Origin IGS: gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctaatgagtacggatatcaaactccttaaacacaatacgtaagtctctctttactctttgacgccctctgaagcgttcatgtcttaagacgcgttctaactcttcttgtttgtcnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 nnnnnatagctcactagatcgagtgaccctgcgccgtaaatgtgccggcgctagaacaatttactgcagcggaggatacctktataggtatggtaggagagtgttctatgtgtgwtgaaggtrtrccgtgaggagcgttggaacgcatagaagtgagaatgcctggtatgagnnnnnttaattaattaannnnngacaaacaagaagagttagaacgcgtcttaagacatgaacgcttcagagggcgtcaaagagtaaagagagacttacgtattgtgtttaaggagtttgatatccgtactcattagggagtcatacaaaaaaacataaaaagtttacaaaagttgttgacaagtcagaaaaagtgtgtataatagtaagagtkgaaaatamcagctcaggtccgtcggtcnnnnnttaattaattaannnnnctgtatctcgaaagggggacgtc Mask Tandem Repeat Region ================================================ gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctaatgagtacggatatcaaactccttaaacacaatacgtaagtctctctttactctttgacgccctctgaagcgttcatgtcttaagacgcgttctaactcttcttgtttgtcnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Find is-nt database================================================ Query_seq: SMT_2048:SMT_2049|SMT_2048:SMT_2049:competence-specific global transcription modulator:3-oxoacyl-:<-<-:1958369..1958825 457 gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctaatgagtacggatatcaaactccttaaacacaatacgtaagtctctctttactctttgacgccctctgaagcgttcatgtcttaagacgcgttctaactcttcttgtttgtcnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_2048:SMT_2049|SMT_2048:SMT_2049:competence-specific global transcription modulator:3-oxoacyl-:<-<-:1958369..1958825 457 gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctaatgagtacggatatcaaactccttaaacacaatacgtaagtctctctttactctttgacgccctctgaagcgttcatgtcttaagacgcgttctaactcttcttgtttgtcnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_2048:SMT_2049|SMT_2048:SMT_2049:competence-specific global transcription modulator:3-oxoacyl-:<-<-:1958369..1958825 457 gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctaatgagtacggatatcaaactccttaaacacaatacgtaagtctctctttactctttgacgccctctgaagcgttcatgtcttaagacgcgttctaactcttcttgtttgtcnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 153 Max: 263 Len: 111 Subject: UniRef90_Q9R2W8 Cluster: ComX2; n=4; Streptococcus pneumoniae|Rep: ComX2 - Streptococcus pneumoniae HSP 1 e-value: 4.0E-10 bit: 65.9 Len: 111 Query Start:153 Query End:263 Subject Strand: null Subject Start: 123 Subject End: 159 ........................................................................................................................................................ D K Q E E L E R V L R H E R F R G R Q R V K R D L R I V F K E F D I R T H .................................................................................................................................................................................................. ........................................................................................................................................................ E K Q E E L E R V L S N E R F R G R Q R V L R D L R I V F K E F T I R T H .................................................................................................................................................................................................. gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 276 End: 404 ................................................................................................................................................................................................................................................................................... M X X X H T R H S H F Y A F Q R S S R X T F X T H R T L S Y H T Y X G I L R C S K L F ..................................................... Protein_Len: 51 Strand: + Start: 289 End: 441 ................................................................................................................................................................................................................................................................................................ M P G I L T S M R S N A P H G X P S X H I E H S P T I P I X V S S A A V N C S S A G T F T A Q G H S I ................ Protein_Len: 31 Strand: - Start: 343 End: 435 ...................................................................................................................................................................................................................................................................................................................................................... X V Y F V R R G Y R Y L Y G G S C Y I T R A G A C K R R L T M ...................... gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_2048:SMT_2049|SMT_2048:SMT_2049:competence-specific global transcription modulator:3-oxoacyl-:<-<-:1958369..1958825 457 gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatgtttttttgtatgactccctannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctatnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 452 Len: 452 Subject: smit_SMT_2048_SMT_2049|competence-specific global transcription modulator:3-oxoacyl-|NEGATIVE:NEGATIVE|[1958369, 1958825]|457 HSP 1 e-value: 3.0E-87 bit: 323.0 Len: 184 Query Start:269 Query End:452 Subject Strand: POSITIVE Subject Start: 269 Subject End: 452 ............................................................................................................................................................................................................................................................................ttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctat..... ............................................................................................................................................................................................................................................................................ttaattaattaannnnnctcataccaggcattctcacttctatgcgttccaacgctcctcacggyayaccttcawcacacatagaacactctcctaccatacctatamaggtatcctccgctgcagtaaattgttctagcgccggcacatttacggcgcagggtcactcgatctagtgagctat..... HSP 2 e-value: 3.0E-49 bit: 197.0 Len: 132 Query Start:1 Query End:132 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatg..................................................................................................................................................................................................................................................................................................................................... gacgtccccctttcgagatacagnnnnnttaattaattaannnnngaccgacggacctgagctgktattttcmactcttactattatacacactttttctgacttgtcaacaacttttgtaaactttttatg..................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACGUCCCCCUUUCGAGAUACAGNNNNNUUAAUUAAUUAANNNNNGACCGACGGACCUGAGCUGKUAUUUUCMACUCUUACUAUUAUACACACUUUUUCUGACUUGUCAACAACUUUUGUAAACUUUUUAUGUUUUUUUGUAUGACUCCCUAAUGAGUACGGAUAUCAAACUCCUUAAACACAAUACGUAAGUCUCUCUUUACUCUUUGACGCCCUCUGAAGCGUUCAUGUCUUAAGACGCGUUCUAACUCUUCUUGUUUGUCNNNNNUUAAUUAAUUAANNNNNCUCAUACCAGGCAUUCUCACUUCUAUGCGUUCCAACGCUCCUCACGGYAYACCUUCAWCACACAUAGAACACUCUCCUACCAUACCUAUAMAGGUAUCCUCCGCUGCAGUAAAUUGUUCUAGCGCCGGCACAUUUACGGCGCAGGGUCACUCGAUCUAGUGAGCUAU ...(((........(((...........((((((((((((.....(((.((((((...(((............................................(((((........(((((...(((((((....((((...((((......))))..(((........)))......)))).)))))))......)))))...))))).......((((((((..........))))).)))...))).)).)))).))).....)))))))))))).....)))......)))...((((((.....((((....))))......(((...((((..........(((((((..........((((((....)))))).....((....))....)))))))((((((.........)))))).))))...)))....)))))).... (-76.73) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGCUCACUAGAUCGAGUGACCCUGCGCCGUAAAUGUGCCGGCGCUAGAACAAUUUACUGCAGCGGAGGAUACCUKUAUAGGUAUGGUAGGAGAGUGUUCUAUGUGUGWUGAAGGURURCCGUGAGGAGCGUUGGAACGCAUAGAAGUGAGAAUGCCUGGUAUGAGNNNNNUUAAUUAAUUAANNNNNGACAAACAAGAAGAGUUAGAACGCGUCUUAAGACAUGAACGCUUCAGAGGGCGUCAAAGAGUAAAGAGAGACUUACGUAUUGUGUUUAAGGAGUUUGAUAUCCGUACUCAUUAGGGAGUCAUACAAAAAAACAUAAAAAGUUUACAAAAGUUGUUGACAAGUCAGAAAAAGUGUGUAUAAUAGUAAGAGUKGAAAAUAMCAGCUCAGGUCCGUCGGUCNNNNNUUAAUUAAUUAANNNNNCUGUAUCUCGAAAGGGGGACGUC ....((((((...((..(((..((.((((.........(((.(((((((((((.(((.((((........((((((....)))))).)))).))).))))))).))))......)))...((....)).)))).))..)))...)))))))).(((((((((((.((.....((((((((((((.....(((..((..((.(((((...((..(((....))).(((.((((......)))))))....)).........(((((.(((((((..((.....((((((.(((.((.....)).)))((((.((((..((((.......)))).......))))))))..)))))).....))..)))))))))))).............)))))...)).))..))).....)))))))))))).....))))))).(....).))).))). (-98.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 707 100 51 191 142 smit:SMT_2048|5end_competence-specific_global_transcription_modulator_1958278..1958508_NEGATIVE 366 426 386 49 6 smit:SMT_1999|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1922792..1923022_NEGATIVE 366 426 386 49 6 smit:SMT_1665|5end_cell_wall_surface_anchor_family_protein_1656335..1656565_NEGATIVE 347 428 386 53 1 smit:SMT_314|5end_biotin_carboxylase_254277..254507_POSITIVE 342 434 392 227 185 smit:SMT_1403|5end_dihydrolipoamide_dehydrogenase_1379204..1379434_POSITIVE 341 263 239 25 1 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 340 450 404 80 33 smit:SMT_1382|5end_glutamate_5-kinase_1360744..1360974_NEGATIVE 335 444 406 132 79 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 334 444 402 171 107 smit:SMT_1966|5end_DNA_polymerase_III_alpha_subunit_1897934..1898164_POSITIVE 330 446 401 169 105 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 328 225 196 47 11 smit:SMT_1553|5end_K04074_cell_division_initiation_protein_1535913..1536143_POSITIVE 324 450 401 183 145 smit:SMT_1816|5end_K02026_multiple_sugar_transport_system_permease_protein_1790813..1791043_POSITIVE 323 444 406 218 161 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 322 444 406 172 115 smit:SMT_1926|5end_mevalonate_kinase_1867692..1867922_POSITIVE 322 430 384 111 63 smit:SMT_448|5end_K03707_transcriptional_activator_TenA_386789..387019_POSITIVE 320 417 377 57 16 smit:SMT_460|5end_6-phospho-beta-glucosidase_397819..398049_POSITIVE 315 444 410 192 145 smit:SMT_2030|5end_chromosomal_replication_initiator_protein_DnaA_1945167..1945397_NEGATIVE 315 444 410 132 85 smit:SMT_2002|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1924405..1924635_NEGATIVE 315 444 410 215 168 smit:SMT_1927|5end_cell_division_protein_FtsH_1868779..1869009_NEGATIVE 315 444 410 153 106 smit:SMT_1885|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1840057..1840287_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 837 190 141 131 82 smit:SMT_2027|3end_competence-specific_global_transcription_modulator_1943025..1943175_NEGATIVE 837 190 141 131 82 smit:SMT_1091|3end_competence-specific_global_transcription_modulator_1032561..1032711_NEGATIVE 837 190 141 131 82 smit:SMT_102|3end_competence-specific_global_transcription_modulator_34667..34817_POSITIVE 649 90 46 62 18 smit:SMT_1039|3end_tRNA_(uracil-5-)_-methyltransferase_981343..981493_NEGATIVE 427 118 78 41 1 smit:SMT_1133|3end_cytidine/deoxycytidylate_deaminase_family_protein,_putative_1074556..1074706_NEGATIVE 348 449 406 70 34 smit:SMT_481|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_417641..417791_NEGATIVE 328 225 196 38 2 smit:SMT_1552|3end_RNA_binding_protein_1535984..1536134_POSITIVE 315 444 410 52 5 smit:SMT_1630|3end_hypothetical_protein_1618141..1618291_POSITIVE 305 449 407 58 16 smit:SMT_313|3end_3R-hydroxymyristoyl_ACP_dehydrase_254345..254495_POSITIVE 297 435 400 55 23 smit:SMT_826|3end_hypothetical_protein_749591..749741_NEGATIVE 290 220 172 122 70 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 288 430 386 106 55 smit:SMT_1902|3end_proton-translocating_NADH-quinone_oxidoreductase,_chain_L_1852028..1852178_NEGATIVE 287 450 401 52 1 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 285 430 381 63 3 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE 285 450 403 105 50 smit:SMT_1153|3end_alpha-mannosidase_1097383..1097533_NEGATIVE 284 448 407 59 15 smit:SMT_1952|3end_hypothetical_protein_1886932..1887082_POSITIVE 284 438 401 135 82 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 283 426 386 148 104 smit:SMT_1756|3end_hypothetical_protein_1733967..1734117_NEGATIVE 282 449 410 69 36 smit:SMT_1559|3end_6-phosphofructokinase_1544614..1544764_NEGATIVE 282 448 402 131 68 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE