Origin IGS: aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca .........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 tgtaaaaggattgctcagctcaggcaatctttttattttgtgcttttacccaatgaaaatcaaagtgctaactactcaaatcatagctttgagattgcagataaagcgacgtgttttgaagagtattaccatcaaaatctcagctacaattcacccatccttgctctaggaacccatttcctatttcccgttttagatttctttaaggtttttattatatcctgtagaactctacaatttaaaaacattaacaatctaggtagagaaattgttcgtaaaaaaggagatactt Mask Tandem Repeat Region ================================================ aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Find is-nt database================================================ Query_seq: SMT_205:SMT_206|SMT_205:SMT_206:K02012 iron(III) transport system substrate-binding protein:K07720 two-component system, response regulator YesN:<-<-:137265..137556 292 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_205:SMT_206|SMT_205:SMT_206:K02012 iron(III) transport system substrate-binding protein:K07720 two-component system, response regulator YesN:<-<-:137265..137556 292 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_205:SMT_206|SMT_205:SMT_206:K02012 iron(III) transport system substrate-binding protein:K07720 two-component system, response regulator YesN:<-<-:137265..137556 292 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 24 End: 146 ....................... M S L P R L L M F L N C R V L Q D I I K T L K K S K T G N R K W V P R A R M G E L .................................................................................................................................................. Protein_Len: 52 Strand: - Start: 127 End: 282 .............................................................................................................................. L L S P H I T A S I K I T I S K L V R R K I Q L R L A I I Q T T L V K I K M P Y F C L I F L N G S S L M .......... Protein_Len: 60 Strand: - Start: 2 End: 283 . P F L F H T G L A L I P S N Y S L N Q H Y Y E E F C T A K D A I E F S H N S Y N A S Q N E N P L L V F Y F S Q R L Q A M ......... aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca 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: 82 Start: 50 End: 79 .................................................TTTAAATTGTAGAGTTCTACAGGATATAAT..................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 61 HP_score: -5.2 Tail_Score: -3.76815 Start: 110 End: 126 Full_Region: cacccatccttgctc taggaa cccat ttccta tttcccgttttagat .............................................................................................................taggaacccatttccta...................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_205:SMT_206|SMT_205:SMT_206:K02012 iron(III) transport system substrate-binding protein:K07720 two-component system, response regulator YesN:<-<-:137265..137556 292 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: smit_SMT_205_SMT_206|K02012 iron(III) transport system substrate-binding protein:K07720 two-component system, response regulator YesN|NEGATIVE:NEGATIVE|[137265,137556]|292 HSP 1 e-value: 1.0E-164 bit: 579.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca aagtatctccttttttacgaacaatttctctacctagattgttaatgtttttaaattgtagagttctacaggatataataaaaaccttaaagaaatctaaaacgggaaataggaaatgggttcctagagcaaggatgggtgaattgtagctgagattttgatggtaatactcttcaaaacacgtcgctttatctgcaatctcaaagctatgatttgagtagttagcactttgattttcattgggtaaaagcacaaaataaaaagattgcctgagctgagcaatccttttaca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGUAUCUCCUUUUUUACGAACAAUUUCUCUACCUAGAUUGUUAAUGUUUUUAAAUUGUAGAGUUCUACAGGAUAUAAUAAAAACCUUAAAGAAAUCUAAAACGGGAAAUAGGAAAUGGGUUCCUAGAGCAAGGAUGGGUGAAUUGUAGCUGAGAUUUUGAUGGUAAUACUCUUCAAAACACGUCGCUUUAUCUGCAAUCUCAAAGCUAUGAUUUGAGUAGUUAGCACUUUGAUUUUCAUUGGGUAAAAGCACAAAAUAAAAAGAUUGCCUGAGCUGAGCAAUCCUUUUACA .....((((((((((((.((((.(((((.(((((((((((.((((.(((((((..((((((....)))))).......))))))).))))...))))).....)))...))))))))..)))).))))).))))).))..((((..(((((((((((((((.((.....))..))))).......((.......)).)))))..)))))..))))..((..(((.(.(..((.....))..)).)))..))......(((((.(((((((......).)))))).))))).. (-63.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUAAAAGGAUUGCUCAGCUCAGGCAAUCUUUUUAUUUUGUGCUUUUACCCAAUGAAAAUCAAAGUGCUAACUACUCAAAUCAUAGCUUUGAGAUUGCAGAUAAAGCGACGUGUUUUGAAGAGUAUUACCAUCAAAAUCUCAGCUACAAUUCACCCAUCCUUGCUCUAGGAACCCAUUUCCUAUUUCCCGUUUUAGAUUUCUUUAAGGUUUUUAUUAUAUCCUGUAGAACUCUACAAUUUAAAAACAUUAACAAUCUAGGUAGAGAAAUUGUUCGUAAAAAAGGAGAUACUU .((((((((((((((.......)))))))))))))).((((((................((((((..(......((((((.......)))))).((((.......)))).)..)))))).(((.(((........)))))).)).))))........((((......))))....(((((((.(((..((.....((((((((((..(((((((........(((((....)))))...)))))))..............))))))))))...))..))).))))))).... (-61.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 901 140 91 231 182 smit:SMT_205|5end_K02012_iron(III)_transport_system_substrate-binding_protein_137174..137404_NEGATIVE 623 220 171 223 173 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 596 220 171 231 181 smit:SMT_1592|5end_putative_hemolysin_1579655..1579885_POSITIVE 456 229 182 62 13 smit:SMT_1911|5end_hypothetical_protein_1857614..1857844_POSITIVE 456 229 182 62 13 smit:SMT_867|5end_hypothetical_protein_816316..816546_POSITIVE 416 207 170 177 138 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 409 217 173 231 186 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 389 226 182 219 174 smit:SMT_604|5end_DNA_polymerase_III,_epsilon_chain_518693..518923_POSITIVE 372 226 182 58 13 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 364 220 182 52 13 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 364 220 182 52 13 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 313 158 111 163 108 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 297 150 103 159 113 smit:SMT_341|5end_ThiJ/PfpI_family_protein_280969..281199_POSITIVE 293 230 181 179 138 smit:SMT_1250|5end_hypothetical_protein_1211345..1211575_NEGATIVE 291 146 101 176 129 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 284 154 111 60 1 smit:SMT_481|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_418240..418470_NEGATIVE 284 154 111 60 1 smit:SMT_480|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417433..417663_NEGATIVE 284 154 111 60 1 smit:SMT_475|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_412997..413227_NEGATIVE 284 154 111 60 1 smit:SMT_474|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_411894..412124_NEGATIVE 284 154 111 60 1 smit:SMT_473|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_410614..410844_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 529 229 181 51 1 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 460 226 182 51 6 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 416 207 170 81 42 smit:SMT_1782|3end_hypothetical_protein_1759740..1759890_POSITIVE 388 229 182 55 6 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 365 255 219 61 25 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 357 226 181 51 4 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 333 257 219 66 29 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 313 158 111 148 93 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 311 240 191 70 2 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 295 251 219 65 30 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 295 251 219 62 27 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 289 270 225 53 1 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 287 250 201 73 16 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 278 47 5 136 81 smit:SMT_2045|3end_K+_transport_system,_NAD-binding_component_1956758..1956908_POSITIVE 278 246 201 90 37 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 278 47 5 136 81 smit:SMT_1668|3end_K+_transport_system,_NAD-binding_component_1657623..1657773_NEGATIVE 271 252 219 42 5 smit:SMT_1570|3end_hypothetical_protein_1563250..1563400_NEGATIVE 270 229 182 151 99 smit:SMT_740|3end_50S_ribosomal_protein_L10_643715..643865_NEGATIVE 265 209 161 98 51 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 265 139 97 147 105 smit:SMT_919|3end_hypothetical_protein_871741..871891_NEGATIVE