Origin IGS: atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaat Mask Tandem Repeat Region ================================================ atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Find is-nt database================================================ Query_seq: SMT_2003:SMT_2004|SMT_2003:SMT_2004:serine protease:K00783 hypothetical protein:<-->:1924900..1925069 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2003:SMT_2004|SMT_2003:SMT_2004:serine protease:K00783 hypothetical protein:<-->:1924900..1925069 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2003:SMT_2004|SMT_2003:SMT_2004:serine protease:K00783 hypothetical protein:<-->:1924900..1925069 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 38 End: 154 ..................................... N Y S L C L L K V C I T S L K L F D T T K E A L I L R K N Q S Y S T F F Y L M ................ atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc 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: 83 Start: 38 End: 67 .....................................TGTGTAAAACTTTTGTGTTTAAGTTATAAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2003:SMT_2004|SMT_2003:SMT_2004:serine protease:K00783 hypothetical protein:<-->:1924900..1925069 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 3 Min: 1 Max: 170 Len: 170 Subject: smit_SMT_2094_SMT_2095|serine protease:K00783 hypothetical protein|NEGATIVE:POSITIVE|[1989834,1990015]|182 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 13 Subject End: 182 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: smit_SMT_2003_SMT_2004|serine protease:K00783 hypothetical protein|NEGATIVE:POSITIVE|[1924900,1925069]|170 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: smit_SMT_86_SMT_87|K00783 hypothetical protein:serine protease|NEGATIVE:POSITIVE|[17605,17786]|182 HSP 1 e-value: 7.0E-92 bit: 337.0 Len: 170 Query Start:1 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 170 atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Inter-species Hit: Count: 3 Min: 4 Max: 170 Len: 167 Subject: NC_008533_SPD_2067_SPD_2068|hypothetical protein:serine protease|NEGATIVE:POSITIVE|[2043724,2043905]|182 HSP 1 e-value: 3.0E-32 bit: 139.0 Len: 78 Query Start:4 Query End:81 Subject Strand: NEGATIVE Subject Start: 90 Subject End: 167 ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataact......................................................................................... ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacaaactgtggataact......................................................................................... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:118 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 53 .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: NC_003098_spr2044_spr2045|hypothetical protein:Serine protease|NEGATIVE:POSITIVE|[2036224,2036393]|170 HSP 1 e-value: 3.0E-32 bit: 139.0 Len: 78 Query Start:4 Query End:81 Subject Strand: NEGATIVE Subject Start: 90 Subject End: 167 ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataact......................................................................................... ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacaaactgtggataact......................................................................................... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:118 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 53 .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: NC_003028_SP_2238_SP_2239|hypothetical protein:serine protease|NEGATIVE:POSITIVE|[2158647,2158828]|182 HSP 1 e-value: 3.0E-32 bit: 139.0 Len: 78 Query Start:4 Query End:81 Subject Strand: NEGATIVE Subject Start: 90 Subject End: 167 ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataact......................................................................................... ...tttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacaaactgtggataact......................................................................................... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:118 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 53 .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .....................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAUUACUGAAAGUAUAAACUGACUAGCUUAAUUAUAACUUAAACACAAAAGUUUUACACAGAUUGUGGAUAACUUUAAAAAAUCUGUGGUUUUCUCGGCUAAAAUUAACCUUUUAUUUUGUGAAUAAGAUGUGAAAAAAUAGAGAAUAUGUUAGAAUAGAGUC ......................(((((...(((..(((((.((((..(((((((......((((((((.((((....))))...))))))))........((.((....)).)).....)))))))..)))).))))).......))).....)))))......... (-24.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUCUAUUCUAACAUAUUCUCUAUUUUUUCACAUCUUAUUCACAAAAUAAAAGGUUAAUUUUAGCCGAGAAAACCACAGAUUUUUUAAAGUUAUCCACAAUCUGUGUAAAACUUUUGUGUUUAAGUUAUAAUUAAGCUAGUCAGUUUAUACUUUCAGUAAUUCAAA .(((...............................((((..(((((((.....(((((....)))))........((((((((................))))))))......)))))))..)))).......((((((....)))))).......)))........ (-23.49) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 771 110 61 216 167 smit:SMT_2094|5end_serine_protease_1989743..1989973_NEGATIVE 771 110 61 204 155 smit:SMT_2003|5end_serine_protease_1924809..1925039_NEGATIVE 771 110 61 216 167 smit:SMT_87|5end_serine_protease_17647..17877_POSITIVE 245 101 63 60 23 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 219 109 77 182 150 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 215 106 66 185 133 smit:SMT_1687|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1670400..1670630_POSITIVE 215 100 54 128 81 smit:SMT_1556|5end_phosphoglycerate_mutase_1541194..1541424_POSITIVE 214 138 93 149 92 smit:SMT_1898|5end_aminotransferase_(class_V),_putative_1849929..1850159_NEGATIVE 213 126 89 205 161 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 209 135 91 46 2 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 208 127 88 208 165 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 205 127 88 157 116 smit:SMT_1324|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1293801..1294031_POSITIVE 203 55 23 94 52 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 201 104 63 195 158 smit:SMT_1577|5end_ribose_ABC_transporter,_ATP-binding_protein_1569362..1569592_POSITIVE 201 139 98 168 121 smit:SMT_1576|5end_ribose_ABC_transporter_protein_RbsD_1568950..1569180_POSITIVE 199 102 67 204 167 smit:SMT_786|5end_hypothetical_protein_697964..698194_NEGATIVE 192 122 87 80 40 smit:SMT_665|5end_NAD+_kinase_576745..576975_NEGATIVE 189 125 88 205 172 smit:SMT_1289|5end_hypothetical_protein_1252208..1252438_POSITIVE 187 116 88 76 45 smit:SMT_1469|5end_GTP_pyrophosphokinase_1450582..1450812_POSITIVE 186 125 85 172 123 smit:SMT_961|5end_K02016_iron_complex_transport_system_substrate-binding_protein_907809..908039_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 101 63 76 39 smit:SMT_1679|3end_hypothetical_protein_1663590..1663740_POSITIVE 221 138 92 52 2 smit:SMT_982|3end_D-tyrosyl-tRNA(Tyr)_deacylase_929211..929361_NEGATIVE 215 106 66 61 9 smit:SMT_1686|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1670356..1670506_POSITIVE 208 36 11 100 69 smit:SMT_882|3end_acetyl_esterase_829662..829812_NEGATIVE 205 127 88 48 7 smit:SMT_1323|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1293772..1293922_POSITIVE 203 55 23 73 31 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 199 102 67 80 43 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 192 122 87 96 56 smit:SMT_666|3end_GTP_pyrophosphokinase-like_protein_576729..576879_NEGATIVE 187 100 52 65 9 smit:SMT_1242|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1203027..1203177_NEGATIVE 185 107 72 77 43 smit:SMT_423|3end_sensory_transduction_protein_kinase_367531..367681_POSITIVE 180 127 86 102 50 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 180 124 85 144 103 smit:SMT_962|3end_putative_hemin_transport_system_ATP-binding_protein_fecE_907829..907979_NEGATIVE 178 118 91 36 11 smit:SMT_914|3end_sucrose-6-phosphate_hydrolase_867673..867823_POSITIVE 177 116 81 50 8 smit:SMT_496|3end_superoxide_dismutase,_manganese-dependent_431118..431268_POSITIVE 174 119 84 151 120 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 173 129 91 114 79 smit:SMT_1589|3end_hypothetical_protein_1578606..1578756_POSITIVE 173 70 26 51 6 smit:SMT_731|3end_hypothetical_protein_predicted_by_Glimmer/Critica_638387..638537_NEGATIVE 169 104 62 148 104 smit:SMT_1553|3end_K04074_cell_division_initiation_protein_1536868..1537018_POSITIVE 169 104 87 123 104 smit:SMT_749|3end_shikimate_kinase_653495..653645_NEGATIVE 169 107 66 123 77 smit:SMT_675|3end_DNA_repair_protein_582297..582447_NEGATIVE