Origin IGS: atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .........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 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Mask Tandem Repeat Region ================================================ atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Find is-nt database================================================ Query_seq: SMT_2094:SMT_2095|SMT_2094:SMT_2095:serine protease:K00783 hypothetical protein:<-->:1989834..1990015 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2094:SMT_2095|SMT_2094:SMT_2095:serine protease:K00783 hypothetical protein:<-->:1989834..1990015 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2094:SMT_2095|SMT_2094:SMT_2095:serine protease:K00783 hypothetical protein:<-->:1989834..1990015 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: - Start: 50 End: 166 ................................................. 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 ................ atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc 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: 50 End: 79 .................................................TGTGTAAAACTTTTGTGTTTAAGTTATAAT....................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2094:SMT_2095|SMT_2094:SMT_2095:serine protease:K00783 hypothetical protein:<-->:1989834..1990015 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Intra-Species Hit: Count: 3 Min: 1 Max: 182 Len: 182 Subject: smit_SMT_2094_SMT_2095|serine protease:K00783 hypothetical protein|NEGATIVE:POSITIVE|[1989834,1990015]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: smit_SMT_86_SMT_87|K00783 hypothetical protein:serine protease|NEGATIVE:POSITIVE|[17605,17786]|182 HSP 1 e-value: 5.0E-99 bit: 361.0 Len: 182 Query Start:1 Query End:182 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Subject: smit_SMT_2003_SMT_2004|serine protease:K00783 hypothetical protein|NEGATIVE:POSITIVE|[1924900,1925069]|170 HSP 1 e-value: 8.0E-92 bit: 337.0 Len: 170 Query Start:13 Query End:182 Subject Strand: POSITIVE Subject Start: 1 Subject End: 170 ............atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc ............atttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Inter-species Hit: Count: 3 Min: 1 Max: 182 Len: 182 Subject: NC_008533_SPD_2067_SPD_2068|hypothetical protein:serine protease|NEGATIVE:POSITIVE|[2043724,2043905]|182 HSP 1 e-value: 1.0E-38 bit: 161.0 Len: 93 Query Start:1 Query End:93 Subject Strand: NEGATIVE Subject Start: 90 Subject End: 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataact......................................................................................... atttgcctccatatgtttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacaaactgtggataact......................................................................................... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:130 Query End:182 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: 1.0E-38 bit: 161.0 Len: 93 Query Start:1 Query End:93 Subject Strand: NEGATIVE Subject Start: 90 Subject End: 182 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataact......................................................................................... atttgcctccatatgtttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacaaactgtggataact......................................................................................... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:130 Query End:182 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: 4.0E-32 bit: 139.0 Len: 78 Query Start:16 Query End:93 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:130 Query End:182 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 53 .................................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc .................................................................................................................................ttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGCCUCCAUAUUUUUGAAUUACUGAAAGUAUAAACUGACUAGCUUAAUUAUAACUUAAACACAAAAGUUUUACACAGAUUGUGGAUAACUUUAAAAAAUCUGUGGUUUUCUCGGCUAAAAUUAACCUUUUAUUUUGUGAAUAAGAUGUGAAAAAAUAGAGAAUAUGUUAGAAUAGAGUC ......(((.((((((((........))))))))...(((((...(((..(((((.((((..(((((((......((((((((.((((....))))...))))))))........((.((....)).)).....)))))))..)))).))))).......))).....)))))....))).. (-29.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUCUAUUCUAACAUAUUCUCUAUUUUUUCACAUCUUAUUCACAAAAUAAAAGGUUAAUUUUAGCCGAGAAAACCACAGAUUUUUUAAAGUUAUCCACAAUCUGUGUAAAACUUUUGUGUUUAAGUUAUAAUUAAGCUAGUCAGUUUAUACUUUCAGUAAUUCAAAAAUAUGGAGGCAAAU ..................(((((((.((((.....((((..(((((((.....(((((....)))))........((((((((................))))))))......)))))))..)))).......((((((....))))))................)))).)))))))..... (-30.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 120 71 211 162 smit:SMT_2094|5end_serine_protease_1989743..1989973_NEGATIVE 776 120 71 199 150 smit:SMT_2003|5end_serine_protease_1924809..1925039_NEGATIVE 776 120 71 211 162 smit:SMT_87|5end_serine_protease_17647..17877_POSITIVE 245 116 78 60 23 smit:SMT_1680|5end_hypothetical_protein_1663494..1663724_POSITIVE 235 150 105 46 1 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 224 129 81 191 133 smit:SMT_1687|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1670400..1670630_POSITIVE 219 124 92 182 150 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 215 148 103 163 116 smit:SMT_1324|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1293801..1294031_POSITIVE 213 141 104 205 161 smit:SMT_288|5end_hypothetical_protein_231184..231414_POSITIVE 208 142 103 208 165 smit:SMT_166|5end_hypothetical_protein_112987..113217_POSITIVE 203 70 38 94 52 smit:SMT_608|5end_laminin-binding_surface_protein_520757..520987_POSITIVE 201 119 78 195 158 smit:SMT_1577|5end_ribose_ABC_transporter,_ATP-binding_protein_1569362..1569592_POSITIVE 201 154 113 168 121 smit:SMT_1576|5end_ribose_ABC_transporter_protein_RbsD_1568950..1569180_POSITIVE 201 118 71 73 20 smit:SMT_1255|5end_cell_division_protein_FtsH_1221811..1222041_NEGATIVE 200 86 41 52 6 smit:SMT_730|5end_hypothetical_protein_638387..638617_NEGATIVE 199 117 82 204 167 smit:SMT_786|5end_hypothetical_protein_697964..698194_NEGATIVE 196 48 1 227 188 smit:SMT_691|5end_endonuclease_III_603008..603238_NEGATIVE 192 115 71 128 83 smit:SMT_1556|5end_phosphoglycerate_mutase_1541194..1541424_POSITIVE 192 140 92 205 167 smit:SMT_1289|5end_hypothetical_protein_1252208..1252438_POSITIVE 192 137 102 80 40 smit:SMT_665|5end_NAD+_kinase_576745..576975_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 245 116 78 76 39 smit:SMT_1679|3end_hypothetical_protein_1663590..1663740_POSITIVE 224 129 81 67 9 smit:SMT_1686|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1670356..1670506_POSITIVE 215 148 103 54 7 smit:SMT_1323|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1293772..1293922_POSITIVE 208 51 26 100 69 smit:SMT_882|3end_acetyl_esterase_829662..829812_NEGATIVE 203 70 38 73 31 smit:SMT_607|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_520816..520966_POSITIVE 200 49 9 67 24 smit:SMT_981|3end_hypothetical_protein_929202..929352_POSITIVE 200 86 41 52 6 smit:SMT_731|3end_hypothetical_protein_predicted_by_Glimmer/Critica_638387..638537_NEGATIVE 199 117 82 80 43 smit:SMT_787|3end_K02440_glycerol_uptake_facilitator_protein_698088..698238_NEGATIVE 193 145 107 44 2 smit:SMT_982|3end_D-tyrosyl-tRNA(Tyr)_deacylase_929211..929361_NEGATIVE 192 137 102 96 56 smit:SMT_666|3end_GTP_pyrophosphokinase-like_protein_576729..576879_NEGATIVE 186 48 4 143 104 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 185 122 87 77 43 smit:SMT_423|3end_sensory_transduction_protein_kinase_367531..367681_POSITIVE 183 139 91 98 41 smit:SMT_1443|3end_23S_rRNA_m(5)U_1939_methyltransferase_1426503..1426653_NEGATIVE 180 139 100 144 103 smit:SMT_962|3end_putative_hemin_transport_system_ATP-binding_protein_fecE_907829..907979_NEGATIVE 180 47 6 68 10 smit:SMT_807|3end_hypothetical_protein_predicted_by_Glimmer/Critica_716708..716858_NEGATIVE 179 47 5 62 21 smit:SMT_1643|3end_2-isopropylmalate_synthase_1630772..1630922_POSITIVE 178 109 67 57 9 smit:SMT_1242|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1203027..1203177_NEGATIVE 177 32 4 121 94 smit:SMT_1288|3end_replicative_DNA_helicase_1252286..1252436_POSITIVE 177 131 96 50 8 smit:SMT_496|3end_superoxide_dismutase,_manganese-dependent_431118..431268_POSITIVE 176 49 3 57 4 smit:SMT_1735|3end_K03596_GTP-binding_protein_LepA_1719549..1719699_POSITIVE