Origin IGS: ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttactatcctccataaaaagaccggattgctccgatctttttaagtttcgctctaagaaaatcaaagaataaacaaggcatcgaaccgcaggcagtactgaagtacggcaaggtgaagataacacagtttaaatttgattttcgacgagaggaa Mask Tandem Repeat Region ================================================ ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Find is-nt database================================================ Query_seq: SMT_456:SMT_457|SMT_456:SMT_457:pyruvate oxidase:hypothetical protein:->->:396152..396305 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_456:SMT_457|SMT_456:SMT_457:pyruvate oxidase:hypothetical protein:->->:396152..396305 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_456:SMT_457|SMT_456:SMT_457:pyruvate oxidase:hypothetical protein:->->:396152..396305 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 35 End: 148 .................................. M F T L P Y F S T A C G S M P C L F F D F L R A K L K K I G A I R S F Y G G ...... Protein_Len: 41 Strand: + Start: 30 End: 152 ............................. M L S S P C R T S V L P A V R C L V Y S L I F L E R N L K R S E Q S G L F M E D S .. Protein_Len: 43 Strand: - Start: 1 End: 129 E E R R F D F K F Q T I K V K G Y K L V A Q P E I G Q K N K S K R L A F S L F I P A M ......................... ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa 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================================================ ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 84 HP_score: -7.7 Tail_Score: -4.83615 Start: 118 End: 135 Full_Region: AGCGAAACTTAAAAA GATCGGA GCAA TCCGGTC TTTTTATGGAGGATA .....................................................................................................................GATCGGAGCAATCCGGTC................... Find igs database================================================ Query_seq: SMT_456:SMT_457|SMT_456:SMT_457:pyruvate oxidase:hypothetical protein:->->:396152..396305 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Intra-Species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: smit_SMT_456_SMT_457|pyruvate oxidase:hypothetical protein|POSITIVE:POSITIVE|[396152,396305]|154 HSP 1 e-value: 2.0E-82 bit: 305.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa Inter-species Hit: Count: 1 Min: 1 Max: 154 Len: 154 Subject: NC_009009_SSA_0391_SSA_0392|Pyruvate oxidase, putative:hypothetical protein|POSITIVE:POSITIVE|[387862,388015]|154 HSP 1 e-value: 1.0E-53 bit: 210.0 Len: 154 Query Start:1 Query End:154 Subject Strand: POSITIVE Subject Start: 1 Subject End: 154 ttcctctcgtcgaaaatcaaatttaaactgtgttatcttcaccttgccgtacttcagtactgcctgcggttcgatgccttgtttattctttgattttcttagagcgaaacttaaaaagatcggagcaatccggtctttttatggaggatagtaa ttcctctcgccgaaaatcaaatgtaaactgtgtcatcttaaccttgccgtacagcagtactgcctgcggttcgatgtcttgtttataacttgattttcttagagcggaacttgaaaagatcggagcaatccggtctttttatggaggatagtaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCCUCUCGUCGAAAAUCAAAUUUAAACUGUGUUAUCUUCACCUUGCCGUACUUCAGUACUGCCUGCGGUUCGAUGCCUUGUUUAUUCUUUGAUUUUCUUAGAGCGAAACUUAAAAAGAUCGGAGCAAUCCGGUCUUUUUAUGGAGGAUAGUAA .((((((....((((((((((..(((((...(.((((...(((..((.((((....)))).))....)))..)))).)..)))))...)))))))))).............(((((((((((((....))))))))))))).))))))...... (-48.40) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUACUAUCCUCCAUAAAAAGACCGGAUUGCUCCGAUCUUUUUAAGUUUCGCUCUAAGAAAAUCAAAGAAUAAACAAGGCAUCGAACCGCAGGCAGUACUGAAGUACGGCAAGGUGAAGAUAACACAGUUUAAAUUUGAUUUUCGACGAGAGGAA ......((((((.((((((((.((((....)))).)))))))).............((((((((((...(((((..(..(((..(((....((.((((....)))).))..)))...)))..)...)))))..))))))))))...).))))). (-46.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 552 69 21 189 141 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 538 69 21 206 158 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 510 69 21 171 123 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 510 69 21 171 123 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 510 69 21 171 123 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 498 60 11 227 178 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 394 50 1 198 149 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 372 107 62 101 53 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 361 83 41 51 3 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 353 86 41 60 5 smit:SMT_1731|5end_K06442_putative_hemolysin_1715643..1715873_POSITIVE 352 89 41 98 41 smit:SMT_1693|5end_dimethyladenosine_transferase_1675800..1676030_POSITIVE 339 77 33 134 88 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 336 80 37 142 93 smit:SMT_573|5end_1-phosphofructokinase_490976..491206_POSITIVE 327 78 31 135 92 smit:SMT_2067|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1973432..1973662_POSITIVE 324 78 32 57 12 smit:SMT_886|5end_single-stranded-DNA-specific_exonuclease_RecJ_834575..834805_NEGATIVE 322 98 51 89 43 smit:SMT_867|5end_hypothetical_protein_816316..816546_POSITIVE 315 109 62 103 53 smit:SMT_1911|5end_hypothetical_protein_1857614..1857844_POSITIVE 310 140 103 60 8 smit:SMT_1168|5end_potassium_uptake_protein_KtrB_1116552..1116782_NEGATIVE 308 48 4 214 170 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 304 98 51 89 30 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 510 69 21 56 8 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 510 69 21 56 8 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 510 69 21 56 8 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 432 69 21 53 5 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 431 68 22 52 6 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 398 90 42 53 5 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 386 50 1 146 97 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 385 98 56 46 4 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 353 86 41 67 12 smit:SMT_1730|3end_geranyltranstransferase_1715730..1715880_POSITIVE 350 105 62 89 46 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 348 104 62 88 46 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 348 104 62 74 32 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 339 77 33 141 95 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 336 80 37 145 96 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 335 104 62 88 46 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 315 109 62 63 13 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 298 98 56 48 8 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 293 98 56 44 2 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 291 71 35 145 103 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 286 81 42 80 35 smit:SMT_230|3end_hypothetical_protein_predicted_by_Glimmer/Critica_165666..165816_NEGATIVE