Origin IGS: ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcaagtggagcaataaggggatttgtggcgatactcttgctagcagttgctttatcaatgggcttggtcttgttgtttgaaagcttccaaggaatccccttaaccagtcaaaaaaaggatgcatttctcaagaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aattctagcagttttttcctcttcctgatctttagtattttgattggtcttatttgcttcttgagaaatgcatcctttttttgactggttaaggggattccttggaagctttcaaacaacaagaccaagcccattgataaagcaactgctagcaagagtatcgccacaaatccccttattgctccacttgcgataactcctaaaaagtttacaaagcctctcacaaaatgaaaaactggtccacggttatggctatcttgggctctttggcatctcattctcccctannnnnttaattaattaannnnncttcctgttcgccattgcaaattatgccgtcctcgtcaatgataaaggtggagaa Mask Tandem Repeat Region ================================================ ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcaagtggagcaataaggggatttgtggcgatactcttgctagcagttgctttatcaatgggcttggtcttgttgtttgaaagcttccaaggaatccccttaaccagtcaaaaaaaggatgcatttctcaagaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Find is-nt database================================================ Query_seq: SMT_1681:SMT_1682|SMT_1681:SMT_1682:D-alanine-activating enzyme:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):->->:1665113..1665476 364 ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcaagtggagcaataaggggatttgtggcgatactcttgctagcagttgctttatcaatgggcttggtcttgttgtttgaaagcttccaaggaatccccttaaccagtcaaaaaaaggatgcatttctcaagaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1681:SMT_1682|SMT_1681:SMT_1682:D-alanine-activating enzyme:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):->->:1665113..1665476 364 ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcaagtggagcaataaggggatttgtggcgatactcttgctagcagttgctttatcaatgggcttggtcttgttgtttgaaagcttccaaggaatccccttaaccagtcaaaaaaaggatgcatttctcaagaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1681:SMT_1682|SMT_1681:SMT_1682:D-alanine-activating enzyme:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):->->:1665113..1665476 364 ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcaagtggagcaataaggggatttgtggcgatactcttgctagcagttgctttatcaatgggcttggtcttgttgtttgaaagcttccaaggaatccccttaaccagtcaaaaaaaggatgcatttctcaagaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 176 Max: 304 Len: 129 Subject: UniRef90_Q8CYL1 Cluster: Hypothetical protein spr1309; n=2; Streptococcus pneumoniae|Rep: Hypothetical protein spr1309 - Streptococcus pneumoniae (strain ATCC BAA-255 / R6) HSP 1 e-value: 1.0E-9 bit: 64.7 Len: 129 Query Start:176 Query End:304 Subject Strand: null Subject Start: 28 Subject End: 70 ............................................................................................................................................................................... L R N A S F F * L V K G I P W K L S N N K T K P I D K A T A S K S I A T N P L I A P L ............................................................ ............................................................................................................................................................................... L R N S I S F L T S Q G I P W K L S N N K T K P I D K P T A S K S I A T N P L L L H L ............................................................ ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 87 End: 362 ...................................................................................... M R C Q R A Q D S H N R G P V F H F V R G F V N F L G V I A S G A I R G F V A I L L L A V A L S M G L V L L F E S F Q G .. Protein_Len: 42 Strand: - Start: 172 End: 297 ........................................................................................................................................................................... R L H L L L P I Q P S V R A L L Q K I L P S P R T T Q F S G L F G R L W D F F P H M ................................................................... Protein_Len: 48 Strand: - Start: 137 End: 280 ........................................................................................................................................ K T L P K T F K K P T I A L P A I L P N T A I S K S A T A K D I P K T K N N S L K W P I G K V M .................................................................................... ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 198 End: 214 .....................................................................................................................................................................................................GTGGCGATACTCTTGCT...................................................................................................................................................... ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1681:SMT_1682|SMT_1681:SMT_1682:D-alanine-activating enzyme:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):->->:1665113..1665476 364 ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Intra-Species Hit: Count: 1 Min: 1 Max: 364 Len: 364 Subject: smit_SMT_1681_SMT_1682|D-alanine-activating enzyme:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein)|POSITIVE:POSITIVE|[1665113,1665476]|364 HSP 1 e-value: 1.0E-76 bit: 287.0 Len: 175 Query Start:1 Query End:175 Subject Strand: POSITIVE Subject Start: 1 Subject End: 175 ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgc............................................................................................................................................................................................. ttctccacctttatcattgacgaggacggcataatttgcaatggcgaacaggaagnnnnnttaattaattaannnnntaggggagaatgagatgccaaagagcccaagatagccataaccgtggaccagtttttcattttgtgagaggctttgtaaactttttaggagttatcgc............................................................................................................................................................................................. HSP 2 e-value: 3.0E-25 bit: 117.0 Len: 59 Query Start:306 Query End:364 Subject Strand: POSITIVE Subject Start: 306 Subject End: 364 .................................................................................................................................................................................................................................................................................................................aagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt .................................................................................................................................................................................................................................................................................................................aagcaaataagaccaatcaaaatactaaagatcaggaagaggaaaaaactgctagaatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUCCACCUUUAUCAUUGACGAGGACGGCAUAAUUUGCAAUGGCGAACAGGAAGNNNNNUUAAUUAAUUAANNNNNUAGGGGAGAAUGAGAUGCCAAAGAGCCCAAGAUAGCCAUAACCGUGGACCAGUUUUUCAUUUUGUGAGAGGCUUUGUAAACUUUUUAGGAGUUAUCGCAAGUGGAGCAAUAAGGGGAUUUGUGGCGAUACUCUUGCUAGCAGUUGCUUUAUCAAUGGGCUUGGUCUUGUUGUUUGAAAGCUUCCAAGGAAUCCCCUUAACCAGUCAAAAAAAGGAUGCAUUUCUCAAGAAGCAAAUAAGACCAAUCAAAAUACUAAAGAUCAGGAAGAGGAAAAAACUGCUAGAAUU ((((((.(((...((......))...((.(((........))).))................................))))))))).(((((((((.(((.(((...((.((..((...((((...((((((((((...)))))))))).....(((((.....))))).))))...))..)).))...))).))).)))).)).)))...(((((((((.((((.((....((.(((((((((((((((((((((.(((((((.....))))...............))).)).)))).....)))).)))))))))))))......(....).....)).))))....))))))))).... (-82.56) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUUCUAGCAGUUUUUUCCUCUUCCUGAUCUUUAGUAUUUUGAUUGGUCUUAUUUGCUUCUUGAGAAAUGCAUCCUUUUUUUGACUGGUUAAGGGGAUUCCUUGGAAGCUUUCAAACAACAAGACCAAGCCCAUUGAUAAAGCAACUGCUAGCAAGAGUAUCGCCACAAAUCCCCUUAUUGCUCCACUUGCGAUAACUCCUAAAAAGUUUACAAAGCCUCUCACAAAAUGAAAAACUGGUCCACGGUUAUGGCUAUCUUGGGCUCUUUGGCAUCUCAUUCUCCCCUANNNNNUUAAUUAAUUAANNNNNCUUCCUGUUCGCCAUUGCAAAUUAUGCCGUCCUCGUCAAUGAUAAAGGUGGAGAA ....(((((((((......((.....)).(((((.........((((((((....((((((...((.....((((((((...........))))))))))...))))))...........)))))))).........))))).)))))))))...(((.((.((((.....(((.(((((((.......)))))))..................((((..(((.....)))..(((((.....)))))..)))).....))).....)))))))))..((((((((.................................((....))..(((((..((....))...)))))..))).))))). (-74.33) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 349 248 201 72 21 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 341 236 191 212 157 smit:SMT_952|5end_hypothetical_protein_900912..901142_NEGATIVE 324 260 211 216 156 smit:SMT_1410|5end_exonuclease_RexA_1392182..1392412_NEGATIVE 321 135 95 129 88 smit:SMT_1457|5end_16S_rRNA_m(2)G_1207_methyltransferase_1440209..1440439_NEGATIVE 321 290 241 152 98 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 313 217 174 196 139 smit:SMT_178|5end_50S_ribosomal_protein_L29_119161..119391_POSITIVE 311 228 181 60 1 smit:SMT_1852|5end_1,4-alpha-glucan_branching_enzyme_1817690..1817920_NEGATIVE 310 150 101 118 61 smit:SMT_1631|5end_phosphopantothenoylcysteine_synthase/decarboxylase_1618359..1618589_NEGATIVE 309 140 91 66 17 smit:SMT_1607|5end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1596648..1596878_POSITIVE 299 215 175 131 89 smit:SMT_1775|5end_K07478_putative_ATPase_1751836..1752066_NEGATIVE 298 245 201 216 169 smit:SMT_1351|5end_dephospho-CoA_kinase_1329817..1330047_NEGATIVE 298 260 212 186 131 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 297 208 161 83 38 smit:SMT_1581|5end_transcriptional_regulator,_biotin_repressor_family_1573635..1573865_NEGATIVE 297 216 174 225 177 smit:SMT_685|5end_LPS_biosynthesis_protein_594354..594584_POSITIVE 295 128 89 167 129 smit:SMT_501|5end_ABC_transporter,_ATP-binding_protein_433227..433457_POSITIVE 294 225 181 155 117 smit:SMT_1538|5end_two-component_response_regulator_YvqC_1523301..1523531_NEGATIVE 293 240 195 59 12 smit:SMT_321|5end_hypothetical_protein_259930..260160_POSITIVE 291 218 180 205 162 smit:SMT_769|5end_spermidine/putrescine-binding_periplasmic_protein_680589..680819_NEGATIVE 289 139 92 142 90 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 287 219 174 218 172 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 345 115 81 40 9 smit:SMT_1866|3end_extramembranal_protein_1827939..1828089_POSITIVE 311 228 181 63 4 smit:SMT_1853|3end_1,4-alpha-glucan_branching_enzyme_1817687..1817837_NEGATIVE 310 150 101 106 49 smit:SMT_1632|3end_hypothetical_protein_1618371..1618521_NEGATIVE 309 140 91 69 20 smit:SMT_1606|3end_glutamate_racemase_1596731..1596881_POSITIVE 302 219 173 56 6 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 299 215 175 75 33 smit:SMT_1776|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_1751892..1752042_NEGATIVE 295 114 78 38 3 smit:SMT_1488|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468982..1469132_POSITIVE 294 273 233 148 108 smit:SMT_2066|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1973346..1973496_POSITIVE 294 225 181 141 103 smit:SMT_1539|3end_sensor_histidine_kinase,_putative_1523315..1523465_NEGATIVE 284 320 279 146 106 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 283 218 179 57 23 smit:SMT_821|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_734060..734210_POSITIVE 276 247 201 133 94 smit:SMT_829|3end_putative_mucus_binding_protein_761037..761187_NEGATIVE 276 250 208 147 99 smit:SMT_195|3end_30S_ribosomal_protein_S13_127322..127472_POSITIVE 275 248 201 129 87 smit:SMT_1786|3end_phenylalanyl-tRNA_synthetase_beta_chain_1763235..1763385_NEGATIVE 275 239 191 73 33 smit:SMT_1484|3end_exonuclease_RexA_1464256..1464406_NEGATIVE 275 246 201 85 46 smit:SMT_115|3end_hypothetical_protein_66482..66632_POSITIVE 274 224 187 133 98 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 272 47 16 57 22 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 269 219 183 50 11 smit:SMT_946|3end_hypothetical_protein_895918..896068_NEGATIVE 268 224 190 55 11 smit:SMT_2068|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974183..1974333_NEGATIVE