Origin IGS: tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaattattatgcaagctcttatttttataatagctcctttttatcaagttttttactattagataaactttccagttaaactattagaatgttttttatatcttgtggtattttagtaacaataatacttgcaactccaatacatggagtcctatatcaataatacaatctgcatttctaataacatctaaatcatgtttaataaccattacagttgcttctaattgaataatattttcttttcattttgtcaaaaaaattacttgttaaaactaaaaaataataaataagatagccaaaaaaaatcttctttgctataattataatatctaaaaagtattgtgaaaataaaaggagaatttaata Mask Tandem Repeat Region ================================================ tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Find is-nt database================================================ Query_seq: FN0878:FN0879|FN0878:FN0879:Transcriptional regulator, GntR family:ABC transporter integral membrane protein:<-<-:1539885..1540250 366 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0878:FN0879|FN0878:FN0879:Transcriptional regulator, GntR family:ABC transporter integral membrane protein:<-<-:1539885..1540250 366 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0878:FN0879|FN0878:FN0879:Transcriptional regulator, GntR family:ABC transporter integral membrane protein:<-<-:1539885..1540250 366 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Predict ORF larger than 30AA ================================================ Protein_Len: 53 Strand: + Start: 7 End: 165 ...... M L L L F S Q Y F L D I I I I A K K I F F G Y L I Y Y F L V L T S N F F D K M K R K Y Y S I R S N C N G Y ......................................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 134 End: 268 ..................................................................................................................................... M I Q L E A T V M V I K H D L D V I R N A D C I I D I G L H V L E L Q V L L L L K Y H K I .................................................................................................. Protein_Len: 42 Strand: - Start: 142 End: 267 ............................................................................................................................................. N S A V T I T I L C S K S T I L F A S Q I I S I P S W T N S N C T N N N S F Y W L M ................................................................................................... tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: - Score: 86 Start: 46 End: 75 .............................................ATAGCCAAAAAAAATCTTCTTTGCTATAAT................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 18 End: 47 .................ATTTTCACAATACTTTTTAGATATTATAAT............................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0878:FN0879|FN0878:FN0879:Transcriptional regulator, GntR family:ABC transporter integral membrane protein:<-<-:1539885..1540250 366 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaagattttttttggctatcttatttattattttttagttttaacaagtaatttttttgacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt Intra-Species Hit: Count: 1 Min: 1 Max: 366 Len: 366 Subject: NC_003454_FN0878_FN0879|Transcriptional regulator, GntR family:ABC transporter integral membrane protein|NEGATIVE:NEGATIVE|[1539885,1540250]|366 HSP 1 e-value: 1.0E-140 bit: 500.0 Len: 252 Query Start:115 Query End:366 Subject Strand: POSITIVE Subject Start: 115 Subject End: 366 ..................................................................................................................gacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt ..................................................................................................................gacaaaatgaaaagaaaatattattcaattagaagcaactgtaatggttattaaacatgatttagatgttattagaaatgcagattgtattattgatataggactccatgtattggagttgcaagtattattgttactaaaataccacaagatataaaaaacattctaatagtttaactggaaagtttatctaatagtaaaaaacttgataaaaaggagctattataaaaataagagcttgcataataattt HSP 2 e-value: 7.0E-26 bit: 119.0 Len: 60 Query Start:1 Query End:60 Subject Strand: POSITIVE Subject Start: 1 Subject End: 60 tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaag.................................................................................................................................................................................................................................................................................................................. tattaaattctccttttattttcacaatactttttagatattataattatagcaaagaag.................................................................................................................................................................................................................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUAAAUUCUCCUUUUAUUUUCACAAUACUUUUUAGAUAUUAUAAUUAUAGCAAAGAAGAUUUUUUUUGGCUAUCUUAUUUAUUAUUUUUUAGUUUUAACAAGUAAUUUUUUUGACAAAAUGAAAAGAAAAUAUUAUUCAAUUAGAAGCAACUGUAAUGGUUAUUAAACAUGAUUUAGAUGUUAUUAGAAAUGCAGAUUGUAUUAUUGAUAUAGGACUCCAUGUAUUGGAGUUGCAAGUAUUAUUGUUACUAAAAUACCACAAGAUAUAAAAAACAUUCUAAUAGUUUAACUGGAAAGUUUAUCUAAUAGUAAAAAACUUGAUAAAAAGGAGCUAUUAUAAAAAUAAGAGCUUGCAUAAUAAUUU (((((.....((((((((((.......((((..(((((((........(((((((((((....)))))).)))))..........(((((((((((..(((.....((((((((..(.....)..))))))))........(((((((....(((((....(((...(((((.......)))))..)))...))))).(((((((.(((......(((((((.....)))))))...((((.......)))).........))))))))))......))))))).))).))))))))))).))))))).))))........))).)))))))(((.((((....)))).))).....))))).... (-60.06) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUAUUAUGCAAGCUCUUAUUUUUAUAAUAGCUCCUUUUUAUCAAGUUUUUUACUAUUAGAUAAACUUUCCAGUUAAACUAUUAGAAUGUUUUUUAUAUCUUGUGGUAUUUUAGUAACAAUAAUACUUGCAACUCCAAUACAUGGAGUCCUAUAUCAAUAAUACAAUCUGCAUUUCUAAUAACAUCUAAAUCAUGUUUAAUAACCAUUACAGUUGCUUCUAAUUGAAUAAUAUUUUCUUUUCAUUUUGUCAAAAAAAUUACUUGUUAAAACUAAAAAAUAAUAAAUAAGAUAGCCAAAAAAAAUCUUCUUUGCUAUAAUUAUAAUAUCUAAAAAGUAUUGUGAAAAUAAAAGGAGAAUUUAAUA ...(((((((...((((.((((....)))).))))...(((((.(((((..(((..(((((((((((((....))))....(((((((((((...((.(((....((((((...((((.......))))....((((((.....))))))...))))))...))).))...))).))))))))............))))))))).......((((((....)))))).............................)))..))))).))))).......)))))))...................((((((((.......(((((((((.......))))))))).....))))))))........ (-50.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 648 60 11 151 102 NC_003454:FN0878|5end_Transcriptional_regulator,_GntR_family_1539794..1540024_NEGATIVE 265 236 195 193 145 NC_003454:FN0679|5end_GTPase_1334596..1334826_POSITIVE 258 234 193 119 77 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 226 238 193 227 178 NC_003454:FN0206|5end_Activator_of_(R)-2-hydroxyglutaryl-CoA_dehydratase_832758..832988_POSITIVE 224 260 218 78 31 NC_003454:FN1940|5end_Na+_driven_multidrug_efflux_pump_440955..441185_NEGATIVE 207 220 183 75 39 NC_003454:FN0610|5end_hypothetical_protein_1264815..1265045_POSITIVE 206 120 80 157 114 NC_003454:FN0795|5end_CBS_domain_containing_protein_1452400..1452630_POSITIVE 206 226 186 195 152 NC_003454:FN1604|5end_hypothetical_protein_113822..114052_NEGATIVE 204 250 212 47 9 NC_003454:FN0889|5end_Dihydrolipoamide_acyltransferase_1551393..1551623_NEGATIVE 202 243 206 187 153 NC_003454:FN0295|5end_Transketolase_927986..928216_POSITIVE 201 239 191 61 7 NC_003454:FN0397|5end_Dipeptide_transport_system_permease_protein_dppB_1035822..1036052_POSITIVE 200 237 196 112 72 NC_003454:FN0647|5end_Hypothetical_cytosolic_protein_1304520..1304750_NEGATIVE 198 217 172 167 116 NC_003454:FN1046|5end_hypothetical_protein_1696371..1696601_POSITIVE 198 180 133 206 164 NC_003454:FN2066|5end_hypothetical_protein_576277..576507_POSITIVE 196 50 6 120 66 NC_003454:FN0464|5end_hypothetical_protein_1109675..1109905_POSITIVE 195 268 230 141 106 NC_003454:FN0616|5end_hypothetical_protein_1276511..1276741_NEGATIVE 195 240 191 65 18 NC_003454:FN1751|5end_Pyruvate-flavodoxin_oxidoreductase_248067..248297_POSITIVE 194 114 74 178 135 NC_003454:FN0169|5end_Coproporphyrinogen_III_oxidase_794741..794971_POSITIVE 194 255 213 59 10 NC_003454:FN2014|5end_ATP-dependent_protease_La_516974..517204_NEGATIVE 192 250 208 78 35 NC_003454:FN0671|5end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326616..1326846_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 224 222 183 151 108 NC_003454:FN0678|3end_Ser/Thr_protein_kinase_1334651..1334801_POSITIVE 215 350 305 104 58 NC_003454:FN1288|3end_hypothetical_protein_1944830..1944980_POSITIVE 209 310 261 74 23 NC_003454:FN0053|3end_Branched-chain_amino_acid_transport_system_carrier_protein_690694..690844_POSITIVE 200 237 196 100 60 NC_003454:FN0648|3end_Exoenzyme_regulatory_protein_aepA_precursor_1304532..1304682_NEGATIVE 197 97 51 129 86 NC_003454:FN0571|3end_DNA_processing_chain_A_1222390..1222540_POSITIVE 195 268 230 50 15 NC_003454:FN0617|3end_DNA_polymerase_III,_beta_chain_1276602..1276752_NEGATIVE 192 250 208 81 38 NC_003454:FN0670|3end_High-affinity_zinc_uptake_system_membrane_protein_znuB_1326699..1326849_POSITIVE 192 337 291 72 30 NC_003454:FN0502|3end_Phosphoheptose_isomerase_1152063..1152213_NEGATIVE 191 43 12 100 73 NC_003454:FN0741|3end_Glutamate_formiminotransferase_1398991..1399141_NEGATIVE 191 237 192 38 1 NC_003454:FN0051|3end_hypothetical_protein_688783..688933_NEGATIVE 190 110 61 69 19 NC_003454:FN0180|3end_Tetratricopeptide_repeat_family_protein_804846..804996_NEGATIVE 189 197 151 57 12 NC_003454:FN1529|3end_hypothetical_protein_42993..43143_NEGATIVE 187 259 227 43 14 NC_003454:FN0906|3end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1564124..1564274_NEGATIVE 183 255 214 49 1 NC_003454:FN2015|3end_ATP-dependent_protease_ATP-binding_subunit_516984..517134_NEGATIVE 182 250 218 43 6 NC_003454:FN0791|3end_histidine_ammonia-lyase_1448326..1448476_POSITIVE 181 260 215 97 59 NC_003454:FN1463|3end_pyridoxine_biosynthesis_protein_2145924..2146074_POSITIVE 181 236 204 63 28 NC_003454:FN1282|3end_LSU_ribosomal_protein_L17P_1941269..1941419_NEGATIVE 180 238 191 57 22 NC_003454:FN1194|3end_hypothetical_protein_1855668..1855818_POSITIVE 180 54 11 124 86 NC_003454:FN0755|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_C_1414663..1414813_NEGATIVE 180 248 201 119 63 NC_003454:FN0131|3end_Hemolysin_activator_protein_precursor_761327..761477_POSITIVE