Origin IGS: tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agctataaatactttactcttatagtaaatgaaaaataaggatttcgagagaacaaaatcgttctctctttttttatctgaatattttaagtaaaaggttaagctattctttcataaaacaagacagaatggttgcctccaaagtctcatcataagagaacagttatattctctggatctacttttgagatggtaaaaatagatatactgatatccattccttttatcatatccttgatttcttaagttttaaagacagtttaatcaggattccttttatatatcgattaagaaataaataatctgtcttgaatcctactatagatgtataaagagtcattttgttttttgtttcgtatcagtatcaatccgttctgatattgttttttgaattgtagaaaattctagtatagtagttaggaagtttttataaatttattgtatttaattcttgagttgagacctttacttttttagctaattatgtaataatattaacaatacaaataaatgaaagttggtgtttcta Mask Tandem Repeat Region ================================================ tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Find is-nt database================================================ Query_seq: SMT_781:SMT_782|SMT_781:SMT_782:hypothetical protein:GMP synthase:<-<-:692518..693046 529 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_781:SMT_782|SMT_781:SMT_782:hypothetical protein:GMP synthase:<-<-:692518..693046 529 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_781:SMT_782|SMT_781:SMT_782:hypothetical protein:GMP synthase:<-<-:692518..693046 529 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 95 End: 190 .............................................................................................. M Y K N F L T T I L E F S T I Q K T I S E R I D T D T K Q K T K ................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 37 Strand: + Start: 190 End: 300 ............................................................................................................................................................................................. M T L Y T S I V G F K T D Y L F L N R Y I K G I L I K L S L K L K K S R I ..................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 326 End: 415 ..................................................................................................................................................................................................................................................................................................................................... M Y F Y H L K S R S R E Y N C S L M M R L W R Q P F C L V L .................................................................................................................. Protein_Len: 39 Strand: - Start: 378 End: 494 ......................................................................................................................................................................................................................................................................................................................................................................................... S S V K S A V M R D Q K I F S Y S L R K S L I N L Y F F L S R N Q E R S I R M ................................... Protein_Len: 37 Strand: - Start: 287 End: 397 .............................................................................................................................................................................................................................................................................................. S I L S I I F P I S I L I D I K V M E F T S G S F I V T R K H H S K P P M .................................................................................................................................... Protein_Len: 30 Strand: - Start: 142 End: 231 ............................................................................................................................................. F V I D S R I S V S V F C F V F H S K I C R Y Y S E L C I M .......................................................................................................................................................................................................................................................................................................... tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct 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: 84 Start: 275 End: 304 ..................................................................................................................................................................................................................................................................................CTTTAAAACTTAAGAAATCAAGGATATGAT................................................................................................................................................................................................................................. PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 37 End: 66 ....................................CTTTACTTTTTTAGCTAATTATGTAATAAT............................................................................................................................................................................................................................................................................................................................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 45 End: 74 ............................................GTTGAGACCTTTACTTTTTTAGCTAATTAT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -8.8 Tail_Score: -5.72616 Start: 462 End: 483 Full_Region: aaaaataaggatttc gagagaac aaaatc gttctctc tttttttatctgaat .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................gagagaacaaaatcgttctctc.............................................. Find igs database================================================ Query_seq: SMT_781:SMT_782|SMT_781:SMT_782:hypothetical protein:GMP synthase:<-<-:692518..693046 529 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Intra-Species Hit: Count: 1 Min: 1 Max: 529 Len: 529 Subject: smit_SMT_781_SMT_782|hypothetical protein:GMP synthase|NEGATIVE:NEGATIVE|[692518,693046]|529 HSP 1 e-value: 0.0 bit: 1007.0 Len: 529 Query Start:1 Query End:529 Subject Strand: POSITIVE Subject Start: 1 Subject End: 529 tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagatnnnnnnngagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct tagaaacaccaactttcatttatttgtattgttaatattattacataattagctaaaaaagtaaaggtctcaactcaagaattaaatacaataaatttataaaaacttcctaactactatactagaattttctacaattcaaaaaacaatatcagaacggattgatactgatacgaaacaaaaaacaaaatgactctttatacatctatagtaggattcaagacagattatttatttcttaatcgatatataaaaggaatcctgattaaactgtctttaaaacttaagaaatcaaggatatgataaaaggaatggatatcagtatatctatttttaccatctcaaaagtagatccagagaatataactgttctcttatgatgagactttggaggcaaccattctgtcttgttttatgaaagaatagcttaaccttttacttaaaatattcagataaaaaaagagagaacgattttgttctctcgaaatccttatttttcatttactataagagtaaagtatttatagct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGAAACACCAACUUUCAUUUAUUUGUAUUGUUAAUAUUAUUACAUAAUUAGCUAAAAAAGUAAAGGUCUCAACUCAAGAAUUAAAUACAAUAAAUUUAUAAAAACUUCCUAACUACUAUACUAGAAUUUUCUACAAUUCAAAAAACAAUAUCAGAACGGAUUGAUACUGAUACGAAACAAAAAACAAAAUGACUCUUUAUACAUCUAUAGUAGGAUUCAAGACAGAUUAUUUAUUUCUUAAUCGAUAUAUAAAAGGAAUCCUGAUUAAACUGUCUUUAAAACUUAAGAAAUCAAGGAUAUGAUAAAAGGAAUGGAUAUCAGUAUAUCUAUUUUUACCAUCUCAAAAGUAGAUCCAGAGAAUAUAACUGUUCUCUUAUGAUGAGACUUUGGAGGCAACCAUUCUGUCUUGUUUUAUGAAAGAAUAGCUUAACCUUUUACUUAAAAUAUUCAGAUAAAAAAAGAGAGAACGAUUUUGUUCUCUCGAAAUCCUUAUUUUUCAUUUACUAUAAGAGUAAAGUAUUUAUAGCU ..((((............((((((((....((((((...........)))))).....((((((((((((.......)))...............(((((((((.........((((((((...(((((......)))))......((.((((((......)))))).))....................................))))))))....(((((((((...(((((.((......))...))))).((.(((((((((......((((........)))))))).)))))........((((((((((((....))))))))))))....((((.(((((..(((.((((((((....))))))))...)))...))))).))))...))..)))))))))))))))))).............)))))))))........))))))))....(((((((((....)))))))))............)))).((((((.....))))))............ (-94.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUAUAAAUACUUUACUCUUAUAGUAAAUGAAAAAUAAGGAUUUCGAGAGAACAAAAUCGUUCUCUCUUUUUUUAUCUGAAUAUUUUAAGUAAAAGGUUAAGCUAUUCUUUCAUAAAACAAGACAGAAUGGUUGCCUCCAAAGUCUCAUCAUAAGAGAACAGUUAUAUUCUCUGGAUCUACUUUUGAGAUGGUAAAAAUAGAUAUACUGAUAUCCAUUCCUUUUAUCAUAUCCUUGAUUUCUUAAGUUUUAAAGACAGUUUAAUCAGGAUUCCUUUUAUAUAUCGAUUAAGAAAUAAAUAAUCUGUCUUGAAUCCUACUAUAGAUGUAUAAAGAGUCAUUUUGUUUUUUGUUUCGUAUCAGUAUCAAUCCGUUCUGAUAUUGUUUUUUGAAUUGUAGAAAAUUCUAGUAUAGUAGUUAGGAAGUUUUUAUAAAUUUAUUGUAUUUAAUUCUUGAGUUGAGACCUUUACUUUUUUAGCUAAUUAUGUAAUAAUAUUAACAAUACAAAUAAAUGAAAGUUGGUGUUUCUA (((((.......((((((.....))))))...((((((.((((...((((((((......)))))))).......))))...))))))(((((((.((((..(((((...((((.(((((((..((((((((((((((((((((....(((...((((((........)))))).)))....))))).)).)))))........((((((((((......(((..((((......)))).....)))......((((((...((.((((((..((((((((((((((((((((.............))))).)))........))))))).)))))..)))))).)).)))))).))))))))))....))))))))...))))))).))))...((((....))))..)))))..(((((((.....(((((.....))))).....))))))).....)))))))))))...)))))...........(((((((((.................))))))))).... (-104.15) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 693 90 41 181 132 smit:SMT_781|5end_hypothetical_protein_692427..692657_NEGATIVE 258 412 372 152 116 smit:SMT_1561|5end_putative_mucus_binding_protein_1553809..1554039_NEGATIVE 246 436 391 102 47 smit:SMT_1534|5end_signal_peptidase_I_1517218..1517448_POSITIVE 246 439 391 216 162 smit:SMT_320|5end_alcohol_dehydrogenase,_zinc-containing_259492..259722_NEGATIVE 244 310 263 166 114 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 242 414 371 146 96 smit:SMT_1404|5end_lipoate-protein_ligase_A_1380967..1381197_POSITIVE 238 396 354 216 172 smit:SMT_915|5end_sucrose_operon_repressor_867574..867804_POSITIVE 238 80 31 180 134 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 230 359 311 205 156 smit:SMT_1684|5end_acetyltransferase,_GNAT_family_1667757..1667987_NEGATIVE 225 360 313 120 82 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 224 400 351 90 27 smit:SMT_624|5end_K07584_hypothetical_protein_529870..530100_POSITIVE 224 368 321 222 171 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 223 407 371 64 26 smit:SMT_1934|5end_homoserine_dehydrogenase_1872402..1872632_POSITIVE 222 416 376 72 32 smit:SMT_1216|5end_hypothetical_protein_1174879..1175109_POSITIVE 222 344 308 168 133 smit:SMT_639|5end_6-phospho-beta-galactosidase_544885..545115_NEGATIVE 221 508 461 173 128 smit:SMT_924|5end_primosomal_protein_N'_879903..880133_NEGATIVE 219 303 261 158 117 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 218 415 371 162 94 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 218 408 366 104 59 smit:SMT_465|5end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_protein_403244..403474_POSITIVE 218 408 366 104 59 smit:SMT_417|5end_short_chain_dehydrogenase_360373..360603_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 426 381 138 92 smit:SMT_2167|3end_hypothetical_protein_2040711..2040861_POSITIVE 246 436 391 98 43 smit:SMT_1533|3end_ribonuclease_HIII_1517294..1517444_POSITIVE 245 410 368 74 32 smit:SMT_540|3end_DNA_gyrase,_B_subunit_457157..457307_POSITIVE 244 428 386 44 3 smit:SMT_346|3end_K01992_ABC-2_type_transport_system_permease_protein_285849..285999_POSITIVE 242 414 371 86 36 smit:SMT_1403|3end_dihydrolipoamide_dehydrogenase_1380987..1381137_POSITIVE 228 406 362 129 75 smit:SMT_1435|3end_phosphoribosylanthranilate_isomerase_1419807..1419957_NEGATIVE 228 419 371 149 107 smit:SMT_1193|3end_phosphoribosylglycinamide_formyltransferase_1151607..1151757_NEGATIVE 225 360 313 86 48 smit:SMT_1169|3end_phosphorylase,_Pnp/UDP_family_1116586..1116736_NEGATIVE 224 407 382 63 36 smit:SMT_1854|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1818952..1819102_POSITIVE 224 398 366 31 1 smit:SMT_1774|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1750151..1750301_NEGATIVE 221 508 461 107 62 smit:SMT_925|3end_DNA-directed_RNA_polymerase_omega_chain_879969..880119_NEGATIVE 220 405 373 128 90 smit:SMT_1945|3end_putative_dihydrolipoamide_S-acetyltransferase_1880646..1880796_POSITIVE 218 415 371 101 33 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 218 408 366 83 38 smit:SMT_464|3end_ribonuclease_Z_403303..403453_POSITIVE 218 408 366 83 38 smit:SMT_416|3end_ribonuclease_Z_360432..360582_POSITIVE 216 407 364 145 92 smit:SMT_1792|3end_K03307_solute:Na+_symporter,_SSS_family_1766575..1766725_NEGATIVE 216 428 381 51 5 smit:SMT_1243|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1204469..1204619_POSITIVE 216 413 373 83 32 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 215 437 396 44 12 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 214 357 313 58 1 smit:SMT_1610|3end_tyrosine_recombinase_1599385..1599535_POSITIVE