Origin IGS: aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc .........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 gagacttctccttttctattcttatccctattatacaatctttttgtaaatctatcaaacgcttacatttctttttcaaaattcagaaaagtatgaataagctagcaaaaagagctctgaaatagagctctctgaatgaaggtaagatacatttcattcgattttttcaattattagaaattaaccttttaatgtagataaagattgctttacaatctatatctgtcaactaaaaaggtcccctggactataatgatgattacttcgtaatcctcatccaccgactaaaacaatccagtggattgtt Mask Tandem Repeat Region ================================================ aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Find is-nt database================================================ Query_seq: SMT_493:SMT_494|SMT_493:SMT_494:K01996 branched-chain amino acid transport system ATP-binding protein:K04767 acetoin utilization protein AcuB:->->:427988..428294 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_493:SMT_494|SMT_493:SMT_494:K01996 branched-chain amino acid transport system ATP-binding protein:K04767 acetoin utilization protein AcuB:->->:427988..428294 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_493:SMT_494|SMT_493:SMT_494:K01996 branched-chain amino acid transport system ATP-binding protein:K04767 acetoin utilization protein AcuB:->->:427988..428294 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: - Start: 186 End: 290 ......................................................................................................................................................................................... K L A R K A L K N M S K Q I K F F F H L R K I S K C F S Q I I P I L M ................. aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc 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: 89 Start: 249 End: 278 ........................................................................................................................................................................................................................................................TTTGATAGATTTACAAAAAGATTGTATAAT............................. PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 92 End: 121 ...........................................................................................TTTTAATGTAGATAAAGATTGCTTTACAAT.......................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 274 End: 303 .................................................................................................................................................................................................................................................................................CTTCTCCTTTTCTATTCTTATCCCTATTAT.... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -8.9 Tail_Score: -4.77759 Start: 178 End: 196 Full_Region: TTACCTTCATTCAGA GAGCTCT ATTTC AGAGCTC TTTTTGCTAGCTTAT .................................................................................................................................................................................GAGCTCTATTTCAGAGCTC............................................................................................................... Find igs database================================================ Query_seq: SMT_493:SMT_494|SMT_493:SMT_494:K01996 branched-chain amino acid transport system ATP-binding protein:K04767 acetoin utilization protein AcuB:->->:427988..428294 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Intra-Species Hit: Count: 1 Min: 1 Max: 307 Len: 307 Subject: smit_SMT_493_SMT_494|K01996 branched-chain amino acid transport system ATP-binding protein:K04767 acetoin utilization protein AcuB|POSITIVE:POSITIVE|[427988,428294]|307 HSP 1 e-value: 1.0E-173 bit: 609.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Inter-species Hit: Count: 3 Min: 1 Max: 307 Len: 307 Subject: NC_003028_SP_0753_SP_0754|branched-chain amino acid ABC transporter, ATP-binding protein:acetoin utilization protein AcuB, putative|POSITIVE:POSITIVE|[712632,712938]|307 HSP 1 e-value: 1.0E-113 bit: 410.0 Len: 307 Query Start:1 Query End:307 Subject Strand: POSITIVE Subject Start: 1 Subject End: 307 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc aacaatccagtggattgttttagtcggcagatggagattacgaagtaatcatcaatatagtccgggggacctttttagtcggtagattgagattgcaaacaaatctgcatctacattgaaagcttaatttctaataattgaaaaaatcgaatgaaaaatttcttaccttcattcacagagctcgatttcagagctctttttgctagcttattcatacttttctgaatttcgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc Subject: NC_008533_SPD_0656_SPD_0657|branched-chain amino acid ABC transporter, ATP-binding protein:acetoin utilization protein AcuB, putative|POSITIVE:POSITIVE|[674718,675130]|413 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 296 Query Start:12 Query End:307 Subject Strand: POSITIVE Subject Start: 118 Subject End: 413 ...........ggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc ...........ggattgttttagccggcagatggagattacgaagtaatcatcaatatagtcctggggacctttttagtcggtggatagagattgcaaacaaatatgcatctacattgaaagcttaatttctaataattgaaaaaatcgaatgaaaaatttcttaccttcattcacagagctctatttcagagctctttttgctagcttattcatacttttttgaatttcgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatggggataagaatagaaaaggagaagtctc HSP 2 e-value: 1.0E-17 bit: 91.7 Len: 62 Query Start:1 Query End:62 Subject Strand: POSITIVE Subject Start: 1 Subject End: 62 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtc..................................................................................................................................................................................................................................................... aacaatccagtggattgttttagtcggcagatgaagattacgaagtaatcatcattatagtc..................................................................................................................................................................................................................................................... Subject: NC_003098_spr0663_spr0664|ABC transporter ATP-binding protein - branched chain amino acid transport:hypothetical protein|POSITIVE:POSITIVE|[667187,667599]|413 HSP 1 e-value: 1.0E-102 bit: 373.0 Len: 296 Query Start:12 Query End:307 Subject Strand: POSITIVE Subject Start: 118 Subject End: 413 ...........ggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtccaggggacctttttagttgacagatatagattgtaaagcaatctttatctacattaaaaggttaatttctaataattgaaaaaatcgaatgaaatgtatcttaccttcattcagagagctctatttcagagctctttttgctagcttattcatacttttctgaattttgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatagggataagaatagaaaaggagaagtctc ...........ggattgttttagccggcagatggagattacgaagtaatcatcaatatagtcctggggacctttttagtcggtggatagagattgcaaacaaatatgcatctacattgaaagcttaatttctaataattgaaaaaatcgaatgaaaaatttcttaccttcattcacagagctctatttcagagctctttttgctagcttattcatacttttttgaatttcgaaaaagaaatgtaagcgtttgatagatttacaaaaagattgtataatggggataagaatagaaaaggagaagtctc HSP 2 e-value: 1.0E-17 bit: 91.7 Len: 62 Query Start:1 Query End:62 Subject Strand: POSITIVE Subject Start: 1 Subject End: 62 aacaatccactggattgttttagtcggtggatgaggattacgaagtaatcatcattatagtc..................................................................................................................................................................................................................................................... aacaatccagtggattgttttagtcggcagatgaagattacgaagtaatcatcattatagtc..................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAAUCCACUGGAUUGUUUUAGUCGGUGGAUGAGGAUUACGAAGUAAUCAUCAUUAUAGUCCAGGGGACCUUUUUAGUUGACAGAUAUAGAUUGUAAAGCAAUCUUUAUCUACAUUAAAAGGUUAAUUUCUAAUAAUUGAAAAAAUCGAAUGAAAUGUAUCUUACCUUCAUUCAGAGAGCUCUAUUUCAGAGCUCUUUUUGCUAGCUUAUUCAUACUUUUCUGAAUUUUGAAAAAGAAAUGUAAGCGUUUGAUAGAUUUACAAAAAGAUUGUAUAAUAGGGAUAAGAAUAGAAAAGGAGAAGUCUC .....(((.(((((((((...........(((((.((((((...)))))).))))))))))))))..((((((((....((..(((((.((((((.....)))))).))))).))..))))))))..((((((....((((.....))))..........(((((((((((...((((((((((.....))))))))))......((((((......(((((........)))))......))))))...)))......(((((.....))))).....))).))))).)))))).)))........ (-74.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAGACUUCUCCUUUUCUAUUCUUAUCCCUAUUAUACAAUCUUUUUGUAAAUCUAUCAAACGCUUACAUUUCUUUUUCAAAAUUCAGAAAAGUAUGAAUAAGCUAGCAAAAAGAGCUCUGAAAUAGAGCUCUCUGAAUGAAGGUAAGAUACAUUUCAUUCGAUUUUUUCAAUUAUUAGAAAUUAACCUUUUAAUGUAGAUAAAGAUUGCUUUACAAUCUAUAUCUGUCAACUAAAAAGGUCCCCUGGACUAUAAUGAUGAUUACUUCGUAAUCCUCAUCCACCGACUAAAACAAUCCAGUGGAUUGUU (((....)))..((((((...............(((((.....)))))............((((((((...((((((........)))))).)))..)))))........(((((((((...)))))))))..(((((((((((...))).))))))))...............))))))...(((((((..((((((((.((((((.....)))))).)))))).))....)))))))....((((......(((.((((((...)))))).)))))))........((((((((...)))))))) (-65.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 295 198 152 210 164 smit:SMT_1651|5end_chromosome_segregation_SMC_protein_1636998..1637228_POSITIVE 294 68 26 230 192 smit:SMT_242|5end_PTS_system,_mannose-specific_IID_component_180074..180304_NEGATIVE 287 207 165 231 197 smit:SMT_581|5end_ATP_synthase_A_chain_498402..498632_POSITIVE 274 200 151 170 116 smit:SMT_1843|5end_transposase,_TnpA_1808100..1808330_POSITIVE 274 200 151 170 116 smit:SMT_1238|5end_transposase,_TnpA_1198738..1198968_POSITIVE 271 207 167 109 55 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 271 205 161 162 113 smit:SMT_461|5end_mannose-6-phosphate_isomerase_399379..399609_POSITIVE 270 201 168 229 187 smit:SMT_1464|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1444721..1444951_POSITIVE 266 69 21 68 34 smit:SMT_450|5end_hydroxyethylthiazole_kinase_388139..388369_POSITIVE 263 83 43 68 29 smit:SMT_464|5end_ribonuclease_Z_402867..403097_POSITIVE 262 52 14 223 180 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 257 208 163 84 46 smit:SMT_2065|5end_transcriptional_regulator,_MarR_family_1972665..1972895_POSITIVE 257 208 163 84 46 smit:SMT_1320|5end_transcriptional_regulator,_MarR_family_1290234..1290464_POSITIVE 256 64 26 100 69 smit:SMT_725|5end_hypothetical_protein_630415..630645_NEGATIVE 254 207 165 56 15 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 252 223 182 231 188 smit:SMT_1361|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1341402..1341632_NEGATIVE 249 209 161 218 171 smit:SMT_1493|5end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1475737..1475967_POSITIVE 245 203 169 171 134 smit:SMT_1661|5end_K02986_small_subunit_ribosomal_protein_S4_1651110..1651340_NEGATIVE 244 206 162 158 114 smit:SMT_168|5end_anaerobic_ribonucleoside-triphosphate_reductase_activating_protein_113670..113900_POSITIVE 243 68 24 220 172 smit:SMT_1698|5end_CMP-binding_factor_1680092..1680322_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 330 69 25 131 76 smit:SMT_2122|3end_cell_surface_protein_precursor_2007319..2007469_NEGATIVE 294 33 1 107 72 smit:SMT_493|3end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427927..428077_POSITIVE 284 196 152 61 15 smit:SMT_964|3end_cadmium_resistance_transporter,_putative_909891..910041_NEGATIVE 278 59 12 63 4 smit:SMT_198|3end_50S_ribosomal_protein_L17_129281..129431_POSITIVE 271 207 167 112 58 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 270 201 168 71 29 smit:SMT_1463|3end_phosphate_transport_system_protein_PhoU_1444643..1444793_POSITIVE 266 69 21 68 34 smit:SMT_449|3end_hypothetical_protein_388219..388369_POSITIVE 257 88 41 51 1 smit:SMT_1848|3end_K03458_nucleobase:cation_symporter-2,_NCS2_family_1812694..1812844_NEGATIVE 257 43 3 119 77 smit:SMT_476|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_413313..413463_NEGATIVE 256 64 26 103 72 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 252 229 190 145 110 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 252 202 161 58 19 smit:SMT_1036|3end_alpha-galactosidase_978160..978310_NEGATIVE 252 85 44 43 1 smit:SMT_211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_144316..144466_POSITIVE 250 70 28 45 1 smit:SMT_1357|3end_endo-beta-N-acetylglucosaminidase_1334450..1334600_NEGATIVE 247 70 27 57 11 smit:SMT_1471|3end_hypothetical_protein_1453442..1453592_NEGATIVE 241 204 166 63 19 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 238 204 162 133 76 smit:SMT_1337|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1312054..1312204_NEGATIVE 237 207 175 108 78 smit:SMT_2167|3end_hypothetical_protein_2040711..2040861_POSITIVE 235 65 26 34 2 smit:SMT_1071|3end_hypothetical_protein_1010386..1010536_POSITIVE 235 47 9 53 5 smit:SMT_737|3end_hypothetical_protein_642270..642420_NEGATIVE