Origin IGS: aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt .........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 acctcgcaactgtgctctgtccattcgtattctattttagaaacaaaagtaaaaataatggagcaatgaatatgaagtggcatttacaattcggaagaaactgcagagtcgggaaaacgtgagattgtttcattcggaaaaaacttttatctttacggatgaacaattaacgaaacgattcatcattcgggtgtaattggttttctgacaaaattgattcaaagcatttaataaagtaaggaggatttttt Mask Tandem Repeat Region ================================================ aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Find is-nt database================================================ Query_seq: PG2050:PG2052|PG2050:PG2052:hypothetical protein:dihydrodipicolinate synthase:<-->:2149525..2149775 251 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG2050:PG2052|PG2050:PG2052:hypothetical protein:dihydrodipicolinate synthase:<-->:2149525..2149775 251 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG2050:PG2052|PG2050:PG2052:hypothetical protein:dihydrodipicolinate synthase:<-->:2149525..2149775 251 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 6 End: 119 ..... M L L T L L N A L N Q F C Q K T N Y T R M M N R F V N C S S V K I K V F S E .................................................................................................................................... Protein_Len: 44 Strand: + Start: 86 End: 217 ..................................................................................... M F I R K D K S F F R M K Q S H V F P T L Q F L P N C K C H F I F I A P L F L L L F L K .................................. Protein_Len: 36 Strand: - Start: 133 End: 240 .................................................................................................................................... T K G V R C N R G F Q L H W K M N M A G N N K S K N R F Y F V F P C L M ........... Protein_Len: 39 Strand: - Start: 59 End: 175 .......................................................... V R I I F R K T L Q E D T F I F T K E S H F L R V N E R S Q L K K R I T F A M ............................................................................ aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt 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================================================ aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG2050:PG2052|PG2050:PG2052:hypothetical protein:dihydrodipicolinate synthase:<-->:2149525..2149775 251 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Intra-Species Hit: Count: 1 Min: 1 Max: 251 Len: 251 Subject: NC_002950_PG2050_PG2052|hypothetical protein:dihydrodipicolinate synthase|NEGATIVE:POSITIVE|[2149525,2149775]|251 HSP 1 e-value: 1.0E-140 bit: 498.0 Len: 251 Query Start:1 Query End:251 Subject Strand: POSITIVE Subject Start: 1 Subject End: 251 aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt aaaaaatcctccttactttattaaatgctttgaatcaattttgtcagaaaaccaattacacccgaatgatgaatcgtttcgttaattgttcatccgtaaagataaaagttttttccgaatgaaacaatctcacgttttcccgactctgcagtttcttccgaattgtaaatgccacttcatattcattgctccattatttttacttttgtttctaaaatagaatacgaatggacagagcacagttgcgaggt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAAUCCUCCUUACUUUAUUAAAUGCUUUGAAUCAAUUUUGUCAGAAAACCAAUUACACCCGAAUGAUGAAUCGUUUCGUUAAUUGUUCAUCCGUAAAGAUAAAAGUUUUUUCCGAAUGAAACAAUCUCACGUUUUCCCGACUCUGCAGUUUCUUCCGAAUUGUAAAUGCCACUUCAUAUUCAUUGCUCCAUUAUUUUUACUUUUGUUUCUAAAAUAGAAUACGAAUGGACAGAGCACAGUUGCGAGGU .......((((...(((........(((((((..........(((.((((((..............(((((((....))))))).((((((((.((.(((((.......))))).)).))).)))))......))))))..)))..((((((((.....))))))))....(((.(((.(((((..........((((((.((....))....))))))))))).)))))).))))))).)))...)))). (-42.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUCGCAACUGUGCUCUGUCCAUUCGUAUUCUAUUUUAGAAACAAAAGUAAAAAUAAUGGAGCAAUGAAUAUGAAGUGGCAUUUACAAUUCGGAAGAAACUGCAGAGUCGGGAAAACGUGAGAUUGUUUCAUUCGGAAAAAACUUUUAUCUUUACGGAUGAACAAUUAACGAAACGAUUCAUCAUUCGGGUGUAAUUGGUUUUCUGACAAAAUUGAUUCAAAGCAUUUAAUAAAGUAAGGAGGAUUUUUU .((((...((((((((((((((((((((((((..(((((...................)))))....))))))).))))).........(((....)))...)))).(((((((((.(((..(((((((.((((((...................))))))))))))).)))...(((((((((.....)))).))))).))))))))).............))))).......)))...))))....... (-55.13) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 821 100 51 191 142 NC_002950:PG2050|5end_hypothetical_protein_2149434..2149664_NEGATIVE 329 180 132 78 21 NC_002950:PG1521|5end_O-succinylbenzoic_acid--CoA_ligase_1599103..1599333_NEGATIVE 312 177 139 220 177 NC_002950:PG0484|5end_hypothetical_protein_524858..525088_NEGATIVE 296 173 131 179 137 NC_002950:PG1995|5end_hypothetical_protein_2085584..2085814_POSITIVE 290 178 136 94 55 NC_002950:PG1500|5end_hypothetical_protein_1576099..1576329_POSITIVE 289 178 133 39 3 NC_002950:PG2024|5end_hemagglutinin_protein_HagE_2124203..2124433_NEGATIVE 287 175 133 231 169 NC_002950:PG0393|5end_ribosomal_protein_L7/L12_424560..424790_POSITIVE 287 160 114 211 146 NC_002950:PG0390|5end_50S_ribosomal_protein_L11_422822..423052_POSITIVE 281 81 41 141 105 NC_002950:PG1533|5end_Toprim_domain_protein_1613761..1613991_NEGATIVE 281 190 144 176 119 NC_002950:PG0728|5end_hypothetical_protein_779807..780037_NEGATIVE 280 190 141 96 43 NC_002950:PG0268|5end_tRNA_(5-methylaminomethyl-2-thiouridylate)-methyltransferase_300898..301128_POSITIVE 275 167 128 202 153 NC_002950:PG2114|5end_hypothetical_protein_2224158..2224388_NEGATIVE 275 178 133 209 146 NC_002950:PG1057|5end_hypothetical_protein_1123419..1123649_POSITIVE 273 180 138 40 6 NC_002950:PG1772|5end_endonuclease_III_1859079..1859309_POSITIVE 270 197 151 181 133 NC_002950:PG0283|5end_efflux_transporter,_MFP_component,_RND_family_318245..318475_NEGATIVE 269 160 116 198 156 NC_002950:PG2119|5end_oxidoreductase,_Gfo/Idh/MocA_family_2226547..2226777_POSITIVE 268 174 133 165 120 NC_002950:PG1619|5end_biotin_synthesis_protein_BioC,_putative_1698568..1698798_POSITIVE 267 190 141 99 57 NC_002950:PG0205|5end_peptide_chain_release_factor_3_242093..242323_NEGATIVE 265 159 114 223 171 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 265 162 128 71 41 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 329 180 132 81 24 NC_002950:PG1522|3end_mandelate_racemase/muconate_lactonizing_enzyme_family_protein_1599100..1599250_NEGATIVE 312 177 139 92 49 NC_002950:PG0485|3end_preprotein_translocase,_YajC_subunit_524986..525136_NEGATIVE 287 160 114 142 77 NC_002950:PG0389|3end_transcription_antitermination_protein_NusG_422833..422983_POSITIVE 281 81 41 144 108 NC_002950:PG1534|3end_hypothetical_protein_1613758..1613908_NEGATIVE 280 190 141 91 38 NC_002950:PG0267|3end_arginyl-tRNA_synthetase_300973..301123_POSITIVE 274 178 133 132 77 NC_002950:PG1357|3end_hypothetical_protein_1436327..1436477_NEGATIVE 272 193 152 141 103 NC_002950:PG1162|3end_ATP:cob(I)alamin_adenosyltransferase,_putative_1241473..1241623_NEGATIVE 263 161 128 90 59 NC_002950:PG1855|3end_carboxyl-terminal_protease_1953842..1953992_NEGATIVE 259 173 131 79 42 NC_002950:PG1587|3end_PAP2_superfamily_protein_1665779..1665929_POSITIVE 259 99 59 84 30 NC_002950:PG0213|3end_precorrin-3_methylase/precorrin-8X_methylmutase_249058..249208_NEGATIVE 258 104 63 49 6 NC_002950:PG0647|3end_iron_compound_ABC_transporter,_permease_protein_699079..699229_NEGATIVE 256 149 114 119 79 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE 255 161 124 131 98 NC_002950:PG1459|3end_hypothetical_protein_1539632..1539782_NEGATIVE 254 187 144 151 100 NC_002950:PG0729|3end_D-alanylalanine_synthetase_779826..779976_NEGATIVE 253 174 134 69 31 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 252 97 52 103 61 NC_002950:PG1651|3end_TPR_domain_protein_1733393..1733543_POSITIVE 251 117 76 85 41 NC_002950:PG1738|3end_hypothetical_protein_1824097..1824247_NEGATIVE 249 167 139 75 37 NC_002950:PG1055|3end_thiol_protease_1121202..1121352_NEGATIVE 248 159 111 139 83 NC_002950:PG1154|3end_hypothetical_protein_1235697..1235847_NEGATIVE 243 160 111 65 20 NC_002950:PG2100|3end_immunoreactive_63_kDa_antigen_PG102_2208527..2208677_NEGATIVE