Origin IGS: cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat .........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 atttgaaaattctccttctttctatagttctatcataccctttaaatattaccgtttcttgacacttttatgtagaaatattacaaaattattttttatttctctaaataagccattttttgttacaaaagatgcttttttatgctatttgtagtgtaaaaaggttttcatccacaattaaagccaagaccttcattctttgatataatagagataagaatttttataaggggaaactg Mask Tandem Repeat Region ================================================ cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Find is-nt database================================================ Query_seq: SMT_133:SMT_134|SMT_133:SMT_134:L-serine dehydratase beta subunit:LysM domain protein:<-->:85328..85566 239 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_133:SMT_134|SMT_133:SMT_134:L-serine dehydratase beta subunit:LysM domain protein:<-->:85328..85566 239 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_133:SMT_134|SMT_133:SMT_134:L-serine dehydratase beta subunit:LysM domain protein:<-->:85328..85566 239 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 89 End: 208 ........................................................................................ L Y C L F A D K T V F F P K N L S I F F L K T I N R C L L T L F R Y Y K F P I M ............................... Protein_Len: 31 Strand: - Start: 40 End: 132 ....................................... L I F T K A K I T S S F R K V S C I A Y F L M K Q L L F H S M ........................................................................................................... cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat 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: 153 End: 182 ........................................................................................................................................................CTTGACACTTTTATGTAGAAATATTACAAA......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 78 HP_score: -4.2 Tail_Score: -5.38321 Start: 105 End: 127 Full_Region: atttctctaaataag ccattttttg tta caaaagatgc ttttttatgctattt ........................................................................................................ccattttttgttacaaaagatgc................................................................................................................ TransTerm Strand: - Conf: 72 HP_score: -7.7 Tail_Score: -3.80552 Start: 106 End: 126 Full_Region: tttctctaaataagc cattttttg tta caaaagatg cttttttatgctatt .........................................................................................................cattttttgttacaaaagatg................................................................................................................. Find igs database================================================ Query_seq: SMT_133:SMT_134|SMT_133:SMT_134:L-serine dehydratase beta subunit:LysM domain protein:<-->:85328..85566 239 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactacaaatagcataaaaaagcatcttttgtaacaaaaaatggcttatttagagaaataaaaaataattttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Intra-Species Hit: Count: 1 Min: 1 Max: 239 Len: 239 Subject: smit_SMT_133_SMT_134|L-serine dehydratase beta subunit:LysM domain protein|NEGATIVE:POSITIVE|[85328,85566]|239 HSP 1 e-value: 2.0E-43 bit: 176.0 Len: 89 Query Start:1 Query End:89 Subject Strand: POSITIVE Subject Start: 1 Subject End: 89 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactac...................................................................................................................................................... cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaacctttttacactac...................................................................................................................................................... HSP 2 e-value: 3.0E-42 bit: 172.0 Len: 87 Query Start:153 Query End:239 Subject Strand: POSITIVE Subject Start: 153 Subject End: 239 ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttcaaat Inter-species Hit: Count: 3 Min: 1 Max: 235 Len: 235 Subject: NC_008533_SPD_0103_SPD_0104|L-serine dehydratase, iron-sulfur-dependent, beta subunit:LysM domain protein|NEGATIVE:POSITIVE|[103670,103910]|241 HSP 1 e-value: 8.0E-40 bit: 165.0 Len: 83 Query Start:153 Query End:235 Subject Strand: POSITIVE Subject Start: 155 Subject End: 237 ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... HSP 2 e-value: 3.0E-33 bit: 143.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... cagtttccccttataaaaattcttatctctattatatcaaagaatgaggggcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... Subject: NC_003098_spr0095_spr0096|L-serine dehydratase beta subunit:hypothetical protein|NEGATIVE:POSITIVE|[103670,103910]|241 HSP 1 e-value: 8.0E-40 bit: 165.0 Len: 83 Query Start:153 Query End:235 Subject Strand: POSITIVE Subject Start: 155 Subject End: 237 ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... HSP 2 e-value: 3.0E-33 bit: 143.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... cagtttccccttataaaaattcttatctctattatatcaaagaatgaggggcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... Subject: NC_003028_SP_0106_SP_0107|L-serine dehydratase, iron-sulfur-dependent, beta subunit:LysM domain protein|NEGATIVE:POSITIVE|[109163,109403]|241 HSP 1 e-value: 8.0E-40 bit: 165.0 Len: 83 Query Start:153 Query End:235 Subject Strand: POSITIVE Subject Start: 155 Subject End: 237 ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... ........................................................................................................................................................tttgtaatatttctacataaaagtgtcaagaaacggtaatatttaaagggtatgatagaactatagaaagaaggagaattttc.... HSP 2 e-value: 3.0E-33 bit: 143.0 Len: 80 Query Start:1 Query End:80 Subject Strand: POSITIVE Subject Start: 1 Subject End: 80 cagtttccccttataaaaattcttatctctattatatcaaagaatgaaggtcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... cagtttccccttataaaaattcttatctctattatatcaaagaatgaggggcttggctttaattgtggatgaaaaccttt............................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGUUUCCCCUUAUAAAAAUUCUUAUCUCUAUUAUAUCAAAGAAUGAAGGUCUUGGCUUUAAUUGUGGAUGAAAACCUUUUUACACUACAAAUAGCAUAAAAAAGCAUCUUUUGUAACAAAAAAUGGCUUAUUUAGAGAAAUAAAAAAUAAUUUUGUAAUAUUUCUACAUAAAAGUGUCAAGAAACGGUAAUAUUUAAAGGGUAUGAUAGAACUAUAGAAAGAAGGAGAAUUUUC ....(((.((((.......((((....(((((((((((....(((.(((((....))))).))).((((((...(((((((((((((..........((((.((((...((((......))))...)))).)))).(((((((..(((....)))....))))))).......)))))..))))).)))..))))))...))))))))))).....))))..)))).)))..... (-39.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAAAUUCUCCUUCUUUCUAUAGUUCUAUCAUACCCUUUAAAUAUUACCGUUUCUUGACACUUUUAUGUAGAAAUAUUACAAAAUUAUUUUUUAUUUCUCUAAAUAAGCCAUUUUUUGUUACAAAAGAUGCUUUUUUAUGCUAUUUGUAGUGUAAAAAGGUUUUCAUCCACAAUUAAAGCCAAGACCUUCAUUCUUUGAUAUAAUAGAGAUAAGAAUUUUUAUAAGGGGAAACUG .....((((((((........(((((((((......................(((((...((((..(((.((......((((((......(((((((....))))))).....)))))).......((.((((((((((((((....))))))))))))))..)).)).)))...)))).)))))...(((.....))).........))).)))))).....)))))))).... (-38.82) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 801 90 41 181 132 smit:SMT_133|5end_L-serine_dehydratase_beta_subunit_85237..85467_NEGATIVE 280 88 41 65 3 smit:SMT_1430|5end_hypothetical_protein_1414857..1415087_POSITIVE 280 49 3 116 56 smit:SMT_216|5end_Holliday_junction_DNA_helicase_RuvB_148257..148487_POSITIVE 280 49 3 116 56 smit:SMT_212|5end_Holliday_junction_DNA_helicase_RuvB_144830..145060_POSITIVE 262 230 200 84 53 smit:SMT_1025|5end_hypothetical_protein_960557..960787_NEGATIVE 261 68 27 179 120 smit:SMT_1985|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1914571..1914801_NEGATIVE 261 68 27 179 120 smit:SMT_299|5end_recombination_protein_U_243495..243725_NEGATIVE 255 229 181 45 4 smit:SMT_399|5end_cytochrome_c-type_biogenesis_protein_CcdA_328366..328596_POSITIVE 248 87 44 138 106 smit:SMT_1305|5end_glycerol_kinase_1268217..1268447_POSITIVE 238 69 21 146 101 smit:SMT_272|5end_hypothetical_protein_213315..213545_NEGATIVE 234 228 186 161 111 smit:SMT_1217|5end_hypothetical_protein_1176603..1176833_NEGATIVE 228 67 25 95 45 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 222 69 21 158 99 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 218 100 53 71 15 smit:SMT_1688|5end_putative_N-acylglucosamine-6-phosphate_2-epimerase_1671350..1671580_POSITIVE 218 35 1 135 99 smit:SMT_534|5end_hypothetical_protein_predicted_by_Glimmer/Critica_453571..453801_POSITIVE 218 35 1 135 99 smit:SMT_531|5end_hypothetical_protein_predicted_by_Glimmer/Critica_452672..452902_POSITIVE 218 35 1 135 99 smit:SMT_527|5end_hypothetical_protein_predicted_by_Glimmer/Critica_451502..451732_POSITIVE 218 35 1 135 99 smit:SMT_511|5end_hypothetical_protein_predicted_by_Glimmer/Critica_439391..439621_POSITIVE 218 35 1 135 99 smit:SMT_478|5end_hypothetical_protein_predicted_by_Glimmer/Critica_414644..414874_POSITIVE 217 80 31 177 125 smit:SMT_1485|5end_exodeoxyribonuclease_1465825..1466055_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 88 41 64 2 smit:SMT_1429|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1414936..1415086_POSITIVE 234 228 186 76 26 smit:SMT_1218|3end_DNA_polymerase_I_1176688..1176838_NEGATIVE 232 57 20 138 99 smit:SMT_1964|3end_sodium/hydrogen_exchanger_family_protein_1896596..1896746_NEGATIVE 221 71 42 133 106 smit:SMT_2093|3end_hypothetical_protein_LOC618557_1989186..1989336_POSITIVE 217 67 26 47 7 smit:SMT_167|3end_acetyltransferase,_GNAT_family_113757..113907_POSITIVE 214 81 49 40 3 smit:SMT_1481|3end_endopeptidase_O_1463094..1463244_POSITIVE 208 70 26 49 3 smit:SMT_1135|3end_glucose-6-phosphate_isomerase_1076592..1076742_NEGATIVE 207 202 168 151 117 smit:SMT_1163|3end_hypothetical_protein_1109096..1109246_NEGATIVE 205 56 25 65 39 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 204 58 21 130 89 smit:SMT_275|3end_transcriptional_activator-exopolysaccharide_biosynthesis_218894..219044_POSITIVE 203 88 47 69 21 smit:SMT_1007|3end_radical_SAM_domain_protein_947549..947699_POSITIVE 201 75 47 65 30 smit:SMT_887|3end_ABC-type_polar_amino_acid_transport_system,_ATPase_component_835528..835678_POSITIVE 200 55 22 112 68 smit:SMT_1500|3end_K03742_competence/damage-inducible_protein_CinA_N-terminal_domain_1484426..1484576_POSITIVE 198 58 20 127 88 smit:SMT_806|3end_hypothetical_protein_715867..716017_NEGATIVE 198 87 48 51 9 smit:SMT_533|3end_RNA_binding_protein_453537..453687_POSITIVE 198 87 48 51 9 smit:SMT_530|3end_RNA_binding_protein_452638..452788_POSITIVE 198 87 48 51 9 smit:SMT_526|3end_RNA_binding_protein_451468..451618_POSITIVE 198 87 48 51 9 smit:SMT_510|3end_hypothetical_protein_439357..439507_POSITIVE 197 71 32 77 19 smit:SMT_864|3end_K07485_transposase_814971..815121_POSITIVE 196 69 21 137 82 smit:SMT_981|3end_hypothetical_protein_929202..929352_POSITIVE