Origin IGS: agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag .........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 ctcttgaatccgtttatttaatttatcaaaatcaaaagttgttgtttcagtgaaaatttctggatccggtataaagtgaactgttgttccagttttatccgtatctccaccacctcaggtctgcgacacatgacacgacggtatcttggtatgaaatctaccattttgtggacatgacatctaatgagttgaaaggcnnnnnttaattaattaannnnnagatatgtcctagttcttttttctctaacttaatctwatccatcccaaaaatcgatttccagaaaggagctgggtaaattcttatcaaaaagaatgacttctgtgttggaactgacatkggttttatctcagtcttgctagtatctgtagcggcattct Mask Tandem Repeat Region ================================================ agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Find is-nt database================================================ Query_seq: SMT_539:SMT_540|SMT_539:SMT_540:sensor histidine kinase CiaH:DNA gyrase, B subunit:->->:456120..456497 378 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_539:SMT_540|SMT_539:SMT_540:sensor histidine kinase CiaH:DNA gyrase, B subunit:->->:456120..456497 378 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_539:SMT_540|SMT_539:SMT_540:sensor histidine kinase CiaH:DNA gyrase, B subunit:->->:456120..456497 378 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 33 End: 173 ................................ M K P M S V P T Q K S F F L I R I Y P A P F W K S I F G M D X I K L E K K E L G H I X X L I N ............................................................................................................................................................................................................. Protein_Len: 55 Strand: + Start: 194 End: 358 ................................................................................................................................................................................................. M R C H V H K M V D F I P R Y R R V M C R R P E V V E I R I K L E Q Q F T L Y R I Q K F S L K Q Q L L I L I N .................... Protein_Len: 50 Strand: - Start: 205 End: 354 ............................................................................................................................................................................................................ T W L I T S K M G L Y R R T M H R L G S T T S I R I F S S C C N V K Y R I W F N E S F C C S K I K M ........................ Protein_Len: 41 Strand: - Start: 176 End: 298 ............................................................................................................................................................................... X X G K L E N S T M D V F H Y I E Y W S V T T D H T A S R L H H L Y P Y F Q F L M ................................................................................ agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_539:SMT_540|SMT_539:SMT_540:sensor histidine kinase CiaH:DNA gyrase, B subunit:->->:456120..456497 378 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Intra-Species Hit: Count: 1 Min: 1 Max: 378 Len: 378 Subject: smit_SMT_539_SMT_540|sensor histidine kinase CiaH:DNA gyrase, B subunit|POSITIVE:POSITIVE|[456120,456497]|378 HSP 1 e-value: 0.0 bit: 684.0 Len: 378 Query Start:1 Query End:378 Subject Strand: POSITIVE Subject Start: 1 Subject End: 378 agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag agaatgccgctacagatactagcaagactgagataaaaccmatgtcagttccaacacagaagtcattctttttgataagaatttacccagctcctttctggaaatcgatttttgggatggatwagattaagttagagaaaaaagaactaggacatatctnnnnnttaattaattaannnnngcctttcaactcattagatgtcatgtccacaaaatggtagatttcataccaagataccgtcgtgtcatgtgtcgcagacctgaggtggtggagatacggataaaactggaacaacagttcactttataccggatccagaaattttcactgaaacaacaacttttgattttgataaattaaataaacggattcaagag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAAUGCCGCUACAGAUACUAGCAAGACUGAGAUAAAACCMAUGUCAGUUCCAACACAGAAGUCAUUCUUUUUGAUAAGAAUUUACCCAGCUCCUUUCUGGAAAUCGAUUUUUGGGAUGGAUWAGAUUAAGUUAGAGAAAAAAGAACUAGGACAUAUCUNNNNNUUAAUUAAUUAANNNNNGCCUUUCAACUCAUUAGAUGUCAUGUCCACAAAAUGGUAGAUUUCAUACCAAGAUACCGUCGUGUCAUGUGUCGCAGACCUGAGGUGGUGGAGAUACGGAUAAAACUGGAACAACAGUUCACUUUAUACCGGAUCCAGAAAUUUUCACUGAAACAACAACUUUUGAUUUUGAUAAAUUAAAUAAACGGAUUCAAGAG .(((.((((((.(((...((.((..((((((.((.......)).))))))...((((.((((((.((((((((..(...((((((......(((.(((..((((....))))..))).)))......))))))..)..))))))))...((((((((((.....................................))))...))))))...........)))))).......(((((....)))))..)))).))))..))).))))))(((....((((((((((((......))))....))))).)))..))).......))).............(((((((.((((..............)))).))))))) (-76.63) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUGAAUCCGUUUAUUUAAUUUAUCAAAAUCAAAAGUUGUUGUUUCAGUGAAAAUUUCUGGAUCCGGUAUAAAGUGAACUGUUGUUCCAGUUUUAUCCGUAUCUCCACCACCUCAGGUCUGCGACACAUGACACGACGGUAUCUUGGUAUGAAAUCUACCAUUUUGUGGACAUGACAUCUAAUGAGUUGAAAGGCNNNNNUUAAUUAAUUAANNNNNAGAUAUGUCCUAGUUCUUUUUUCUCUAACUUAAUCUWAUCCAUCCCAAAAAUCGAUUUCCAGAAAGGAGCUGGGUAAAUUCUUAUCAAAAAGAAUGACUUCUGUGUUGGAACUGACAUKGGUUUUAUCUCAGUCUUGCUAGUAUCUGUAGCGGCAUUCU .....(((((((((..((((((((((....(((((..(..(((((.((((((.........((((.(((.((((((.((((....))))...))))))))).))))..(((......)))......))).))).)))))..)...)))))......(((((......)))))...........))))))))))..........................((((((..((((((((((((((.........((((..................))))...))))))))))))))...((((((......)))))).....(((.(.(((((((......))))))).).)))........))))))..))))).)))). (-72.57) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 314 280 238 71 25 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 309 274 234 192 141 smit:SMT_1990|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1917565..1917795_POSITIVE 304 280 232 197 138 smit:SMT_2022|5end_hypothetical_protein_1938257..1938487_POSITIVE 303 300 252 80 20 smit:SMT_1010|5end_hypothetical_protein_948292..948522_POSITIVE 294 280 239 120 80 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 282 119 72 199 147 smit:SMT_1113|5end_hypothetical_protein_1052071..1052301_NEGATIVE 281 280 233 163 111 smit:SMT_1471|5end_hypothetical_protein_1453933..1454163_NEGATIVE 281 100 59 37 2 smit:SMT_1150|5end_hypothetical_protein_1094803..1095033_NEGATIVE 280 280 233 42 5 smit:SMT_1015|5end_galactose_operon_repressor_951938..952168_POSITIVE 278 280 234 220 163 smit:SMT_1982|5end_conserved_hypothetical_protein_1913036..1913266_POSITIVE 278 275 236 174 127 smit:SMT_1851|5end_ABC_transporter,_permease_protein,_putative_1815721..1815951_NEGATIVE 278 280 234 208 151 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 278 280 234 216 152 smit:SMT_323|5end_amino_acid_transport_ATP-binding_protein_261872..262102_NEGATIVE 277 300 255 47 6 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 276 275 231 196 146 smit:SMT_1088|5end_hypothetical_protein_1024346..1024576_NEGATIVE 275 280 231 68 8 smit:SMT_1401|5end_pyruvate_dehydrogenase_E1_component_beta_subunit_1377013..1377243_POSITIVE 275 270 221 174 127 smit:SMT_247|5end_K02996_small_subunit_ribosomal_protein_S9_183062..183292_POSITIVE 272 293 253 57 6 smit:SMT_2082|5end_ATP-dependent_nuclease_subunit_B_1982286..1982516_NEGATIVE 267 256 215 187 140 smit:SMT_177|5end_K02878_large_subunit_ribosomal_protein_L16_118738..118968_POSITIVE 265 285 246 37 3 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 300 252 68 8 smit:SMT_1009|3end_hypothetical_protein_predicted_by_Glimmer/Critica_948360..948510_POSITIVE 303 299 251 72 22 smit:SMT_82|3end_transcriptional_regulator,_TetR_family_14330..14480_POSITIVE 294 280 232 52 3 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 294 291 255 43 1 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE 291 120 71 146 97 smit:SMT_305|3end_seryl-tRNA_synthetase_247577..247727_NEGATIVE 285 121 87 59 20 smit:SMT_1752|3end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1730451..1730601_POSITIVE 281 280 233 145 93 smit:SMT_1472|3end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1453951..1454101_NEGATIVE 274 275 238 142 97 smit:SMT_1074|3end_catabolite_control_protein_A_1012275..1012425_NEGATIVE 273 268 229 144 110 smit:SMT_270|3end_ATP-binding_subunit_of_Clp_protease_and_DnaK/DnaJ_chaperones_211225..211375_POSITIVE 272 274 232 145 95 smit:SMT_2021|3end_K06201_copper_homeostasis_protein_1938294..1938444_POSITIVE 268 278 233 116 64 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 261 280 234 58 5 smit:SMT_1954|3end_6-phospho-beta-glucosidase_1888831..1888981_POSITIVE 260 295 260 44 7 smit:SMT_264|3end_hypothetical_protein_203321..203471_NEGATIVE 259 273 231 55 13 smit:SMT_2116|3end_extramembranal_protein_2003774..2003924_POSITIVE 257 139 91 129 85 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 257 245 204 151 102 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 256 36 6 72 36 smit:SMT_869|3end_hypothetical_protein_817228..817378_NEGATIVE 254 300 251 81 41 smit:SMT_843|3end_hypothetical_protein_789264..789414_NEGATIVE 254 276 232 123 70 smit:SMT_576|3end_transcriptional_regulator,_LysR_family_495407..495557_POSITIVE 252 279 231 149 92 smit:SMT_2033|3end_hydrolase,_haloacid_dehalogenase-like_family_1946739..1946889_POSITIVE