Origin IGS: aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tacaaacccacctctctctttaaaccttgactatctttgactattataccgaaattttctcatttttaaaagaaaaagggcgctggtaaaggataatcttcaccaactccctattttt Mask Tandem Repeat Region ================================================ aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Find is-nt database================================================ Query_seq: SMT_1294:SMT_1295|SMT_1294:SMT_1295:K02049 sulfonate/nitrate/taurine transport system ATP-binding protein:transcriptional regulator CtsR:->->:1256852..1256969 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1294:SMT_1295|SMT_1294:SMT_1295:K02049 sulfonate/nitrate/taurine transport system ATP-binding protein:transcriptional regulator CtsR:->->:1256852..1256969 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1294:SMT_1295|SMT_1294:SMT_1295:K02049 sulfonate/nitrate/taurine transport system ATP-binding protein:transcriptional regulator CtsR:->->:1256852..1256969 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Predict ORF larger than 30AA ================================================ aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta 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: 85 Start: 47 End: 76 ..............................................CTTTTAAAAATGAGAAAATTTCGGTATAAT.......................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 72 End: 101 .......................................................................CTTTAAACCTTGACTATCTTTGACTATTAT................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1294:SMT_1295|SMT_1294:SMT_1295:K02049 sulfonate/nitrate/taurine transport system ATP-binding protein:transcriptional regulator CtsR:->->:1256852..1256969 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Intra-Species Hit: Count: 1 Min: 1 Max: 118 Len: 118 Subject: smit_SMT_1294_SMT_1295|K02049 sulfonate/nitrate/taurine transport system ATP-binding protein:transcriptional regulator CtsR|POSITIVE:POSITIVE|[1256852,1256969]|118 HSP 1 e-value: 5.0E-61 bit: 234.0 Len: 118 Query Start:1 Query End:118 Subject Strand: POSITIVE Subject Start: 1 Subject End: 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgta Inter-species Hit: Count: 2 Min: 1 Max: 117 Len: 117 Subject: NC_008533_SPD_2023_SPD_2024|transcriptional regulator CtsR:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[2003354,2003471]|118 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 117 Query Start:1 Query End:117 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgt. aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaacaaggtcaaggtttaaagagagaggtgggtttgt. Subject: NC_003028_SP_2195_SP_2196|transcriptional regulator CtsR:ABC transporter, ATP-binding protein|NEGATIVE:NEGATIVE|[2118301,2118418]|118 HSP 1 e-value: 3.0E-53 bit: 208.0 Len: 117 Query Start:1 Query End:117 Subject Strand: NEGATIVE Subject Start: 2 Subject End: 118 aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaagatagtcaaggtttaaagagagaggtgggtttgt. aaaaatagggagttggtgaagattatcctttaccagcgccctttttcttttaaaaatgagaaaatttcggtataatagtcaaacaaggtcaaggtttaaagagagaggtgggtttgt. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAUAGGGAGUUGGUGAAGAUUAUCCUUUACCAGCGCCCUUUUUCUUUUAAAAAUGAGAAAAUUUCGGUAUAAUAGUCAAAGAUAGUCAAGGUUUAAAGAGAGAGGUGGGUUUGU ......((((.((((((((((......)))))))))).))))(((((((((.(((....((..((((..(.........)..))))..))....))).))))))))).......... (-27.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAACCCACCUCUCUCUUUAAACCUUGACUAUCUUUGACUAUUAUACCGAAAUUUUCUCAUUUUUAAAAGAAAAAGGGCGCUGGUAAAGGAUAAUCUUCACCAACUCCCUAUUUUU .............(((.((((((...(((..(..((((..........))))..)...)))..)))))))))...((((.(.((((.(((......))).)))).).))))...... (-15.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 279 40 7 138 103 smit:SMT_1444|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1427979..1428209_NEGATIVE 279 40 7 190 155 smit:SMT_1443|5end_23S_rRNA_m(5)U_1939_methyltransferase_1427927..1428157_NEGATIVE 273 37 9 49 27 smit:SMT_866|5end_50S_ribosomal_protein_L11_816234..816464_NEGATIVE 262 45 1 147 113 smit:SMT_1279|5end_translation_elongation_factor_Ts_1242331..1242561_POSITIVE 262 41 7 196 147 smit:SMT_659|5end_hypothetical_protein_570545..570775_NEGATIVE 256 49 3 60 12 smit:SMT_855|5end_dihydrofolate_reductase_799998..800228_NEGATIVE 255 40 5 164 121 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 254 45 1 153 107 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 253 55 11 65 10 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 253 38 2 158 126 smit:SMT_687|5end_carbamoyl-phosphate_synthase,_large_subunit_599264..599494_NEGATIVE 250 50 12 201 159 smit:SMT_295|5end_hypothetical_protein_predicted_by_Glimmer/Critica_237992..238222_POSITIVE 249 69 23 130 88 smit:SMT_478|5end_hypothetical_protein_predicted_by_Glimmer/Critica_414644..414874_POSITIVE 248 49 4 179 120 smit:SMT_680|5end_choline_transport_protein_589962..590192_NEGATIVE 245 50 4 167 112 smit:SMT_2015|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1932655..1932885_POSITIVE 237 109 68 86 52 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 236 59 11 108 54 smit:SMT_1247|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1207409..1207639_POSITIVE 234 47 2 179 127 smit:SMT_1505|5end_purine-nucleoside_phosphorylase_1488515..1488745_NEGATIVE 231 43 8 154 109 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 230 68 25 150 105 smit:SMT_313|5end_3R-hydroxymyristoyl_ACP_dehydrase_253843..254073_POSITIVE 230 50 5 143 90 smit:SMT_115|5end_hypothetical_protein_65521..65751_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 374 48 7 92 49 smit:SMT_1294|3end_K02049_sulfonate/nitrate/taurine_transport_system_ATP-binding_protein_1256791..1256941_POSITIVE 295 39 4 101 66 smit:SMT_2119|3end_mercuric_reductase_2006145..2006295_POSITIVE 295 39 4 101 66 smit:SMT_1236|3end_mercuric_reductase_1197698..1197848_POSITIVE 275 40 1 68 22 smit:SMT_872|3end_hypothetical_protein_820331..820481_NEGATIVE 275 40 1 68 22 smit:SMT_385|3end_hypothetical_protein_320262..320412_POSITIVE 262 45 1 68 34 smit:SMT_1278|3end_30S_ribosomal_protein_S2_1242332..1242482_POSITIVE 254 45 1 82 36 smit:SMT_1306|3end_alpha-glycerophosphate_oxidase_1271673..1271823_POSITIVE 250 50 12 147 105 smit:SMT_294|3end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_238018..238168_POSITIVE 244 69 26 57 19 smit:SMT_1328|3end_hypothetical_protein_1304310..1304460_NEGATIVE 240 48 1 115 49 smit:SMT_903|3end_hypothetical_protein_851945..852095_NEGATIVE 238 48 7 47 7 smit:SMT_83|3end_K07707_two-component_system,_AgrA_family,_response_regulator_AgrA_14543..14693_NEGATIVE 236 60 14 145 99 smit:SMT_457|3end_hypothetical_protein_396593..396743_POSITIVE 234 50 11 138 100 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 233 50 12 141 100 smit:SMT_258|3end_alpha-glucosidase,_family_31_of_glycosyl_hydrolase_197342..197492_POSITIVE 230 50 5 71 18 smit:SMT_114|3end_alpha-mannosidase_65529..65679_POSITIVE 229 40 7 148 116 smit:SMT_574|3end_PTS_system,_fructose_specific_IIABC_components_493847..493997_POSITIVE 225 38 5 39 1 smit:SMT_1193|3end_phosphoribosylglycinamide_formyltransferase_1151607..1151757_NEGATIVE 219 39 5 59 30 smit:SMT_1753|3end_tryptophan_synthase_beta_chain_1731652..1731802_POSITIVE 219 43 7 64 32 smit:SMT_1108|3end_acetate_kinase_1048122..1048272_NEGATIVE 217 47 7 88 56 smit:SMT_1065|3end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1005452..1005602_POSITIVE