Origin IGS: gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag .........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 cttctacccccaacttctttatcttttcattataccatattttagaagttttccaaaaaggaaaaaagtctggaaattttcaagtctaagcgaatactctaataccccaatacaagaattagaatgatatcttttttcagtcctcattttatttcaaacaaataaaaacagcaaatcttgttgatttaccgtttaaaacatgatacaagaaaactctctaaaaatttcttttattctataaatcaactagaataagcttcttcaaccctattcgctatatctggacttacctcccaaatcccaacatagggttgctcaatatactgtttttctttcatagtatatagataggctacactatcatktaatcattctgatgagtgannnnnttaattaattaannnnnattgagttagtagcatc Mask Tandem Repeat Region ================================================ gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Find is-nt database================================================ Query_seq: SMT_575:SMT_576|SMT_575:SMT_576:pyruvate kinase:transcriptional regulator, LysR family:->->:494874..495296 423 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_575:SMT_576|SMT_575:SMT_576:pyruvate kinase:transcriptional regulator, LysR family:->->:494874..495296 423 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_575:SMT_576|SMT_575:SMT_576:pyruvate kinase:transcriptional regulator, LysR family:->->:494874..495296 423 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 86 End: 178 ..................................................................................... M K E K Q Y I E Q P Y V G I W E V S P D I A N R V E E A Y S S ..................................................................................................................................................................................................................................................... Protein_Len: 42 Strand: + Start: 277 End: 402 .................................................................................................................................................................................................................................................................................... M R T E K R Y H S N S C I G V L E Y S L R L E N F Q T F F L F G K L L K Y G I M K R ..................... Protein_Len: 32 Strand: - Start: 300 End: 395 ........................................................................................................................................................................................................................................................................................................... E L E Q I P T N S Y E S L S S F K W V K K R K P F S R F Y P I M ............................ Protein_Len: 31 Strand: - Start: 80 End: 172 ............................................................................... I S H F F F L I N L L G I N P N P L Y T W I Y R I P N F F S M ........................................................................................................................................................................................................................................................... gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag 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: 83 Start: 248 End: 277 .......................................................................................................................................................................................................................................................TTTGCTGTTTTTATTTGTTTGAAATAAAAT.................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 83 Start: 365 End: 394 ............................................................................................................................................................................................................................................................................................................................................................................TTTTGGAAAACTTCTAAAATATGGTATAAT............................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 85 HP_score: -4.9 Tail_Score: -5.5454 Start: 233 End: 255 Full_Region: GTATCATGTTTTAAA CGGTAAATC AACAA GATTTGCTG TTTTTATTTGTTTGA ........................................................................................................................................................................................................................................CGGTAAATCAACAAGATTTGCTG........................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_575:SMT_576|SMT_575:SMT_576:pyruvate kinase:transcriptional regulator, LysR family:->->:494874..495296 423 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagacttttttcctttttggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Intra-Species Hit: Count: 1 Min: 1 Max: 423 Len: 423 Subject: smit_SMT_575_SMT_576|pyruvate kinase:transcriptional regulator, LysR family|POSITIVE:POSITIVE|[494874,495296]|423 HSP 1 e-value: 0.0 bit: 643.0 Len: 356 Query Start:1 Query End:356 Subject Strand: POSITIVE Subject Start: 1 Subject End: 356 gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagac................................................................... gatgctactaactcaatnnnnnttaattaattaannnnntcactcatcagaatgattamatgatagtgtagcctatctatatactatgaaagaaaaacagtatattgagcaaccctatgttgggatttgggaggtaagtccagatatagcgaatagggttgaagaagcttattctagttgatttatagaataaaagaaatttttagagagttttcttgtatcatgttttaaacggtaaatcaacaagatttgctgtttttatttgtttgaaataaaatgaggactgaaaaaagatatcattctaattcttgtattggggtattagagtattcgcttagacttgaaaatttccagac................................................................... HSP 2 e-value: 3.0E-22 bit: 107.0 Len: 54 Query Start:370 Query End:423 Subject Strand: POSITIVE Subject Start: 370 Subject End: 423 .................................................................................................................................................................................................................................................................................................................................................................................ggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag .................................................................................................................................................................................................................................................................................................................................................................................ggaaaacttctaaaatatggtataatgaaaagataaagaagttgggggtagaag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGCUACUAACUCAAUNNNNNUUAAUUAAUUAANNNNNUCACUCAUCAGAAUGAUUAMAUGAUAGUGUAGCCUAUCUAUAUACUAUGAAAGAAAAACAGUAUAUUGAGCAACCCUAUGUUGGGAUUUGGGAGGUAAGUCCAGAUAUAGCGAAUAGGGUUGAAGAAGCUUAUUCUAGUUGAUUUAUAGAAUAAAAGAAAUUUUUAGAGAGUUUUCUUGUAUCAUGUUUUAAACGGUAAAUCAACAAGAUUUGCUGUUUUUAUUUGUUUGAAAUAAAAUGAGGACUGAAAAAAGAUAUCAUUCUAAUUCUUGUAUUGGGGUAUUAGAGUAUUCGCUUAGACUUGAAAAUUUCCAGACUUUUUUCCUUUUUGGAAAACUUCUAAAAUAUGGUAUAAUGAAAAGAUAAAGAAGUUGGGGGUAGAAG ..(((..(((((((..........................((((.((((...........)))))))).....(((((.(((((((((.....................(((((((((((((..(((((((.......))))))).))))..))))))))).(((((.((((((((.........))))))))..(((((((((((..(((((((((((.(((......((((((((((((.....)))))))))))).........))).))))...))))))).....(((.....((((((((((((.....)))).)))))))).....)))....))))))))))).......((((((.....)))))))))))....)))))))))......)))))..).))))))..))).... (-91.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCUACCCCCAACUUCUUUAUCUUUUCAUUAUACCAUAUUUUAGAAGUUUUCCAAAAAGGAAAAAAGUCUGGAAAUUUUCAAGUCUAAGCGAAUACUCUAAUACCCCAAUACAAGAAUUAGAAUGAUAUCUUUUUUCAGUCCUCAUUUUAUUUCAAACAAAUAAAAACAGCAAAUCUUGUUGAUUUACCGUUUAAAACAUGAUACAAGAAAACUCUCUAAAAAUUUCUUUUAUUCUAUAAAUCAACUAGAAUAAGCUUCUUCAACCCUAUUCGCUAUAUCUGGACUUACCUCCCAAAUCCCAACAUAGGGUUGCUCAAUAUACUGUUUUUCUUUCAUAGUAUAUAGAUAGGCUACACUAUCAUKUAAUCAUUCUGAUGAGUGANNNNNUUAAUUAAUUAANNNNNAUUGAGUUAGUAGCAUC ...((((.(((............................(((((((..((((((.....))))))...)))))))......(((((((((((((((...................(((.((((((((...((......))...)))))))).)))..............(((...(((.(((((((((..(..(((((.........(((......))).........)))))..)..))))))))).)))....)))..........)))))))).....)))))))....................)))..((((((((((((((.........))))))))..(((((......)))))......((((((....)))))).......................))))))..)))).... (-76.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 305 158 118 54 2 smit:SMT_938|5end_hypothetical_protein_891274..891504_NEGATIVE 295 168 126 160 114 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 292 160 115 211 164 smit:SMT_1692|5end_hypothetical_protein_1675169..1675399_POSITIVE 285 143 102 227 183 smit:SMT_391|5end_PTS_system,_galactose-specific_IIC_component_322647..322877_POSITIVE 279 418 375 222 178 smit:SMT_326|5end_K02029_polar_amino_acid_transport_system_permease_protein_263864..264094_NEGATIVE 272 150 108 85 44 smit:SMT_519|5end_glutathione_reductase_444884..445114_NEGATIVE 265 372 333 109 66 smit:SMT_663|5end_phosphate_acetyltransferase_574990..575220_NEGATIVE 261 146 108 66 21 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 258 143 112 147 115 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 257 119 73 59 21 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 257 160 118 221 182 smit:SMT_1703|5end_recombination_protein_RecR_1686660..1686890_POSITIVE 257 159 112 201 160 smit:SMT_1671|5end_hypothetical_protein_1659757..1659987_NEGATIVE 257 119 73 59 21 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 257 160 113 68 13 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 254 164 121 67 28 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 253 257 219 83 49 smit:SMT_92|5end_GTP-binding_protein,_probable_translation_factor_22857..23087_POSITIVE 251 168 121 121 57 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 249 160 122 74 29 smit:SMT_1614|5end_K08998_hypothetical_protein_1601330..1601560_POSITIVE 249 170 122 67 14 smit:SMT_997|5end_integral_membrane_protein_938243..938473_POSITIVE 248 142 106 211 167 smit:SMT_1868|5end_thymidine_kinase_1828775..1829005_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 375 160 112 148 107 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 339 149 103 145 89 smit:SMT_1597|3end_K02032_peptide/nickel_transport_system_ATP-binding_protein_1587987..1588137_POSITIVE 305 158 118 76 24 smit:SMT_939|3end_phosphomethylpyrimidine_kinase_891252..891402_NEGATIVE 272 150 108 88 47 smit:SMT_520|3end_glutathione_reductase_444881..445031_NEGATIVE 271 167 123 53 3 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 269 161 122 117 78 smit:SMT_979|3end_K03709_Mn-dependent_transcriptional_regulator_927399..927549_POSITIVE 265 372 333 65 22 smit:SMT_664|3end_ribosomal_large_subunit_pseudouridine_synthase,_RluD_subfamily_575034..575184_NEGATIVE 261 146 108 69 24 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 258 107 61 65 17 smit:SMT_1164|3end_hypothetical_protein_1110482..1110632_POSITIVE 258 143 112 68 36 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 257 160 113 59 4 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 256 160 111 145 95 smit:SMT_1637|3end_hypothetical_protein_1623848..1623998_POSITIVE 251 167 123 132 97 smit:SMT_997|3end_integral_membrane_protein_939243..939393_POSITIVE 251 168 121 151 87 smit:SMT_942|3end_hypothetical_protein_893528..893678_NEGATIVE 249 160 122 74 29 smit:SMT_1613|3end_ribosomal_large_subunit_pseudouridine_synthase_B_1601410..1601560_POSITIVE 249 150 105 114 67 smit:SMT_479|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_415604..415754_NEGATIVE 241 178 147 141 111 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 240 170 122 52 8 smit:SMT_320|3end_alcohol_dehydrogenase,_zinc-containing_259241..259391_NEGATIVE 238 152 112 138 96 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 234 169 121 117 57 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE