Origin IGS: aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc .........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 ggtaagtctcccatctattcgtttattcacgattgaaggtcgtgtgtgcttaacgattgaaggtcgcttgagcagtattcattataacatgcttggttggagaagacaagaaagaggatgtcaatcgaccaacctctttgtaaatacatatataattgtttaaaaagagggtaatttatagcttaatccctctactgcttattatcttatttataaaataaactaaaaatgatatactatattgaggaggaatacgtacatgatcccttaaagatactaccatccatgtacgtagaacgatt Mask Tandem Repeat Region ================================================ aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Find is-nt database================================================ Query_seq: SMT_137:SMT_138|SMT_137:SMT_138:hypothetical protein:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:<-->:89100..89401 302 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_137:SMT_138|SMT_137:SMT_138:hypothetical protein:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:<-->:89100..89401 302 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_137:SMT_138|SMT_137:SMT_138:hypothetical protein:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:<-->:89100..89401 302 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Predict ORF larger than 30AA ================================================ Protein_Len: 41 Strand: + Start: 2 End: 124 . M V L R T W M V V S L R D H V R I P P Q Y S I S F L V Y F I N K I I S S R G I K L .................................................................................................................................................................................. Protein_Len: 41 Strand: + Start: 128 End: 250 ............................................................................................................................... M T L F L N N Y I C I Y K E V G R L T S S F L S S P T K H V I M N T A Q A T F N R .................................................... Protein_Len: 50 Strand: + Start: 124 End: 273 ........................................................................................................................... M N Y P L F K Q L Y M Y L Q R G W S I D I L F L V F S N Q A C Y N E Y C S S D L Q S L S T H D L Q S ............................. Protein_Len: 48 Strand: - Start: 143 End: 286 .............................................................................................................................................. V I I Y T N V F L N T S Q C G R E Q R R W G L M N Y H I S S L R G E I T L C V R G E I T F L R M ................ aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc 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: 87 Start: 193 End: 222 ................................................................................................................................................................................................CTTGTCTTCTCCAACCAAGCATGTTATAAT................................................................................ PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 65 End: 94 ................................................................ATTTATAAAATAAACTAAAAATGATATACT................................................................................................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_137:SMT_138|SMT_137:SMT_138:hypothetical protein:tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase:<-->:89100..89401 302 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Intra-Species Hit: Count: 1 Min: 1 Max: 302 Len: 302 Subject: smit_SMT_137_SMT_138|hypothetical protein:tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase|NEGATIVE:POSITIVE|[89100,89401]|302 HSP 1 e-value: 1.0E-170 bit: 599.0 Len: 302 Query Start:1 Query End:302 Subject Strand: POSITIVE Subject Start: 1 Subject End: 302 aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc aatcgttctacgtacatggatggtagtatctttaagggatcatgtacgtattcctcctcaatatagtatatcatttttagtttattttataaataagataataagcagtagagggattaagctataaattaccctctttttaaacaattatatatgtatttacaaagaggttggtcgattgacatcctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Inter-species Hit: Count: 2 Min: 187 Max: 302 Len: 116 Subject: NC_008533_SPD_0126_SPD_0127|pneumococcal surface protein A:tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase|POSITIVE:POSITIVE|[130216,130615]|400 HSP 1 e-value: 8.0E-50 bit: 198.0 Len: 116 Query Start:187 Query End:302 Subject Strand: POSITIVE Subject Start: 285 Subject End: 400 ..........................................................................................................................................................................................ctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc ..........................................................................................................................................................................................ctcttccttgtcttctctaaccaagcgtgttataatgaatactgctcaagcgaccttcaatcgtgaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Subject: NC_003028_SP_0117_SP_0118|pneumococcal surface protein A:tRNA (5-methylaminomethyl-2-thiouridylate)- methyltransferase|POSITIVE:POSITIVE|[120658,121057]|400 HSP 1 e-value: 8.0E-50 bit: 198.0 Len: 116 Query Start:187 Query End:302 Subject Strand: POSITIVE Subject Start: 285 Subject End: 400 ..........................................................................................................................................................................................ctctttcttgtcttctccaaccaagcatgttataatgaatactgctcaagcgaccttcaatcgttaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc ..........................................................................................................................................................................................ctcttccttgtcttctctaaccaagcgtgttataatgaatactgctcaagcgaccttcaatcgtgaagcacacacgaccttcaatcgtgaataaacgaatagatgggagacttacc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUUUCUUGUCUUCUCCAACCAAGCAUGUUAUAAUGAAUACUGCUCAAGCGACCUUCAAUCGUUAAGCACACACGACCUUCAAUCGUGAAUAAACGAAUAGAUGGGAGACUUACC ...(((((..(((..((........(((......))).....((((..(((((.......))))).))))..(((((.......))))).......))..)))..)))))...... (-21.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUAAGUCUCCCAUCUAUUCGUUUAUUCACGAUUGAAGGUCGUGUGUGCUUAACGAUUGAAGGUCGCUUGAGCAGUAUUCAUUAUAACAUGCUUGGUUGGAGAAGACAAGAAAGAG .....((((((((.(((..(((((((.((((((.....))))))..(((((((((((.....)))).))))))).........)))).)))..))).))).).))))......... (-28.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 297 58 13 64 12 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 294 84 50 72 38 smit:SMT_605|5end_DNA-binding_protein_HU_519034..519264_POSITIVE 284 87 43 74 26 smit:SMT_1191|5end_phosphoribosylamine--glycine_ligase_1149737..1149967_NEGATIVE 275 80 35 189 147 smit:SMT_1573|5end_MutT/NUDIX_family_protein_1566413..1566643_POSITIVE 269 87 41 65 15 smit:SMT_1588|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1577062..1577292_POSITIVE 268 89 44 228 161 smit:SMT_493|5end_K01996_branched-chain_amino_acid_transport_system_ATP-binding_protein_427137..427367_POSITIVE 261 88 41 213 170 smit:SMT_615|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_524884..525114_POSITIVE 259 83 42 98 55 smit:SMT_676|5end_DNA_helicase_II_585266..585496_NEGATIVE 257 88 42 66 22 smit:SMT_1704|5end_D-alanine-D-alanine_ligase_1687431..1687661_POSITIVE 246 88 42 119 76 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 242 88 41 219 158 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 242 86 44 140 86 smit:SMT_261|5end_ImpB/MucB/SamB_family_protein_200160..200390_POSITIVE 241 87 43 74 26 smit:SMT_2076|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1978592..1978822_NEGATIVE 241 87 43 181 133 smit:SMT_2075|5end_phosphoribosylamine--glycine_ligase_1978485..1978715_NEGATIVE 240 89 45 137 93 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 239 62 24 105 62 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 235 89 42 53 1 smit:SMT_1785|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763277..1763507_NEGATIVE 235 79 42 192 155 smit:SMT_1585|5end_phosphopantetheine_adenylyltransferase_1575242..1575472_POSITIVE 235 47 1 196 156 smit:SMT_1512|5end_hypothetical_protein_1494747..1494977_NEGATIVE 235 88 45 111 62 smit:SMT_148|5end_glycoprotein_endopeptidase_98033..98263_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 259 83 42 61 18 smit:SMT_677|3end_DNA_topoisomerase_I_585303..585453_NEGATIVE 251 90 45 142 95 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 242 88 41 91 30 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 242 86 44 136 82 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 241 90 48 70 31 smit:SMT_932|3end_tellurite_resistance_protein_885402..885552_POSITIVE 239 62 24 103 60 smit:SMT_1262|3end_ribosomal_protein_L11_methyltransferase_1228182..1228332_POSITIVE 235 89 42 95 43 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 231 86 44 41 3 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 226 59 17 54 1 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 224 58 12 70 24 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 223 110 71 129 92 smit:SMT_1749|3end_anthranilate_synthase_component_II_1728080..1728230_POSITIVE 221 50 15 68 27 smit:SMT_1542|3end_phosphomevalonate_kinase_1526077..1526227_NEGATIVE 219 70 21 148 102 smit:SMT_2014|3end_tryptophan_synthase_beta_chain_1932727..1932877_POSITIVE 219 89 44 41 1 smit:SMT_147|3end_K02027_multiple_sugar_transport_system_substrate-binding_protein_98016..98166_POSITIVE 218 60 11 150 97 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 218 70 21 90 39 smit:SMT_1447|3end_hypothetical_protein_1429610..1429760_NEGATIVE 217 110 67 146 110 smit:SMT_765|3end_hypothetical_protein_672135..672285_NEGATIVE 216 52 11 97 37 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 216 56 16 115 75 smit:SMT_1780|3end_PTS_system,_glucose-specific_IIABC_component_1755960..1756110_NEGATIVE 215 55 13 68 16 smit:SMT_1752|3end_N-(5'-phosphoribosyl)-anthranilate_isomerase_1730451..1730601_POSITIVE