Origin IGS: gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag .........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 cttgttttccaagatggcaatctcttcctctaaaccttcgaggtcaaagagaccccctgaaagaagctaatttttcacgatttgcgtcaattttctgacgaatttctgaaatgtccataaatactccttttttacattatttcattatagcatattttatcatttctttccatcttttgctctaatcccttattacacgtaaaaagaagcctttcggcttcccttc Mask Tandem Repeat Region ================================================ gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Find is-nt database================================================ Query_seq: SMT_494:SMT_495|SMT_494:SMT_495:K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2):->->:428952..429177 226 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_494:SMT_495|SMT_494:SMT_495:K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2):->->:428952..429177 226 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_494:SMT_495|SMT_494:SMT_495:K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2):->->:428952..429177 226 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Predict ORF larger than 30AA ================================================ gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag 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: 84 Start: 54 End: 83 .....................................................ATGGAAAGAAATGATAAAATATGCTATAAT............................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_494:SMT_495|SMT_494:SMT_495:K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2):->->:428952..429177 226 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Intra-Species Hit: Count: 1 Min: 1 Max: 226 Len: 226 Subject: smit_SMT_494_SMT_495|K04767 acetoin utilization protein AcuB:bacterial peptide chain release factor 2 (RF-2)|POSITIVE:POSITIVE|[428952,429177]|226 HSP 1 e-value: 1.0E-125 bit: 448.0 Len: 226 Query Start:1 Query End:226 Subject Strand: POSITIVE Subject Start: 1 Subject End: 226 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaacaag Inter-species Hit: Count: 4 Min: 1 Max: 222 Len: 222 Subject: NC_008533_SPD_0657_SPD_0658|acetoin utilization protein AcuB, putative:peptide chain release factor 2|POSITIVE:POSITIVE|[675788,676000]|213 HSP 1 e-value: 4.0E-94 bit: 345.0 Len: 214 Query Start:1 Query End:214 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatc............ gaagggaagcccaaaggcttcttttttcatgaaa-aggggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagtaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaagggctagaggaagagattgccatc............ Subject: NC_003098_spr0664_spr0665|hypothetical protein:peptide chain release factor 2|POSITIVE:POSITIVE|[668257,668469]|213 HSP 1 e-value: 4.0E-94 bit: 345.0 Len: 214 Query Start:1 Query End:214 Subject Strand: POSITIVE Subject Start: 1 Subject End: 213 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatc............ gaagggaagcccaaaggcttcttttttcatgaaa-aggggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtatttatggacatttcagtaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaagggctagaggaagagattgccatc............ Subject: NC_009009_SSA_0868_SSA_0869|hypothetical protein:Peptide chain release factor 2, putative|NEGATIVE:POSITIVE|[861626,862053]|428 HSP 1 e-value: 2.0E-40 bit: 167.0 Len: 120 Query Start:103 Query End:222 Subject Strand: POSITIVE Subject Start: 305 Subject End: 424 ......................................................................................................gtatttatggacatttcagaaattcgtcagaaaattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacctcgaaggtttagaggaagagattgccatcttggaaaa.... ......................................................................................................gtatttatggacatttcagaaattcgtcaaaagattgacgcaaatcgtgaaaaattagcttctttcagggggtctctttgacttagaaggtctggaagaagaaattgccatcttagaaaa.... Subject: NC_003028_SP_0754_SP_0755|acetoin utilization protein AcuB, putative:peptide chain release factor 2|POSITIVE:POSITIVE|[713596,713702]|107 HSP 1 e-value: 5.0E-38 bit: 159.0 Len: 108 Query Start:1 Query End:108 Subject Strand: POSITIVE Subject Start: 1 Subject End: 107 gaagggaagccgaaaggcttctttttacgtgtaataagggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtattt...................................................................................................................... gaagggaagcccaaaggcttcttttttcatgaaa-aggggattagagcaaaagatggaaagaaatgataaaatatgctataatgaaataatgtaaaaaaggagtattt...................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAAGGGAAGCCGAAAGGCUUCUUUUUACGUGUAAUAAGGGAUUAGAGCAAAAGAUGGAAAGAAAUGAUAAAAUAUGCUAUAAUGAAAUAAUGUAAAAAAGGAGUAUUUAUGGACAUUUCAGAAAUUCGUCAGAAAAUUGACGCAAAUCGUGAAAAAUUAGCUUCUUUCAGGGGGUCUCUUUGACCUCGAAGGUUUAGAGGAAGAGAUUGCCAUCUUGGAAAA (((((((((((....)))))))))))...(((..(((....)))..))).((((..(((((((.((((.....(((((((((........................)))))).)))((((((....((((((....))))))....)).))))..))))..))))))).((.((((((((...((((.........)))))))))))).)).))))...... (-55.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUCCAAGAUGGCAAUCUCUUCCUCUAAACCUUCGAGGUCAAAGAGACCCCCUGAAAGAAGCUAAUUUUUCACGAUUUGCGUCAAUUUUCUGACGAAUUUCUGAAAUGUCCAUAAAUACUCCUUUUUUACAUUAUUUCAUUAUAGCAUAUUUUAUCAUUUCUUUCCAUCUUUUGCUCUAAUCCCUUAUUACACGUAAAAAGAAGCCUUUCGGCUUCCCUUC ......(((((((...((((((((((.........))))...)))))).....(((((...((((.........((....(((((......)))))....)).((((((.....(((........))).....))))))....))))...)))))..........))))))).............................((((((....))))))..... (-41.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 311 206 170 175 139 smit:SMT_1048|5end_K06518_holin-like_protein_988142..988372_POSITIVE 288 204 161 208 166 smit:SMT_413|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_356677..356907_POSITIVE 285 209 167 80 30 smit:SMT_1524|5end_peptidase_T_1504564..1504794_POSITIVE 277 217 171 196 144 smit:SMT_989|5end_hypothetical_protein_933548..933778_NEGATIVE 268 217 171 68 15 smit:SMT_1717|5end_DNA-3-methyladenine_glycosylase_I_1704274..1704504_NEGATIVE 268 219 172 97 42 smit:SMT_1472|5end_hypothetical_protein,_coenzyme_PQQ_synthesis_homologue_1454262..1454492_NEGATIVE 268 45 1 198 149 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 267 193 151 67 17 smit:SMT_1523|5end_ferrochelatase_1504460..1504690_NEGATIVE 265 200 155 95 52 smit:SMT_541|5end_K03697_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpE_457842..458072_NEGATIVE 262 46 10 133 88 smit:SMT_1701|5end_transcriptional_regulator,_RpiR_family_1684450..1684680_NEGATIVE 259 48 3 186 143 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 257 193 158 112 79 smit:SMT_1873|5end_K02006_cobalt_transport_system_ATP-binding_protein_1831936..1832166_POSITIVE 257 209 167 44 4 smit:SMT_1693|5end_dimethyladenosine_transferase_1675800..1676030_POSITIVE 256 219 171 142 93 smit:SMT_1407|5end_ribonuclease_HII_1386309..1386539_NEGATIVE 256 218 174 66 26 smit:SMT_920|5end_serine/threonine_protein_kinase_874501..874731_NEGATIVE 255 220 176 132 96 smit:SMT_2044|5end_transcriptional_activator_TipA,_putative_1955885..1956115_NEGATIVE 253 202 164 210 166 smit:SMT_959|5end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_905283..905513_POSITIVE 252 219 174 117 69 smit:SMT_1691|5end_putative_deoxyribonuclease_1674978..1675208_POSITIVE 251 219 171 134 74 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 250 208 167 186 142 smit:SMT_418|5end_putative_transcriptional_regulator_362140..362370_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 286 200 157 125 76 smit:SMT_1086|3end_K01992_ABC-2_type_transport_system_permease_protein_1022542..1022692_NEGATIVE 269 201 162 58 13 smit:SMT_1512|3end_hypothetical_protein_1493896..1494046_NEGATIVE 268 217 171 58 5 smit:SMT_1718|3end_Holliday_junction_DNA_helicase_RuvA_1704284..1704434_NEGATIVE 268 45 1 94 45 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 267 218 171 47 1 smit:SMT_1481|3end_endopeptidase_O_1463094..1463244_POSITIVE 256 218 174 69 29 smit:SMT_921|3end_putative_PP2C_protein_phosphatase_874498..874648_NEGATIVE 254 193 160 146 101 smit:SMT_804|3end_S-adenosylmethionine_synthetase_713884..714034_NEGATIVE 253 190 148 150 100 smit:SMT_990|3end_hypothetical_protein_933558..933708_NEGATIVE 253 202 164 86 42 smit:SMT_958|3end_hypothetical_protein_predicted_by_Glimmer/Critica_905239..905389_POSITIVE 253 204 161 89 42 smit:SMT_593|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_510317..510467_POSITIVE 248 201 169 83 56 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 243 200 156 139 90 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 240 200 157 50 9 smit:SMT_665|3end_NAD+_kinase_575927..576077_NEGATIVE 239 49 2 72 9 smit:SMT_1710|3end_magnesium-translocating_P-type_ATPase_1695578..1695728_NEGATIVE 238 199 163 66 18 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 236 48 3 58 15 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 236 48 3 56 13 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 235 215 171 92 35 smit:SMT_2088|3end_glucose-1-phosphate_thymidylyltransferase_1985066..1985216_POSITIVE 235 220 171 70 12 smit:SMT_1722|3end_x-prolyl-dipeptidyl_aminopeptidase_1709012..1709162_POSITIVE 235 200 151 52 6 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE