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IntaRNA 4935127

Input and runtime details for job 4935127 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_003197
? 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 4935127 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:12:23 CET 2020
?IntaRNA Started@ Mon Jan 27 14:14:40 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:16:11 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:17:25 CET 2020
?Job Completed@ Mon Jan 27 14:17:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

Description of the job

GcvB - E. coli

? Output [zip]

Downloadable files

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


heatmap

? Identified Interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
STM3909 -34 -14 GcvB 67 88 -21.24 6.85e-05 0.2036716 ilvC ketol-acid reductoisomerase
STM3630 -43 -2 GcvB 51 92 -20.93 9.35e-05 0.2036716 dppA ABC transporter substrate-binding protein
STM1107 4 61 GcvB 36 82 -20.55 0.0001353 0.2036716 hpaX 4-hydroxyphenylacetate permease
STM3251 -5 39 GcvB 45 87 -20.16 0.0001949 0.2200421 sugar kinase
STM4398 -30 6 GcvB 125 169 -19.27 0.000428 0.3847632 cycA D-serine/D-alanine/glycine transporter
STM0369 2 69 GcvB 31 91 -18.82 0.0006231 0.3847632 prpC 2-methylcitrate synthase
STM1953 -28 28 GcvB 31 87 -18.8 0.0006334 0.3847632 yedO D-cysteine desulfhydrase
STM0001 -71 -15 GcvB 141 186 -18.71 0.0006816 0.3847632 thrL thr operon leader peptide
STM3344 -70 -27 GcvB 48 102 -18.35 0.0009093 0.4343002 rpsI 30S ribosomal protein S9
STM1098 -69 -36 GcvB 62 90 -18.25 0.0009836 0.4343002 hpaC 4-hydroxyphenylacetate 3-monooxygenase reductase component
STM2818 -20 -9 GcvB 153 164 -18.09 0.001114 0.4343002 gshA glutamate--cysteine ligase
STM1743 -4 21 GcvB 35 59 -18.01 0.0011849 0.4343002 oppD oligopeptide ABC transporter ATP-binding protein OppD
STM3707 -35 -23 GcvB 147 159 -17.94 0.0012502 0.4343002 yibD putative glycosyltransferase
STM0849 -26 -9 GcvB 140 162 -17.84 0.0013491 0.4351811 yliB glutathione ABC transporter substrate-binding protein GsiB
STM1789 -10 11 GcvB 35 55 -17.32 0.0019866 0.598099 hydrogenase expression/formation protein
STM3609 2 53 GcvB 25 91 -17.04 0.0024321 0.659913 yhjE MFS transporter
STM1856 -40 -18 GcvB 64 87 -17.01 0.0024848 0.659913 similar to E. coli orf hypothetical protein (AAC74245.1) Blastp hit to AAC74245.1 (134 aa) 40% identity in aa 1 - 127
STM1538 -52 -14 GcvB 51 90 -16.93 0.0026303 0.659913 putative hydrogenase-1 large subunit
STM0510 -35 -21 GcvB 66 80 -16.54 0.003456 0.6975035 sfbA metal ABC transporter substrate-binding protein
STM0283 41 60 GcvB 152 169 -16.47 0.0036267 0.6975035
STM1787 -64 2 GcvB 34 90 -16.39 0.0038311 0.6975035 [Ni/Fe] hydrogenase large subunit
STM0634 20 62 GcvB 35 77 -16.39 0.0038311 0.6975035 ybeF putative LysR family transcriptional regulator
STM1715 -75 -43 GcvB 42 71 -16.36 0.0039103 0.6975035 yciN similar to E. coli orf hypothetical protein (AAC74355.1) Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83
STM3495 52 64 GcvB 181 193 -16.35 0.0039371 0.6975035 yrfF Intracellular growth attenuator protein igaA
STM2909 41 74 GcvB 47 83 -16.31 0.0040457 0.6975035 mutS DNA mismatch repair protein MutS
STM1498 -54 -38 GcvB 76 92 -16.29 0.0041011 0.6975035 dimethyl sulfoxide reductase subunit A
STM0689 -9 15 GcvB 66 90 -16.13 0.0045687 0.6975035 citA citrate-proton symporter
STM2355 -57 -39 GcvB 72 91 -16.13 0.0045687 0.6975035 argT histidine ABC transporter substrate-binding protein HisJ
STM3089 56 73 GcvB 157 174 -16.07 0.0047561 0.6975035 yqgD similar to E. coli orf hypothetical protein (AAC75978.1) Blastp hit to AAC75978.1 (83 aa) 52% identity in aa 1 - 78
STM1179 22 44 GcvB 35 58 -16.06 0.004788 0.6975035 flgG flagellar basal-body rod protein FlgG
STM1564 19 40 GcvB 72 90 -16.06 0.004788 0.6975035 yddX biofilm-dependent modulation protein
STM4465 -72 -28 GcvB 43 78 -15.94 0.005186 0.7318742 putative ornithine carbamoyltransferase
STM4014 56 73 GcvB 36 58 -15.86 0.0054675 0.7419678 putative periplasmic protein
STM3665 -33 -19 GcvB 154 169 -15.78 0.0057627 0.7419678 avtA valine--pyruvate transaminase
STM0604 4 22 GcvB 62 80 -15.71 0.0060327 0.7419678 ybdM similar to E. coli orf hypothetical protein (AAC73702.1) Blastp hit to AAC73702.1 (209 aa) 77% identity in aa 5 - 209
STM3600 -75 -47 GcvB 155 182 -15.65 0.0062731 0.7419678 fructoselysine 6-kinase
STM1524 -72 -45 GcvB 148 177 -15.64 0.006314 0.7419678 yneI putative succinate-semialdehyde dehydrogenase
STM0399 -32 12 GcvB 43 76 -15.64 0.006314 0.7419678 brnQ branched-chain amino acid transport system II carrier protein
STM3093 -66 -41 GcvB 72 101 -15.59 0.006522 0.7419678 endA deoxyribonuclease I
STM1351 -23 26 GcvB 145 186 -15.56 0.0066498 0.7419678 ydiT ferredoxin family protein
STM3236 25 40 GcvB 154 169 -15.54 0.0067362 0.7419678 yhaK similar to E. coli orf hypothetical protein (AAC76141.1) Blastp hit to AAC76141.1 (233 aa) 84% identity in aa 1 - 233
STM3574 -53 -35 GcvB 150 169 -15.48 0.0070016 0.7528387 yhhM similar to E. coli putative receptor (AAC76492.1) Blastp hit to AAC76492.1 (119 aa) 84% identity in aa 1 - 116
STM1749 51 71 GcvB 36 55 -15.39 0.0074172 0.7711365 adhE bifunctional acetaldehyde-CoA/alcohol dehydrogenase
STM3567 -51 -28 GcvB 63 87 -15.35 0.0076089 0.7711365 livJ high-affinity branched-chain amino acid transporter
STM2189 -6 10 GcvB 155 171 -15.31 0.0078051 0.7711365 mglA galactose/methyl galactoside ABC transporter ATP-binding protein MglA
STM1129 -11 38 GcvB 139 186 -15.3 0.0078548 0.7711365 N-acetylmannosamine-6-phosphate 2-epimerase
STM1571 -69 -46 GcvB 65 89 -15.24 0.0081593 0.7799855 yddG putative permease
STM2801 35 49 GcvB 151 164 -15.18 0.0084743 0.7799855 ygaC similar to E. coli orf hypothetical protein (AAC75718.1) Blastp hit to AAC75718.1 (114 aa) 88% identity in aa 1 - 112
STM3523 7 24 GcvB 72 89 -15.15 0.0086358 0.7799855 glpR DeoR/GlpR family transcriptional regulator
STM3598 58 75 GcvB 62 79 -15.15 0.0086358 0.7799855 putative L-asparaginase
STM3083 -36 -6 GcvB 130 160 -15.04 0.009252 0.7883581 fructuronate reductase
STM1033 42 70 GcvB 132 162 -15.02 0.0093682 0.7883581 Gifsy-2 prophage Clp protease-like protein
STM0085 63 75 GcvB 152 164 -14.92 0.009969 0.7883581 yabF glutathione-regulated potassium-efflux system ancillary protein KefF
STM0412 27 72 GcvB 35 73 -14.92 0.009969 0.7883581 putative inner membrane protein
STM0680 -43 -18 GcvB 71 90 -14.91 0.0100309 0.7883581 asnB asparagine synthetase B
STM3843 7 49 GcvB 37 85 -14.9 0.0100932 0.7883581 trmE tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE
STM0069 -71 -52 GcvB 60 81 -14.87 0.0102821 0.7883581 caiE phenylacetic acid degradation protein PaaY
STM1282 56 70 GcvB 36 50 -14.86 0.0103458 0.7883581 yeaK putative cytoplasmic protein
STM3527 -66 -47 GcvB 139 163 -14.85 0.0104098 0.7883581 similar to E. coli orf hypothetical protein (AAC73602.1) Blastp hit to AAC73602.1 (86 aa) 35% identity in aa 21 - 85
STM4558 -7 58 GcvB 36 91 -14.84 0.0104742 0.7883581 rimI ribosomal-protein-alanine N-acetyltransferase
STM2745 -21 11 GcvB 36 61 -14.8 0.0107353 0.7904009
STM2179 -46 -27 GcvB 69 90 -14.7 0.0114137 0.7904009 4-hydroxybenzoate transporter
STM3810 -30 -11 GcvB 72 91 -14.7 0.0114137 0.7904009 yidQ putative outer membrane lipoprotein
STM2384 -30 -16 GcvB 77 90 -14.64 0.0118389 0.7904009 aroC chorismate synthase
STM4250 10 38 GcvB 49 80 -14.64 0.0118389 0.7904009 yjbQ similar to E. coli orf hypothetical protein (AAC77026.1) Blastp hit to AAC77026.1 (138 aa) 78% identity in aa 1 - 138
STM0670 -75 -37 GcvB 36 78 -14.61 0.0120567 0.7904009 miaB tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB
STM3021 29 67 GcvB 50 91 -14.5 0.0128866 0.7904009 putative inner membrane protein
STM2925 58 74 GcvB 153 170 -14.45 0.0132805 0.7904009 nlpD lipoprotein NlpD
STM1879 -34 15 GcvB 49 86 -14.44 0.0133605 0.7904009 ptrB oligopeptidase B
STM0516 31 40 GcvB 154 163 -14.42 0.0135219 0.7904009 allR transcriptional regulator
STM1871 -72 -28 GcvB 143 187 -14.41 0.0136032 0.7904009 putative phage integrase protein
STM3786 27 38 GcvB 178 189 -14.4 0.013685 0.7904009 yicN similar to E. coli orf hypothetical protein (AAC76686.1) Blastp hit to AAC76686.1 (159 aa) 82% identity in aa 10 - 159
STM2096 18 30 GcvB 152 164 -14.39 0.0137672 0.7904009 rfbD dTDP-4-dehydrorhamnose reductase
STM0900 -48 -8 GcvB 36 81 -14.38 0.0138499 0.7904009 putative Fels-1 prophage DNA or RNA helicases of superfamily II
STM3564 -44 -17 GcvB 65 90 -14.37 0.013933 0.7904009 livK leucine ABC transporter subunit substrate-binding protein LivK
STM2526 -32 -17 GcvB 71 86 -14.36 0.0140165 0.7904009 ndk nucleoside-diphosphate kinase
STM0022 -74 -55 GcvB 127 147 -14.36 0.0140165 0.7904009 bcfB fimbrial chaperone protein
STM1822 43 69 GcvB 162 185 -14.36 0.0140165 0.7904009 yoaB similar to E. coli orf hypothetical protein (AAC74879.1) Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130
STM3076 -22 13 GcvB 35 75 -14.34 0.0141849 0.7904009 tktA transketolase
STM0470 27 75 GcvB 38 91 -14.3 0.0145273 0.7904009 rpmJ2 50S ribosomal protein L36
STM1287 4 34 GcvB 47 79 -14.28 0.0147012 0.7904009 anaerobic sulfatase maturase
STM2793 -73 -48 GcvB 49 72 -14.28 0.0147012 0.7904009 gabP GABA permease
STM1576 4 30 GcvB 61 86 -14.27 0.0147888 0.7904009 narU nitrate/nitrite transporter NarU
STM3680 58 70 GcvB 48 60 -14.26 0.0148769 0.7904009 aldB aldehyde dehydrogenase
STM3261 59 74 GcvB 54 69 -14.26 0.0148769 0.7904009 galactitol-1-phosphate 5-dehydrogenase
STM1057 1 43 GcvB 37 81 -14.2 0.0154155 0.7979576 pepN aminopeptidase N
STM0532 -28 7 GcvB 131 164 -14.18 0.0155989 0.7979576 arcC putative carbamate kinase
PSLT042 2 70 GcvB 37 91 -14.17 0.0156913 0.7979576 putative integrase protein
STM0330 -25 -8 GcvB 152 170 -14.16 0.0157842 0.7979576 3-isopropylmalate dehydratase small subunit
STM2328 11 48 GcvB 32 75 -14.14 0.0159714 0.7979576 nuoA NADH-quinone oxidoreductase subunit A
STM4228 -39 -26 GcvB 1 15 -14.12 0.0161607 0.7979576 malF maltose ABC transporter permease MalF
STM3720 14 23 GcvB 154 163 -14.11 0.016256 0.7979576 yibR putative inner membrane protein
STM3984 -15 -3 GcvB 148 161 -14.06 0.0167404 0.8089837 pepQ Xaa-Pro dipeptidase
STM0804 -70 -36 GcvB 36 76 -14.05 0.0168389 0.8089837 moaC molybdenum cofactor biosynthesis protein C
STM3257 -68 -44 GcvB 46 81 -13.98 0.0175423 0.8300455 D-tagatose-16-bisphosphate aldolase subunit GatZ
STM2573 -66 -17 GcvB 42 84 -13.97 0.0176449 0.8300455 2-dehydropantoate 2-reductase
STM4312 -24 24 GcvB 53 90 -13.95 0.0178517 0.8311163
STM1257 -35 -12 GcvB 166 189 -13.92 0.018166 0.8371189 peptide ABC transporter permease
STM4007 -39 -20 GcvB 63 85 -13.85 0.0189185 0.8629894 glnA type I glutamate--ammonia ligase
STM4083 -40 -22 GcvB 138 155 -13.8 0.0194729 0.8669559 yiiR similar to E. coli orf hypothetical protein (AAC76903.1) Blastp hit to AAC76903.1 (146 aa) 90% identity in aa 1 - 141

Details of Selected Interaction Download Interaction Details 

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



		 
	

			





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