Origin IGS: ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ggtctctctccaattttgtgatgttactattataccatttttgagggaatttggtctcgttctattctatacttttctattttaccttgctctagaatttttaaactgctatacttataacaaaaaacccttccaaggaggtagcgg Mask Tandem Repeat Region ================================================ ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Find is-nt database================================================ Query_seq: SMT_207:SMT_208|SMT_207:SMT_208:putative two-component sensor histidine kinase:leucyl-tRNA synthetase:<-->:139970..140116 147 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_207:SMT_208|SMT_207:SMT_208:putative two-component sensor histidine kinase:leucyl-tRNA synthetase:<-->:139970..140116 147 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_207:SMT_208|SMT_207:SMT_208:putative two-component sensor histidine kinase:leucyl-tRNA synthetase:<-->:139970..140116 147 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 3 End: 119 .. S G G Q F P K K N Y T Y C N L F E L A L Y F L F T Y F L V L G F E R L F P I M ............................ ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_207:SMT_208|SMT_207:SMT_208:putative two-component sensor histidine kinase:leucyl-tRNA synthetase:<-->:139970..140116 147 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Intra-Species Hit: Count: 2 Min: 1 Max: 147 Len: 147 Subject: smit_SMT_207_SMT_208|putative two-component sensor histidine kinase:leucyl-tRNA synthetase|NEGATIVE:POSITIVE|[139970,140116]|147 HSP 1 e-value: 3.0E-78 bit: 291.0 Len: 147 Query Start:1 Query End:147 Subject Strand: POSITIVE Subject Start: 1 Subject End: 147 ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc ccgctacctccttggaagggttttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaaatggtataatagtaacatcacaaaattggagagagacc Subject: smit_SMT_212_SMT_213|Holliday junction DNA helicase RuvB:leucyl-tRNA synthetase|POSITIVE:POSITIVE|[145360,145531]|172 HSP 1 e-value: 1.0E-49 bit: 196.0 Len: 126 Query Start:22 Query End:147 Subject Strand: POSITIVE Subject Start: 11 Subject End: 137 .....................tttttgttataagtatagcagtttaaaaattctagagcaaggtaaaatagaaaagtatagaatagaacgagaccaaattccctcaaaa-atggtataatagtaacatcacaaaattggagagagacc .....................tttttgttataagtatagcagtttaaaaattctagagcaaggtaaattagaaaagtatagaatagaccgagsccaaattccctcaaaatggggtataatagtaacatcacaaaattggagagagacc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCGCUACCUCCUUGGAAGGGUUUUUUGUUAUAAGUAUAGCAGUUUAAAAAUUCUAGAGCAAGGUAAAAUAGAAAAGUAUAGAAUAGAACGAGACCAAAUUCCCUCAAAAAUGGUAUAAUAGUAACAUCACAAAAUUGGAGAGAGACC ...((..((((..((((.(((((((((((((....))))))).......((((((..((................)).)))))).....))))))...)))).......(((.(((....))).))).........))))..))... (-22.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUCUCUCUCCAAUUUUGUGAUGUUACUAUUAUACCAUUUUUGAGGGAAUUUGGUCUCGUUCUAUUCUAUACUUUUCUAUUUUACCUUGCUCUAGAAUUUUUAAACUGCUAUACUUAUAACAAAAAACCCUUCCAAGGAGGUAGCGG ..((((((...(((..(((((((....)))))))..)))...))))))..........((((((............................)))))).......((((((.................((((.....)))))))))) (-18.31) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 821 50 1 141 92 smit:SMT_207|5end_putative_two-component_sensor_histidine_kinase_139879..140109_NEGATIVE 307 60 12 231 177 smit:SMT_636|5end_ribonucleoside-diphosphate_reductase_beta_chain_541153..541383_POSITIVE 243 46 3 187 134 smit:SMT_1094|5end_membrane_carboxypeptidase_(penicillin-binding_protein)_1036336..1036566_NEGATIVE 239 45 2 226 183 smit:SMT_348|5end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_286456..286686_POSITIVE 236 40 2 43 1 smit:SMT_1689|5end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1671542..1671772_POSITIVE 230 123 88 65 15 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 222 140 94 203 156 smit:SMT_954|5end_cation-transporting_ATPase,_E1-E2_family_904025..904255_NEGATIVE 221 49 2 145 95 smit:SMT_1021|5end_K05846_osmoprotectant_transport_system_permease_protein_957999..958229_NEGATIVE 217 106 78 102 70 smit:SMT_1132|5end_glutamate--cysteine_ligase,_putative,_truncated_1068108..1068338_NEGATIVE 217 40 2 54 19 smit:SMT_423|5end_sensory_transduction_protein_kinase_366012..366242_POSITIVE 216 50 4 136 94 smit:SMT_978|5end_hypothetical_protein_926607..926837_NEGATIVE 216 46 1 126 82 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 216 22 1 189 158 smit:SMT_242|5end_PTS_system,_mannose-specific_IID_component_180074..180304_NEGATIVE 216 112 78 190 154 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 215 27 3 135 109 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 212 37 1 134 88 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 208 45 1 87 26 smit:SMT_308|5end_trans-2-enoyl-ACP_reductase_II_249439..249669_POSITIVE 206 130 92 120 86 smit:SMT_1985|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1914571..1914801_NEGATIVE 206 130 92 120 86 smit:SMT_299|5end_recombination_protein_U_243495..243725_NEGATIVE 205 41 4 46 10 smit:SMT_500|5end_hypothetical_protein_432770..433000_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 47 1 71 20 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 216 112 78 40 4 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 212 48 2 151 102 smit:SMT_1022|3end_glycine_betaine_transport_ATP-binding_protein_957992..958142_NEGATIVE 205 64 23 45 1 smit:SMT_635|3end_ribonucleoside-diphosphate_reductase_alpha_chain_541043..541193_POSITIVE 204 24 7 57 38 smit:SMT_902|3end_hypothetical_protein_851424..851574_NEGATIVE 200 29 1 79 49 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 198 57 13 105 52 smit:SMT_1978|3end_hypothetical_protein_1908766..1908916_NEGATIVE 194 44 3 149 108 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 193 39 1 96 55 smit:SMT_1139|3end_rRNA_(guanine-N1-)-methyltransferase_1080683..1080833_POSITIVE 191 60 22 39 3 smit:SMT_1491|3end_capsular_polysaccharide_biosynthesis_protein,_putative_1471967..1472117_POSITIVE 190 128 81 70 9 smit:SMT_1315|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1280952..1281102_POSITIVE 188 103 61 151 110 smit:SMT_941|3end_hypothetical_protein_892863..893013_NEGATIVE 187 60 11 74 10 smit:SMT_710|3end_hypothetical_protein_predicted_by_Glimmer/Critica_619270..619420_NEGATIVE 186 44 3 137 90 smit:SMT_1873|3end_K02006_cobalt_transport_system_ATP-binding_protein_1832351..1832501_POSITIVE 185 78 33 73 27 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 185 29 1 95 69 smit:SMT_1142|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1086897..1087047_POSITIVE 185 47 2 88 42 smit:SMT_173|3end_50S_ribosomal_protein_L2_117407..117557_POSITIVE 184 96 52 75 16 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 183 105 69 128 92 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 182 44 5 133 77 smit:SMT_988|3end_N-acetylneuraminate_lyase_932242..932392_NEGATIVE