Origin IGS: tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cttcattctccctactttctaatgcaagccttttctttttattatatcacagataagtatttctttcacaattgaattgaacttcctatctattttctataaatcctaaaggctgtaatactttcaatccttgtcattttgtgatatcatgtagaggtaatgaaaggagagaaa Mask Tandem Repeat Region ================================================ tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Find is-nt database================================================ Query_seq: SMT_565:SMT_566|SMT_565:SMT_566:polypeptide deformylase:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):<-->:483464..483637 174 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_565:SMT_566|SMT_565:SMT_566:polypeptide deformylase:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):<-->:483464..483637 174 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_565:SMT_566|SMT_565:SMT_566:polypeptide deformylase:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):<-->:483464..483637 174 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Predict ORF larger than 30AA ================================================ tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag 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: 84 Start: 105 End: 134 ........................................................................................................TGTGAAAGAAATACTTATCTGTGATATAAT........................................ PromScan Matrix: RpoD-17 Strand: - Score: 82 Start: 25 End: 54 ........................CTTTCAATCCTTGTCATTTTGTGATATCAT........................................................................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_565:SMT_566|SMT_565:SMT_566:polypeptide deformylase:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein):<-->:483464..483637 174 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Intra-Species Hit: Count: 1 Min: 1 Max: 174 Len: 174 Subject: smit_SMT_565_SMT_566|polypeptide deformylase:K07282 poly-gamma-glutamate synthesis protein (capsule biosynthesis protein)|NEGATIVE:POSITIVE|[483464,483637]|174 HSP 1 e-value: 3.0E-94 bit: 345.0 Len: 174 Query Start:1 Query End:174 Subject Strand: POSITIVE Subject Start: 1 Subject End: 174 tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag tttctctcctttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag Inter-species Hit: Count: 2 Min: 11 Max: 174 Len: 164 Subject: NC_008533_SPD_1284_SPD_1285|hypothetical protein:peptide deformylase|POSITIVE:POSITIVE|[1307971,1308293]|323 HSP 1 e-value: 8.0E-67 bit: 254.0 Len: 164 Query Start:11 Query End:174 Subject Strand: NEGATIVE Subject Start: 77 Subject End: 240 ..........ttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag ..........ttcatttcctctacatgatatcacaaaatgacaagaattgaaagcattatggcatttaggatttatagaaaatagatgggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcataagaaagtagggagaacgaag Subject: NC_003098_spr1309_spr1310|hypothetical protein:peptide deformylase|POSITIVE:POSITIVE|[1300440,1300762]|323 HSP 1 e-value: 8.0E-67 bit: 254.0 Len: 164 Query Start:11 Query End:174 Subject Strand: NEGATIVE Subject Start: 77 Subject End: 240 ..........ttcattacctctacatgatatcacaaaatgacaaggattgaaagtattacagcctttaggatttatagaaaatagataggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcattagaaagtagggagaatgaag ..........ttcatttcctctacatgatatcacaaaatgacaagaattgaaagcattatggcatttaggatttatagaaaatagatgggaagttcaattcaattgtgaaagaaatacttatctgtgatataataaaaagaaaaggcttgcataagaaagtagggagaacgaag Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUUACCUCUACAUGAUAUCACAAAAUGACAAGGAUUGAAAGUAUUACAGCCUUUAGGAUUUAUAGAAAAUAGAUAGGAAGUUCAAUUCAAUUGUGAAAGAAAUACUUAUCUGUGAUAUAAUAAAAAGAAAAGGCUUGCAUUAGAAAGUAGGGAGAAUGAAG ((((((..((((((......(((.....)))............(((....(((((((.....(((((....(((((((((...(((..((((....)))).)))...)))))))))..)))))........))))))))))........))))))..)))))). (-34.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUCAUUCUCCCUACUUUCUAAUGCAAGCCUUUUCUUUUUAUUAUAUCACAGAUAAGUAUUUCUUUCACAAUUGAAUUGAACUUCCUAUCUAUUUUCUAUAAAUCCUAAAGGCUGUAAUACUUUCAAUCCUUGUCAUUUUGUGAUAUCAUGUAGAGGUAAUGAA ..(((((..((((((.......((((.((((((....(((((........(((((.(...(((.((((....))))..)))...).))))).......)))))....))))))))))..............((((((...))))))....)))).)).))))). (-30.26) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 60 11 161 112 smit:SMT_565|5end_polypeptide_deformylase_483373..483603_NEGATIVE 243 155 127 230 199 smit:SMT_520|5end_glutathione_reductase_445285..445515_NEGATIVE 218 64 28 42 1 smit:SMT_837|5end_cation_transport_ATPase_782667..782897_NEGATIVE 216 159 114 68 21 smit:SMT_162|5end_hypothetical_protein_106593..106823_POSITIVE 210 160 117 131 87 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 203 42 11 63 31 smit:SMT_981|5end_hypothetical_protein_928709..928939_POSITIVE 202 159 111 151 97 smit:SMT_266|5end_S-adenosyl-methyltransferase_204190..204420_POSITIVE 199 112 72 91 45 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 194 54 11 203 157 smit:SMT_1766|5end_sucrose-6-phosphate_hydrolase_1741702..1741932_POSITIVE 193 120 72 156 109 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 193 87 54 45 13 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 189 159 112 228 180 smit:SMT_1899|5end_hypothetical_protein_1850018..1850248_POSITIVE 188 85 50 184 150 smit:SMT_1233|5end_cadmium_resistance_protein_1194306..1194536_POSITIVE 188 148 108 50 3 smit:SMT_880|5end_beta-lactam_resistance_factor_828300..828530_NEGATIVE 187 64 30 193 161 smit:SMT_1794|5end_SOS_responce_UmuC_protein_1769074..1769304_NEGATIVE 187 64 30 221 189 smit:SMT_1066|5end_holo-(acyl_carrier_protein)_synthase_1005411..1005641_POSITIVE 186 159 129 170 137 smit:SMT_1069|5end_acetyl_xylan_esterase,_putative_1009330..1009560_POSITIVE 186 147 106 156 119 smit:SMT_984|5end_transcriptional_regulator_Spx_930898..931128_NEGATIVE 185 44 14 168 136 smit:SMT_1490|5end_putative_undecaprenyl-phosphate_galactose_phosphotransferase_1470853..1471083_POSITIVE 183 155 134 52 36 smit:SMT_1878|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836577..1836807_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 230 88 51 69 26 smit:SMT_271|3end_autoinducer-2_production_protein_211254..211404_NEGATIVE 216 85 43 90 50 smit:SMT_2038|3end_zinc_metalloprotease_ZmpB,_truncated_1949615..1949765_POSITIVE 212 146 108 94 50 smit:SMT_1094|3end_membrane_carboxypeptidase_(penicillin-binding_protein)_1034141..1034291_NEGATIVE 205 85 42 109 64 smit:SMT_405|3end_zinc_metalloprotease_ZmpB,_truncated_339938..340088_POSITIVE 199 112 72 94 48 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 199 90 51 148 112 smit:SMT_774|3end_hypothetical_protein_684479..684629_NEGATIVE 193 45 5 75 37 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 191 80 34 139 93 smit:SMT_1884|3end_hypothetical_protein_1839238..1839388_POSITIVE 190 120 73 141 92 smit:SMT_1971|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1903526..1903676_POSITIVE 187 64 30 82 50 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE 186 60 13 130 85 smit:SMT_1507|3end_purine_nucleoside_phosphorylase_1490202..1490352_NEGATIVE 183 119 73 73 15 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 183 155 134 62 46 smit:SMT_1879|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836567..1836717_NEGATIVE 182 143 109 55 22 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 181 58 33 66 37 smit:SMT_1283|3end_K02240_competence_protein_ComFA_1247045..1247195_POSITIVE 178 100 68 57 25 smit:SMT_536|3end_oxidoreductase,_aldo/keto_reductase_family_454743..454893_POSITIVE 177 114 77 72 31 smit:SMT_1307|3end_glycerol_uptake_facilitator_protein_1272448..1272598_POSITIVE 177 41 1 65 28 smit:SMT_486|3end_hypothetical_protein_421460..421610_NEGATIVE 177 68 29 66 28 smit:SMT_368|3end_hypothetical_protein_303996..304146_POSITIVE 173 46 2 57 16 smit:SMT_141|3end_K03495_glucose_inhibited_division_protein_A_93401..93551_POSITIVE