Origin IGS: gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc .........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 gatggaacatcgaaagtttttgcttgattttaagcatgctttgtgctatagtatttgataactaaatattcctttaaacctgtcccgtgaggcaggcaaggagaacgattaagtagtagggtgaagtctatactgtttgcagtagggctcgcttggctatacatttcaagtctccttgtttaaggagacttttctttttggaggtttgtc Mask Tandem Repeat Region ================================================ gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Find is-nt database================================================ Query_seq: SMT_690:SMT_691|SMT_690:SMT_691:pyrimidine regulatory protein:endonuclease III:<-<-:602259..602468 210 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_690:SMT_691|SMT_690:SMT_691:pyrimidine regulatory protein:endonuclease III:<-<-:602259..602468 210 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_690:SMT_691|SMT_690:SMT_691:pyrimidine regulatory protein:endonuclease III:<-<-:602259..602468 210 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 47 End: 178 .............................................. M Y S Q A S P T A N S I D F T L L L N R S P C L P H G T G L K E Y L V I K Y Y S T K H A ................................ gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc 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: 159 End: 188 ..............................................................................................................................................................CTTGATTTTAAGCATGCTTTGTGCTATAGT...................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.8 Tail_Score: -5.26119 Start: 22 End: 41 Full_Region: ggctatacatttcaa gtctcctt gttt aaggagac ttttctttttggagg .....................gtctccttgtttaaggagac......................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_690:SMT_691|SMT_690:SMT_691:pyrimidine regulatory protein:endonuclease III:<-<-:602259..602468 210 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Intra-Species Hit: Count: 1 Min: 1 Max: 210 Len: 210 Subject: smit_SMT_690_SMT_691|pyrimidine regulatory protein:endonuclease III|NEGATIVE:NEGATIVE|[602259,602468]|210 HSP 1 e-value: 1.0E-115 bit: 416.0 Len: 210 Query Start:1 Query End:210 Subject Strand: POSITIVE Subject Start: 1 Subject End: 210 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgttccatc Inter-species Hit: Count: 3 Min: 1 Max: 204 Len: 204 Subject: NC_008533_SPD_1134_SPD_1135|pyrimidine operon regulatory protein/uracil phosphoribosyltransferase:endonuclease III|NEGATIVE:NEGATIVE|[1168362,1168571]|210 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgt...... gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatttatagccaagcgagccctactgcacacagtatagacttcacccttctactttatcgcgctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcatttactatagcacaaagcatgcttaaaatcaagcaaaaagtttcaatgt...... Subject: NC_003098_spr1156_spr1157|pyrimidine regulatory protein PyrR:endonuclease III (DNA repair)|NEGATIVE:NEGATIVE|[1160831,1161040]|210 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgt...... gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatttatagccaagcgagccctactgcacacagtatagacttcacccttctactttatcgcgctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcatttactatagcacaaagcatgcttaaaatcaagcaaaaagtttcaatgt...... Subject: NC_003028_SP_1278_SP_1279|pyrimidine regulatory protein PyrR:endonuclease III|NEGATIVE:NEGATIVE|[1214221,1214430]|210 HSP 1 e-value: 3.0E-88 bit: 325.0 Len: 204 Query Start:1 Query End:204 Subject Strand: POSITIVE Subject Start: 1 Subject End: 204 gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatgtatagccaagcgagccctactgcaaacagtatagacttcaccctactacttaatcgttctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcaaatactatagcacaaagcatgcttaaaatcaagcaaaaactttcgatgt...... gacaaacctccaaaaagaaaagtctccttaaacaaggagacttgaaatttatagccaagcgagccctactgcacacagtatagacttcacccttctactttatcgcgctccttgcctgcctcacgggacaggtttaaaggaatatttagttatcatttactatagcacaaagcatgcttaaaatcaagcaaaaagtttcaatgt...... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACAAACCUCCAAAAAGAAAAGUCUCCUUAAACAAGGAGACUUGAAAUGUAUAGCCAAGCGAGCCCUACUGCAAACAGUAUAGACUUCACCCUACUACUUAAUCGUUCUCCUUGCCUGCCUCACGGGACAGGUUUAAAGGAAUAUUUAGUUAUCAAAUACUAUAGCACAAAGCAUGCUUAAAAUCAAGCAAAAACUUUCGAUGU .(((...............((((((((((....))))))))))((((.((...((..(((((....(((((....)))))(((........)))........))))).((((((((((((.....)).)))))...))))).......(((((........))))).....)).(((((......)))))...))))))..))) (-42.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAUCGAAAGUUUUUGCUUGAUUUUAAGCAUGCUUUGUGCUAUAGUAUUUGAUAACUAAAUAUUCCUUUAAACCUGUCCCGUGAGGCAGGCAAGGAGAACGAUUAAGUAGUAGGGUGAAGUCUAUACUGUUUGCAGUAGGGCUCGCUUGGCUAUACAUUUCAAGUCUCCUUGUUUAAGGAGACUUUUCUUUUUGGAGGUUUGUC ......(((((...((((((....)))))).))))).......((((((((.....))))))))....(((((((...((....))....(((((((((.......(((((..(((((.((((.(((((....))))))))))))))..))))).......((((((((((....))))))))))))))))))).))))))).. (-61.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 997 130 81 221 172 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 369 134 91 51 5 smit:SMT_895|5end_cysteinyl-tRNA_synthetase_843037..843267_NEGATIVE 369 134 91 51 5 smit:SMT_383|5end_cysteinyl-tRNA_synthetase_318689..318919_POSITIVE 363 129 81 231 187 smit:SMT_434|5end_orotidine_5'-phosphate_decarboxylase_376107..376337_POSITIVE 310 94 51 98 57 smit:SMT_1113|5end_hypothetical_protein_1052071..1052301_NEGATIVE 285 130 83 59 11 smit:SMT_1074|5end_catabolite_control_protein_A_1013285..1013515_NEGATIVE 283 129 84 146 99 smit:SMT_370|5end_acetyltransferase,_GNAT_family_304688..304918_POSITIVE 282 128 88 60 19 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 276 130 87 126 93 smit:SMT_962|5end_putative_hemin_transport_system_ATP-binding_protein_fecE_908584..908814_NEGATIVE 275 50 5 204 166 smit:SMT_1339|5end_hypothetical_protein_1314746..1314976_NEGATIVE 274 65 23 222 188 smit:SMT_1608|5end_hypothetical_protein_1597595..1597825_POSITIVE 271 96 51 225 181 smit:SMT_1605|5end_hypothetical_protein_1595406..1595636_POSITIVE 269 78 32 69 29 smit:SMT_1862|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1824094..1824324_POSITIVE 269 78 32 69 29 smit:SMT_1763|5end_K02027_multiple_sugar_transport_system_substrate-binding_protein_1738537..1738767_POSITIVE 269 141 103 166 133 smit:SMT_851|5end_conserved_hypothetical_protein,_translation_initiation_inhibitor_protein_797446..797676_NEGATIVE 269 135 104 113 81 smit:SMT_546|5end_DNA_topoisomerase_IV_subunit_A_461377..461607_POSITIVE 267 89 51 183 134 smit:SMT_1085|5end_sensor_histidine_kinase_(homolog_to_HK11_Spn)_1022267..1022497_NEGATIVE 264 60 15 222 170 smit:SMT_1953|5end_hypothetical_protein_1886897..1887127_POSITIVE 262 126 81 57 7 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 262 128 85 68 22 smit:SMT_361|5end_hypothetical_protein_295914..296144_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 94 51 93 52 smit:SMT_1114|3end_competence_protein_1052076..1052226_NEGATIVE 276 130 87 124 91 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 269 135 104 80 48 smit:SMT_545|3end_hypothetical_protein_predicted_by_Glimmer/Critica_461424..461574_POSITIVE 269 79 44 136 106 smit:SMT_242|3end_PTS_system,_mannose-specific_IID_component_179163..179313_NEGATIVE 263 140 95 84 29 smit:SMT_625|3end_50S_ribosomal_protein_L27_530400..530550_POSITIVE 262 128 85 75 29 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE 261 151 111 149 102 smit:SMT_1339|3end_hypothetical_protein_1313751..1313901_NEGATIVE 261 70 21 130 93 smit:SMT_463|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_402839..402989_POSITIVE 261 70 21 130 93 smit:SMT_407|3end_para-aminobenzoate_synthetase_component_I_/_4-amino-4-deoxychorismate_lyase_353166..353316_POSITIVE 259 69 22 62 18 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 254 130 82 122 56 smit:SMT_1377|3end_hypothetical_protein_1355556..1355706_NEGATIVE 250 133 98 148 114 smit:SMT_852|3end_K03978_GTP-binding_protein_797457..797607_NEGATIVE 249 123 84 139 95 smit:SMT_572|3end_fructose_repressor_491059..491209_POSITIVE 248 47 7 70 21 smit:SMT_459|3end_hypothetical_protein_397690..397840_POSITIVE 248 65 23 127 99 smit:SMT_365|3end_hypothetical_protein_301747..301897_POSITIVE 247 133 107 37 1 smit:SMT_1444|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1427887..1428037_NEGATIVE 247 77 36 54 21 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 245 64 22 147 101 smit:SMT_1011|3end_xanthine_phosphoribosyltransferase_949234..949384_POSITIVE 244 79 35 95 50 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 241 136 91 65 11 smit:SMT_1182|3end_K02796_PTS_system,_mannose-specific_IID_component_1139821..1139971_NEGATIVE