Origin IGS: tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac .........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 gtgtctttacattcnnnnnttaattaattaannnnntgctaataaagtgactcccgcaagagccaatactttccttgttttcatagtattctcctttgtttttctatccattatagaccctttttaaagtcctgtcaacagaattttcagaattttagaaaattattttttaaacaatagatttgcaaaaatatgaataatatcaaaaatacctcaactacattaggtagtcaaggaattattaatcatatttgaaaatagcatctgagaaacagttttaattctttaatctaactcatttcttacacactgcaaagctgttgtcatgagaatattatatctattattttcgtggggagttcattaacgaccaggattcaaa Mask Tandem Repeat Region ================================================ tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Find is-nt database================================================ Query_seq: SMT_293:SMT_294|SMT_293:SMT_294:dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase:->->:236923..237304 382 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_293:SMT_294|SMT_293:SMT_294:dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase:->->:236923..237304 382 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_293:SMT_294|SMT_293:SMT_294:dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase:->->:236923..237304 382 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 206 End: 295 ............................................................................................................................................................................................................. Q K F F L K R F N Q F N Q Q C S K L F P R Y H I S F C L L M ....................................................................................... tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac 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: 89 Start: 244 End: 273 ...................................................................................................................................................................................................................................................GTTGACAGGACTTTAAAAAGGGTCTATAAT............................................................................................................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 148 End: 177 ...................................................................................................................................................CTTGACTACCTAATGTAGTTGAGGTATTTT............................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 72 HP_score: -4.6 Tail_Score: -4.93316 Start: 145 End: 173 Full_Region: AAATATGATTAATAA TTCCTTGACTAC CTAAT GTAGTTGAGGTA TTTTTGATATTATTC ................................................................................................................................................TTCCTTGACTACCTAATGTAGTTGAGGTA................................................................................................................................................................................................................. TransTerm Strand: + Conf: 75 HP_score: -7.2 Tail_Score: -4.06487 Start: 147 End: 171 Full_Region: ATATGATTAATAATT CCTTGACTAC CTAAT GTAGTTGAGG TATTTTTGATATTAT ..................................................................................................................................................CCTTGACTACCTAATGTAGTTGAGG................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_293:SMT_294|SMT_293:SMT_294:dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase:->->:236923..237304 382 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Intra-Species Hit: Count: 2 Min: 1 Max: 382 Len: 382 Subject: smit_SMT_293_SMT_294|dTDP-4-dehydrorhamnose reductase:alpha-glucosidase, family 31 of glycosyl hydrolase|POSITIVE:POSITIVE|[236923,237304]|382 HSP 1 e-value: 0.0 bit: 698.0 Len: 382 Query Start:1 Query End:382 Subject Strand: POSITIVE Subject Start: 1 Subject End: 382 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatactatgaaaacaaggaaagtattggctcttgcgggagtcactttattagcannnnnttaattaattaannnnngaatgtaaagacac Subject: smit_SMT_296_SMT_297|hypothetical protein predicted by Glimmer/Critica:ABC transporter substrate-binding protein - oligopeptide transport|POSITIVE:POSITIVE|[238389,238686]|298 HSP 1 e-value: 1.0E-168 bit: 591.0 Len: 298 Query Start:1 Query End:298 Subject Strand: POSITIVE Subject Start: 1 Subject End: 298 tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact.................................................................................... tttgaatcctggtcgttaatgaactccccacgaaaataatagatataatattctcatgacaacagctttgcagtgtgtaagaaatgagttagattaaagaattaaaactgtttctcagatgctattttcaaatatgattaataattccttgactacctaatgtagttgaggtatttttgatattattcatatttttgcaaatctattgtttaaaaaataattttctaaaattctgaaaattctgttgacaggactttaaaaagggtctataatggatagaaaaacaaaggagaatact.................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAUCCUGGUCGUUAAUGAACUCCCCACGAAAAUAAUAGAUAUAAUAUUCUCAUGACAACAGCUUUGCAGUGUGUAAGAAAUGAGUUAGAUUAAAGAAUUAAAACUGUUUCUCAGAUGCUAUUUUCAAAUAUGAUUAAUAAUUCCUUGACUACCUAAUGUAGUUGAGGUAUUUUUGAUAUUAUUCAUAUUUUUGCAAAUCUAUUGUUUAAAAAAUAAUUUUCUAAAAUUCUGAAAAUUCUGUUGACAGGACUUUAAAAAGGGUCUAUAAUGGAUAGAAAAACAAAGGAGAAUACUAUGAAAACAAGGAAAGUAUUGGCUCUUGCGGGAGUCACUUUAUUAGCANNNNNUUAAUUAAUUAANNNNNGAAUGUAAAGACAC ..............((((((((((((((((.((..........((((.(((((((..(((((.((.((((((((((.(.((((((.((((.((((....))))..)))))))))).).)))).......((((((((.(((((((.(((..(((((.....)))))..))).))......))))).)))))))).)))))).)).)))))..........(((((((.............(((((((...(((((((....))))))).))))))))))))))......))))))).))))....(((........)))..)).)).))))))....))))))))..................................... (-76.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUCUUUACAUUCNNNNNUUAAUUAAUUAANNNNNUGCUAAUAAAGUGACUCCCGCAAGAGCCAAUACUUUCCUUGUUUUCAUAGUAUUCUCCUUUGUUUUUCUAUCCAUUAUAGACCCUUUUUAAAGUCCUGUCAACAGAAUUUUCAGAAUUUUAGAAAAUUAUUUUUUAAACAAUAGAUUUGCAAAAAUAUGAAUAAUAUCAAAAAUACCUCAACUACAUUAGGUAGUCAAGGAAUUAUUAAUCAUAUUUGAAAAUAGCAUCUGAGAAACAGUUUUAAUUCUUUAAUCUAACUCAUUUCUUACACACUGCAAAGCUGUUGUCAUGAGAAUAUUAUAUCUAUUAUUUUCGUGGGGAGUUCAUUAACGACCAGGAUUCAAA (.(((.....................((((.........))))..((((((((((.(((.(((............(((((((...(((...((..((((((.(((((.....)))))...((((((((((.(((.............))).))))))))))..........))))))..))..)))..((((((((.(((((......((.(((..(((((.....)))))..))).))))))).)))))))))))))))(((..(((((((.((((((((....))))...))))..))))))).....)))...))).))).((((((((((.((....)).))))))))))))))).)))))...)))).......... (-67.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 269 330 284 58 12 smit:SMT_134|5end_LysM_domain_protein_85427..85657_POSITIVE 264 346 306 56 14 smit:SMT_1350|5end_multidrug_resistance_efflux_pump_1329225..1329455_NEGATIVE 261 346 306 90 35 smit:SMT_1917|5end_ATP-dependent_nuclease_subunit_B_1861765..1861995_NEGATIVE 259 339 291 79 34 smit:SMT_297|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_238547..238777_POSITIVE 255 278 231 214 171 smit:SMT_1006|5end_6-pyruvoyl_tetrahydrobiopterin_synthase,_putative_946599..946829_POSITIVE 252 178 136 76 37 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 248 336 299 52 9 smit:SMT_1932|5end_K02008_cobalt_transport_system_permease_protein_1872001..1872231_NEGATIVE 235 330 286 137 73 smit:SMT_1291|5end_hypothetical_protein_1253875..1254105_POSITIVE 234 45 3 74 24 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 233 198 157 220 177 smit:SMT_1231|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1192622..1192852_POSITIVE 233 337 293 59 3 smit:SMT_1136|5end_K02025_multiple_sugar_transport_system_permease_protein_1078101..1078331_NEGATIVE 230 197 153 81 40 smit:SMT_1296|5end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1257290..1257520_POSITIVE 230 93 60 52 13 smit:SMT_669|5end_ribose-phosphate_pyrophosphokinase_578160..578390_POSITIVE 227 106 63 230 192 smit:SMT_1123|5end_hypothetical_protein_1059292..1059522_POSITIVE 227 276 231 210 157 smit:SMT_654|5end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_566058..566288_NEGATIVE 227 346 312 209 168 smit:SMT_592|5end_amino_acid_ABC_transporter,_ATP-binding_protein_508759..508989_POSITIVE 226 330 288 229 184 smit:SMT_432|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase_373553..373783_POSITIVE 225 181 144 64 24 smit:SMT_1152|5end_hypothetical_protein_1097197..1097427_NEGATIVE 225 330 289 210 158 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 223 82 42 41 2 smit:SMT_1008|5end_hypothetical_protein_948021..948251_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 346 306 69 27 smit:SMT_1351|3end_dephospho-CoA_kinase_1329212..1329362_NEGATIVE 248 336 299 67 24 smit:SMT_1933|3end_K02006_cobalt_transport_system_ATP-binding_protein_1871986..1872136_NEGATIVE 237 209 168 50 4 smit:SMT_1604|3end_K05833_putative_ABC_transport_system_ATP-binding_protein_1595163..1595313_POSITIVE 234 45 3 52 2 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 230 197 153 79 38 smit:SMT_1295|3end_transcriptional_regulator_CtsR_1257368..1257518_POSITIVE 229 333 309 124 97 smit:SMT_997|3end_integral_membrane_protein_939243..939393_POSITIVE 220 341 317 45 18 smit:SMT_2154|3end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2028892..2029042_POSITIVE 220 90 54 118 80 smit:SMT_2002|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1924145..1924295_NEGATIVE 217 93 54 142 96 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 214 94 54 121 80 smit:SMT_1927|3end_cell_division_protein_FtsH_1868408..1868558_NEGATIVE 214 96 55 145 109 smit:SMT_1801|3end_heavy_metal_translocating_P-type_ATPase_1775408..1775558_POSITIVE 212 97 56 81 33 smit:SMT_1392|3end_dihydroxyacetone_kinase_1369186..1369336_POSITIVE 211 188 147 91 58 smit:SMT_1419|3end_hypothetical_protein_1404582..1404732_POSITIVE 210 83 59 144 113 smit:SMT_1039|3end_tRNA_(uracil-5-)_-methyltransferase_981343..981493_NEGATIVE 209 336 317 147 125 smit:SMT_1892|3end_hypothetical_protein_1846193..1846343_POSITIVE 207 346 311 149 118 smit:SMT_1916|3end_glutamine_amidotransferase_1861200..1861350_POSITIVE 207 92 54 57 19 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 207 345 306 147 105 smit:SMT_1470|3end_K06188_aquaporin_Z_1453266..1453416_POSITIVE 206 90 54 59 23 smit:SMT_334|3end_K03713_MerR_family_transcriptional_regulator,_glutamine_synthetase_repressor_273796..273946_POSITIVE 205 35 8 136 113 smit:SMT_1690|3end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1673370..1673520_NEGATIVE