Origin IGS: aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa .........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 ttaattaannnnngctggaagtctcgtacccactggtatgagaattaccgcttattgttcaaaaagaaaaagtcggtgctattttttcaatctatacttttcaatccttttttcctattcctagcttactcggcctagcctccattctcaccttatgtatattcttcctctacttctggcaagcaagacgaattgctcataagattgctacacacaacgctgttcctattgaaagcttagtttaccaacttcaagaaattcccaaacaagcagaaaaaagactttctctacaaacaggtgatgagtttgaattt Mask Tandem Repeat Region ================================================ aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Find is-nt database================================================ Query_seq: SMT_1988:SMT_1989|SMT_1988:SMT_1989:two-component sensor kinase YesM:multimodular transpeptidase-transglycosylase:<-<-:1916895..1917208 314 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1988:SMT_1989|SMT_1988:SMT_1989:two-component sensor kinase YesM:multimodular transpeptidase-transglycosylase:<-<-:1916895..1917208 314 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1988:SMT_1989|SMT_1988:SMT_1989:two-component sensor kinase YesM:multimodular transpeptidase-transglycosylase:<-<-:1916895..1917208 314 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: - Start: 180 End: 311 ................................................................................................................................................................................... A S Y A L F L F F P N F L I S Q F F L V S K K K K F L L R Y N E Y W H T R S K W X X X M ... Protein_Len: 60 Strand: - Start: 1 End: 261 E I P V A N H T A I K H A I R R A Q W F Y L F F I C L T L I S A L G L L S P I P F F S Q F T Y I S F I A G V K E K Q V M ..................................................... aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa 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================================================ aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1988:SMT_1989|SMT_1988:SMT_1989:two-component sensor kinase YesM:multimodular transpeptidase-transglycosylase:<-<-:1916895..1917208 314 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagcnnnnnttaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 301 Len: 301 Subject: smit_SMT_1988_SMT_1989|two-component sensor kinase YesM:multimodular transpeptidase- transglycosylase|NEGATIVE:NEGATIVE|[1916895,1917208]|314 HSP 1 e-value: 1.0E-170 bit: 597.0 Len: 301 Query Start:1 Query End:301 Subject Strand: POSITIVE Subject Start: 1 Subject End: 301 aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagc............. aaattcaaactcatcacctgtttgtagagaaagtcttttttctgcttgtttgggaatttcttgaagttggtaaactaagctttcaataggaacagcgttgtgtgtagcaatcttatgagcaattcgtcttgcttgccagaagtagaggaagaatatacataaggtgagaatggaggctaggccgagtaagctaggaataggaaaaaaggattgaaaagtatagattgaaaaaatagcaccgactttttctttttgaacaataagcggtaattctcataccagtgggtacgagacttccagc............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUUCAAACUCAUCACCUGUUUGUAGAGAAAGUCUUUUUUCUGCUUGUUUGGGAAUUUCUUGAAGUUGGUAAACUAAGCUUUCAAUAGGAACAGCGUUGUGUGUAGCAAUCUUAUGAGCAAUUCGUCUUGCUUGCCAGAAGUAGAGGAAGAAUAUACAUAAGGUGAGAAUGGAGGCUAGGCCGAGUAAGCUAGGAAUAGGAAAAAAGGAUUGAAAAGUAUAGAUUGAAAAAAUAGCACCGACUUUUUCUUUUUGAACAAUAAGCGGUAAUUCUCAUACCAGUGGGUACGAGACUUCCAGC .........((((((..((((((.((..(((((.(((..((.((((..((..((.....))..))...))))))..))))))))..)).))))))..(((((((((((..((....))))..(((.(((.((((.....))))))).)))...)))))))))))))))..((((((....((((..((..(((....)))...(((((((...((((((....(((.....))).......)))))))))))))......))..))))...((((.((((....)))).)))))))))).. (-70.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGGAAGUCUCGUACCCACUGGUAUGAGAAUUACCGCUUAUUGUUCAAAAAGAAAAAGUCGGUGCUAUUUUUUCAAUCUAUACUUUUCAAUCCUUUUUUCCUAUUCCUAGCUUACUCGGCCUAGCCUCCAUUCUCACCUUAUGUAUAUUCUUCCUCUACUUCUGGCAAGCAAGACGAAUUGCUCAUAAGAUUGCUACACACAACGCUGUUCCUAUUGAAAGCUUAGUUUACCAACUUCAAGAAAUUCCCAAACAAGCAGAAAAAAGACUUUCUCUACAAACAGGUGAUGAGUUUGAAUUU (((((((.(((((((((....)))))))))..((((((((....(((.....))).))).))))).......................................)))).)))......(((...)))...((((((((((..((((..(((((..........((((((((((......)))))........)))))........(((.(((.....))))))................)))))..............(((((......))))).))))...)))))).))))........ (-54.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 140 91 231 182 smit:SMT_1988|5end_two-component_sensor_kinase_YesM_1916804..1917034_NEGATIVE 382 293 272 22 1 smit:SMT_2118|5end_putative_two-component_sensor_histidine_kinase_2005489..2005719_NEGATIVE 321 149 110 58 11 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 313 216 175 69 23 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 309 204 162 175 133 smit:SMT_125|5end_hypothetical_protein_77664..77894_NEGATIVE 296 120 74 221 177 smit:SMT_1654|5end_K03110_signal_recognition_particle_receptor_1642150..1642380_POSITIVE 293 185 141 203 161 smit:SMT_1595|5end_oligopeptide_transport_system_permease_protein_OppC_1584968..1585198_POSITIVE 293 140 95 82 38 smit:SMT_605|5end_DNA-binding_protein_HU_519034..519264_POSITIVE 292 179 135 193 145 smit:SMT_1272|5end_K02006_cobalt_transport_system_ATP-binding_protein_1236097..1236327_POSITIVE 291 202 163 52 8 smit:SMT_1571|5end_CAAX_amino_terminal_protease_family_protein_1563780..1564010_POSITIVE 287 180 135 59 10 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 282 140 92 198 146 smit:SMT_169|5end_30S_ribosomal_protein_S10_114515..114745_POSITIVE 280 148 121 124 95 smit:SMT_1420|5end_K02004_1406582..1406812_NEGATIVE 279 148 107 216 165 smit:SMT_760|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_666442..666672_NEGATIVE 276 196 161 60 23 smit:SMT_997|5end_integral_membrane_protein_938243..938473_POSITIVE 273 177 138 156 116 smit:SMT_2028|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1943729..1943959_NEGATIVE 273 177 138 156 116 smit:SMT_1754|5end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1733022..1733252_NEGATIVE 272 88 41 87 39 smit:SMT_2152|5end_cell_division_protein_2025649..2025879_POSITIVE 272 178 135 94 47 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 271 210 162 57 6 smit:SMT_350|5end_immunity_protein_BlpL_289864..290094_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 216 175 76 30 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 299 202 161 151 96 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 287 180 135 69 20 smit:SMT_1618|3end_K02015_iron_complex_transport_system_permease_protein_1604490..1604640_NEGATIVE 280 148 121 122 93 smit:SMT_1421|3end_K02003_1406584..1406734_NEGATIVE 275 140 96 120 72 smit:SMT_1517|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1498497..1498647_POSITIVE 270 201 163 53 25 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 269 209 162 66 13 smit:SMT_1367|3end_K02237_competence_protein_ComEA_1346872..1347022_NEGATIVE 268 188 145 81 30 smit:SMT_203|3end_putative_ABC_transporter_BitD_133821..133971_NEGATIVE 266 132 93 71 25 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 266 132 93 71 25 smit:SMT_290|3end_glucose-1-phosphate_thymidylyltransferase_234276..234426_POSITIVE 263 200 172 102 67 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 261 147 108 74 24 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 257 196 156 72 26 smit:SMT_1121|3end_hypothetical_protein_1057105..1057255_NEGATIVE 256 186 143 64 16 smit:SMT_1062|3end_hypothetical_protein_1000648..1000798_POSITIVE 254 137 91 60 16 smit:SMT_801|3end_glycyl-tRNA_synthetase_alpha_chain_709892..710042_NEGATIVE 253 210 165 141 99 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 253 201 163 61 25 smit:SMT_1321|3end_K02074_zinc/manganese_transport_system_ATP-binding_protein_1291458..1291608_POSITIVE 253 72 32 73 26 smit:SMT_1031|3end_MSM_(multiple_sugar_metabolism)_operon_regulatory_protein_968827..968977_POSITIVE 251 137 95 68 7 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 250 129 88 96 64 smit:SMT_1174|3end_acylneuraminate_cytidylyltransferase_1125617..1125767_NEGATIVE