Origin IGS: atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa .........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 ttgttccctcccatttcagtttttactattatagcacattttaaaagtaatgaacagaagaaaattcttgaattttcagaaaattctatacatatataaacattttaaattaaaaacaacaaagcggatcagggcactttctgattaccagaatatgcttttaatccgcttgctttaaataacgtaatgtaatttttacagaagttctttcagataagtgtatttaacat Mask Tandem Repeat Region ================================================ atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Find is-nt database================================================ Query_seq: SMT_1568:SMT_1569|SMT_1568:SMT_1569:putative transketolase C-terminal section:dihydroxy-acid dehydratase:->->:1561195..1561424 230 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1568:SMT_1569|SMT_1568:SMT_1569:putative transketolase C-terminal section:dihydroxy-acid dehydratase:->->:1561195..1561424 230 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1568:SMT_1569|SMT_1568:SMT_1569:putative transketolase C-terminal section:dihydroxy-acid dehydratase:->->:1561195..1561424 230 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 136 End: 228 ....................................................................................................................................... M C I E F S E N S R I F F C S L L L K C A I I V K T E M G G N .. Protein_Len: 32 Strand: - Start: 135 End: 230 ...................................................................................................................................... I H I S N E S F E L I K K Q E N S K F H A I I T F V S I P P F M Protein_Len: 46 Strand: - Start: 56 End: 193 ....................................................... L L R I L L M N Q Y D S L A R I R K T T K L K F H K Y I Y L I K Q F N L F K R R N M V K L M ..................................... atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa 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: 199 End: 228 ......................................................................................................................................................................................................GTTCCCTCCCATTTCAGTTTTTACTATTAT.. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1568:SMT_1569|SMT_1568:SMT_1569:putative transketolase C-terminal section:dihydroxy-acid dehydratase:->->:1561195..1561424 230 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Intra-Species Hit: Count: 1 Min: 1 Max: 230 Len: 230 Subject: smit_SMT_1568_SMT_1569|putative transketolase C-terminal section:dihydroxy-acid dehydratase|POSITIVE:POSITIVE|[1561195,1561424]|230 HSP 1 e-value: 1.0E-127 bit: 456.0 Len: 230 Query Start:1 Query End:230 Subject Strand: POSITIVE Subject Start: 1 Subject End: 230 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgtttatatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggagggaacaa Inter-species Hit: Count: 3 Min: 1 Max: 226 Len: 226 Subject: NC_008533_SPD_1956_SPD_1957|dihydroxy-acid dehydratase:transketolase, C-terminal subunit|NEGATIVE:NEGATIVE|[1925236,1925467]|232 HSP 1 e-value: 1.0E-78 bit: 293.0 Len: 226 Query Start:1 Query End:226 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 232 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaa-gcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgttt-atatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggaggga.... atgttaaatacacttatttgaaagaatttctgtaaaaattacagtacgttatttaaagaaagcggattaaaaagcatattctggtcatcagaaagtgcactaatccgctttgttgtttttaattttaaatatttcacatgcgtatagaattttctgaaaattcaagaattttattctgttcattgcctttaaattgtgctataatagtaaaaactgaaatgggaggga.... Subject: NC_003098_spr1935_spr1936|dihydroxy-acid dehydratase:Putative transketolase c-terminal section|NEGATIVE:NEGATIVE|[1917704,1917935]|232 HSP 1 e-value: 1.0E-78 bit: 293.0 Len: 226 Query Start:1 Query End:226 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 232 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggattaaaa-gcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgttt-atatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggaggga.... atgttaaatacacttatttgaaagaatttctgtaaaaattacagtacgttatttaaagaaagcggattaaaaagcatattctggtcatcagaaagtgcactaatccgctttgttgtttttaattttaaatatttcacatgcgtatagaattttctgaaaattcaagaattttattctgttcattgcctttaaattgtgctataatagtaaaaactgaaatgggaggga.... Subject: NC_003028_SP_2126_SP_2127|dihydroxy-acid dehydratase:transketolase, C-terminal subunit|NEGATIVE:NEGATIVE|[2038564,2038795]|232 HSP 1 e-value: 5.0E-69 bit: 262.0 Len: 226 Query Start:1 Query End:226 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 232 atgttaaatacacttatctgaaagaacttctgtaaaaattacattacgttatttaaagcaagcggatt-aaaagcatattctggtaatcagaaagtgccctgatccgctttgttgtttttaatttaaaatgttt-atatatgtatagaattttctgaaaattcaagaattttcttctgttcattacttttaaaatgtgctataatagtaaaaactgaaatgggaggga.... atgttaaatacacttatttgaaagaatttctgtaaaaattacagtacgttatttaaagaaagcggattaaaaagcatattctggtcatcagaaagtgcactaatccgctttgttgtttttaattttaaatatttcacatgtgtatagaattttctgaaaattcaagaattttattctgttcttcatgcgaaaattgtgctataatagtaaaaactgaaatgggaggga.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUUAAAUACACUUAUCUGAAAGAACUUCUGUAAAAAUUACAUUACGUUAUUUAAAGCAAGCGGAUUAAAAGCAUAUUCUGGUAAUCAGAAAGUGCCCUGAUCCGCUUUGUUGUUUUUAAUUUAAAAUGUUUAUAUAUGUAUAGAAUUUUCUGAAAAUUCAAGAAUUUUCUUCUGUUCAUUACUUUUAAAAUGUGCUAUAAUAGUAAAAACUGAAAUGGGAGGGA ................((((((((((.(((((((......(((((..((((.....(((((((((((((...((((.(((((.....))))).))))..)))))))).))))).....))))....))))).........)))))))..)))).....))).)))..(..(((((((((((((((.(((..........))).)))))....)).))))))))..) (-45.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCCUCCCAUUUCAGUUUUUACUAUUAUAGCACAUUUUAAAAGUAAUGAACAGAAGAAAAUUCUUGAAUUUUCAGAAAAUUCUAUACAUAUAUAAACAUUUUAAAUUAAAAACAACAAAGCGGAUCAGGGCACUUUCUGAUUACCAGAAUAUGCUUUUAAUCCGCUUGCUUUAAAUAACGUAAUGUAAUUUUUACAGAAGUUCUUUCAGAUAAGUGUAUUUAACAU .........((((.(((((((((.(((..........))).))))).))))....(((((((....))))))).)))).....((((((.(((........................((((((((.((((((..(((((.....)))))..))))))..)))))))).....(((.(((....((((.....))))...))).)))...))).))))))....... (-40.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 322 118 79 73 33 smit:SMT_1690|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1674779..1675009_NEGATIVE 298 108 63 128 84 smit:SMT_1127|5end_transcriptional_regulator,_MarR_family_1061556..1061786_NEGATIVE 285 112 71 45 7 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 282 207 162 160 120 smit:SMT_1411|5end_ATP-dependent_nuclease_subunit_B_1395478..1395708_NEGATIVE 271 110 77 57 22 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 264 118 80 126 78 smit:SMT_1917|5end_ATP-dependent_nuclease_subunit_B_1861765..1861995_NEGATIVE 239 113 79 231 198 smit:SMT_141|5end_K03495_glucose_inhibited_division_protein_A_91408..91638_POSITIVE 236 116 71 168 128 smit:SMT_1922|5end_exonuclease_RexA_1865998..1866228_NEGATIVE 236 116 71 168 128 smit:SMT_1484|5end_exonuclease_RexA_1464936..1465166_NEGATIVE 236 105 61 188 144 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 235 109 61 175 121 smit:SMT_121|5end_hypothetical_protein_73303..73533_POSITIVE 234 124 81 217 168 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 232 107 62 55 4 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 232 117 71 226 169 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 231 110 61 58 14 smit:SMT_1962|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1895639..1895869_NEGATIVE 231 110 61 58 14 smit:SMT_823|5end_putative_mucus_binding_protein_746790..747020_NEGATIVE 228 119 71 78 34 smit:SMT_610|5end_hypothetical_protein_521659..521889_POSITIVE 228 113 73 68 19 smit:SMT_599|5end_glucosamine-1-phosphate_N-acetyltransferase_/_UDP-N-acetylglucosamine_pyrophosphorylase_514918..515148_POSITIVE 227 114 72 58 16 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 227 114 72 58 16 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 118 80 75 27 smit:SMT_1918|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1861816..1861966_NEGATIVE 256 118 80 36 1 smit:SMT_1568|3end_putative_transketolase_C-terminal_section_1561134..1561284_POSITIVE 252 106 77 147 120 smit:SMT_1835|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1804072..1804222_POSITIVE 241 119 71 75 24 smit:SMT_1814|3end_amino_acid_transporter_1788640..1788790_POSITIVE 239 198 152 103 65 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 237 120 72 93 52 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 229 117 72 141 103 smit:SMT_150|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_99400..99550_POSITIVE 228 115 71 138 102 smit:SMT_1301|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1263836..1263986_POSITIVE 228 108 61 58 10 smit:SMT_862|3end_hypothetical_protein_predicted_by_Glimmer/Critica_809191..809341_POSITIVE 228 119 71 70 26 smit:SMT_609|3end_laminin-binding_surface_protein_521731..521881_POSITIVE 227 114 72 61 19 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 222 116 80 79 47 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 220 199 160 116 65 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 219 118 73 132 83 smit:SMT_1492|3end_DNA-directed_RNA_polymerase_beta_chain_1475778..1475928_POSITIVE 217 104 61 96 60 smit:SMT_1114|3end_competence_protein_1052076..1052226_NEGATIVE 214 114 71 50 7 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 213 114 71 45 5 smit:SMT_394|3end_K07729_putative_transcriptional_regulator_324549..324699_POSITIVE 213 114 73 138 99 smit:SMT_229|3end_mechanosensitive_ion_channel_165429..165579_NEGATIVE 211 120 87 93 52 smit:SMT_1511|3end_hypothetical_protein_1493902..1494052_POSITIVE 211 107 72 64 27 smit:SMT_403|3end_two-component_sensor_kinase_YesM_333351..333501_POSITIVE