Origin IGS: aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 cacttgtgaaactatggtataataaatgaaaggagttttctatgcaagaatttattcaaacctacctcaataagcattgatataacaacgattattgagaatatcttaaccaagttaatttctctgttatttctatttttgctattctatatagctaannnnnttaattaattaannnnngggcaccagaaggcgtcgccgtcgtcacacgaaaagcaattatttaaacacagaaaggaaagggttgtctaaattcgtgcgtgccctgagagcccacagcgaatacttttcactgtggtgtcagttggtacaagtgattgtaccaactgcggaaaatttgagaccttaggctcaaattttagtcatgaaagtccgaaggactttgctgacgtccgtcaccacttcagaaaagtataaaaagaaactcttttaagaaaatt Mask Tandem Repeat Region ================================================ aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Find is-nt database================================================ Query_seq: SMT_995:SMT_996|SMT_995:SMT_996:K07574 putative RNA-binding protein containing KH domain:K03309 dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family:<-->:936559..936998 440 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_995:SMT_996|SMT_995:SMT_996:K07574 putative RNA-binding protein containing KH domain:K03309 dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family:<-->:936559..936998 440 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_995:SMT_996|SMT_995:SMT_996:K07574 putative RNA-binding protein containing KH domain:K03309 dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family:<-->:936559..936998 440 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 322 End: 426 ................................................................................................................................................................................................................................................................................................................................. M N L V K I F S I I V V I S M L I E V G L N K F L H R K L L S F I I P .............. Protein_Len: 50 Strand: - Start: 273 End: 422 ................................................................................................................................................................................................................................................................................ N X X X A I Y F L L F L F L L S I L K T L I N E I I T T I D I S I S T P K F L N K C L F S R E N I M .................. Protein_Len: 34 Strand: - Start: 95 End: 196 .............................................................................................. P R L N E A T P V I V Q V L Q C W L S F Y E S H A R L A R V F K S M .................................................................................................................................................................................................................................................... Protein_Len: 54 Strand: - Start: 27 End: 188 .......................... V K R F H H R V D A F D K P S E H S F N S G L T E F K G C N T C D S T G V S V V T F L I R Q P S E P C A R M ............................................................................................................................................................................................................................................................ aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg 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: 82 Start: 393 End: 422 ........................................................................................................................................................................................................................................................................................................................................................................................................CTTGCATAGAAAACTCCTTTCATTTATTAT.................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 70 HP_score: -5.8 Tail_Score: -4.30576 Start: 85 End: 104 Full_Region: accaactgcggaaaa tttgagacc tta ggctcaaa ttttagtcatgaaag ....................................................................................tttgagaccttaggctcaaa................................................................................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 49 HP_score: -4.9 Tail_Score: -2.56715 Start: 141 End: 168 Full_Region: tgcgtgccctgagag cccacagcgaa tactt ttcactgtggtg tcagttggtacaagt ............................................................................................................................................cccacagcgaatacttttcactgtggtg................................................................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 43 HP_score: -3.1 Tail_Score: -2.67209 Start: 146 End: 164 Full_Region: tgccctgagagccca cagcgaa tactt ttcactg tggtgtcagttggta .................................................................................................................................................cagcgaatacttttcactg.................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 54 HP_score: -6.3 Tail_Score: -2.66451 Start: 341 End: 376 Full_Region: ACTTGGTTAAGATAT TCTCAATAATCGTTG TTATAT CAATGCTTATTGAGG TAGGTTTGAATAAAT ....................................................................................................................................................................................................................................................................................................................................................TCTCAATAATCGTTGTTATATCAATGCTTATTGAGG................................................................ Find igs database================================================ Query_seq: SMT_995:SMT_996|SMT_995:SMT_996:K07574 putative RNA-binding protein containing KH domain:K03309 dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family:<-->:936559..936998 440 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Intra-Species Hit: Count: 1 Min: 1 Max: 440 Len: 440 Subject: smit_SMT_995_SMT_996|K07574 putative RNA-binding protein containing KH domain:K03309 dicarboxylate/amino acid:cation (Na+ or H+) symporter, DAACS family|NEGATIVE:POSITIVE|[936559,936998]|440 HSP 1 e-value: 0.0 bit: 813.0 Len: 440 Query Start:1 Query End:440 Subject Strand: POSITIVE Subject Start: 1 Subject End: 440 aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg aattttcttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgtgggctctcagggcacgcacgaatttagacaaccctttcctttctgtgtttaaataattgcttttcgtgtgacgacggcgacgccttctggtgcccnnnnnttaattaattaannnnnttagctatatagaatagcaaaaatagaaataacagagaaattaacttggttaagatattctcaataatcgttgttatatcaatgcttattgaggtaggtttgaataaattcttgcatagaaaactcctttcatttattataccatagtttcacaagtg Inter-species Hit: Count: 2 Min: 8 Max: 212 Len: 205 Subject: NC_008533_SPD_1558_SPD_1559|conserved hypothetical protein TIGR00253:GTP-binding protein|NEGATIVE:NEGATIVE|[1579140,1579353]|214 HSP 1 e-value: 2.0E-79 bit: 297.0 Len: 205 Query Start:8 Query End:212 Subject Strand: POSITIVE Subject Start: 8 Subject End: 213 .......ttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgt-gggctctcagggcacgcacgaatttagacaaccctttcctttctgtg.................................................................................................................................................................................................................................... .......ttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaacttacaccacagcgaaaagtattctctatggggctcgccttgctcgcccaaattcagacaaccctttcctttctgtg.................................................................................................................................................................................................................................... Subject: NC_003098_spr1593_spr1594|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[1571609,1571822]|214 HSP 1 e-value: 2.0E-79 bit: 297.0 Len: 205 Query Start:8 Query End:212 Subject Strand: POSITIVE Subject Start: 8 Subject End: 213 .......ttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaactgacaccacagtgaaaagtattcgctgt-gggctctcagggcacgcacgaatttagacaaccctttcctttctgtg.................................................................................................................................................................................................................................... .......ttaaaagagtttctttttatacttttctgaagtggtgacggacgtcagcaaagtccttcggactttcatgactaaaatttgagcctaaggtctcaaattttccgcagttggtacaatcacttgtaccaacttacaccacagcgaaaagtattctctatggggctcgccttgctcgcccaaattcagacaaccctttcctttctgtg.................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAAGAGUUUCUUUUUAUACUUUUCUGAAGUGGUGACGGACGUCAGCAAAGUCCUUCGGACUUUCAUGACUAAAAUUUGAGCCUAAGGUCUCAAAUUUUCCGCAGUUGGUACAAUCACUUGUACCAACUGACACCACAGUGAAAAGUAUUCGCUGUGGGCUCUCAGGGCACGCACGAAUUUAGACAACCCUUUCCUUUCUGUG ...((((.((((((....(((((((((....((((((.((((.((((..(((((((...)))))))..))))..(((((((((((...)).)))))))))))))((((((((((((....)))))))))))).))))))...)))))))))(((.((((.(((.....))).)))))))....))).))).)))).......... (-72.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CACAGAAAGGAAAGGGUUGUCUAAAUUCGUGCGUGCCCUGAGAGCCCACAGCGAAUACUUUUCACUGUGGUGUCAGUUGGUACAAGUGAUUGUACCAACUGCGGAAAAUUUGAGACCUUAGGCUCAAAUUUUAGUCAUGAAAGUCCGAAGGACUUUGCUGACGUCCGUCACCACUUCAGAAAAGUAUAAAAAGAAACUCUUUUAA .........(((((((((.(((....((((..(((..(.....)..))).))))(((((((((...((((((.((((((((((((....))))))))))))(((((((((((((.((...)))))))))))..((((..(((((((...)))))))..)))).)))).))))))....)))))))))....)))))))))))).. (-75.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 954 70 21 168 119 smit:SMT_995|5end_K07574_putative_RNA-binding_protein_containing_KH_domain_936468..936698_NEGATIVE 400 69 23 178 133 smit:SMT_340|5end_chaperone_protein_278663..278893_POSITIVE 358 90 41 190 141 smit:SMT_1190|5end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1148232..1148462_NEGATIVE 332 149 103 83 31 smit:SMT_1634|5end_2,3,4,5-tetrahydropyridine-2-carboxylate_N-succinyltransferase,_putative_1621074..1621304_POSITIVE 316 177 136 192 138 smit:SMT_346|5end_K01992_ABC-2_type_transport_system_permease_protein_284720..284950_POSITIVE 308 68 21 80 25 smit:SMT_2026|5end_K03466_DNA_segregation_ATPase_FtsK/SpoIIIE,_S-DNA-T_family_1942432..1942662_NEGATIVE 308 120 78 73 26 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 294 132 97 64 27 smit:SMT_702|5end_hypothetical_protein_612311..612541_NEGATIVE 293 70 22 187 130 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 292 141 102 177 130 smit:SMT_953|5end_hypothetical_protein_901576..901806_NEGATIVE 291 199 153 51 1 smit:SMT_1262|5end_ribosomal_protein_L11_methyltransferase_1227152..1227382_POSITIVE 289 47 10 130 94 smit:SMT_357|5end_tRNA_(guanine-N7-)-methyltransferase_293185..293415_POSITIVE 285 187 153 134 93 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 284 193 155 83 51 smit:SMT_1791|5end_hypothetical_protein_1765907..1766137_POSITIVE 284 95 58 231 185 smit:SMT_1257|5end_acetolactate_synthase_small_subunit_1223173..1223403_NEGATIVE 281 72 31 198 148 smit:SMT_852|5end_K03978_GTP-binding_protein_798044..798274_NEGATIVE 280 166 121 217 164 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 279 69 22 61 19 smit:SMT_2150|5end_threonyl-tRNA_synthetase_2024673..2024903_POSITIVE 279 69 22 61 19 smit:SMT_2146|5end_threonyl-tRNA_synthetase_2022048..2022278_POSITIVE 278 55 11 139 101 smit:SMT_1912|5end_D-alanyl-D-alanine_carboxypeptidase_1857920..1858150_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 141 102 76 29 smit:SMT_954|3end_cation-transporting_ATPase,_E1-E2_family_901677..901827_NEGATIVE 289 47 10 133 97 smit:SMT_356|3end_hypothetical_protein_293268..293418_POSITIVE 286 192 156 115 83 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 278 179 147 33 3 smit:SMT_1663|3end_DNA-binding_response_regulator_1652357..1652507_NEGATIVE 276 72 31 49 11 smit:SMT_1997|3end_K03294_basic_amino_acid/polyamine_antiporter,_APA_family_1921123..1921273_NEGATIVE 275 59 11 141 85 smit:SMT_218|3end_undecaprenyl_pyrophosphate_synthetase_150993..151143_POSITIVE 272 194 152 76 27 smit:SMT_2044|3end_transcriptional_activator_TipA,_putative_1955274..1955424_NEGATIVE 272 194 152 76 27 smit:SMT_2016|3end_tyrosine_recombinase_1933021..1933171_NEGATIVE 272 194 152 86 37 smit:SMT_2001|3end_membrane_protease_protein_family_1923889..1924039_POSITIVE 272 194 152 86 37 smit:SMT_1985|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1914407..1914557_NEGATIVE 272 194 152 76 27 smit:SMT_1957|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1890829..1890979_POSITIVE 272 197 153 66 8 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 272 194 152 76 27 smit:SMT_1886|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1841198..1841348_POSITIVE 272 194 152 76 27 smit:SMT_1658|3end_hypothetical_protein_1648937..1649087_POSITIVE 272 194 152 76 27 smit:SMT_1558|3end_hypothetical_protein_1543855..1544005_NEGATIVE 272 194 152 76 27 smit:SMT_1155|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_1099183..1099333_NEGATIVE 270 192 154 80 32 smit:SMT_1896|3end_lysine_decarboxylase_1848073..1848223_NEGATIVE 269 197 154 59 10 smit:SMT_1669|3end_potassium_uptake_protein_KtrB_1658302..1658452_NEGATIVE 269 68 22 146 102 smit:SMT_935|3end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_888749..888899_POSITIVE 268 128 82 151 111 smit:SMT_216|3end_Holliday_junction_DNA_helicase_RuvB_149335..149485_POSITIVE