Origin IGS: gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtacgtattattattgcttaattggttgttgttgaaatcgattaactttgttgcccgcgaaagtactgaaactctttcatatagagggaaaaataacgataaattcagacaagagacgatagacaagagtatcagaacataaaaggagcgagtctcacgactcactccttcccaaattaaccaaaaccttaactatgaaaaatcttacttttccatcacaaacataatgagcacgaagtagttttacaaacttttgtcggtaataatcgagataatacgacaatttgatataacatacaagc Mask Tandem Repeat Region ================================================ gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Find is-nt database================================================ Query_seq: PG1012:PG1013|PG1012:PG1013:tRNA-i(6)A37 modification enzyme MiaB:acetyl-CoA hydrolase/transferase family protein:<-->:1071571..1071873 303 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1012:PG1013|PG1012:PG1013:tRNA-i(6)A37 modification enzyme MiaB:acetyl-CoA hydrolase/transferase family protein:<-->:1071571..1071873 303 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1012:PG1013|PG1012:PG1013:tRNA-i(6)A37 modification enzyme MiaB:acetyl-CoA hydrolase/transferase family protein:<-->:1071571..1071873 303 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 14 End: 145 ............. M K L S Y Y L D Y Y R Q K F V K L L R A H Y V C D G K V R F F I V K V L V N L G R S E S .............................................................................................................................................................. Protein_Len: 59 Strand: + Start: 126 End: 302 ............................................................................................................................. M W E G V S R E T R S F Y V L I L L S I V S C L N L S L F F P L Y E R V S V L S R A T K L I D F N N N Q L S N N N T Y . Protein_Len: 42 Strand: - Start: 164 End: 289 ................................................................................................................................................................... T R I S K D I T E Q R F K D N N K G R Y S L T E T S E R A V F N I S K L L L W N L M .............. gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact 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: 2 End: 31 .CTTGTATGTTATATCAAATTGTCGTATTAT................................................................................................................................................................................................................................................................................ PromScan Matrix: RpoD-17 Strand: + Score: 81 Start: 53 End: 82 ....................................................TTTGTAAAACTACTTCGTGCTCATTATGTT............................................................................................................................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.2 Tail_Score: -4.75289 Start: 135 End: 158 Full_Region: TGGTTAATTTGGGAA GGAGTGAGTC GTGA GACTCGCTCC TTTTATGTTCTGATA ......................................................................................................................................GGAGTGAGTCGTGAGACTCGCTCC................................................................................................................................................. Find igs database================================================ Query_seq: PG1012:PG1013|PG1012:PG1013:tRNA-i(6)A37 modification enzyme MiaB:acetyl-CoA hydrolase/transferase family protein:<-->:1071571..1071873 303 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Intra-Species Hit: Count: 1 Min: 1 Max: 303 Len: 303 Subject: NC_002950_PG1012_PG1013|tRNA-i(6)A37 modification enzyme MiaB:acetyl-CoA hydrolase/transferase family protein|NEGATIVE:POSITIVE|[1071571,1071873]|303 HSP 1 e-value: 1.0E-171 bit: 601.0 Len: 303 Query Start:1 Query End:303 Subject Strand: POSITIVE Subject Start: 1 Subject End: 303 gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact gcttgtatgttatatcaaattgtcgtattatctcgattattaccgacaaaagtttgtaaaactacttcgtgctcattatgtttgtgatggaaaagtaagatttttcatagttaaggttttggttaatttgggaaggagtgagtcgtgagactcgctccttttatgttctgatactcttgtctatcgtctcttgtctgaatttatcgttatttttccctctatatgaaagagtttcagtactttcgcgggcaacaaagttaatcgatttcaacaacaaccaattaagcaataataatacgtact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUUGUAUGUUAUAUCAAAUUGUCGUAUUAUCUCGAUUAUUACCGACAAAAGUUUGUAAAACUACUUCGUGCUCAUUAUGUUUGUGAUGGAAAAGUAAGAUUUUUCAUAGUUAAGGUUUUGGUUAAUUUGGGAAGGAGUGAGUCGUGAGACUCGCUCCUUUUAUGUUCUGAUACUCUUGUCUAUCGUCUCUUGUCUGAAUUUAUCGUUAUUUUUCCCUCUAUAUGAAAGAGUUUCAGUACUUUCGCGGGCAACAAAGUUAAUCGAUUUCAACAACAACCAAUUAAGCAAUAAUAAUACGUACU (.((((.((((..(((...((((((((.((.......)).)).))))))..(((((..(((.((((....((((.((((((....((.(((((((((((((..(((((((.((((((.(..(..(((...((((((((((((((....))))))))))))))..))))..).)).)))).)))............))))...))).)))))))))).)).))))))..))))...)))).)))..))))).............)))...)))))))).)........................ (-74.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUACGUAUUAUUAUUGCUUAAUUGGUUGUUGUUGAAAUCGAUUAACUUUGUUGCCCGCGAAAGUACUGAAACUCUUUCAUAUAGAGGGAAAAAUAACGAUAAAUUCAGACAAGAGACGAUAGACAAGAGUAUCAGAACAUAAAAGGAGCGAGUCUCACGACUCACUCCUUCCCAAAUUAACCAAAACCUUAACUAUGAAAAAUCUUACUUUUCCAUCACAAACAUAAUGAGCACGAAGUAGUUUUACAAACUUUUGUCGGUAAUAAUCGAGAUAAUACGACAAUUUGAUAUAACAUACAAGC .((.(((((((((.....((((((((((........))))))))))..((((((((.((((((((..(((((((.((((.....((.((((((.(((.(((...((((.....(((..((((........)))).........((((((.(((((....))))).)))))).................))).....))))..)))))).)))))).)).....(.....).....)))).)))))))...)))))))).))))))))....)))))))))))..................... (-70.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 817 90 41 181 132 NC_002950:PG1012|5end_tRNA-i(6)A37_modification_enzyme_MiaB_1071480..1071710_NEGATIVE 332 173 135 188 154 NC_002950:PG2133|5end_lipoprotein,_putative_2239002..2239232_POSITIVE 318 159 116 201 165 NC_002950:PG2201|5end_peptide_deformylase_2309412..2309642_NEGATIVE 317 159 114 68 11 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 294 160 119 200 164 NC_002950:PG2008|5end_TonB-dependent_receptor,_putative_2095243..2095473_POSITIVE 294 180 131 167 106 NC_002950:PG0670|5end_lipoprotein,_putative_720752..720982_POSITIVE 286 160 114 187 138 NC_002950:PG1772|5end_endonuclease_III_1859079..1859309_POSITIVE 284 157 114 139 98 NC_002950:PG1561|5end_dTDP-4-dehydrorhamnose_reductase_1640995..1641225_NEGATIVE 283 269 228 61 15 NC_002950:PG1771|5end_phenylalanyl-tRNA_synthetase_alpha_subunit_1858038..1858268_POSITIVE 283 190 143 208 165 NC_002950:PG1334|5end_band_7/Mec-2_family_protein_1416402..1416632_NEGATIVE 280 156 115 203 160 NC_002950:PG0109|5end_hypothetical_protein_131331..131561_POSITIVE 279 165 127 147 115 NC_002950:PG1963|5end_Sua5/YciO/YrdC/YwlC_family_protein_2052338..2052568_POSITIVE 279 170 129 194 152 NC_002950:PG0598|5end_hypothetical_protein_654477..654707_POSITIVE 277 264 223 190 156 NC_002950:PG2167|5end_immunoreactive_53_kDa_antigen_PG123_2273543..2273773_NEGATIVE 277 196 153 119 80 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 276 178 135 178 130 NC_002950:PG1795|5end_hypothetical_protein_1889776..1890006_NEGATIVE 275 89 64 118 93 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 275 145 107 231 186 NC_002950:PG1551|5end_hmuY_protein_1628438..1628668_POSITIVE 274 170 129 159 127 NC_002950:PG2187|5end_1,4-dihydroxy-2-naphthoate_octaprenyltransferase_2294643..2294873_NEGATIVE 273 159 129 207 163 NC_002950:PG1433|5end_hydrolase_1518831..1519061_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 332 173 135 49 15 NC_002950:PG2132|3end_fimbrilin_2238943..2239093_POSITIVE 324 192 151 58 16 NC_002950:PG1449|3end_hypothetical_protein_1533582..1533732_NEGATIVE 324 192 151 75 33 NC_002950:PG1196|3end_hypothetical_protein_1275359..1275509_POSITIVE 324 192 151 58 16 NC_002950:PG0824|3end_hypothetical_protein_881930..882080_POSITIVE 318 159 116 96 60 NC_002950:PG2202|3end_Holliday_junction_resolvase-like_protein_2309517..2309667_NEGATIVE 317 159 114 64 7 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 299 249 201 103 46 NC_002950:PG2091|3end_dihydroneopterin_aldolase_2191610..2191760_POSITIVE 291 196 151 111 57 NC_002950:PG0322|3end_serine/threonine_transporter_356966..357116_POSITIVE 286 177 132 81 32 NC_002950:PG2072|3end_UvrD/REP_helicase_domain_protein_2170757..2170907_POSITIVE 285 169 130 110 69 NC_002950:PG0173|3end_transcriptional_regulator,_putative_194388..194538_NEGATIVE 284 157 114 142 101 NC_002950:PG1562|3end_dTDP-4-dehydrorhamnose_3,5-epimerase_1640992..1641142_NEGATIVE 281 190 141 59 5 NC_002950:PG2062|3end_histidyl-tRNA_synthetase_2160415..2160565_POSITIVE 277 264 223 145 111 NC_002950:PG2168|3end_hypothetical_protein_2273588..2273738_NEGATIVE 277 196 153 105 66 NC_002950:PG2099|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_2206649..2206799_NEGATIVE 276 145 105 97 64 NC_002950:PG1711|3end_alpha-1,2-mannosidase_family_protein_1796652..1796802_NEGATIVE 275 89 64 121 96 NC_002950:PG2200|3end_TPR_domain_protein_2306720..2306870_NEGATIVE 271 156 111 89 49 NC_002950:PG1781|3end_uridine_kinase_1870732..1870882_POSITIVE 267 198 169 57 25 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 264 162 130 105 73 NC_002950:PG2163|3end_acid_phosphatase_2268801..2268951_NEGATIVE 264 190 145 64 16 NC_002950:PG0507|3end_hypothetical_protein_548190..548340_POSITIVE