Origin IGS: tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtttgactctccttttgttctttcttttttgagttatatgtgataacccttacaatttggtattatatcatcttctaggatttttttcaagcattttatgggatttattcgatttcctttcagataacttgctgaaaatcttctattctagataacaaaacacaggatatagttttccaaaaaactacttctaggataattatcactatttcataaaacaaacactacatattgtgttttgcaacctttagtagaaaaatagaccactatatttagtttcaaatcattgacaaaaatttattttctgatatactaagaaagtaatctattttgaaagaggagttacaca Mask Tandem Repeat Region ================================================ tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Find is-nt database================================================ Query_seq: SMT_1384:SMT_1385|SMT_1384:SMT_1385:glutaredoxin:phosphocarrier protein HPr:<-->:1362318..1362667 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1384:SMT_1385|SMT_1384:SMT_1385:glutaredoxin:phosphocarrier protein HPr:<-->:1362318..1362667 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1384:SMT_1385|SMT_1384:SMT_1385:glutaredoxin:phosphocarrier protein HPr:<-->:1362318..1362667 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: + Start: 129 End: 227 ................................................................................................................................ M F Y E I V I I I L E V V F W K T I S C V L L S R I E D F Q Q V I ........................................................................................................................... Protein_Len: 39 Strand: - Start: 198 End: 314 ..................................................................................................................................................................................................... R S Y F I K L L N D S L F D F L D W L I S S F F G L L H Y L V L N Y P N D C M .................................... tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact 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: 90 Start: 259 End: 288 ..................................................................................................................................................................................................................................................................CTTGAAAAAAATCCTAGAAGATGATATAAT.............................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1384:SMT_1385|SMT_1384:SMT_1385:glutaredoxin:phosphocarrier protein HPr:<-->:1362318..1362667 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Intra-Species Hit: Count: 1 Min: 1 Max: 350 Len: 350 Subject: smit_SMT_1384_SMT_1385|glutaredoxin:phosphocarrier protein HPr|NEGATIVE:POSITIVE|[1362318,1362667]|350 HSP 1 e-value: 0.0 bit: 652.0 Len: 350 Query Start:1 Query End:350 Subject Strand: POSITIVE Subject Start: 1 Subject End: 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgnnnnnnntcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggtctatttttctactaaaggttgcaaaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaataaatcccataaaatgcttgaaaaaaatcctagaagatgatataataccaaattgtaagggttatcacatataactcaaaaaagaaagaacaaaaggagagtcaaact Inter-species Hit: Count: 3 Min: 1 Max: 350 Len: 350 Subject: NC_008533_SPD_1040_SPD_1041|phosphocarrier protein HPr:glutaredoxin-like protein NrdH|NEGATIVE:POSITIVE|[1069169,1069518]|350 HSP 1 e-value: 3.0E-62 bit: 240.0 Len: 240 Query Start:111 Query End:350 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 242 ..............................................................................................................aaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaa-taaatcccataaaatgcttgnnnnnnntcctagaagatgatataataccaaattgtaagggttatcacatataactc-aaaaaagaaagaacaaaaggagagtcaaact ..............................................................................................................aaacacaatatatagtgtttgtattgtgaaatagcaatgattatcctataaattgtttttaaagaaactatatcctgtgttttgttatctaggatagaagattttcagcaagttatctgaaaggaaattgaaggaaaatccagaaaatgcttgaaaaaaatcctagaagatggtataatactaaattgtaagggttatcacatataactcaaaaaaagaaagaacaaaaggagagtcaaact HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 87 Query Start:1 Query End:87 Subject Strand: NEGATIVE Subject Start: 266 Subject End: 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggt....................................................................................................................................................................................................................................................................... tgtgtaactcctctt-caaaatttaatactatcttagtatatcagaaaataaaattttgtcaatgatttg-aactaaatatagtggt....................................................................................................................................................................................................................................................................... Subject: NC_003098_spr1063_spr1064|Histidine-containing phosphocarrier protein of the PTS:Glutaredoxin-like protein involved in electron transport system for ribonucleotide reductase system NrdEF|NEGATIVE:POSITIVE|[1061638,1061969]|332 HSP 1 e-value: 3.0E-62 bit: 240.0 Len: 240 Query Start:111 Query End:350 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 242 ..............................................................................................................aaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaa-taaatcccataaaatgcttgnnnnnnntcctagaagatgatataataccaaattgtaagggttatcacatataactc-aaaaaagaaagaacaaaaggagagtcaaact ..............................................................................................................aaacacaatatatagtgtttgtattgtgaaatagcaatgattatcctataaattgtttttaaagaaactatatcctgtgttttgttatctaggatagaagattttcagcaagttatctgaaaggaaattgaaggaaaatccagaaaatgcttgaaaaaaatcctagaagatggtataatactaaattgtaagggttatcacatataactcaaaaaaagaaagaacaaaaggagagtcaaact HSP 2 e-value: 6.0E-17 bit: 89.7 Len: 61 Query Start:27 Query End:87 Subject Strand: NEGATIVE Subject Start: 266 Subject End: 325 ..........................tactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggt....................................................................................................................................................................................................................................................................... ..........................tactatcttagtatatcagaaaataaaattttgtcaatgatttg-aactaaatatagtggt....................................................................................................................................................................................................................................................................... Subject: NC_003028_SP_1177_SP_1178|phosphocarrier protein HPr:NrdH-redoxin|NEGATIVE:POSITIVE|[1115581,1115930]|350 HSP 1 e-value: 3.0E-62 bit: 240.0 Len: 240 Query Start:111 Query End:350 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 242 ..............................................................................................................aaacacaatatgtagtgtttgttttatgaaatagtgataattatcctagaagtagttttttggaaaactatatcctgtgttttgttatctagaatagaagattttcagcaagttatctgaaaggaaatcgaa-taaatcccataaaatgcttgnnnnnnntcctagaagatgatataataccaaattgtaagggttatcacatataactc-aaaaaagaaagaacaaaaggagagtcaaact ..............................................................................................................aaacacaatatatagtgtttgtattgtgaaatagcaatgattatcctataaattgtttttaaagaaactatatcctgtgttttgttatctaggatagaagattttcagcaagttatctgaaaggaaattgaaggaaaatccagaaaatgcttgaaaaaaatcctagaagatggtataatactaaattgtaagggttatcacatataactcaaaaaaagaaagaacaaaaggagagtcaaact HSP 2 e-value: 2.0E-20 bit: 101.0 Len: 87 Query Start:1 Query End:87 Subject Strand: NEGATIVE Subject Start: 266 Subject End: 350 tgtgtaactcctctttcaaaatagattactttcttagtatatcagaaaataaatttttgtcaatgatttgaaactaaatatagtggt....................................................................................................................................................................................................................................................................... tgtgtaactcctctt-caaaatttaatactatcttagtatatcagaaaataaaattttgtcaatgatttg-aactaaatatagtggt....................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUGUAACUCCUCUUUCAAAAUAGAUUACUUUCUUAGUAUAUCAGAAAAUAAAUUUUUGUCAAUGAUUUGAAACUAAAUAUAGUGGUCUAUUUUUCUACUAAAGGUUGCAAAACACAAUAUGUAGUGUUUGUUUUAUGAAAUAGUGAUAAUUAUCCUAGAAGUAGUUUUUUGGAAAACUAUAUCCUGUGUUUUGUUAUCUAGAAUAGAAGAUUUUCAGCAAGUUAUCUGAAAGGAAAUCGAAUAAAUCCCAUAAAAUGCUUGAAAAAAAUCCUAGAAGAUGAUAUAAUACCAAAUUGUAAGGGUUAUCACAUAUAACUCAAAAAAGAAAGAACAAAAGGAGAGUCAAACU .......((((((((((.((((((((((((...(((((....((((((.....))))))((((....)))).)))))....))))))))))))..........(((((..((((((........)))))).............((((((...(((((.((.((((((((....)))))))).))..(((((.((((((((....(((..((((((...(((((.........(((...........)))........)))))...)))))))))..)))))))).))))).........)))))))))))...))))).......))))))......))))......... (-70.53) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUGACUCUCCUUUUGUUCUUUCUUUUUUGAGUUAUAUGUGAUAACCCUUACAAUUUGGUAUUAUAUCAUCUUCUAGGAUUUUUUUCAAGCAUUUUAUGGGAUUUAUUCGAUUUCCUUUCAGAUAACUUGCUGAAAAUCUUCUAUUCUAGAUAACAAAACACAGGAUAUAGUUUUCCAAAAAACUACUUCUAGGAUAAUUAUCACUAUUUCAUAAAACAAACACUACAUAUUGUGUUUUGCAACCUUUAGUAGAAAAAUAGACCACUAUAUUUAGUUUCAAAUCAUUGACAAAAAUUUAUUUUCUGAUAUACUAAGAAAGUAAUCUAUUUUGAAAGAGGAGUUACACA .((.((((((..(((((...........((((((..(((((((.............(((((.((((((((....((((((((..((((((.(((..((((((((...........)))).....))))..)))))))))......)))))))).............))))))))...)))))...(((((...(((....((((.........))))...((((((........)))))).....)))..)))))..........))).)))).....))))))..............(((((((((.........)))))))))........)))))..)))))).)). (-65.53) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 759 130 81 221 172 smit:SMT_1384|5end_glutaredoxin_1362227..1362457_NEGATIVE 279 229 184 75 19 smit:SMT_1221|5end_choline_binding_protein_A_1185539..1185769_NEGATIVE 247 34 7 124 95 smit:SMT_1474|5end_K02003_1455170..1455400_POSITIVE 246 98 54 106 62 smit:SMT_1389|5end_dihydroxyacetone_kinase_1366890..1367120_NEGATIVE 245 220 178 68 22 smit:SMT_222|5end_beta-glucosidase_154971..155201_POSITIVE 239 230 185 230 179 smit:SMT_1677|5end_transcription-repair_coupling_factor_1662112..1662342_NEGATIVE 235 147 101 185 130 smit:SMT_506|5end_K07729_putative_transcriptional_regulator_437635..437865_NEGATIVE 235 147 101 185 130 smit:SMT_503|5end_K07729_putative_transcriptional_regulator_436204..436434_NEGATIVE 229 49 1 140 94 smit:SMT_1277|5end_PcsB_protein_1240000..1240230_POSITIVE 225 249 204 60 15 smit:SMT_161|5end_putative_folyl-polyglutamate_synthetase_105358..105588_POSITIVE 223 196 151 185 132 smit:SMT_1383|5end_ribonucleoside-diphosphate_reductase_alpha_chain_1361928..1362158_NEGATIVE 222 220 176 154 106 smit:SMT_1564|5end_transcriptional_antiterminator,_BglG_family_1555587..1555817_POSITIVE 221 209 166 186 148 smit:SMT_1362|5end_chaperone_protein_hscC_1343078..1343308_NEGATIVE 221 249 215 119 76 smit:SMT_423|5end_sensory_transduction_protein_kinase_366012..366242_POSITIVE 221 46 6 137 97 smit:SMT_414|5end_K03665_GTP-binding_protein_HflX_357554..357784_POSITIVE 216 229 196 48 10 smit:SMT_842|5end_hypothetical_protein_789262..789492_NEGATIVE 209 250 212 177 129 smit:SMT_1164|5end_hypothetical_protein_1110115..1110345_POSITIVE 208 88 44 48 5 smit:SMT_851|5end_conserved_hypothetical_protein,_translation_initiation_inhibitor_protein_797446..797676_NEGATIVE 204 194 151 53 12 smit:SMT_1584|5end_methyltransferase,_putative_1574713..1574943_POSITIVE 203 211 172 227 188 smit:SMT_1300|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1262844..1263074_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 70 23 70 17 smit:SMT_1932|3end_K02008_cobalt_transport_system_permease_protein_1871171..1871321_NEGATIVE 246 98 54 109 65 smit:SMT_1390|3end_hypothetical_protein_1366887..1367037_NEGATIVE 238 240 191 145 90 smit:SMT_221|3end_prolyl-tRNA_synthetase_154952..155102_POSITIVE 223 196 151 104 51 smit:SMT_1384|3end_glutaredoxin_1362009..1362159_NEGATIVE 221 46 6 144 104 smit:SMT_413|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_357641..357791_POSITIVE 216 229 196 46 8 smit:SMT_843|3end_hypothetical_protein_789264..789414_NEGATIVE 206 208 164 143 96 smit:SMT_694|3end_putative_ATP-binding_component_of_a_transport_system_605968..606118_POSITIVE 202 250 204 147 102 smit:SMT_1836|3end_cytidine/deoxycytidylate_deaminase_family_protein_1804100..1804250_NEGATIVE 202 196 155 46 7 smit:SMT_1804|3end_hypothetical_protein_1780314..1780464_POSITIVE 202 230 182 147 98 smit:SMT_1339|3end_hypothetical_protein_1313751..1313901_NEGATIVE 200 49 7 46 9 smit:SMT_1276|3end_rod_shape-determining_protein_MreD_1239986..1240136_POSITIVE 198 319 279 79 45 smit:SMT_422|3end_K02004_365876..366026_POSITIVE 195 45 7 84 36 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 194 246 206 49 12 smit:SMT_1540|3end_hypothetical_protein_1524307..1524457_NEGATIVE 194 150 103 74 9 smit:SMT_987|3end_N-acetylmannosamine_kinase_/_transcriptional_regulator_931655..931805_NEGATIVE 193 262 226 67 25 smit:SMT_606|3end_cytochrome_c-type_biogenesis_protein_CcdA_520147..520297_POSITIVE 192 238 194 57 9 smit:SMT_1299|3end_MutT/NUDIX_family_protein_1262572..1262722_POSITIVE 192 47 5 147 106 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 191 69 21 100 52 smit:SMT_125|3end_hypothetical_protein_76717..76867_NEGATIVE 190 230 183 70 26 smit:SMT_832|3end_hypothetical_protein_774376..774526_NEGATIVE