Origin IGS: ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa .........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 tttctgagatcagcgnnnnnttaattaattaannnnnaaaaagcggttcaaaacgaatcgcttttttatataaggagaccgaatggaaaaagaaagataaataaaatagatatattatcttctggtaatattataatacacaaaaataaggggcttgtcaatagaaaagaagcaatttaattaaaaatattcttgttttttcaaattgcaattaaataagcaattttcagataataattgaaaattcaagctgtttatgttataatgatagcgattaaattcgaggtgaaaa Mask Tandem Repeat Region ================================================ ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Find is-nt database================================================ Query_seq: SMT_1991:SMT_1992|SMT_1991:SMT_1992:K03706 transcriptional pleiotropic repressor:carboxynorspermidine decarboxylase:<-<-:1918355..1918646 292 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1991:SMT_1992|SMT_1991:SMT_1992:K03706 transcriptional pleiotropic repressor:carboxynorspermidine decarboxylase:<-<-:1918355..1918646 292 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1991:SMT_1992|SMT_1991:SMT_1992:K03706 transcriptional pleiotropic repressor:carboxynorspermidine decarboxylase:<-<-:1918355..1918646 292 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 117 End: 224 .................................................................................................................... M A S F L L T S P L F L C I I I L P E D N I S I L F I F L F P F G L L I .................................................................... Protein_Len: 50 Strand: - Start: 116 End: 265 ................................................................................................................... I A E K R N V L G K N K H I I I N G S S L I D I K N I K R K G N P R R I Y F L S E N Q V A K X X X M ........................... ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa 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: 95 Start: 27 End: 56 ..........................ATTGAAAATTCAAGCTGTTTATGTTATAAT............................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 91 Start: 131 End: 160 ..................................................................................................................................ATTGACAAGCCCCTTATTTTTGTGTATTAT.................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1991:SMT_1992|SMT_1991:SMT_1992:K03706 transcriptional pleiotropic repressor:carboxynorspermidine decarboxylase:<-<-:1918355..1918646 292 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Intra-Species Hit: Count: 1 Min: 1 Max: 292 Len: 292 Subject: smit_SMT_1991_SMT_1992|K03706 transcriptional pleiotropic repressor:carboxynorspermidine decarboxylase|NEGATIVE:NEGATIVE|[1918355,1918646]|292 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 292 Query Start:1 Query End:292 Subject Strand: POSITIVE Subject Start: 1 Subject End: 292 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatttaattgcaatttgaaaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgctttttnnnnnttaattaattaannnnncgctgatctcagaaa Inter-species Hit: Count: 3 Min: 1 Max: 255 Len: 255 Subject: NC_008533_SPD_1412_SPD_1413|GTP-sensing transcriptional pleiotropic repressor CodY:ATP-dependent RNA helicase, putative|NEGATIVE:NEGATIVE|[1431056,1431318]|263 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 163 Query Start:93 Query End:255 Subject Strand: POSITIVE Subject Start: 105 Subject End: 262 ............................................................................................aaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgcttttt..................................... ............................................................................................aaaaaccagaatatttttaattaaattgttccttttctattgacaagttgcctatttttgtgtatcataacattataa-aagataatataataattttatttgtcttt----tcacattcggtctccttatataaaaaagcgattcattttgaaccgcttttt..................................... HSP 2 e-value: 3.0E-15 bit: 83.8 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatt...................................................................................................................................................................................................................... ttttcacctcgaatttaatcgctatcattataacataaaaacgtctctttttcaataattatctgaaaattccttatt...................................................................................................................................................................................................................... Subject: NC_003098_spr1439_spr1440|transcriptional repressor CodY:hypothetical protein|NEGATIVE:NEGATIVE|[1423525,1423787]|263 HSP 1 e-value: 1.0E-29 bit: 131.0 Len: 163 Query Start:93 Query End:255 Subject Strand: POSITIVE Subject Start: 105 Subject End: 262 ............................................................................................aaaaacaagaatatttttaattaaattgcttcttttctattgacaagccccttatttttgtgtattataatattaccagaagataatatatctattttatttatctttctttttccattcggtctccttatataaaaaagcgattcgttttgaaccgcttttt..................................... ............................................................................................aaaaaccagaatatttttaattaaattgttccttttctattgacaagttgcctatttttgtgtatcataacattataa-aagataatataataattttatttgtcttt----tcacattcggtctccttatataaaaaagcgattcattttgaaccgcttttt..................................... HSP 2 e-value: 3.0E-15 bit: 83.8 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatt...................................................................................................................................................................................................................... ttttcacctcgaatttaatcgctatcattataacataaaaacgtctctttttcaataattatctgaaaattccttatt...................................................................................................................................................................................................................... Subject: NC_003028_SP_1584_SP_1585|transcriptional repressor CodY:hypothetical protein|NEGATIVE:POSITIVE|[1489503,1489653]|151 HSP 1 e-value: 3.0E-15 bit: 83.8 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 ttttcacctcgaatttaatcgctatcattataacataaacagcttgaattttcaattattatctgaaaattgcttatt...................................................................................................................................................................................................................... ttttcacctcgaatttaatcgctatcattataacataaaaacgtctctttttcaataattatctgaaaattccttatt...................................................................................................................................................................................................................... HSP 2 e-value: 5.0E-11 bit: 69.9 Len: 47 Query Start:93 Query End:139 Subject Strand: POSITIVE Subject Start: 105 Subject End: 151 ............................................................................................aaaaacaagaatatttttaattaaattgcttcttttctattgacaag......................................................................................................................................................... ............................................................................................aaaaaccagaatatttttaattaaattgttccttttctattgacaag......................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCACCUCGAAUUUAAUCGCUAUCAUUAUAACAUAAACAGCUUGAAUUUUCAAUUAUUAUCUGAAAAUUGCUUAUUUAAUUGCAAUUUGAAAAAACAAGAAUAUUUUUAAUUAAAUUGCUUCUUUUCUAUUGACAAGCCCCUUAUUUUUGUGUAUUAUAAUAUUACCAGAAGAUAAUAUAUCUAUUUUAUUUAUCUUUCUUUUUCCAUUCGGUCUCCUUAUAUAAAAAAGCGAUUCGUUUUGAACCGCUUUUU ........(((((...(((((((..................(((((((((((((.........))))))))............((((((((((((((........)))))..)))))))))..............)))))......((((((((((..............((((((((.(((.......)))))))))))......((....))......)))))))))))))))))...))))).......... (-37.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAGCGGUUCAAAACGAAUCGCUUUUUUAUAUAAGGAGACCGAAUGGAAAAAGAAAGAUAAAUAAAAUAGAUAUAUUAUCUUCUGGUAAUAUUAUAAUACACAAAAAUAAGGGGCUUGUCAAUAGAAAAGAAGCAAUUUAAUUAAAAAUAUUCUUGUUUUUUCAAAUUGCAAUUAAAUAAGCAAUUUUCAGAUAAUAAUUGAAAAUUCAAGCUGUUUAUGUUAUAAUGAUAGCGAUUAAAUUCGAGGUGAAAA ((((((((((((.....)))))))))))).............(((((..((..((((.((((((((.......))).)))))))))(.((.(((((((((........(((((.((((((..............(((((((....(((((((....)))))))..)))))))............(((((((((.......))))))))))))))).)))))))))))))).)).)..))..)))))......... (-49.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 744 50 1 141 92 smit:SMT_1991|5end_K03706_transcriptional_pleiotropic_repressor_1918264..1918494_NEGATIVE 271 235 194 223 183 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 260 248 203 200 157 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 260 248 203 200 157 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 260 248 203 200 157 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 260 248 203 200 157 smit:SMT_511|5end_hypothetical_protein_predicted_by_Glimmer/Critica_439391..439621_POSITIVE 243 249 201 223 176 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 238 250 207 73 30 smit:SMT_543|5end_topoisomerase_IV_subunit_B_458372..458602_POSITIVE 237 47 1 211 161 smit:SMT_1867|5end_peptide_chain_release_factor_1_1828218..1828448_NEGATIVE 231 37 1 124 93 smit:SMT_2141|5end_hypothetical_protein_2019976..2020206_NEGATIVE 231 37 1 124 93 smit:SMT_870|5end_hypothetical_protein_818737..818967_NEGATIVE 229 237 191 114 70 smit:SMT_812|5end_acetyltransferase,_GNAT_family_721858..722088_NEGATIVE 228 240 192 57 9 smit:SMT_1552|5end_RNA_binding_protein_1535119..1535349_POSITIVE 225 250 201 152 102 smit:SMT_1059|5end_NAD(P)H-flavin_oxidoreductase_997379..997609_POSITIVE 222 171 135 175 134 smit:SMT_500|5end_hypothetical_protein_432770..433000_POSITIVE 217 217 183 112 81 smit:SMT_747|5end_transcriptional_regulator,_LytR_family_652653..652883_NEGATIVE 216 250 202 137 83 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 214 220 175 161 102 smit:SMT_859|5end_K02086_DNA_replication_protein_804058..804288_NEGATIVE 210 220 178 208 170 smit:SMT_1789|5end_hypothetical_protein_1765318..1765548_POSITIVE 210 240 198 202 155 smit:SMT_76|5end_DNA_repair_and_genetic_recombination_protein_2677..2907_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 260 248 203 86 43 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 260 248 203 86 43 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 260 248 203 86 43 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 260 248 203 86 43 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 229 237 191 105 61 smit:SMT_813|3end_acetyltransferase,_GNAT_family_721867..722017_NEGATIVE 228 240 192 60 12 smit:SMT_1551|3end_K02221_YggT_family_protein_1535202..1535352_POSITIVE 222 171 135 144 103 smit:SMT_499|3end_hypothetical_protein_432819..432969_POSITIVE 217 217 183 115 84 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 216 250 202 137 83 smit:SMT_1352|3end_formamidopyrimidine-DNA_glycosylase_1329817..1329967_NEGATIVE 206 240 195 140 99 smit:SMT_1385|3end_phosphocarrier_protein_HPr_1362871..1363021_POSITIVE 202 144 107 150 109 smit:SMT_458|3end_hypothetical_protein_predicted_by_Glimmer/Critica_396729..396879_NEGATIVE 200 250 203 125 74 smit:SMT_1329|3end_GTP-binding_protein_CgtA_1304478..1304628_NEGATIVE 198 248 202 69 18 smit:SMT_820|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_730734..730884_NEGATIVE 197 244 206 150 119 smit:SMT_1581|3end_transcriptional_regulator,_biotin_repressor_family_1573120..1573270_NEGATIVE 196 221 194 147 122 smit:SMT_1783|3end_peptide_methionine_sulfoxide_reductase_1760774..1760924_POSITIVE 196 122 82 108 68 smit:SMT_714|3end_hypothetical_protein_predicted_by_Glimmer/Critica_620890..621040_NEGATIVE 196 122 82 108 68 smit:SMT_696|3end_K03744_LemA_protein_606885..607035_NEGATIVE 196 217 184 117 76 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 195 219 175 151 93 smit:SMT_860|3end_homoserine_O-succinyltransferase_804067..804217_NEGATIVE 192 156 120 116 73 smit:SMT_2021|3end_K06201_copper_homeostasis_protein_1938294..1938444_POSITIVE