Origin IGS: aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca .........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 tgaaaaacagtccctagggctgttttctctacattaggatataaaaacagactatagctagttagagaaaaactataattgaaaactatatcttcttacagtataataaaaggaacaagtgtttgagatttgacttcaaacacatgcaatgattcctgaaaagtacagttaggagagagtt Mask Tandem Repeat Region ================================================ aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Find is-nt database================================================ Query_seq: SMT_860:SMT_861|SMT_860:SMT_861:homoserine O-succinyltransferase:adenine phosphoribosyltransferase:<-<-:805102..805282 181 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_860:SMT_861|SMT_860:SMT_861:homoserine O-succinyltransferase:adenine phosphoribosyltransferase:<-<-:805102..805282 181 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_860:SMT_861|SMT_860:SMT_861:homoserine O-succinyltransferase:adenine phosphoribosyltransferase:<-<-:805102..805282 181 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Predict ORF larger than 30AA ================================================ aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca 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: 90 Start: 75 End: 104 ..........................................................................ATTGAAAACTATATCTTCTTACAGTATAAT............................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_860:SMT_861|SMT_860:SMT_861:homoserine O-succinyltransferase:adenine phosphoribosyltransferase:<-<-:805102..805282 181 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: smit_SMT_860_SMT_861|homoserine O-succinyltransferase:adenine phosphoribosyltransferase|NEGATIVE:NEGATIVE|[805102, 805282]|181 HSP 1 e-value: 2.0E-98 bit: 359.0 Len: 181 Query Start:1 Query End:181 Subject Strand: POSITIVE Subject Start: 1 Subject End: 181 aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca aactctctcctaactgtacttttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttttca Inter-species Hit: Count: 3 Min: 5 Max: 178 Len: 174 Subject: NC_008533_SPD_1406_SPD_1407|homoserine O-succinyltransferase:adenine phosphoribosyltransferase|NEGATIVE:NEGATIVE|[1426072, 1426252]|181 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 174 Query Start:5 Query End:178 Subject Strand: POSITIVE Subject Start: 5 Subject End: 179 ....ctctcctaactgtact-tttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttt... ....ctctcctaactgtactctttcaggaataattgcatatgtttgaagacaaatctcaaacacttagtccttttattatactgcaagaagatatagttttcaattatagtttttctctaactagttatagtctatttttatatcctagtgtagagaaaacagccctagggactgtttt... Subject: NC_003098_spr1434_spr1435|homoserine O-succinyltransferase:adenine phosphoribosyltransferase|NEGATIVE:NEGATIVE|[1418541, 1418721]|181 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 174 Query Start:5 Query End:178 Subject Strand: POSITIVE Subject Start: 5 Subject End: 179 ....ctctcctaactgtact-tttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttt... ....ctctcctaactgtactctttcaggaataattgcatatgtttgaagacaaatctcaaacacttagtccttttattatactgcaagaagatatagttttcaattatagtttttctctaactagttatagtctatttttatatcctagtgtagagaaaacagccctagggactgtttt... Subject: NC_003028_SP_1576_SP_1577|homoserine O-succinyltransferase:adenine phosphoribosyltransferase|NEGATIVE:NEGATIVE|[1483096, 1483276]|181 HSP 1 e-value: 1.0E-68 bit: 260.0 Len: 174 Query Start:5 Query End:178 Subject Strand: POSITIVE Subject Start: 5 Subject End: 179 ....ctctcctaactgtact-tttcaggaatcattgcatgtgtttgaagtcaaatctcaaacacttgttccttttattatactgtaagaagatatagttttcaattatagtttttctctaactagctatagtctgtttttatatcctaatgtagagaaaacagccctagggactgtttt... ....ctctcctaactgtactctttcaggaataattgcatatgtttgaagacaaatctcaaacacttagtccttttattatactgcaagaagatatagttttcaattatagtttttctctaactagttatagtctatttttatatcctagtgtagagaaaacagccctagggactgtttt... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUCCUAACUGUACUUUUCAGGAAUCAUUGCAUGUGUUUGAAGUCAAAUCUCAAACACUUGUUCCUUUUAUUAUACUGUAAGAAGAUAUAGUUUUCAAUUAUAGUUUUUCUCUAACUAGCUAUAGUCUGUUUUUAUAUCCUAAUGUAGAGAAAACAGCCCUAGGGACUGUUUU ((((.((.((.(((......((((......(((.((((((((.(......))))))))).))))))).......))).)).))..(((((((....(((((((((((...........))))))))).))...))))))).......)))).((((((((....)).)))))). (-37.42) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAACAGUCCCUAGGGCUGUUUUCUCUACAUUAGGAUAUAAAAACAGACUAUAGCUAGUUAGAGAAAAACUAUAAUUGAAAACUAUAUCUUCUUACAGUAUAAUAAAAGGAACAAGUGUUUGAGAUUUGACUUCAAACACAUGCAAUGAUUCCUGAAAAGUACAGUUAGGAGAG .(((((((((...)))))))))((((((.(((((..((((.........)))).)))))))))))......................((((((.((.((((......(((((((.(((((((((.......))))))))).))......))))).....)))).)).)))))). (-42.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 825 50 1 145 96 smit:SMT_860|5end_homoserine_O-succinyltransferase_805011..805241_NEGATIVE 307 170 127 139 94 smit:SMT_1504|5end_topology_modulation_protein_1487204..1487434_POSITIVE 258 170 123 50 6 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 257 170 146 205 179 smit:SMT_122|5end_hypothetical_protein_74456..74686_POSITIVE 250 69 21 105 68 smit:SMT_1169|5end_phosphorylase,_Pnp/UDP_family_1117350..1117580_NEGATIVE 247 169 126 166 121 smit:SMT_1128|5end_surface_antigen_1063140..1063370_NEGATIVE 246 46 2 148 98 smit:SMT_242|5end_PTS_system,_mannose-specific_IID_component_180074..180304_NEGATIVE 232 170 125 66 29 smit:SMT_1143|5end_K02025_multiple_sugar_transport_system_permease_protein_1086928..1087158_POSITIVE 232 80 32 80 32 smit:SMT_846|5end_hypothetical_protein_792769..792999_NEGATIVE 231 70 22 105 48 smit:SMT_1806|5end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781229..1781459_POSITIVE 231 70 22 105 48 smit:SMT_1635|5end_putative_N-acetyldiaminopimelate_deacetylase_1621426..1621656_POSITIVE 231 170 130 141 95 smit:SMT_436|5end_amidase_related_to_nicotinamidase_378198..378428_NEGATIVE 228 68 29 75 35 smit:SMT_1925|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_1867262..1867492_POSITIVE 227 169 124 160 95 smit:SMT_1657|5end_glutamine-binding_protein_/_glutamine_transport_system_permease_protein_GlnP_1648077..1648307_NEGATIVE 227 134 94 47 4 smit:SMT_734|5end_hypothetical_protein_639967..640197_POSITIVE 226 89 58 123 93 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 226 63 21 227 190 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 223 160 116 215 170 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 223 87 45 39 3 smit:SMT_376|5end_DNA_(cytosine-5-)-methyltransferase_312900..313130_POSITIVE 222 100 58 171 128 smit:SMT_2081|5end_glycosyltransferase_1980870..1981100_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 170 127 86 41 smit:SMT_1503|3end_SSU_ribosomal_protein_S20P_1487231..1487381_POSITIVE 257 42 1 141 94 smit:SMT_1264|3end_oligoendopeptidase_F_1230734..1230884_POSITIVE 257 170 146 83 57 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 246 46 2 133 83 smit:SMT_243|3end_PTS_system,_mannose-specific_IIC_component_180089..180239_NEGATIVE 224 69 22 69 31 smit:SMT_341|3end_ThiJ/PfpI_family_protein_281681..281831_POSITIVE 222 100 58 136 93 smit:SMT_2080|3end_glycosyl_transferase_CpsE_1980915..1981065_POSITIVE 222 100 58 136 93 smit:SMT_279|3end_glycosyl_transferase_CpsE_222421..222571_POSITIVE 217 167 139 66 36 smit:SMT_934|3end_pyridine_nucleotide-disulfide_oxidoreductase_887307..887457_POSITIVE 217 96 60 77 41 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 215 160 115 55 13 smit:SMT_2061|3end_K02011_iron(III)_transport_system_permease_protein_1970802..1970952_POSITIVE 215 160 115 55 13 smit:SMT_202|3end_K02011_iron(III)_transport_system_permease_protein_132173..132323_NEGATIVE 213 126 83 100 61 smit:SMT_1616|3end_putative_ABC-type_cobalamin_Fe3+-siderophores_transport_system_ATPase_component_1602795..1602945_NEGATIVE 211 58 11 151 108 smit:SMT_1291|3end_hypothetical_protein_1254296..1254446_POSITIVE 211 42 2 41 6 smit:SMT_497|3end_hypothetical_protein_431810..431960_POSITIVE 207 129 96 122 87 smit:SMT_1139|3end_rRNA_(guanine-N1-)-methyltransferase_1080683..1080833_POSITIVE 207 47 1 63 15 smit:SMT_654|3end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_564157..564307_NEGATIVE 206 170 129 83 28 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE 205 25 2 55 27 smit:SMT_905|3end_hypothetical_protein_predicted_by_Glimmer/Critica_852766..852916_NEGATIVE 199 58 11 137 87 smit:SMT_1535|3end_exodeoxyribonuclease_V_alpha_chain_1520513..1520663_POSITIVE 198 128 85 106 61 smit:SMT_1233|3end_cadmium_resistance_protein_1195000..1195150_POSITIVE