Origin IGS: gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat .........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 atttgcctccatatttttgaattactgaaagtataaactgactagcttaattataacttaaacacaaaagttttacacagattgtggataactttaaaaaatctgtggttttctcggctaaaattaaccttttattttgtgaataagatgtgaaaaaatagagaatatgttagaatagagtc Mask Tandem Repeat Region ================================================ gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Find is-nt database================================================ Query_seq: SMT_86:SMT_87|SMT_86:SMT_87:K00783 hypothetical protein:serine protease:<-->:17605..17786 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_86:SMT_87|SMT_86:SMT_87:K00783 hypothetical protein:serine protease:<-->:17605..17786 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_86:SMT_87|SMT_86:SMT_87:K00783 hypothetical protein:serine protease:<-->:17605..17786 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Predict ORF larger than 30AA ================================================ Protein_Len: 39 Strand: + Start: 17 End: 133 ................ M L Y F F T S Y S Q N K R L I L A E K T T D F L K L S T I C V K L L C L S Y N ................................................. gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat 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: 104 End: 133 .......................................................................................................TGTGTAAAACTTTTGTGTTTAAGTTATAAT................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_86:SMT_87|SMT_86:SMT_87:K00783 hypothetical protein:serine protease:<-->:17605..17786 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat 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: NEGATIVE Subject Start: 1 Subject End: 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat 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: POSITIVE Subject Start: 1 Subject End: 182 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat 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:1 Query End:170 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 170 gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaat............ gactctattctaacatattctctattttttcacatcttattcacaaaataaaaggttaattttagccgagaaaaccacagattttttaaagttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaat............ 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:90 Query End:182 Subject Strand: POSITIVE Subject Start: 90 Subject End: 182 .........................................................................................agttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat .........................................................................................agttatccacagtttgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaacatatggaggcaaat HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:1 Query End:53 Subject Strand: POSITIVE Subject Start: 1 Subject End: 53 gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. 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:90 Query End:182 Subject Strand: POSITIVE Subject Start: 90 Subject End: 182 .........................................................................................agttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaaaatatggaggcaaat .........................................................................................agttatccacagtttgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaacatatggaggcaaat HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:1 Query End:53 Subject Strand: POSITIVE Subject Start: 1 Subject End: 53 gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. 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:90 Query End:167 Subject Strand: POSITIVE Subject Start: 90 Subject End: 167 .........................................................................................agttatccacaatctgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaa............... .........................................................................................agttatccacagtttgtgtaaaacttttgtgtttaagttataattaagctagtcagtttatactttcagtaattcaaa............... HSP 2 e-value: 5.0E-22 bit: 105.0 Len: 53 Query Start:1 Query End:53 Subject Strand: POSITIVE Subject Start: 1 Subject End: 53 gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. gactctattctaacatattctctattttttcacatcttattcacaaaataaaa................................................................................................................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACUCUAUUCUAACAUAUUCUCUAUUUUUUCACAUCUUAUUCACAAAAUAAAAGGUUAAUUUUAGCCGAGAAAACCACAGAUUUUUUAAAGUUAUCCACAAUCUGUGUAAAACUUUUGUGUUUAAGUUAUAAUUAAGCUAGUCAGUUUAUACUUUCAGUAAUUCAAAAAUAUGGAGGCAAAU ..................(((((((.((((.....((((..(((((((.....(((((....)))))........((((((((................))))))))......)))))))..)))).......((((((....))))))................)))).)))))))..... (-30.19) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUUGCCUCCAUAUUUUUGAAUUACUGAAAGUAUAAACUGACUAGCUUAAUUAUAACUUAAACACAAAAGUUUUACACAGAUUGUGGAUAACUUUAAAAAAUCUGUGGUUUUCUCGGCUAAAAUUAACCUUUUAUUUUGUGAAUAAGAUGUGAAAAAAUAGAGAAUAUGUUAGAAUAGAGUC ......(((.((((((((........))))))))...(((((...(((..(((((.((((..(((((((......((((((((.((((....))))...))))))))........((.((....)).)).....)))))))..)))).))))).......))).....)))))....))).. (-29.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 776 110 61 201 152 smit:SMT_2095|5end_K00783_hypothetical_protein_1989876..1990106_POSITIVE 776 110 61 201 152 smit:SMT_2004|5end_K00783_hypothetical_protein_1924930..1925160_POSITIVE 776 110 61 201 152 smit:SMT_86|5end_K00783_hypothetical_protein_17514..17744_NEGATIVE 230 44 3 108 74 smit:SMT_1037|5end_alpha-galactosidase_979609..979839_NEGATIVE 230 44 3 108 74 smit:SMT_1030|5end_alpha-galactosidase_967829..968059_NEGATIVE 225 86 48 169 130 smit:SMT_1517|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1498313..1498543_POSITIVE 225 180 136 126 80 smit:SMT_988|5end_N-acetylneuraminate_lyase_932889..933119_NEGATIVE 225 55 12 165 119 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 224 94 52 157 112 smit:SMT_1092|5end_transcription_antitermination_factor_1033696..1033926_NEGATIVE 210 39 7 117 82 smit:SMT_1528|5end_K03310_alanine_or_glycine:cation_symporter,_AGCS_family_1512667..1512897_NEGATIVE 206 177 136 81 38 smit:SMT_825|5end_aspartate_aminotransferase_749594..749824_NEGATIVE 204 116 75 155 105 smit:SMT_1607|5end_K03341_putative_deoxyribonucleotide_triphosphate_pyrophosphatase_1596648..1596878_POSITIVE 203 106 75 230 194 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 202 106 64 141 108 smit:SMT_1738|5end_peptidyl-prolyl_cis-trans_isomerase_1720497..1720727_POSITIVE 202 178 131 171 125 smit:SMT_893|5end_leucine_rich_protein_841311..841541_NEGATIVE 197 55 14 225 181 smit:SMT_1784|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1760755..1760985_POSITIVE 195 45 1 111 59 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 194 147 113 63 29 smit:SMT_1641|5end_arginyl-tRNA_synthetase_1628253..1628483_NEGATIVE 192 97 64 137 110 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 192 97 64 137 110 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 180 136 66 20 smit:SMT_989|3end_hypothetical_protein_932949..933099_NEGATIVE 224 94 52 103 58 smit:SMT_1093|3end_K03073_preprotein_translocase_SecE_subunit_1033750..1033900_NEGATIVE 216 145 102 42 3 smit:SMT_1921|3end_D-alanine-activating_enzyme_1864101..1864251_POSITIVE 216 93 59 98 60 smit:SMT_674|3end_K07010_putative_glutamine_amidotransferase_582330..582480_POSITIVE 206 177 136 84 41 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 203 106 75 144 108 smit:SMT_1493|3end_DNA-directed_RNA_polymerase,_beta'_subunit/160_kD_subunit_1479494..1479644_POSITIVE 201 159 113 127 87 smit:SMT_739|3end_50S_ribosomal_protein_L7/L12_643274..643424_NEGATIVE 195 107 64 118 77 smit:SMT_154|3end_K03647_protein_involved_in_ribonucleotide_reduction_102474..102624_POSITIVE 193 43 3 97 41 smit:SMT_1181|3end_phosphotransferase_system,_mannose/fructose-specific_component_IIA_1139413..1139563_NEGATIVE 188 176 136 68 21 smit:SMT_1778|3end_ATP-dependent_RNA_helicase_1753611..1753761_NEGATIVE 187 111 80 120 84 smit:SMT_809|3end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_718420..718570_NEGATIVE 184 37 1 106 62 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 184 110 81 129 100 smit:SMT_1166|3end_DNA-binding_response_regulator_CiaR_1111810..1111960_NEGATIVE 184 110 81 129 100 smit:SMT_538|3end_DNA-binding_response_regulator_CiaR_455842..455992_POSITIVE 183 47 3 150 109 smit:SMT_1442|3end_hypothetical_protein_1425762..1425912_NEGATIVE 178 42 18 129 104 smit:SMT_1994|3end_phosphoglycerate_mutase_1920058..1920208_NEGATIVE 178 42 18 129 104 smit:SMT_201|3end_phosphoglycerate_mutase_132101..132251_POSITIVE 177 160 114 124 81 smit:SMT_1949|3end_IS1381_transposase_protein_B_1883987..1884137_POSITIVE 175 84 60 37 8 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 174 78 51 150 129 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE