Origin IGS: gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc .........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 gacctctccaattctatactaagatattaaggacgaagagctccgtacctaaaagatacaaagtttctcgtcagctttattttgtttacataacttatcttatgtaattctattctttgttatatgttttacgaatggcatctttgatgctttcaaccggttggaatcattgcattttctaggttttgtgcataaggcattggcacnnnnnttaattaattaannnnngacgctttcatatcttgtgtacacttatattttagtttcgatatgtattttgaaatgtttatggcttgaaagtagtttcagaaacaagccatc Mask Tandem Repeat Region ================================================ gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Find is-nt database================================================ Query_seq: SMT_1890:SMT_1891|SMT_1890:SMT_1891:hypothetical protein:putative dihydrolipoamide S-acetyltransferase:->->:1844192..1844512 321 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1890:SMT_1891|SMT_1890:SMT_1891:hypothetical protein:putative dihydrolipoamide S-acetyltransferase:->->:1844192..1844512 321 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1890:SMT_1891|SMT_1890:SMT_1891:hypothetical protein:putative dihydrolipoamide S-acetyltransferase:->->:1844192..1844512 321 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 106 End: 219 ......................................................................................................... M X X X A N A L C T K P R K C N D S N R L K A S K M P F V K H I T K N R I T ...................................................................................................... Protein_Len: 55 Strand: - Start: 102 End: 266 ..................................................................................................... N I L X X A L A K H V F G L F H L S E L R N F A D F I G N T F C I V F F L I V Y S L N H L C F L A S S F S Q M ....................................................... gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc 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================================================ gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -7.7 Tail_Score: -3.55622 Start: 172 End: 184 Full_Region: tatgttttacgaatg gcatc ttt gatgc tttcaaccggttgga ...........................................................................................................................................................................gcatctttgatgc......................................................................................................................................... TransTerm Strand: - Conf: 59 HP_score: -4.6 Tail_Score: -3.96154 Start: 215 End: 236 Full_Region: tcagctttattttgt ttacataa cttatc ttatgtaa ttctattctttgtta ......................................................................................................................................................................................................................ttacataacttatcttatgtaa..................................................................................... Find igs database================================================ Query_seq: SMT_1890:SMT_1891|SMT_1890:SMT_1891:hypothetical protein:putative dihydrolipoamide S-acetyltransferase:->->:1844192..1844512 321 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Intra-Species Hit: Count: 2 Min: 1 Max: 321 Len: 321 Subject: smit_SMT_1890_SMT_1891|hypothetical protein:putative dihydrolipoamide S-acetyltransferase|POSITIVE:POSITIVE|[1844192, 1844512]|321 HSP 1 e-value: 1.0E-164 bit: 577.0 Len: 321 Query Start:1 Query End:321 Subject Strand: POSITIVE Subject Start: 1 Subject End: 321 gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc gatggcttgtttctgaaactactttcaagccataaacatttcaaaatacatatcgaaactaaaatataagtgtacacaagatatgaaagcgtcnnnnnttaattaattaannnnngtgccaatgccttatgcacaaaacctagaaaatgcaatgattccaaccggttgaaagcatcaaagatgccattcgtaaaacatataacaaagaatagaattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Subject: smit_SMT_1401_SMT_1402|pyruvate dehydrogenase E1 component beta subunit:pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)|POSITIVE:POSITIVE|[1378146, 1378254]|109 HSP 1 e-value: 4.0E-55 bit: 216.0 Len: 109 Query Start:213 Query End:321 Subject Strand: POSITIVE Subject Start: 1 Subject End: 109 ....................................................................................................................................................................................................................aattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc ....................................................................................................................................................................................................................aattacataagataagttatgtaaacaaaataaagctgacgagaaactttgtatcttttaggtacggagctcttcgtccttaatatcttagtatagaattggagaggtc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGGCUUGUUUCUGAAACUACUUUCAAGCCAUAAACAUUUCAAAAUACAUAUCGAAACUAAAAUAUAAGUGUACACAAGAUAUGAAAGCGUCNNNNNUUAAUUAAUUAANNNNNGUGCCAAUGCCUUAUGCACAAAACCUAGAAAAUGCAAUGAUUCCAACCGGUUGAAAGCAUCAAAGAUGCCAUUCGUAAAACAUAUAACAAAGAAUAGAAUUACAUAAGAUAAGUUAUGUAAACAAAAUAAAGCUGACGAGAAACUUUGUAUCUUUUAGGUACGGAGCUCUUCGUCCUUAAUAUCUUAGUAUAGAAUUGGAGAGGUC .((((((((................))))))))....(((((......((((((...(((........)))........)))))).................................(((((...((((((.....((((((((.((((((.(.(((....((((((((.(((((...)))))..))).........................((((((((......)))))))).........)))))....))).).)))))).))))))))(((((....))))).............)))))).))))).))))). (-57.89) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACCUCUCCAAUUCUAUACUAAGAUAUUAAGGACGAAGAGCUCCGUACCUAAAAGAUACAAAGUUUCUCGUCAGCUUUAUUUUGUUUACAUAACUUAUCUUAUGUAAUUCUAUUCUUUGUUAUAUGUUUUACGAAUGGCAUCUUUGAUGCUUUCAACCGGUUGGAAUCAUUGCAUUUUCUAGGUUUUGUGCAUAAGGCAUUGGCACNNNNNUUAAUUAAUUAANNNNNGACGCUUUCAUAUCUUGUGUACACUUAUAUUUUAGUUUCGAUAUGUAUUUUGAAAUGUUUAUGGCUUGAAAGUAGUUUCAGAAACAAGCCAUC (((((.(((((((......(((((((.....(((((..((((..(((.(.....).)))..))))..))))).....))))))).((((((((......)))))))).........................(((.((((((...)))))))))....)))))))...............))))).((((((((((..((.(((.......((((....))))........)))...))..))))))))))...........(((((((........)))))))....((((((((................)))))))). (-61.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 290 245 163 120 smit:SMT_1402|5end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1378115..1378345_POSITIVE 273 285 247 219 181 smit:SMT_1816|5end_K02026_multiple_sugar_transport_system_permease_protein_1790813..1791043_POSITIVE 265 289 245 76 33 smit:SMT_1142|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1085546..1085776_POSITIVE 257 308 263 148 99 smit:SMT_1933|5end_K02006_cobalt_transport_system_ATP-binding_protein_1872222..1872452_NEGATIVE 247 290 244 47 2 smit:SMT_1540|5end_hypothetical_protein_1525005..1525235_NEGATIVE 247 319 271 182 129 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 247 319 271 54 1 smit:SMT_545|5end_hypothetical_protein_predicted_by_Glimmer/Critica_461249..461479_POSITIVE 246 320 273 148 86 smit:SMT_1834|5end_cell_division_protein_1803695..1803925_NEGATIVE 246 302 268 114 82 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 244 317 271 128 85 smit:SMT_1388|5end_hypothetical_protein_1365214..1365444_POSITIVE 241 199 154 62 9 smit:SMT_1084|5end_hypothetical_protein_1021925..1022155_NEGATIVE 241 300 251 110 63 smit:SMT_412|5end_hypothetical_protein_predicted_by_Glimmer/Critica_356606..356836_NEGATIVE 241 318 271 133 76 smit:SMT_155|5end_hypothetical_protein_102704..102934_NEGATIVE 240 287 245 158 115 smit:SMT_1705|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_1688558..1688788_POSITIVE 236 320 274 175 127 smit:SMT_817|5end_aminotransferase_728699..728929_NEGATIVE 233 293 252 105 53 smit:SMT_2117|5end_transcription-repair_coupling_factor_2004560..2004790_NEGATIVE 233 290 248 52 5 smit:SMT_765|5end_hypothetical_protein_672620..672850_NEGATIVE 229 190 145 70 26 smit:SMT_1716|5end_hypothetical_protein_1703314..1703544_POSITIVE 228 290 247 210 156 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 228 174 137 35 1 smit:SMT_980|5end_hypothetical_protein_927440..927670_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 286 246 76 23 smit:SMT_1482|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1463061..1463211_NEGATIVE 321 290 245 53 10 smit:SMT_1401|3end_pyruvate_dehydrogenase_E1_component_beta_subunit_1378085..1378235_POSITIVE 255 320 273 125 60 smit:SMT_1934|3end_homoserine_dehydrogenase_1873150..1873300_POSITIVE 251 180 138 45 4 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 247 319 271 149 96 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 246 302 268 121 89 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 244 317 271 71 28 smit:SMT_1387|3end_hypothetical_protein_1365237..1365387_POSITIVE 241 199 154 61 8 smit:SMT_1085|3end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1021926..1022076_NEGATIVE 240 287 245 74 31 smit:SMT_1704|3end_D-alanine-D-alanine_ligase_1688554..1688704_POSITIVE 235 282 244 141 87 smit:SMT_864|3end_K07485_transposase_814971..815121_POSITIVE 235 294 251 93 52 smit:SMT_116|3end_beta-N-acetylhexosaminidase_68356..68506_POSITIVE 232 297 256 82 44 smit:SMT_340|3end_chaperone_protein_280566..280716_POSITIVE 229 286 246 85 44 smit:SMT_110|3end_alpha-L-fucosidase_59207..59357_POSITIVE 226 290 246 71 26 smit:SMT_541|3end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457120..457270_NEGATIVE 223 184 147 68 27 smit:SMT_2057|3end_cell_division_protein_FtsH_1966897..1967047_NEGATIVE 222 188 156 144 113 smit:SMT_1951|3end_ABC_transporter,_ATP-binding_protein_1885141..1885291_NEGATIVE 220 180 138 133 84 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 220 194 164 34 4 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 218 299 266 68 36 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 216 284 247 138 101 smit:SMT_2052|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1960662..1960812_NEGATIVE