Origin IGS: agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc .........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 gatatacctctattatcaatttttatttcattttattatatcataaaaaaatacacttgtgagataaatccgcttaggtaaggcgttttcatcttctttccgaaacattctttttgatttgcaaacaattacatcaataaatttactatataaacatcaaaaaggtcccttacggaacctcattcatct Mask Tandem Repeat Region ================================================ agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Find is-nt database================================================ Query_seq: SMT_274:SMT_275|SMT_274:SMT_275:ABC transporter substrate-binding protein - oligopeptide transport:transcriptional activator-exopolysaccharide biosynthesis:->->:217320..217508 189 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_274:SMT_275|SMT_274:SMT_275:ABC transporter substrate-binding protein - oligopeptide transport:transcriptional activator-exopolysaccharide biosynthesis:->->:217320..217508 189 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_274:SMT_275|SMT_274:SMT_275:ABC transporter substrate-binding protein - oligopeptide transport:transcriptional activator-exopolysaccharide biosynthesis:->->:217320..217508 189 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 62 End: 151 ............................................................. M F A N Q K E C F G K K M K T P Y L S G F I S Q V Y F F M I ...................................... Protein_Len: 36 Strand: + Start: 52 End: 159 ................................................... M D V I V C K S K R M F R K E D E N A L P K R I Y L T S V F F Y D I I K .............................. Protein_Len: 40 Strand: - Start: 3 End: 122 .. H I L N R L P G K Q H K Y L L N I S T I T Q L D F L I N R F S S S F A K G L R M ................................................................... agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc 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: 126 End: 155 .............................................................................................................................TCTCACAAGTGTATTTTTTTATGATATAAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_274:SMT_275|SMT_274:SMT_275:ABC transporter substrate-binding protein - oligopeptide transport:transcriptional activator-exopolysaccharide biosynthesis:->->:217320..217508 189 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Intra-Species Hit: Count: 1 Min: 1 Max: 189 Len: 189 Subject: smit_SMT_274_SMT_275|ABC transporter substrate-binding protein - oligopeptide transport:transcriptional activator-exopolysaccharide biosynthesis|POSITIVE:POSITIVE|[217320,217508]|189 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 189 Query Start:1 Query End:189 Subject Strand: POSITIVE Subject Start: 1 Subject End: 189 agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtannnnnnnatgatataataaaatgaaataaaaattgataatagaggtatatc agatgaatgaggttccgtaagggacctttttgatgtttatatagtaaatttattgatgtaattgtttgcaaatcaaaaagaatgtttcggaaagaagatgaaaacgccttacctaagcggatttatctcacaagtgtatttttttatgatataataaaatgaaataaaaattgataatagaggtatatc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUGAAUGAGGUUCCGUAAGGGACCUUUUUGAUGUUUAUAUAGUAAAUUUAUUGAUGUAAUUGUUUGCAAAUCAAAAAGAAUGUUUCGGAAAGAAGAUGAAAACGCCUUACCUAAGCGGAUUUAUCUCACAAGUGUAUUUUUUUAUGAUAUAAUAAAAUGAAAUAAAAAUUGAUAAUAGAGGUAUAUC ..((.((.((((((((....)))))))).)).)).........(((..(((((((.(((((....)))))............(((((((....((.((((((..(((.........)))..)))))))).....((((((.......))))))......)))))))........)))))))..)))... (-38.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUACCUCUAUUAUCAAUUUUUAUUUCAUUUUAUUAUAUCAUAAAAAAAUACACUUGUGAGAUAAAUCCGCUUAGGUAAGGCGUUUUCAUCUUCUUUCCGAAACAUUCUUUUUGAUUUGCAAACAAUUACAUCAAUAAAUUUACUAUAUAAACAUCAAAAAGGUCCCUUACGGAACCUCAUUCAUCU ((((.........)))).............((((((......))))))............(((((.((..(((((.....)))))..)).)))))..(((((......((((((((((.....................................)))))))))).......)))))............ (-22.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 258 140 94 192 130 smit:SMT_1723|5end_hypothetical_protein_1709081..1709311_POSITIVE 256 129 81 87 29 smit:SMT_1328|5end_hypothetical_protein_1304468..1304698_NEGATIVE 238 124 83 156 114 smit:SMT_1260|5end_hypothetical_protein_1225517..1225747_POSITIVE 233 159 113 163 116 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 227 137 106 223 186 smit:SMT_177|5end_K02878_large_subunit_ribosomal_protein_L16_118738..118968_POSITIVE 226 144 101 137 92 smit:SMT_355|5end_hypothetical_protein_291622..291852_POSITIVE 224 149 105 175 130 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 224 128 86 170 114 smit:SMT_342|5end_chaperone_protein_DnaJ_281800..282030_POSITIVE 223 146 106 146 114 smit:SMT_148|5end_glycoprotein_endopeptidase_98033..98263_POSITIVE 222 120 78 116 77 smit:SMT_2022|5end_hypothetical_protein_1938257..1938487_POSITIVE 222 130 81 95 44 smit:SMT_748|5end_prephenate_dehydratase_653498..653728_NEGATIVE 218 105 77 219 183 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 217 36 1 156 118 smit:SMT_487|5end_transcriptional_regulator,_TetR_family_422380..422610_POSITIVE 217 130 86 198 162 smit:SMT_108|5end_hypothetical_protein_53488..53718_POSITIVE 215 49 1 122 71 smit:SMT_964|5end_cadmium_resistance_transporter,_putative_910511..910741_NEGATIVE 213 46 6 95 48 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 213 46 6 179 132 smit:SMT_294|5end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_237165..237395_POSITIVE 210 136 105 187 152 smit:SMT_1768|5end_hydrolase,_alpha/beta_fold_family_1744959..1745189_NEGATIVE 209 150 105 215 164 smit:SMT_808|5end_hypothetical_protein_predicted_by_Glimmer/Critica_718076..718306_NEGATIVE 208 130 82 183 128 smit:SMT_1554|5end_isoleucyl-tRNA_synthetase_1537040..1537270_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 129 81 77 19 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 238 124 83 137 95 smit:SMT_1259|3end_hypothetical_protein_1225578..1225728_POSITIVE 226 149 107 111 71 smit:SMT_1833|3end_tagatose_1,6-diphosphate_aldolase_1802429..1802579_POSITIVE 226 144 101 106 61 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 224 149 105 47 2 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 223 146 106 49 17 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 222 120 78 73 34 smit:SMT_2021|3end_K06201_copper_homeostasis_protein_1938294..1938444_POSITIVE 222 130 81 98 47 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 222 138 102 109 76 smit:SMT_615|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_525617..525767_POSITIVE 220 138 106 133 97 smit:SMT_773|3end_UDP-N-acetylenolpyruvoylglucosamine_reductase_683460..683610_NEGATIVE 219 147 106 122 84 smit:SMT_1157|3end_septation_ring_formation_regulator_EzrA_1100202..1100352_NEGATIVE 217 130 86 80 44 smit:SMT_107|3end_ribose-phosphate_pyrophosphokinase_53450..53600_POSITIVE 213 50 1 92 36 smit:SMT_1389|3end_dihydroxyacetone_kinase_1365901..1366051_NEGATIVE 212 120 82 55 16 smit:SMT_1523|3end_ferrochelatase_1503390..1503540_NEGATIVE 207 37 1 119 78 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 207 44 7 98 57 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 205 48 1 68 15 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 205 119 88 84 40 smit:SMT_1165|3end_sensor_protein_CiaH_1110486..1110636_NEGATIVE 200 56 11 94 59 smit:SMT_728|3end_hypothetical_protein_633203..633353_NEGATIVE 198 35 9 147 113 smit:SMT_2025|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1940995..1941145_NEGATIVE