Origin IGS: gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt .........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 aataatggcaaaaataaggatttgcagaagaaaccgtaaacgaatcctccggatcaaactctaaaaacagatgagaaatactagaagtagccgaatgagtaaaaaaactcgcccctaagggaggaggtttccgtttttgtgaactcaccccaataaatccaaagatcaattccgtattgcagaaccatctaacctgtctttcggcccctatatttcgatctcaccacaagaaaaaactaaaaaaatatatcatcacggcattaacataaaagcccactatc Mask Tandem Repeat Region ================================================ gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Find is-nt database================================================ Query_seq: PG1432:PG1433|PG1432:PG1433:sensor histidine kinase:hydrolase:<-->:1518690..1518970 281 gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1432:PG1433|PG1432:PG1433:sensor histidine kinase:hydrolase:<-->:1518690..1518970 281 gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1432:PG1433|PG1432:PG1433:sensor histidine kinase:hydrolase:<-->:1518690..1518970 281 gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 94 End: 198 ............................................................................................. M V L Q Y G I D L W I Y W G E F T K T E T S S L R G E F F Y S F G Y F ................................................................................... Protein_Len: 60 Strand: + Start: 71 End: 280 ...................................................................... M G A E R Q V R W F C N T E L I F G F I G V S S Q K R K P P P L G A S F F T H S A T S S I S H L F L E F D P E D S F T V . Protein_Len: 38 Strand: - Start: 16 End: 129 ............... T L A T I I Y K K L K K K H H S R F I P A S L C T L H N Q L V S N I K P N M ........................................................................................................................................................ Protein_Len: 35 Strand: - Start: 2 End: 106 . Y H A K I N I G H H Y I K K T K E Q P S I S I Y P G F S L N S P E A M ............................................................................................................................................................................... gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -6.6 Tail_Score: -5.58074 Start: 156 End: 174 Full_Region: CACAAAAACGGAAAC CTCCTCCC TTA GGGGCGAG TTTTTTTACTCATTC ...........................................................................................................................................................CTCCTCCCTTAGGGGCGAG........................................................................................................... Find igs database================================================ Query_seq: PG1432:PG1433|PG1432:PG1433:sensor histidine kinase:hydrolase:<-->:1518690..1518970 281 gatagtgggcttttatgttaatgccgtgatgatatatttttttagttttttcttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt Intra-Species Hit: Count: 1 Min: 1 Max: 281 Len: 281 Subject: NC_002950_PG1432_PG1433|sensor histidine kinase:hydrolase|NEGATIVE:POSITIVE|[1518690,1518970]|281 HSP 1 e-value: 1.0E-115 bit: 414.0 Len: 230 Query Start:52 Query End:281 Subject Strand: POSITIVE Subject Start: 52 Subject End: 281 ...................................................cttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagnnnnnnnactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt ...................................................cttgtggtgagatcgaaatataggggccgaaagacaggttagatggttctgcaatacggaattgatctttggatttattggggtgagttcacaaaaacggaaacctcctcccttaggggcgagtttttttactcattcggctacttctagtatttctcatctgtttttagagtttgatccggaggattcgtttacggtttcttctgcaaatccttatttttgccattatt HSP 2 e-value: 1.0E-11 bit: 71.9 Len: 36 Query Start:1 Query End:36 Subject Strand: POSITIVE Subject Start: 1 Subject End: 36 gatagtgggcttttatgttaatgccgtgatgatata..................................................................................................................................................................................................................................................... gatagtgggcttttatgttaatgccgtgatgatata..................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAGUGGGCUUUUAUGUUAAUGCCGUGAUGAUAUAUUUUUUUAGUUUUUUCUUGUGGUGAGAUCGAAAUAUAGGGGCCGAAAGACAGGUUAGAUGGUUCUGCAAUACGGAAUUGAUCUUUGGAUUUAUUGGGGUGAGUUCACAAAAACGGAAACCUCCUCCCUUAGGGGCGAGUUUUUUUACUCAUUCGGCUACUUCUAGUAUUUCUCAUCUGUUUUUAGAGUUUGAUCCGGAGGAUUCGUUUACGGUUUCUUCUGCAAAUCCUUAUUUUUGCCAUUAUU ((((((((..............((((..(.((...(((.....)))....)))..)))).....(((((.((((((....((((((((((.(((.(((((((.....))))))).....(((((..((.(.((((((((....((((((......(((((.....)))))...))))))..)))))))).).))..)))))....))).))))))))))...(((((...(((((((.(((....)))..))))))))))))))))))))))))))))))) (-66.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAAUGGCAAAAAUAAGGAUUUGCAGAAGAAACCGUAAACGAAUCCUCCGGAUCAAACUCUAAAAACAGAUGAGAAAUACUAGAAGUAGCCGAAUGAGUAAAAAAACUCGCCCCUAAGGGAGGAGGUUUCCGUUUUUGUGAACUCACCCCAAUAAAUCCAAAGAUCAAUUCCGUAUUGCAGAACCAUCUAACCUGUCUUUCGGCCCCUAUAUUUCGAUCUCACCACAAGAAAAAACUAAAAAAAUAUAUCAUCACGGCAUUAACAUAAAAGCCCACUAUC ..(((((.(.......((((((((.....(....).....)))))))).....................(((((((((((.(((.....((((((.((((......)))).......(((..((((((((..(((((((.((...............)))))))))((((.....))))..))))).)))..)))....))))))..)))))))))..(((.......)))..................)))))..).))))).................. (-47.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 949 110 61 201 152 NC_002950:PG1432|5end_sensor_histidine_kinase_1518599..1518829_NEGATIVE 347 266 223 43 4 NC_002950:PG1988|5end_hypothetical_protein_2078867..2079097_NEGATIVE 336 185 150 115 74 NC_002950:PG1831|5end_ATP-dependent_DNA_helicase_RecQ_1925422..1925652_NEGATIVE 326 264 221 181 130 NC_002950:PG1659|5end_hypothetical_protein_1743747..1743977_NEGATIVE 324 76 41 187 148 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 323 266 221 209 148 NC_002950:PG0585|5end_YqeY_family_protein_643272..643502_POSITIVE 322 260 211 131 81 NC_002950:PG2023|5end_methionyl-tRNA_formyltransferase_2118536..2118766_NEGATIVE 321 260 213 199 147 NC_002950:PG1722|5end_hypothetical_protein_1812938..1813168_NEGATIVE 319 171 131 215 173 NC_002950:PG0703|5end_cobalamin_(5'-phosphate)_synthase,_putative_758144..758374_POSITIVE 315 275 231 177 137 NC_002950:PG0327|5end_hypothetical_protein_362061..362291_NEGATIVE 314 277 231 91 42 NC_002950:PG2171|5end_D-isomer_specific_2-hydroxyacid_dehydrogenase_family_protein_2278972..2279202_NEGATIVE 310 178 133 67 14 NC_002950:PG1330|5end_large_conductance_mechanosensitive_channel_protein_1409666..1409896_POSITIVE 310 196 154 65 15 NC_002950:PG0709|5end_peptidyl-prolyl_cis-trans_isomerase_FkpA,_FKBP-type_765417..765647_NEGATIVE 307 85 44 192 153 NC_002950:PG2024|5end_hemagglutinin_protein_HagE_2124203..2124433_NEGATIVE 304 174 131 121 77 NC_002950:PG2159|5end_protoporphyrinogen_oxidase_2264397..2264627_POSITIVE 303 208 161 99 55 NC_002950:PG1387|5end_hypothetical_protein_1470058..1470288_NEGATIVE 299 97 52 84 14 NC_002950:PG2199|5end_ABC_transporter,_ATP-binding_protein,_putative_2306723..2306953_NEGATIVE 298 172 131 217 177 NC_002950:PG1946|5end_ABC_3_transporter_family_protein_2032133..2032363_POSITIVE 298 259 222 217 181 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 297 256 212 53 12 NC_002950:PG0364|5end_hypothetical_protein_399615..399845_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 267 222 71 31 NC_002950:PG0380|3end_excinuclease_ABC_subunit_B_411218..411368_POSITIVE 339 258 213 58 8 NC_002950:PG1410|3end_hypothetical_protein_1493436..1493586_POSITIVE 315 275 231 83 43 NC_002950:PG0328|3end_imidazolonepropionase_362155..362305_NEGATIVE 307 276 232 125 71 NC_002950:PG1332|3end_NAD(P)_transhydrogenase,_beta_subunit_1414110..1414260_POSITIVE 306 180 131 91 35 NC_002950:PG1630|3end_hypothetical_protein_1712142..1712292_POSITIVE 304 174 131 117 73 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 303 208 161 62 18 NC_002950:PG1388|3end_hypothetical_protein_1470095..1470245_NEGATIVE 299 97 52 87 17 NC_002950:PG2200|3end_TPR_domain_protein_2306720..2306870_NEGATIVE 297 256 212 56 15 NC_002950:PG0365|3end_3'-5'_exonuclease_domain_protein_399612..399762_NEGATIVE 296 265 223 114 75 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE 295 174 131 83 26 NC_002950:PG0769|3end_fibronectin_type_III_domain_protein_822555..822705_NEGATIVE 294 258 211 89 34 NC_002950:PG1253|3end_DNA_ligase,_NAD-dependent_1329597..1329747_NEGATIVE 294 197 153 96 33 NC_002950:PG1025|3end_hypothetical_protein_1088309..1088459_POSITIVE 294 237 191 131 84 NC_002950:PG0012|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_15661..15811_POSITIVE 292 257 211 63 17 NC_002950:PG0717|3end_lipoprotein,_putative_769991..770141_NEGATIVE 290 258 212 137 91 NC_002950:PG1997|3end_hypothetical_protein_2087072..2087222_POSITIVE 290 250 204 130 95 NC_002950:PG1664|3end_ABC_transporter,_permease_protein,_putative_1747167..1747317_POSITIVE 289 198 155 118 78 NC_002950:PG2065|3end_conserved_hypothetical_protein_TIGR00048_2162105..2162255_POSITIVE 289 66 21 103 43 NC_002950:PG0308|3end_electron_transport_complex,_RnfABCDGE_type,_A_subunit_343827..343977_POSITIVE 288 99 55 91 34 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE