Origin IGS: agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa .........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 ttctatttaaaatcttactcttcattgtaccacaatttgagcagaaaattatggaaaagcaagaagctttttttcgtttttacagtaagatacgtttttatttattcatccctatattatatgttataatgaatgtaaaagttcaataatctagtctttttccaacacgactcatttaaaggagcctttct Mask Tandem Repeat Region ================================================ agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Find is-nt database================================================ Query_seq: SMT_1701:SMT_1702|SMT_1701:SMT_1702:transcriptional regulator, RpiR family:penicillin-binding protein 2B:<-->:1684541..1684731 191 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1701:SMT_1702|SMT_1701:SMT_1702:transcriptional regulator, RpiR family:penicillin-binding protein 2B:<-->:1684541..1684731 191 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1701:SMT_1702|SMT_1701:SMT_1702:transcriptional regulator, RpiR family:penicillin-binding protein 2B:<-->:1684541..1684731 191 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: - Start: 66 End: 167 ................................................................. L M Y Y L S S Y I F V Y R V T F V F F L K K S K W L K R S L N H Y M ........................ Protein_Len: 45 Strand: - Start: 46 End: 180 ............................................. Q V K V N M I V Y L I P I F L Y F R I K S Y F R F F A E Q K E M I K Q E F Q P V I F L L M ........... agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa 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: 81 Start: 62 End: 91 .............................................................TTTATTCATCCCTATATTATATGTTATAAT.................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1701:SMT_1702|SMT_1701:SMT_1702:transcriptional regulator, RpiR family:penicillin-binding protein 2B:<-->:1684541..1684731 191 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgtaaaaacgaaaaaaagcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Intra-Species Hit: Count: 1 Min: 1 Max: 191 Len: 191 Subject: smit_SMT_1701_SMT_1702|transcriptional regulator, RpiR family:penicillin-binding protein 2B|NEGATIVE:POSITIVE|[1684541,1684731]|191 HSP 1 e-value: 5.0E-56 bit: 218.0 Len: 110 Query Start:1 Query End:110 Subject Strand: POSITIVE Subject Start: 1 Subject End: 110 agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgt................................................................................. agaaaggctcctttaaatgagtcgtgttggaaaaagactagattattgaacttttacattcattataacatataatatagggatgaataaataaaaacgtatcttactgt................................................................................. HSP 2 e-value: 2.0E-30 bit: 133.0 Len: 67 Query Start:125 Query End:191 Subject Strand: POSITIVE Subject Start: 125 Subject End: 191 ............................................................................................................................gcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa ............................................................................................................................gcttcttgcttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaaatagaa Inter-species Hit: Count: 3 Min: 59 Max: 185 Len: 127 Subject: NC_008533_SPD_1486_SPD_1487|penicillin-binding protein 2B:phosphosugar-binding transcriptional regulator, putative|NEGATIVE:POSITIVE|[1503805,1504003]|199 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 53 Query Start:133 Query End:185 Subject Strand: NEGATIVE Subject Start: 8 Subject End: 60 ....................................................................................................................................cttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaa...... ....................................................................................................................................cttttccataattttctactcaaattgtggtacaattaagagtaagattttaa...... HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 46 Query Start:59 Query End:104 Subject Strand: NEGATIVE Subject Start: 97 Subject End: 142 ..........................................................ttcattataacatataatatagggatgaataaataaaaacgtatct....................................................................................... ..........................................................ttcattataacacataatataaggatagataaataaaaacgcatct....................................................................................... Subject: NC_003098_spr1517_spr1518|Penicillin-binding protein 2B:hypothetical protein|NEGATIVE:POSITIVE|[1496274,1496472]|199 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 53 Query Start:133 Query End:185 Subject Strand: NEGATIVE Subject Start: 8 Subject End: 60 ....................................................................................................................................cttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaa...... ....................................................................................................................................cttttccataattttctactcaaattgtggtacaattaagagtaagattttaa...... HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 46 Query Start:59 Query End:104 Subject Strand: NEGATIVE Subject Start: 97 Subject End: 142 ..........................................................ttcattataacatataatatagggatgaataaataaaaacgtatct....................................................................................... ..........................................................ttcattataacacataatataaggatagataaataaaaacgcatct....................................................................................... Subject: NC_003028_SP_1673_SP_1674|penicillin-binding protein 2B:phosphosugar-binding transcriptional regulator, putative|NEGATIVE:POSITIVE|[1575039,1575252]|214 HSP 1 e-value: 3.0E-17 bit: 89.7 Len: 53 Query Start:133 Query End:185 Subject Strand: NEGATIVE Subject Start: 23 Subject End: 75 ....................................................................................................................................cttttccataattttctgctcaaattgtggtacaatgaagagtaagattttaa...... ....................................................................................................................................cttttccataattttctactcaaattgtggtacaattaagagtaagattttaa...... HSP 2 e-value: 7.0E-6 bit: 52.0 Len: 46 Query Start:59 Query End:104 Subject Strand: NEGATIVE Subject Start: 112 Subject End: 157 ..........................................................ttcattataacatataatatagggatgaataaataaaaacgtatct....................................................................................... ..........................................................ttcattataacacataatataaggatagataaataaaaacgcatct....................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAUUAUAACAUAUAAUAUAGGGAUGAAUAAAUAAAAACGUAUCUUACUGUAAAAACGAAAAAAAGCUUCUUGCUUUUCCAUAAUUUUCUGCUCAAAUUGUGGUACAAUGAAGAGUAAGAUUUUAA ((((((.................)))))).............((((((((.(..........((((((.....))))))(((((((((.......)))))))))........).))))))))..... (-20.43) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAAAAUCUUACUCUUCAUUGUACCACAAUUUGAGCAGAAAAUUAUGGAAAAGCAAGAAGCUUUUUUUCGUUUUUACAGUAAGAUACGUUUUUAUUUAUUCAUCCCUAUAUUAUAUGUUAUAAUGAA .....((((((((.(((((((.....)))..))))..((((((...((((((((.....))))))))..))))))..)))))))).............(((((...((((........))))))))) (-18.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 707 70 21 219 170 smit:SMT_1701|5end_transcriptional_regulator,_RpiR_family_1684450..1684680_NEGATIVE 291 106 66 80 44 smit:SMT_951|5end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_900098..900328_NEGATIVE 286 105 66 141 97 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 245 118 71 132 78 smit:SMT_1744|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1725288..1725518_NEGATIVE 241 102 67 127 95 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 232 88 44 165 119 smit:SMT_293|5end_dTDP-4-dehydrorhamnose_reductase_235919..236149_POSITIVE 227 109 70 226 175 smit:SMT_1199|5end_lactococcin_A_ABC_transporter_permease_protein_1161063..1161293_NEGATIVE 226 103 67 47 3 smit:SMT_548|5end_K02035_peptide/nickel_transport_system_substrate-binding_protein_464992..465222_POSITIVE 224 110 66 195 144 smit:SMT_1803|5end_K03693_penicillin_binding_protein_1776804..1777034_POSITIVE 224 94 66 127 100 smit:SMT_1543|5end_diphosphomevalonate_decarboxylase_1528024..1528254_NEGATIVE 223 107 67 130 85 smit:SMT_938|5end_hypothetical_protein_891274..891504_NEGATIVE 221 105 64 79 39 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 216 120 71 190 134 smit:SMT_1739|5end_hypothetical_protein_1721263..1721493_POSITIVE 214 108 65 74 27 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 211 108 69 206 159 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 209 117 82 104 75 smit:SMT_1819|5end_K03442_small_conductance_mechanosensitive_ion_channel,_MscS_family_1793047..1793277_POSITIVE 209 74 36 143 109 smit:SMT_1215|5end_aromatic_amino_acid_aminotransferase_1174588..1174818_NEGATIVE 207 112 74 124 78 smit:SMT_1072|5end_Cof_family_protein_1011193..1011423_NEGATIVE 206 94 68 116 92 smit:SMT_1400|5end_acetoin_dehydrogenase_complex,_E1_component,_alpha_subunit_1376029..1376259_POSITIVE 206 108 65 177 139 smit:SMT_973|5end_signal_transduction_histidine_kinase_922177..922407_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 106 66 63 27 smit:SMT_952|3end_hypothetical_protein_900115..900265_NEGATIVE 286 105 66 148 104 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 245 118 71 148 94 smit:SMT_1745|3end_UDP-glucose_4-epimerase_1725272..1725422_NEGATIVE 241 102 67 130 98 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 232 88 44 99 53 smit:SMT_292|3end_dTDP-glucose_4,6-dehydratase_235933..236083_POSITIVE 224 94 66 145 118 smit:SMT_1544|3end_mevalonate_kinase_1528006..1528156_NEGATIVE 221 105 64 89 49 smit:SMT_878|3end_excinuclease_ABC,_subunit_C_824402..824552_NEGATIVE 213 119 72 128 82 smit:SMT_1888|3end_K02026_multiple_sugar_transport_system_permease_protein_1842842..1842992_POSITIVE 212 98 67 148 113 smit:SMT_2062|3end_phosphoglycerate_mutase_1970913..1971063_NEGATIVE 201 105 61 110 62 smit:SMT_1092|3end_transcription_antitermination_factor_1033160..1033310_NEGATIVE 200 110 67 147 107 smit:SMT_939|3end_phosphomethylpyrimidine_kinase_891252..891402_NEGATIVE 199 105 71 76 43 smit:SMT_383|3end_cysteinyl-tRNA_synthetase_319407..319557_POSITIVE 197 118 76 124 82 smit:SMT_1527|3end_two-component_sensor_kinase_1510566..1510716_NEGATIVE 197 117 75 102 50 smit:SMT_1434|3end_neopullulanase_1417903..1418053_NEGATIVE 194 103 68 128 97 smit:SMT_1733|3end_DNA_repair_protein_RecN_1718636..1718786_POSITIVE 190 115 74 47 4 smit:SMT_477|3end_K03308_neurotransmitter:Na+_symporter,_NSS_family_414232..414382_NEGATIVE 189 110 68 118 69 smit:SMT_2056|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1966735..1966885_POSITIVE 189 107 65 134 81 smit:SMT_154|3end_K03647_protein_involved_in_ribonucleotide_reduction_102474..102624_POSITIVE 188 79 46 49 18 smit:SMT_1931|3end_23S_rRNA_methyltransferase_1870796..1870946_NEGATIVE 188 120 77 148 99 smit:SMT_871|3end_K03311_branched-chain_amino_acid:cation_transporter,_LIVCS_family_818835..818985_NEGATIVE