Origin IGS: gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca .........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 tgagtaatattgtgctctaaaatcgttagaggcaagtcgaagacttgctagagggatatgcaccgccgtactgttatgtggggatttttgaaaccttaggttcaaaaattagtcagctaaatccactttgatgagactgttggaaatcttgatcaatttagtattagatttccatacagactcacaaagttagttagcgacgtccccagtacctaaggtgcatatcaaaaaagattgaagaaaatgtaaaggaaaaaac Mask Tandem Repeat Region ================================================ gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Find is-nt database================================================ Query_seq: SMT_800:SMT_801|SMT_800:SMT_801:glycyl-tRNA synthetase beta chain:glycyl-tRNA synthetase alpha chain:<-<-:709723..709981 259 gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_800:SMT_801|SMT_800:SMT_801:glycyl-tRNA synthetase beta chain:glycyl-tRNA synthetase alpha chain:<-<-:709723..709981 259 gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_800:SMT_801|SMT_800:SMT_801:glycyl-tRNA synthetase beta chain:glycyl-tRNA synthetase alpha chain:<-<-:709723..709981 259 gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 155 End: 259 .......................................................................................................................................................... M N L R F Q K S P H N S T A V H I P L A S L R L A S N D F R A Q Y Y S Protein_Len: 31 Strand: - Start: 47 End: 139 .............................................. T S P V D S V L K T L R Y P F R I S F Q D L N G V T E D F H M ........................................................................................................................ gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca 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================================================ gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_800:SMT_801|SMT_800:SMT_801:glycyl-tRNA synthetase beta chain:glycyl-tRNA synthetase alpha chain:<-<-:709723..709981 259 gttttttcctttacattttcttcaatcttttttgatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Intra-Species Hit: Count: 1 Min: 34 Max: 259 Len: 226 Subject: smit_SMT_800_SMT_801|glycyl-tRNA synthetase beta chain:glycyl-tRNA synthetase alpha chain|NEGATIVE:NEGATIVE|[709723,709981]|259 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:34 Query End:259 Subject Strand: POSITIVE Subject Start: 34 Subject End: 259 .................................gatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca .................................gatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca Inter-species Hit: Count: 4 Min: 34 Max: 259 Len: 226 Subject: NC_008533_SPD_1304_SPD_1305|glycyl-tRNA synthetase, beta subunit:glycyl-tRNA synthetase, alpha subunit|NEGATIVE:NEGATIVE|[1323902,1324160]|259 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 226 Query Start:34 Query End:259 Subject Strand: POSITIVE Subject Start: 34 Subject End: 259 .................................gatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca .................................gatatgcaccttaggtactggggacgtcgctaactaactctgtgagtctgtatggaaatccaatgctaaatttatcaagatttccaacaatctcataaaagtggatttagctgactgatttttgaacctaaggtttcaaaaatccccacataacagtatggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagtacagtattactca Subject: NC_003098_spr1328_spr1329|glycyl-tRNA synthetase beta subunit:glycyl-tRNA synthetase alpha subunit|NEGATIVE:NEGATIVE|[1316371,1316629]|259 HSP 1 e-value: 1.0E-101 bit: 369.0 Len: 226 Query Start:34 Query End:259 Subject Strand: POSITIVE Subject Start: 34 Subject End: 259 .................................gatatgcaccttaggtactggggacgtcgctaactaactttgtgagtctgtatggaaatctaatactaaattgatcaagatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagcacaatattactca .................................gatatgcaccttaggtactggggacgtcgctaactaactctgtgagtctgtatggaaatccaatgctaaatttatcaagatttccaacaatctcataaaagtggatttagctgactgatttttgaacctaaggtttcaaaaatccccacataacagtatggcggtgcatatccctctagcaagtcttcgacttgcctctaacgattttagagtacagtattactca Subject: NC_008532_STER_0539_STER_0540|Glycyl-tRNA synthetase, alpha subunit:Glycyl-tRNA synthetase, beta subunit|POSITIVE:POSITIVE|[485745,486027]|283 HSP 1 e-value: 6.0E-10 bit: 65.9 Len: 122 Query Start:111 Query End:232 Subject Strand: NEGATIVE Subject Start: 53 Subject End: 175 ..............................................................................................................agatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgc--atatccctctagcaagtcttcgacttgcctct........................... ..............................................................................................................agatttccaacagtctcatcaaagtggatttaatcaactga-ttttgaacttgaggtttcaaaaatctccaccaggcagtacggcggcacctctatccctttagcaagcctttgacttgcctct........................... Subject: NC_006449_str0505_str0507|glycyl-tRNA synthetase alpha subunit:glycyl-tRNA synthetase beta subunit|POSITIVE:POSITIVE|[476717,476891]|175 HSP 1 e-value: 6.0E-10 bit: 65.9 Len: 122 Query Start:111 Query End:232 Subject Strand: NEGATIVE Subject Start: 53 Subject End: 175 ..............................................................................................................agatttccaacagtctcatcaaagtggatttagctgactaatttttgaacctaaggtttcaaaaatccccacataacagtacggcggtgc--atatccctctagcaagtcttcgacttgcctct........................... ..............................................................................................................agatttccaacagtctcatcaaagtggatttaatcaactga-ttttgaacttgaggtttcaaaaatctccaccaggcagtacggcggcacctctatccctttagcaagcctttgacttgcctct........................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAUGCACCUUAGGUACUGGGGACGUCGCUAACUAACUUUGUGAGUCUGUAUGGAAAUCUAAUACUAAAUUGAUCAAGAUUUCCAACAGUCUCAUCAAAGUGGAUUUAGCUGACUAAUUUUUGAACCUAAGGUUUCAAAAAUCCCCACAUAACAGUACGGCGGUGCAUAUCCCUCUAGCAAGUCUUCGACUUGCCUCUAACGAUUUUAGAGCACAAUAUUACUCA ((((((((((.(..(((((((((..((((((((...((((((((((.((((.(((((((((....(......)....))))))))))))).)))).))))))....))))).)))..(((((((((((...)).))))))))))))).......))))).).)))))))))).((((((((((((...))))))).((....))...))))).............. (-79.61) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGUAAUAUUGUGCUCUAAAAUCGUUAGAGGCAAGUCGAAGACUUGCUAGAGGGAUAUGCACCGCCGUACUGUUAUGUGGGGAUUUUUGAAACCUUAGGUUCAAAAAUUAGUCAGCUAAAUCCACUUUGAUGAGACUGUUGGAAAUCUUGAUCAAUUUAGUAUUAGAUUUCCAUACAGACUCACAAAGUUAGUUAGCGACGUCCCCAGUACCUAAGGUGCAUAUC .(((((......))))).............((((((((...)))))))).....((((((((((...(((((.......(((((((((((((.((...))))))))))...(((.(((((....((((((.((((.(((((((((((((....(......)....))))))))).)))).))))))))))...)))))))).))))))))))....)))))))))) (-81.91) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 963 50 1 174 125 smit:SMT_800|5end_glycyl-tRNA_synthetase_beta_chain_709632..709862_NEGATIVE 370 140 93 195 143 smit:SMT_995|5end_K07574_putative_RNA-binding_protein_containing_KH_domain_936468..936698_NEGATIVE 347 199 155 178 120 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 335 198 160 49 3 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 332 200 154 159 114 smit:SMT_1697|5end_hypothetical_protein_1678846..1679076_POSITIVE 330 147 103 213 170 smit:SMT_340|5end_chaperone_protein_278663..278893_POSITIVE 315 195 154 147 97 smit:SMT_1915|5end_pyridoxine_biosynthesis_protein_1860329..1860559_POSITIVE 306 197 154 176 117 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 305 43 2 57 8 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 304 197 159 197 151 smit:SMT_1226|5end_ribosomal_protein_S9_1188737..1188967_POSITIVE 304 197 159 95 49 smit:SMT_247|5end_K02996_small_subunit_ribosomal_protein_S9_183062..183292_POSITIVE 302 194 153 204 158 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 298 199 157 53 7 smit:SMT_1453|5end_K07335_basic_membrane_protein_A_and_related_proteins_1437407..1437637_NEGATIVE 288 200 154 184 132 smit:SMT_1734|5end_serine/threonine_protein_phosphatase_1718558..1718788_POSITIVE 288 114 83 166 129 smit:SMT_1398|5end_dihydroorotase_1373204..1373434_POSITIVE 284 200 159 57 13 smit:SMT_756|5end_3-dehydroquinate_dehydratase_660584..660814_NEGATIVE 283 199 154 57 2 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 283 199 154 57 2 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 283 49 7 166 124 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 280 50 1 78 35 smit:SMT_1481|5end_endopeptidase_O_1462229..1462459_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 361 198 155 68 18 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 353 199 163 36 1 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 315 195 154 62 12 smit:SMT_1914|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1860324..1860474_POSITIVE 308 210 162 84 28 smit:SMT_2006|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1926803..1926953_POSITIVE 284 200 159 60 16 smit:SMT_757|3end_K06969_putative_SAM-dependent_methyltransferase_660581..660731_NEGATIVE 283 199 154 60 5 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 280 190 154 147 112 smit:SMT_1696|3end_hypothetical_protein_1678924..1679074_POSITIVE 278 195 152 141 98 smit:SMT_1202|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1163945..1164095_NEGATIVE 276 50 14 119 82 smit:SMT_998|3end_peptide_chain_release_factor_3_939699..939849_NEGATIVE 271 50 8 48 5 smit:SMT_243|3end_PTS_system,_mannose-specific_IIC_component_180089..180239_NEGATIVE 270 210 162 84 28 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 270 210 162 84 28 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 270 210 162 94 38 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 270 210 162 94 38 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 270 210 162 84 28 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 270 210 162 84 28 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 270 210 162 84 28 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 270 210 162 84 28 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 270 210 162 84 28 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 269 190 142 143 93 smit:SMT_818|3end_cystathionine_gamma-synthase_728707..728857_NEGATIVE