Origin IGS: tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca .........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 tgtttttctcctatatatgtaatatatttattctactagaaaatacggaaatattcaaatttttatctatcaattttgtgtaaattaaatttacagcatactttacacaaatccgtaaatagcaaggctgatttattttgataaattacggttatttcattaaaaaaatgctataattgaagggactatatcgaaggagaacaaa Mask Tandem Repeat Region ================================================ tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Find is-nt database================================================ Query_seq: SMT_78:SMT_79|SMT_78:SMT_79:tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein:<-->:6622..6826 205 tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_78:SMT_79|SMT_78:SMT_79:tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein:<-->:6622..6826 205 tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_78:SMT_79|SMT_78:SMT_79:tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein:<-->:6622..6826 205 tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 51 End: 140 .................................................. M T V I Y Q N K S A L L F T D L C K V C C K F N L H K I D R ................................................................. Protein_Len: 43 Strand: + Start: 64 End: 192 ............................................................... M K I N Q P C Y L R I C V K Y A V N L I Y T K L I D K N L N I S V F S S R I N I L H I ............. Protein_Len: 32 Strand: - Start: 68 End: 163 ................................................................... F L D A K S N V S K H L T H Q L N L K C L I S L Y F N S Y K R M .......................................... tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca 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: 88 Start: 147 End: 176 ..................................................................................................................................................TTTGAATATTTCCGTATTTTCTAGTAGAAT............................. PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 40 End: 69 .......................................TTTGATAAATTACGGTTATTTCATTAAAAA........................................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_78:SMT_79|SMT_78:SMT_79:tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein:<-->:6622..6826 205 tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Intra-Species Hit: Count: 1 Min: 1 Max: 205 Len: 205 Subject: smit_SMT_78_SMT_79|tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[6622,6826]|205 HSP 1 e-value: 1.0E-100 bit: 365.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tttgttctccttcgatatagtcccttcaattatagcannnnnnnaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca tttgttctccttcgatatagtcccttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca Inter-species Hit: Count: 3 Min: 1 Max: 205 Len: 205 Subject: NC_003028_SP_2229_SP_2230|tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[2148628,2148832]|205 HSP 1 e-value: 3.0E-76 bit: 285.0 Len: 205 Query Start:1 Query End:205 Subject Strand: POSITIVE Subject Start: 1 Subject End: 205 tttgttctccttcgatatagtcccttcaattatagcannnnnnnaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaaca tttgttctccttcgatatagtcctttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctttttacagatttgtgtaaaggatactgtaaatataatttacacaaaattgacaaataaaaatttgaatatttctgtattttctagtagaataaatatattacacatataggagaaaaaca Subject: NC_008533_SPD_2056_SPD_2057|tryptophanyl-tRNA synthetase:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[2033704,2033908]|205 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 tttgttctccttcgatatagtcccttcaattatagcannnnnnnaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaa.. tttgttctccttcgatatagtcctttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctttttacagatttgtgtaaaggatactgtaaatataatttacacaaaattgacaaataaaaatttgaatatttctgtattttctagtagaataaatatattacacatataggagaaaaa.. Subject: NC_003098_spr2034_spr2035|tryptophanyl-tRNA synthetase:ABC transporter ATP-binding protein - unknown substrate|NEGATIVE:POSITIVE|[2026204,2026408]|205 HSP 1 e-value: 4.0E-75 bit: 281.0 Len: 203 Query Start:1 Query End:203 Subject Strand: POSITIVE Subject Start: 1 Subject End: 203 tttgttctccttcgatatagtcccttcaattatagcannnnnnnaatgaaataaccgtaatttatcaaaataaatcagccttgctatttacggatttgtgtaaagtatgctgtaaatttaatttacacaaaattgatagataaaaatttgaatatttccgtattttctagtagaataaatatattacatatataggagaaaaa.. tttgttctccttcgatatagtcctttcaattatagcatttttttaatgaaataaccgtaatttatcaaaataaatcagccttgctttttacagatttgtgtaaaggatactgtaaatataatttacacaaaattgacaaataaaaatttgaatatttctgtattttctagtagaataaatatattacacatataggagaaaaa.. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGUUCUCCUUCGAUAUAGUCCCUUCAAUUAUAGCAUUUUUUUAAUGAAAUAACCGUAAUUUAUCAAAAUAAAUCAGCCUUGCUAUUUACGGAUUUGUGUAAAGUAUGCUGUAAAUUUAAUUUACACAAAAUUGAUAGAUAAAAAUUUGAAUAUUUCCGUAUUUUCUAGUAGAAUAAAUAUAUUACAUAUAUAGGAGAAAAACA ....(((((((...((((......(((((.(((..((((.....))))..)))......(((((((((..(((((.(((...))))))))....((((((((((.((...........)).)))))))))).)))))))))......))))).......((((((((.....))..)))))).....))))..)))))))..... (-32.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUUUUUCUCCUAUAUAUGUAAUAUAUUUAUUCUACUAGAAAAUACGGAAAUAUUCAAAUUUUUAUCUAUCAAUUUUGUGUAAAUUAAAUUUACAGCAUACUUUACACAAAUCCGUAAAUAGCAAGGCUGAUUUAUUUUGAUAAAUUACGGUUAUUUCAUUAAAAAAAUGCUAUAAUUGAAGGGACUAUAUCGAAGGAGAACAAA (((((((((.(.(((((.((.....(((((((..(.((((...((((((.........................((((((((((.((...........)).))))))))))))))))..((((...)))).)))).)..)))))))..(((((((..((((.....))))..))))))).....))))))).).))))))))).. (-33.01) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 768 120 71 211 162 smit:SMT_78|5end_tryptophanyl-tRNA_synthetase_6531..6761_NEGATIVE 299 97 56 128 85 smit:SMT_301|5end_hypothetical_protein_244086..244316_POSITIVE 265 57 22 117 84 smit:SMT_1159|5end_hypothetical_protein_1104544..1104774_NEGATIVE 256 37 1 130 91 smit:SMT_461|5end_mannose-6-phosphate_isomerase_399379..399609_POSITIVE 241 100 55 123 72 smit:SMT_916|5end_3-hydroxy-3-methylglutaryl-CoA_reductase_870004..870234_NEGATIVE 239 50 8 139 98 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 235 113 78 196 152 smit:SMT_1420|5end_K02004_1406582..1406812_NEGATIVE 231 87 57 229 205 smit:SMT_1322|5end_K02075_zinc/manganese_transport_system_permease_protein_1291371..1291601_POSITIVE 231 50 3 144 95 smit:SMT_259|5end_dipeptide/tripeptide_permease_197629..197859_POSITIVE 226 115 72 156 105 smit:SMT_2079|5end_single_strand_binding_protein_1980144..1980374_POSITIVE 220 114 74 172 118 smit:SMT_1684|5end_acetyltransferase,_GNAT_family_1667757..1667987_NEGATIVE 220 111 76 68 28 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 219 90 46 94 50 smit:SMT_1646|5end_3-isopropylmalate_dehydratase_large_subunit_1632011..1632241_POSITIVE 219 85 54 227 198 smit:SMT_1254|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1220882..1221112_NEGATIVE 216 114 75 209 171 smit:SMT_624|5end_K07584_hypothetical_protein_529870..530100_POSITIVE 215 114 78 226 180 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 214 44 10 97 56 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 213 98 55 144 102 smit:SMT_1378|5end_DNA_polymerase_III,_delta'_subunit_1356803..1357033_NEGATIVE 212 58 19 76 38 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 212 85 44 172 133 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 299 97 56 75 32 smit:SMT_300|3end_hypothetical_protein_244113..244263_POSITIVE 265 57 22 41 8 smit:SMT_1160|3end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1104620..1104770_NEGATIVE 259 119 74 73 31 smit:SMT_1950|3end_Mn2+_and_Fe2+_transporter_of_the_NRAMP_family_1885069..1885219_POSITIVE 241 100 55 123 72 smit:SMT_917|3end_hydroxymethylglutaryl-CoA_synthase_870004..870154_NEGATIVE 228 32 4 56 22 smit:SMT_211|3end_hypothetical_protein_predicted_by_Glimmer/Critica_144316..144466_POSITIVE 219 90 46 90 46 smit:SMT_1645|3end_hypothetical_protein_1632087..1632237_POSITIVE 219 85 54 122 93 smit:SMT_1255|3end_cell_division_protein_FtsH_1220987..1221137_NEGATIVE 216 114 75 71 33 smit:SMT_623|3end_50S_ribosomal_protein_L21_529812..529962_POSITIVE 214 44 10 107 66 smit:SMT_1488|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468982..1469132_POSITIVE 213 32 1 140 111 smit:SMT_1468|3end_pneumococcal_surface_protein,_putative_1448775..1448925_NEGATIVE 213 98 55 147 105 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 211 50 5 110 65 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 204 28 2 136 103 smit:SMT_923|3end_methionyl-tRNA_formyltransferase_876559..876709_NEGATIVE 201 117 75 146 101 smit:SMT_592|3end_amino_acid_ABC_transporter,_ATP-binding_protein_509468..509618_POSITIVE 197 136 97 89 53 smit:SMT_1515|3end_amino_acid_ABC_transporter,_ATP-binding_protein_1496755..1496905_NEGATIVE 197 38 6 118 86 smit:SMT_805|3end_hypothetical_protein_predicted_by_Glimmer/Critica_715692..715842_NEGATIVE 197 36 10 32 1 smit:SMT_515|3end_hypothetical_protein_442526..442676_POSITIVE 196 37 5 63 24 smit:SMT_535|3end_hypothetical_protein_454456..454606_POSITIVE 196 114 75 122 77 smit:SMT_90|3end_DNA_polymerase_III_beta_subunit_22593..22743_POSITIVE 194 36 9 147 125 smit:SMT_1756|3end_hypothetical_protein_1733967..1734117_NEGATIVE