Origin IGS: actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat .........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 atcgttctttccctgatagtgcagggcaaaggtggggaattttgacgaattgccgttcgtaaattatgaataggcacacaacttttatgtctttatagcatattgttaaatctatcctaaaagaatgaaaggcttatgagaaacaagtacataattccatccgcaatgtcgatggcaaggtatatgggcgtatagacgtgcatcctgtattaccttggattataatgcgagaagaatccggggtgtacccttttcctgtttcttgattcgcctttcgcgctgccgatggctctattcgataagaatggactacttttggtacagaaaccatggtagaatgattcagt Mask Tandem Repeat Region ================================================ actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Find is-nt database================================================ Query_seq: PG2156:PG2157|PG2156:PG2157:conserved hypothetical protein TIGR00046:glutamine cyclotransferase-related protein:<-->:2262736..2263082 347 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2156:PG2157|PG2156:PG2157:conserved hypothetical protein TIGR00046:glutamine cyclotransferase-related protein:<-->:2262736..2263082 347 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2156:PG2157|PG2156:PG2157:conserved hypothetical protein TIGR00046:glutamine cyclotransferase-related protein:<-->:2262736..2263082 347 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 2 End: 211 . M N H S T M V S V P K V V H S Y R I E P S A A R K A N Q E T G K G Y T P D S S R I I I Q G N T G C T S I R P Y T L P S T ........................................................................................................................................ Protein_Len: 32 Strand: + Start: 138 End: 233 ......................................................................................................................................... M Q D A R L Y A H I P C H R H C G W N Y V L V S H K P F I L L G .................................................................................................................. Protein_Len: 38 Strand: + Start: 233 End: 346 ........................................................................................................................................................................................................................................ M D L T I C Y K D I K V V C L F I I Y E R Q F V K I P H L C P A L S G K E R . Protein_Len: 35 Strand: - Start: 85 End: 189 .................................................................................... S V P F P Y V G S E E R M I I W P L V P H V D I R G Y V K G D V N R M .............................................................................................................................................................. Protein_Len: 55 Strand: - Start: 2 End: 166 . Q I M R G H N R Y W F Y D M R I S Y L W R C R S L R I L F C S F P V G R I R R A N Y D L T I C S A R R Y A W M ..................................................................................................................................................................................... actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat 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================================================ actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2156:PG2157|PG2156:PG2157:conserved hypothetical protein TIGR00046:glutamine cyclotransferase-related protein:<-->:2262736..2263082 347 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Intra-Species Hit: Count: 1 Min: 1 Max: 347 Len: 347 Subject: NC_002950_PG2156_PG2157|conserved hypothetical protein TIGR00046:glutamine cyclotransferase-related protein|NEGATIVE:POSITIVE|[2262736,2263082]|347 HSP 1 e-value: 0.0 bit: 688.0 Len: 347 Query Start:1 Query End:347 Subject Strand: POSITIVE Subject Start: 1 Subject End: 347 actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat actgaatcattctaccatggtttctgtaccaaaagtagtccattcttatcgaatagagccatcggcagcgcgaaaggcgaatcaagaaacaggaaaagggtacaccccggattcttctcgcattataatccaaggtaatacaggatgcacgtctatacgcccatataccttgccatcgacattgcggatggaattatgtacttgtttctcataagcctttcattcttttaggatagatttaacaatatgctataaagacataaaagttgtgtgcctattcataatttacgaacggcaattcgtcaaaattccccacctttgccctgcactatcagggaaagaacgat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUGAAUCAUUCUACCAUGGUUUCUGUACCAAAAGUAGUCCAUUCUUAUCGAAUAGAGCCAUCGGCAGCGCGAAAGGCGAAUCAAGAAACAGGAAAAGGGUACACCCCGGAUUCUUCUCGCAUUAUAAUCCAAGGUAAUACAGGAUGCACGUCUAUACGCCCAUAUACCUUGCCAUCGACAUUGCGGAUGGAAUUAUGUACUUGUUUCUCAUAAGCCUUUCAUUCUUUUAGGAUAGAUUUAACAAUAUGCUAUAAAGACAUAAAAGUUGUGUGCCUAUUCAUAAUUUACGAACGGCAAUUCGUCAAAAUUCCCCACCUUUGCCCUGCACUAUCAGGGAAAGAACGAU ...((((....((((..((((......))))...))))...)))).....((((((.((((.((((.....(((((((......(((((((((....(((....)))..((((((..(((((........(((((((.......(((..(((....)))..))).)))))))..........)))))..)))))).....))))))))).....)))))))..((((((((.(((..........))).))).))))).......)))))).))))))))........((...(((.....)))............((((.(((((......)))))))))..)).. (-86.47) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUCGUUCUUUCCCUGAUAGUGCAGGGCAAAGGUGGGGAAUUUUGACGAAUUGCCGUUCGUAAAUUAUGAAUAGGCACACAACUUUUAUGUCUUUAUAGCAUAUUGUUAAAUCUAUCCUAAAAGAAUGAAAGGCUUAUGAGAAACAAGUACAUAAUUCCAUCCGCAAUGUCGAUGGCAAGGUAUAUGGGCGUAUAGACGUGCAUCCUGUAUUACCUUGGAUUAUAAUGCGAGAAGAAUCCGGGGUGUACCCUUUUCCUGUUUCUUGAUUCGCCUUUCGCGCUGCCGAUGGCUCUAUUCGAUAAGAAUGGACUACUUUUGGUACAGAAACCAUGGUAGAAUGAUUCAGU .....((((((((((......))))).)))))..((((..((((((((..(((((((((((...))))))).)))).........((((.((....))))))))))))))....))))....(((((((((((..((((((((((.(..((((.(((((((.((...)).))))).))....))))..)........((((((((((.(((..((((.((....)).))))...))).))))))))))........)))))))).))..)))))))...(((((..(((.(((((((.....))))))))))....((((......)))).)))))....))))... (-98.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1052 110 61 201 152 NC_002950:PG2156|5end_conserved_hypothetical_protein_TIGR00046_2262645..2262875_NEGATIVE 364 99 53 68 15 NC_002950:PG0973|5end_alpha-1,2-mannosidase_family_protein_1034167..1034397_POSITIVE 348 189 141 121 74 NC_002950:PG1640|5end_DNA-damage-inducible_protein_F_1721245..1721475_NEGATIVE 342 100 56 66 8 NC_002950:PG0768|5end_hypothetical_protein_822381..822611_NEGATIVE 341 78 34 174 128 NC_002950:PG2214|5end_hypothetical_protein_2326575..2326805_NEGATIVE 340 198 152 205 161 NC_002950:PG2164|5end_peptidyl-prolyl_cis-trans_isomerase,_FKBP-type_2270125..2270355_NEGATIVE 337 336 291 175 129 NC_002950:PG0504|5end_lipoyl_synthase_544234..544464_POSITIVE 327 100 58 57 9 NC_002950:PG1978|5end_hypothetical_protein_2067337..2067567_NEGATIVE 327 109 61 202 139 NC_002950:PG1853|5end_DNA_polymerase_III,_beta_subunit_1953119..1953349_NEGATIVE 325 107 63 110 65 NC_002950:PG2030|5end_hypothetical_protein_2129747..2129977_POSITIVE 322 100 55 54 16 NC_002950:PG1967|5end_TPR_domain_protein_2057168..2057398_POSITIVE 321 78 33 117 76 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 321 69 25 228 183 NC_002950:PG1108|5end_hypothetical_protein_1181108..1181338_NEGATIVE 321 110 61 86 30 NC_002950:PG0139|5end_membrane-bound_lytic_murein_transglycosylase_D,_putative_163141..163371_NEGATIVE 318 338 299 231 190 NC_002950:PG0090|5end_Dps_family_protein_105524..105754_POSITIVE 317 70 21 182 112 NC_002950:PG1743|5end_2-dehydro-3-deoxyphosphooctonate_aldolase_1828348..1828578_NEGATIVE 315 187 142 73 15 NC_002950:PG0882|5end_hypothetical_protein_944195..944425_POSITIVE 312 102 64 64 23 NC_002950:PG1058|5end_OmpA_family_protein_1124034..1124264_POSITIVE 311 77 38 75 25 NC_002950:PG0446|5end_thiF_protein_486599..486829_POSITIVE 310 190 142 219 175 NC_002950:PG2108|5end_thiazole_synthase_2217450..2217680_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 359 80 34 87 35 NC_002950:PG0685|3end_ABC_transporter,_ATP-binding_protein_740855..741005_POSITIVE 353 210 161 140 95 NC_002950:PG0282|3end_ABC_transporter,_ATP-binding_protein_316244..316394_NEGATIVE 348 189 141 106 59 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE 341 78 34 139 93 NC_002950:PG2215|3end_mannose-1-phosphate_guanylyltransferase_2326610..2326760_NEGATIVE 337 336 291 72 26 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 336 87 42 119 65 NC_002950:PG1859|3end_glycerate_kinase_family_protein_1957174..1957324_NEGATIVE 329 80 39 118 71 NC_002950:PG2031|3end_hypothetical_protein_2130871..2131021_POSITIVE 321 110 61 76 20 NC_002950:PG0140|3end_hypothetical_protein_163151..163301_NEGATIVE 319 79 35 102 59 NC_002950:PG0815|3end_hypothetical_protein_876447..876597_POSITIVE 315 185 141 128 73 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 312 102 64 42 1 NC_002950:PG1057|3end_hypothetical_protein_1124092..1124242_POSITIVE 310 179 143 66 23 NC_002950:PG1212|3end_TPR_domain_protein_1292485..1292635_POSITIVE 309 79 34 71 25 NC_002950:PG2107|3end_thiamine_biosynthesis_protein_ThiH_2215546..2215696_NEGATIVE 309 179 131 122 66 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 309 189 143 42 3 NC_002950:PG0212|3end_precorrin-6Y_C5,15-methyltransferase,_decarboxylating_247824..247974_NEGATIVE 307 79 33 73 24 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 307 78 34 62 15 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 306 199 151 148 89 NC_002950:PG0087|3end_SIS_domain_protein_102505..102655_NEGATIVE 302 100 58 55 13 NC_002950:PG1595|3end_ribulose-phosphate_3-epimerase_1673594..1673744_NEGATIVE 301 110 62 147 100 NC_002950:PG0795|3end_hypothetical_protein_849603..849753_POSITIVE