Origin IGS: tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata .........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 tataaataatatagttattattatcaaaatatataccattttattttttcctttcaacaatgttatggttacatattataacatatttcattgcagttgtgaattaatcttatctataaagaattattctaaaaaatgtatttaatattatatacaattaagtatgtttattatactatatcaataaagaaaatgcaaacttgttttttaaattaaaaaagtgtatattattaattgaaattcacaattaaaaaggagaatataaa Mask Tandem Repeat Region ================================================ tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Find is-nt database================================================ Query_seq: FN0540:FN0541|FN0540:FN0541:Glutamate-1-semialdehyde 2,1-aminomutase:Hypothetical cytosolic protein:<-->:1194036..1194301 266 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN0540:FN0541|FN0540:FN0541:Glutamate-1-semialdehyde 2,1-aminomutase:Hypothetical cytosolic protein:<-->:1194036..1194301 266 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN0540:FN0541|FN0540:FN0541:Glutamate-1-semialdehyde 2,1-aminomutase:Hypothetical cytosolic protein:<-->:1194036..1194301 266 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: - Start: 125 End: 265 ............................................................................................................................ I C K K S Y N K I S L I L E C S C H F I N Y Y T V M V N N F P F F L I T Y I K I I I V I N N M . tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata 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: 89 Start: 163 End: 192 ..................................................................................................................................................................ATTCACAACTGCAATGAAATATGTTATAAT.......................................................................... PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 68 End: 97 ...................................................................TTTGCATTTTCTTTATTGATATAGTATAAT......................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN0540:FN0541|FN0540:FN0541:Glutamate-1-semialdehyde 2,1-aminomutase:Hypothetical cytosolic protein:<-->:1194036..1194301 266 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: NC_003454_FN0540_FN0541|Glutamate-1-semialdehyde 2,1-aminomutase:Hypothetical cytosolic protein|NEGATIVE:POSITIVE|[1194036,1194301]|266 HSP 1 e-value: 1.0E-149 bit: 527.0 Len: 266 Query Start:1 Query End:266 Subject Strand: POSITIVE Subject Start: 1 Subject End: 266 tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata tttatattctcctttttaattgtgaatttcaattaataatatacacttttttaatttaaaaaacaagtttgcattttctttattgatatagtataataaacatacttaattgtatataatattaaatacattttttagaataattctttatagataagattaattcacaactgcaatgaaatatgttataatatgtaaccataacattgttgaaaggaaaaaataaaatggtatatattttgataataataactatattatttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAUAUUCUCCUUUUUAAUUGUGAAUUUCAAUUAAUAAUAUACACUUUUUUAAUUUAAAAAACAAGUUUGCAUUUUCUUUAUUGAUAUAGUAUAAUAAACAUACUUAAUUGUAUAUAAUAUUAAAUACAUUUUUUAGAAUAAUUCUUUAUAGAUAAGAUUAAUUCACAACUGCAAUGAAAUAUGUUAUAAUAUGUAACCAUAACAUUGUUGAAAGGAAAAAAUAAAAUGGUAUAUAUUUUGAUAAUAAUAACUAUAUUAUUUAUA .........(((((((...(((((((((....(((....((((.......(((.(((((((((.............((......))..((((((.(((.(((........))).))).))))))......))))))))).))).....))))..)))....)))))))))..((((((...((((((((.....)))).)))).)))))).)))))))..((((((.(((((...((((.....))))...))))).))))))... (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUAAUAUAGUUAUUAUUAUCAAAAUAUAUACCAUUUUAUUUUUUCCUUUCAACAAUGUUAUGGUUACAUAUUAUAACAUAUUUCAUUGCAGUUGUGAAUUAAUCUUAUCUAUAAAGAAUUAUUCUAAAAAAUGUAUUUAAUAUUAUAUACAAUUAAGUAUGUUUAUUAUACUAUAUCAAUAAAGAAAAUGCAAACUUGUUUUUUAAAUUAAAAAAGUGUAUAUUAUUAAUUGAAAUUCACAAUUAAAAAGGAGAAUAUAAA ....(((((((....))))))).................(((((.(((((((((.....((((((((((.....))))))))))..........(((((((((((..((((.......))))...................((((((.(((((((.....((((((.....))))))..........(((((((........)))))))...........))))))).))))))....)))))))))))..))))))))).))))) (-47.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 631 110 61 201 152 NC_003454:FN0540|5end_Glutamate-1-semialdehyde_2,1-aminomutase_1193945..1194175_NEGATIVE 213 104 65 130 92 NC_003454:FN0367|5end_Integral_membrane_protein_996901..997131_NEGATIVE 205 94 64 158 119 NC_003454:FN0145|5end_hypothetical_protein_774306..774536_POSITIVE 196 89 45 63 24 NC_003454:FN1407|5end_Glutamate_formiminotransferase_2066430..2066660_POSITIVE 189 148 102 132 91 NC_003454:FN0377|5end_Iron(III)-transport_system_permease_protein_sfuB_1007464..1007694_POSITIVE 186 92 64 189 163 NC_003454:FN0412|5end_Recombination_protein_recR_1048549..1048779_POSITIVE 183 97 66 81 47 NC_003454:FN0203|5end_Glutaconate_CoA-transferase_subunit_B_828748..828978_POSITIVE 176 174 146 231 206 NC_003454:FN1118|5end_hypothetical_protein_1760559..1760789_POSITIVE 175 86 44 71 27 NC_003454:FN0729|5end_Phosphoglycerate_mutase_1386354..1386584_POSITIVE 173 45 2 173 135 NC_003454:FN1299|5end_dTDP-glucose_4,6-dehydratase_1956624..1956854_NEGATIVE 173 218 177 222 184 NC_003454:FN0453|5end_Xaa-Pro_aminopeptidase_1097547..1097777_POSITIVE 171 47 1 174 114 NC_003454:FN0244|5end_COP_associated_protein_868115..868345_POSITIVE 167 115 72 102 58 NC_003454:FN1103|5end_Excinuclease_ABC_subunit_A_1746559..1746789_POSITIVE 166 173 132 63 27 NC_003454:FN0416|5end_Type_III_restriction-modification_system_methylation_subunit_1054300..1054530_POSITIVE 166 130 81 97 44 NC_003454:FN1559|5end_cell_volume_regulation_protein_CvrA_80827..81057_POSITIVE 165 47 2 159 93 NC_003454:FN1884|5end_hypothetical_protein_370507..370737_NEGATIVE 164 176 144 178 145 NC_003454:FN0714|5end_NADH_oxidase_1372062..1372292_POSITIVE 163 48 1 136 91 NC_003454:FN1232|5end_Transcriptional_regulator,_MarR_family_1889341..1889571_NEGATIVE 163 42 4 55 15 NC_003454:FN2093|5end_General_secretion_pathway_protein_G_603551..603781_NEGATIVE 162 33 4 129 93 NC_003454:FN0753|5end_aspartyl/glutamyl-tRNA_amidotransferase_subunit_B_1413169..1413399_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 196 89 45 45 6 NC_003454:FN1406|3end_histidine_ammonia-lyase_2066492..2066642_POSITIVE 189 148 102 148 107 NC_003454:FN0376|3end_Iron(III)-transport_ATP-binding_protein_sfuC_1007560..1007710_POSITIVE 183 97 66 78 44 NC_003454:FN0202|3end_Glutaconate_CoA-transferase_subunit_A_828825..828975_POSITIVE 176 215 199 146 130 NC_003454:FN0879|3end_ABC_transporter_integral_membrane_protein_1540161..1540311_NEGATIVE 168 104 70 55 23 NC_003454:FN1002|3end_Adenosylmethionine-8-amino-7-oxononanoate_aminotransferase_1658176..1658326_POSITIVE 163 108 70 149 108 NC_003454:FN1236|3end_Choline_transport_protein_1892512..1892662_NEGATIVE 162 33 4 115 79 NC_003454:FN0754|3end_Glutamyl-tRNA(Gln)_amidotransferase_subunit_A_1413183..1413333_NEGATIVE 162 87 45 121 79 NC_003454:FN0422|3end_carbamoyl-phosphate_synthase_large_subunit_1066283..1066433_POSITIVE 162 47 1 64 16 NC_003454:FN0149|3end_Malonyl-CoA-[acyl-carrier-protein]_transacylase_778465..778615_POSITIVE 162 88 47 68 17 NC_003454:FN1649|3end_Oligopeptide_transport_ATP-binding_protein_oppD_143327..143477_NEGATIVE 161 155 116 89 49 NC_003454:FN1127|3end_Hypothetical_membrane-spanning_protein_1770307..1770457_NEGATIVE 160 189 141 90 34 NC_003454:FN1323|3end_Thymidylate_kinase_1978475..1978625_NEGATIVE 159 220 171 106 63 NC_003454:FN1026|3end_tRNA_pseudouridine_synthase_A_1679954..1680104_NEGATIVE 159 222 187 75 38 NC_003454:FN0500|3end_hypothetical_protein_1149592..1149742_POSITIVE 158 65 22 63 10 NC_003454:FN0482|3end_LSU_ribosomal_protein_L31P_1128620..1128770_POSITIVE 157 59 18 99 61 NC_003454:FN0337|3end_hypothetical_protein_971136..971286_NEGATIVE 156 82 42 133 92 NC_003454:FN0450|3end_ABC_transporter_ATP-binding_protein_1094930..1095080_POSITIVE 153 145 109 54 16 NC_003454:FN0603|3end_Transcriptional_regulatory_protein,_LYSR_family_1257501..1257651_NEGATIVE 152 40 1 127 95 NC_003454:FN0401|3end_hypothetical_protein_1039905..1040055_NEGATIVE 151 83 42 134 82 NC_003454:FN1203|3end_GTP-binding_protein_1862311..1862461_NEGATIVE