46 68 -11.42 0.0224751 0.9496255 hofQ DNA catabolic putative fimbrial transporter
b3777 15 47 RyhB 51 84 -11.41 0.0225939 0.9496255 yifN PemK toxin family pseudogene
b2211 -12 13 RyhB 6 30 -11.41 0.0225939 0.9496255 yojI microcin J25 efflux ABC transporter permease/ATPase
b2155 -55 -41 RyhB 41 57 -11.36 0.0231967 0.9496255 cirA colicin IA outer membrane receptor and translocator ferric iron-catecholate transporter
b3835 -35 -4 RyhB 53 86 -11.36 0.0231967 0.9496255 ubiB regulator of octaprenylphenol hydroxylation ubiquinone synthesis regulator of 2'-N-acetyltransferase putative ABC1 family protein kinase
b3311 -68 -41 RyhB 37 60 -11.34 0.0234421 0.9496255 rpsQ 30S ribosomal subunit protein S17
b4516 -39 -2 RyhB 21 62 -11.31 0.0238147 0.9496255 insA IS1 repressor TnpA
b3645 -7 3 RyhB 40 49 -11.31 0.0238147 0.9496255 dinD DNA damage-inducible protein
b0892 -18 15 RyhB 37 66 -11.3 0.0239401 0.9496255 rarA recombination intermediate processing DNA-dependent ATPase
b2525 55 73 RyhB 40 60 -11.22 0.024966 0.9496255 fdx [2Fe-2S] ferredoxin
b1991 -43 -22 RyhB 1 20 -11.2 0.0252289 0.9496255 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
b2095 -73 -39 RyhB 14 49 -11.15 0.0258974 0.9496255 gatZ D-tagatose 16-bisphosphate aldolase 2 subunit
b2135 -9 27 RyhB 21 58 -11.14 0.026033 0.9496255 yohC Yip1 family inner membrane protein
b3668 52 75 RyhB 6 26 -11.13 0.0261694 0.9496255 uhpB sensory histidine kinase in two-component regulatory sytem with UhpA
b2457 2 41 RyhB 1 59 -11.11 0.0264441 0.9496255 eutM ethanolamine utilization protein putative carboxysome structural protein
b4111 -16 -7 RyhB 15 24 -11.08 0.0268612 0.9496255 proP proline/glycine betaine transporter
b2550 -75 -66 RyhB 39 49 -11.07 0.0270016 0.9496255 yphH putative DNA-binding transcriptional regulator
b1588 -19 -1 RyhB 40 56 -11.03 0.0275701 0.9496255 ynfF S- and N-oxide reductase A subunit periplasmic
b0032 -16 -1 RyhB 10 26 -11 0.0280038 0.9496255 carA carbamoyl phosphate synthetase small subunit glutamine amidotransferase
b3365 -9 12 RyhB 38 57 -10.98 0.0282964 0.9496255 nirB nitrite reductase large subunit NAD(P)H-binding
b0728 -74 -59 RyhB 50 64 -10.97 0.0284439 0.9496255 sucC succinyl-CoA synthetase beta subunit
b3492 -66 -42 RyhB 42 65 -10.96 0.028592 0.9496255 yhiN putative oxidoreductase
b0681 57 71 RyhB 32 46 -10.92 0.0291917 0.9496255 chiP chitoporin uptake of chitosugars
b2714 60 72 RyhB 26 38 -10.91 0.0293435 0.9496255 ascG asc operon transcriptional repressor prpBC operon repressor
b3867 -13 5 RyhB 38 58 -10.87 0.0299579 0.9496255 hemN coproporphyrinogen III oxidase SAM and NAD(P)H dependent oxygen-independent
b3032 -67 -43 RyhB 40 63 -10.86 0.0301134 0.9496255 cpdA 3'5' cAMP phosphodiesterase
b4551 57 73 RyhB 39 58 -10.85 0.0302697 0.9496255 yheV DUF2387 family putative metal-binding protein
b4281 -9 2 RyhB 36 46 -10.82 0.0307429 0.9496255 yjhD pseudogene KpLE2 phage-like element
b1279 -12 4 RyhB 46 61 -10.81 0.0309022 0.9496255 yciS DUF1049 family inner membrane protein function unknown

Details of Selected Interaction Download Interaction Details 

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