Origin IGS: ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttaattaannnnngaccttagctttagtagataataaagaagaaggacaagaaattgatcctaaagctgtcattcgtaatttccaaaatctaccaggtcgatattactttggagcagatggtcgtagagtattaccacttccagag Mask Tandem Repeat Region ================================================ ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Find is-nt database================================================ Query_seq: SMT_1987:SMT_1988|SMT_1987:SMT_1988:hypothetical protein predicted by Glimmer/Critica:two-component sensor kinase YesM:<-<-:1916416..1916561 146 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1987:SMT_1988|SMT_1987:SMT_1988:hypothetical protein predicted by Glimmer/Critica:two-component sensor kinase YesM:<-<-:1916416..1916561 146 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1987:SMT_1988|SMT_1987:SMT_1988:hypothetical protein predicted by Glimmer/Critica:two-component sensor kinase YesM:<-<-:1916416..1916561 146 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: - Start: 3 End: 116 .. Q F H Y Y E V V M Q E L T I D V Q Y I K S I V F S L K L I L K K D K K K I M .............................. Protein_Len: 31 Strand: - Start: 1 End: 93 E P L P L V R R G D A G F Y Y R G P L N Q F N R I V A K P D M ..................................................... ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa 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: 60 End: 89 ...........................................................TTTGGAAATTACGAATGACAGCTTTAGGAT......................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1987:SMT_1988|SMT_1987:SMT_1988:hypothetical protein predicted by Glimmer/Critica:two-component sensor kinase YesM:<-<-:1916416..1916561 146 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtcnnnnnttaattaa Intra-Species Hit: Count: 1 Min: 1 Max: 133 Len: 133 Subject: smit_SMT_1987_SMT_1988|hypothetical protein predicted by Glimmer/Critica:two-component sensor kinase YesM|NEGATIVE:NEGATIVE|[1916416,1916561]|146 HSP 1 e-value: 7.0E-70 bit: 264.0 Len: 133 Query Start:1 Query End:133 Subject Strand: POSITIVE Subject Start: 1 Subject End: 133 ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtc............. ctctggaagtggtaatactctacgaccatctgctccaaagtaatatcgacctggtagattttggaaattacgaatgacagctttaggatcaatttcttgtccttcttctttattatctactaaagctaaggtc............. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUCUGGAAGUGGUAAUACUCUACGACCAUCUGCUCCAAAGUAAUAUCGACCUGGUAGAUUUUGGAAAUUACGAAUGACAGCUUUAGGAUCAAUUUCUUGUCCUUCUUCUUUAUUAUCUACUAAAGCUAAGGUC ...(((..((((.......))))..)))..((((....)))).....((((((((((((...((((.....(((.((((.....((((.....)))))))).))))))).....))))))).......))))) (-25.11) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GACCUUAGCUUUAGUAGAUAAUAAAGAAGAAGGACAAGAAAUUGAUCCUAAAGCUGUCAUUCGUAAUUUCCAAAAUCUACCAGGUCGAUAUUACUUUGGAGCAGAUGGUCGUAGAGUAUUACCACUUCCAGAG (((((........((((((...........(((((((....))).))))...((........))..........)))))).))))).......(((((((..((.((((.(((...))).))))))))))))) (-28.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 921 50 1 141 92 smit:SMT_1987|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1916325..1916555_NEGATIVE 366 109 61 193 146 smit:SMT_601|5end_hypothetical_protein_516864..517094_POSITIVE 318 49 4 84 32 smit:SMT_2171|5end_UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-_diaminopimelate--D-alanyl-D-alanine_ligase_2042271..2042501_POSITIVE 279 90 45 52 5 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 268 67 27 136 92 smit:SMT_1846|5end_acyl-ACP_thioesterase,_putative_1811410..1811640_POSITIVE 266 50 5 162 121 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 266 58 18 70 28 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 256 56 18 155 121 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 256 64 26 74 43 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 253 109 70 104 59 smit:SMT_1352|5end_formamidopyrimidine-DNA_glycosylase_1330641..1330871_NEGATIVE 251 55 26 50 15 smit:SMT_2102|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1994533..1994763_NEGATIVE 251 55 26 50 15 smit:SMT_2025|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1941765..1941995_NEGATIVE 248 57 19 203 154 smit:SMT_889|5end_K02029_polar_amino_acid_transport_system_permease_protein_836266..836496_POSITIVE 247 38 2 216 182 smit:SMT_2169|5end_hypothetical_protein_2041847..2042077_NEGATIVE 246 109 71 131 89 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 246 114 75 108 52 smit:SMT_397|5end_NAD(+)_synthetase_326519..326749_POSITIVE 245 120 72 98 43 smit:SMT_1870|5end_K07566_putative_translation_factor_1829819..1830049_NEGATIVE 241 50 1 185 138 smit:SMT_1589|5end_hypothetical_protein_1578332..1578562_POSITIVE 241 66 29 75 42 smit:SMT_1491|5end_capsular_polysaccharide_biosynthesis_protein,_putative_1471588..1471818_POSITIVE 240 52 18 74 44 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 266 58 18 73 31 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 253 109 70 55 10 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE 248 128 81 106 56 smit:SMT_1265|3end_hypothetical_protein_1230872..1231022_NEGATIVE 246 114 75 111 55 smit:SMT_396|3end_putative_nicotinate_phosphoribosyltransferase_326602..326752_POSITIVE 245 120 72 114 59 smit:SMT_1871|3end_modification_methylase,_HemK_family_1829803..1829953_NEGATIVE 244 43 3 150 107 smit:SMT_1885|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1839830..1839980_NEGATIVE 240 52 18 77 47 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 239 127 84 85 38 smit:SMT_1241|3end_hypothetical_protein_1202952..1203102_POSITIVE 232 35 3 63 31 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 229 120 78 65 32 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 228 65 23 72 39 smit:SMT_1177|3end_immunoglobulin_A1_protease_1129193..1129343_NEGATIVE 228 101 71 53 21 smit:SMT_876|3end_hypothetical_protein_predicted_by_Glimmer/Critica_823371..823521_NEGATIVE 226 70 24 146 100 smit:SMT_1888|3end_K02026_multiple_sugar_transport_system_permease_protein_1842842..1842992_POSITIVE 226 66 31 149 111 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 224 129 94 85 49 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 220 98 51 133 79 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 219 58 20 41 11 smit:SMT_1190|3end_phosphoribosylaminoimidazole_carboxylase,_catalytic_subunit_1147741..1147891_NEGATIVE 219 101 61 138 99 smit:SMT_796|3end_K03734_thiamine_biosynthesis_lipoprotein_705184..705334_POSITIVE 216 56 14 59 13 smit:SMT_1804|3end_hypothetical_protein_1780314..1780464_POSITIVE 216 102 72 36 8 smit:SMT_360|3end_K07742_hypothetical_protein_296001..296151_POSITIVE