Origin IGS: gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgagcagaaacttttcaaaaaaataactttttatcttgacaagagctagaaaacttggtatcatgtaaaagttgagaaaagcagaagtgagagcttctcgccttgtgacatgaagttgcctggccctacggatgaaaagtttctaagaaacgctatcataac Mask Tandem Repeat Region ================================================ gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Find is-nt database================================================ Query_seq: SMT_1365:SMT_1366|SMT_1365:SMT_1366:translation initiation factor IF-3:K02238 competence protein ComEC:<-<-:1344576..1344737 162 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1365:SMT_1366|SMT_1365:SMT_1366:translation initiation factor IF-3:K02238 competence protein ComEC:<-<-:1344576..1344737 162 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1365:SMT_1366|SMT_1365:SMT_1366:translation initiation factor IF-3:K02238 competence protein ComEC:<-<-:1344576..1344737 162 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 4 End: 99 ... M I A F L R N F S S V G P G N F M S Q G E K L S L L L F S T F T ............................................................... Protein_Len: 44 Strand: + Start: 30 End: 161 ............................. M R R A R Q L H V T R R E A L T S A F L N F Y M I P S F L A L V K I K S Y F F E K F L L . gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca 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: 99 End: 128 ..................................................................................................CTTGACAAGAGCTAGAAAACTTGGTATCAT.................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 43 HP_score: -2.4 Tail_Score: -3.18446 Start: 66 End: 79 Full_Region: CATGTCACAAGGCGA GAAG CTCTCA CTTC TGCTTTTCTCAACTT .................................................................GAAGCTCTCACTTC................................................................................... Find igs database================================================ Query_seq: SMT_1365:SMT_1366|SMT_1365:SMT_1366:translation initiation factor IF-3:K02238 competence protein ComEC:<-<-:1344576..1344737 162 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Intra-Species Hit: Count: 1 Min: 1 Max: 162 Len: 162 Subject: smit_SMT_1365_SMT_1366|translation initiation factor IF-3:K02238 competence protein ComEC|NEGATIVE:NEGATIVE|[1344576,1344737]|162 HSP 1 e-value: 1.0E-74 bit: 280.0 Len: 162 Query Start:1 Query End:162 Subject Strand: POSITIVE Subject Start: 1 Subject End: 162 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttannnnnnngaaaagtttctgctca gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagttatttttttgaaaagtttctgctca Inter-species Hit: Count: 3 Min: 1 Max: 139 Len: 139 Subject: NC_008533_SPD_0846_SPD_0847|hypothetical protein:translation initiation factor IF-3|POSITIVE:POSITIVE|[862542,862820]|279 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 139 Query Start:1 Query End:139 Subject Strand: NEGATIVE Subject Start: 111 Subject End: 249 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagtta....................... gttatgatagcgtttcttcgaaacttttcatccgtagggccaggcaacttaatgtcacaaggcgagaagctctcacttctgcttttctcaacttttatatgataccaagttttctagctcttgtcaagataaaaagtta....................... Subject: NC_003098_spr0860_spr0861|hypothetical protein:translation initiation factor IF-3|POSITIVE:POSITIVE|[855012,855260]|249 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 139 Query Start:1 Query End:139 Subject Strand: NEGATIVE Subject Start: 111 Subject End: 249 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagtta....................... gttatgatagcgtttcttcgaaacttttcatccgtagggccaggcaacttaatgtcacaaggcgagaagctctcacttctgcttttctcaacttttatatgataccaagttttctagctcttgtcaagataaaaagtta....................... Subject: NC_003028_SP_0958_SP_0959|hypothetical protein:translation initiation factor IF-3|POSITIVE:POSITIVE|[907032,907314]|283 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 139 Query Start:1 Query End:139 Subject Strand: NEGATIVE Subject Start: 115 Subject End: 253 gttatgatagcgtttcttagaaacttttcatccgtagggccaggcaacttcatgtcacaaggcgagaagctctcacttctgcttttctcaacttttacatgataccaagttttctagctcttgtcaagataaaaagtta....................... gttatgatagcgtttcttcgaaacttttcatccgtagggccaggcaacttaatgtcacaaggcgagaagctctcacttctgcttttctcaacttttatatgataccaagttttctagctcttgtcaagataaaaagtta....................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUAUGAUAGCGUUUCUUAGAAACUUUUCAUCCGUAGGGCCAGGCAACUUCAUGUCACAAGGCGAGAAGCUCUCACUUCUGCUUUUCUCAACUUUUACAUGAUACCAAGUUUUCUAGCUCUUGUCAAGAUAAAAAGUUA .....................(((((((.(((...(((((.(((.((((((((((...(((..(((((((..........)))))))....)))..)))))).....)))).))).)))))......))).))))))). (-29.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAACUUUUUAUCUUGACAAGAGCUAGAAAACUUGGUAUCAUGUAAAAGUUGAGAAAAGCAGAAGUGAGAGCUUCUCGCCUUGUGACAUGAAGUUGCCUGGCCCUACGGAUGAAAAGUUUCUAAGAAACGCUAUCAUAAC .((((((((((((.....((.(((((..((((.....((((((..(((.........((((((((....)))))).)))))...))))))))))..))))).))..))))))))))))..................... (-36.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1046 80 31 171 122 smit:SMT_1365|5end_translation_initiation_factor_IF-3_1344485..1344715_NEGATIVE 416 80 31 93 26 smit:SMT_1934|5end_homoserine_dehydrogenase_1872402..1872632_POSITIVE 339 75 33 231 184 smit:SMT_110|5end_alpha-L-fucosidase_57445..57675_POSITIVE 335 50 1 168 114 smit:SMT_349|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_287207..287437_POSITIVE 330 88 41 149 85 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 326 77 31 207 149 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 320 69 22 101 54 smit:SMT_1879|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1836806..1837036_NEGATIVE 317 70 32 117 72 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 310 88 44 53 9 smit:SMT_513|5end_16S_rRNA_processing_protein_RimM_440869..441099_POSITIVE 306 78 34 57 16 smit:SMT_1115|5end_K02245_competence_protein_ComGC_1052796..1053026_NEGATIVE 304 79 32 103 47 smit:SMT_955|5end_acyltransferase_family_protein_904096..904326_POSITIVE 301 70 24 96 58 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 299 70 29 132 85 smit:SMT_387|5end_hypothetical_protein_predicted_by_Glimmer/Critica_320937..321167_POSITIVE 294 82 44 169 128 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 288 83 44 168 124 smit:SMT_455|5end_cation_transport_ATPase_391670..391900_POSITIVE 287 67 23 227 178 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 287 78 37 107 60 smit:SMT_103|5end_adenylosuccinate_synthetase_40766..40996_POSITIVE 281 113 73 141 91 smit:SMT_1451|5end_K02057_simple_sugar_transport_system_permease_protein_1434683..1434913_NEGATIVE 279 47 9 60 21 smit:SMT_1130|5end_MATE_efflux_family_protein_1065210..1065440_NEGATIVE 276 78 33 188 150 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 76 33 50 17 smit:SMT_1115|3end_K02245_competence_protein_ComGC_1052473..1052623_NEGATIVE 330 88 41 100 36 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 306 78 34 55 14 smit:SMT_1116|3end_K02244_competence_protein_ComGB_1052798..1052948_NEGATIVE 305 126 81 54 9 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 299 70 29 117 70 smit:SMT_386|3end_branched-chain_amino_acid_transport_system_II_carrier_protein_321002..321152_POSITIVE 293 79 33 59 8 smit:SMT_1920|3end_ABC_transporter,_ATP-binding_protein_1862736..1862886_NEGATIVE 285 73 31 79 51 smit:SMT_2053|3end_hypothetical_membrane_associated_protein_1963754..1963904_NEGATIVE 281 113 73 148 98 smit:SMT_1452|3end_ABC-type_uncharacterized_transport_system,_ATPase_component_1434676..1434826_NEGATIVE 278 70 24 106 58 smit:SMT_1754|3end_leader_peptidase_(prepilin_peptidase)_/_N-methyltransferase_1732363..1732513_NEGATIVE 275 110 61 116 55 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 270 88 59 88 57 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 268 53 23 81 57 smit:SMT_2125|3end_3-phosphoshikimate_1-carboxyvinyltransferase_2009098..2009248_POSITIVE 266 89 54 58 10 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 265 70 25 140 98 smit:SMT_900|3end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_848367..848517_NEGATIVE 264 88 48 91 53 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 264 88 48 91 53 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 264 88 48 91 53 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 264 88 48 91 53 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 263 98 52 60 11 smit:SMT_993|3end_hypothetical_protein_934883..935033_NEGATIVE 263 78 33 90 37 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE