Origin IGS: gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa .........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 ttcagttccttctttctttcatccattttaccactttttataggagaaggatagcgggaaggtggatttctaagttagtatcttagttttgctctatcttagaaatgaattgtattctcttgcatttgaagtaaaatctaaaaaattccaagattcactcgaaattttattcccaaacaaaaaaacaatccgatgccaaaatcgttcagatttttcataaaatttgcagaaaatagttgacttctccttcttatttctttaaaatagtacaaaactagaaaaaggaaaaaatc Mask Tandem Repeat Region ================================================ gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Find is-nt database================================================ Query_seq: SMT_1745:SMT_1746|SMT_1745:SMT_1746:UDP-glucose 4-epimerase:glutamyl aminopeptidase:<-->:1725632..1725924 293 gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1745:SMT_1746|SMT_1745:SMT_1746:UDP-glucose 4-epimerase:glutamyl aminopeptidase:<-->:1725632..1725924 293 gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1745:SMT_1746|SMT_1745:SMT_1746:UDP-glucose 4-epimerase:glutamyl aminopeptidase:<-->:1725632..1725924 293 gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 22 End: 153 ..................... M Y Y F K E I R R R S Q L F S A N F M K N L N D F G I G L F F C L G I K F R V N L G I F ............................................................................................................................................ Protein_Len: 46 Strand: + Start: 60 End: 197 ........................................................... M F C K F Y E K S E R F W H R I V F L F G N K I S S E S W N F L D F T S N A R E Y N S F L R ................................................................................................ Protein_Len: 46 Strand: - Start: 77 End: 214 ............................................................................ S F D S R N Q C R I T K K N P F L I E L S D Q F K K S K V E F A L S Y L E N R L Y L L V L M ............................................................................... Protein_Len: 31 Strand: - Start: 57 End: 149 ........................................................ S N E A F K I F F R F S K P M P N N K Q K P I F N R T F R P M ................................................................................................................................................ gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa 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: 89 Start: 29 End: 58 ............................GTTGACTTCTCCTTCTTATTTCTTTAAAAT........................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1745:SMT_1746|SMT_1745:SMT_1746:UDP-glucose 4-epimerase:glutamyl aminopeptidase:<-->:1725632..1725924 293 gattttttcctttttctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 2 Min: 16 Max: 293 Len: 278 Subject: smit_SMT_1745_SMT_1746|UDP-glucose 4-epimerase:glutamyl aminopeptidase|NEGATIVE:POSITIVE|[1725632,1725924]|293 HSP 1 e-value: 1.0E-143 bit: 509.0 Len: 278 Query Start:16 Query End:293 Subject Strand: POSITIVE Subject Start: 16 Subject End: 293 ...............ctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgnnnnnnngtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ...............ctagttttgtactattttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaatctgaacgattttggcatcggattgtttttttgtttgggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Subject: smit_SMT_1862_SMT_1863|K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase|POSITIVE:POSITIVE|[1825521,1825767]|247 HSP 1 e-value: 5.0E-94 bit: 345.0 Len: 174 Query Start:120 Query End:293 Subject Strand: POSITIVE Subject Start: 74 Subject End: 247 .......................................................................................................................gggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa .......................................................................................................................gggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Inter-species Hit: Count: 3 Min: 31 Max: 293 Len: 263 Subject: NC_008533_SPD_1647_SPD_1648|glutamyl aminopeptidase PepA:NAD-dependent epimerase/dehydratase family protein|NEGATIVE:POSITIVE|[1662045,1662444]|400 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 125 Query Start:169 Query End:293 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 ........................................................................................................................................................................atgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ........................................................................................................................................................................atgcaagagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 54 Query Start:31 Query End:84 Subject Strand: NEGATIVE Subject Start: 212 Subject End: 265 ..............................tttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaat................................................................................................................................................................................................................. ..............................tttaaagaaagaagaaagggaagtcaactattttctgtaaatttcatgaaaaat................................................................................................................................................................................................................. Subject: NC_003098_spr1682_spr1683|Glutamyl aminopeptidase:UDP-galactose 4-epimerase, truncation|NEGATIVE:POSITIVE|[1654514,1654913]|400 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 125 Query Start:169 Query End:293 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 ........................................................................................................................................................................atgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ........................................................................................................................................................................atgcaagagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 54 Query Start:31 Query End:84 Subject Strand: NEGATIVE Subject Start: 212 Subject End: 265 ..............................tttaaagaaataagaaggagaagtcaactattttctgcaaattttatgaaaaat................................................................................................................................................................................................................. ..............................tttaaagaaagaagaaagggaagtcaactattttctgtaaatttcatgaaaaat................................................................................................................................................................................................................. Subject: NC_003028_SP_1865_SP_1866|glutamyl-aminopeptidase:hypothetical protein|NEGATIVE:POSITIVE|[1772988,1773106]|119 HSP 1 e-value: 7.0E-47 bit: 188.0 Len: 119 Query Start:175 Query End:293 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 ..............................................................................................................................................................................gagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ..............................................................................................................................................................................gagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAAGAAAUAAGAAGGAGAAGUCAACUAUUUUCUGCAAAUUUUAUGAAAAAUCUGAACGAUUUUGGCAUCGGAUUGUUUUUUUGUUUGGGAAUAAAAUUUCGAGUGAAUCUUGGAAUUUUUUAGAUUUUACUUCAAAUGCAAGAGAAUACAAUUCAUUUCUAAGAUAGAGCAAAACUAAGAUACUAACUUAGAAAUCCACCUUCCCGCUAUCCUUCUCCUAUAAAAAGUGGUAAAAUGGAUGAAAGAAAGAAGGAACUGAA .............(((((..........(((((((((((..............((..(((((....((((......))))...)))))..))...(((((((((((.....))))))))))).................))).))))))))......(((((((((.(((..(........)...))).)))))))))...)))))......(((((((..........((......))...........)))))))...... (-49.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGUUCCUUCUUUCUUUCAUCCAUUUUACCACUUUUUAUAGGAGAAGGAUAGCGGGAAGGUGGAUUUCUAAGUUAGUAUCUUAGUUUUGCUCUAUCUUAGAAAUGAAUUGUAUUCUCUUGCAUUUGAAGUAAAAUCUAAAAAAUUCCAAGAUUCACUCGAAAUUUUAUUCCCAAACAAAAAAACAAUCCGAUGCCAAAAUCGUUCAGAUUUUUCAUAAAAUUUGCAGAAAAUAGUUGACUUCUCCUUCUUAUUUCUUUAAA .....(((((.((.((((((.(((..................))))))))).)).)))))((((((...(((((.......)))))......))))))..((((((((..((((......))))...(((((.....(((.((((((.(.((.....)).).)))))).(((..................((((......))))..((((((((....))))))))..)))..)))...)))))......))))))))..... (-41.87) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 110 61 231 182 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 253 53 15 191 148 smit:SMT_300|5end_hypothetical_protein_243512..243742_POSITIVE 247 94 53 126 80 smit:SMT_575|5end_pyruvate_kinase_493849..494079_POSITIVE 245 173 132 216 176 smit:SMT_595|5end_phosphoglycerate_mutase_512593..512823_NEGATIVE 240 70 21 187 137 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 239 247 202 138 101 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 238 246 212 96 58 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 238 127 83 227 181 smit:SMT_126|5end_hypothetical_membrane_associated_protein_78250..78480_NEGATIVE 234 203 165 195 145 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 228 236 200 42 14 smit:SMT_977|5end_conserved_hypothetical_protein,_Rrf2_family_protein_925689..925919_NEGATIVE 227 224 182 175 120 smit:SMT_349|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_287207..287437_POSITIVE 227 117 76 185 150 smit:SMT_282|5end_hypothetical_protein_224866..225096_POSITIVE 226 222 181 50 5 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 225 150 103 155 108 smit:SMT_845|5end_hypothetical_protein_791868..792098_NEGATIVE 221 223 181 116 69 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 219 218 171 70 23 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 216 210 161 178 111 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 215 89 59 127 90 smit:SMT_930|5end_ATP-dependent_RNA_helicase_884435..884665_NEGATIVE 214 220 173 216 170 smit:SMT_1541|5end_isopentenyl-diphosphate_delta-isomerase_1526093..1526323_NEGATIVE 214 120 73 185 149 smit:SMT_911|5end_hypothetical_protein_862023..862253_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 256 109 61 141 87 smit:SMT_1924|3end_isoleucyl-tRNA_synthetase_1866843..1866993_POSITIVE 247 128 82 85 29 smit:SMT_1253|3end_beta-galactosidase_1212912..1213062_NEGATIVE 240 70 21 121 71 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 239 247 202 151 114 smit:SMT_1088|3end_hypothetical_protein_1024152..1024302_NEGATIVE 238 246 212 62 24 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 237 244 207 68 21 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 234 235 200 54 13 smit:SMT_820|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_730734..730884_NEGATIVE 227 117 76 39 4 smit:SMT_281|3end_glycosyl_transferase,_group_1_224800..224950_POSITIVE 226 180 132 142 101 smit:SMT_912|3end_fructokinase_862733..862883_NEGATIVE 226 94 54 44 2 smit:SMT_574|3end_PTS_system,_fructose_specific_IIABC_components_493847..493997_POSITIVE 226 226 182 109 54 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 222 152 111 53 7 smit:SMT_892|3end_K02023_multiple_sugar_transport_system_ATP-binding_protein_839199..839349_NEGATIVE 220 233 191 55 20 smit:SMT_549|3end_hypothetical_cytosolic_protein_467367..467517_POSITIVE 219 235 203 99 71 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 219 218 171 51 4 smit:SMT_232|3end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_172717..172867_POSITIVE 214 210 170 142 105 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 212 68 27 54 14 smit:SMT_1664|3end_hypothetical_protein_1653176..1653326_NEGATIVE 212 248 206 133 94 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 212 198 153 51 11 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 212 220 171 115 68 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE