Origin IGS: taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccttagccttatgaatttaaagaaagcgaagctgtattctagcaataagttatctattgataaatggtttgtttataggaaaggacaagaagggggagaaaattagaaaccgcacttctaaagtgcggtcattttcacgggtgtttttta Mask Tandem Repeat Region ================================================ taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Find is-nt database================================================ Query_seq: AA00168:AA00169|AA00168:AA00169:possible sigma 54 modulation protein:conserved hypothetical protein:->->:120301..120451 151 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00168:AA00169|AA00168:AA00169:possible sigma 54 modulation protein:conserved hypothetical protein:->->:120301..120451 151 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00168:AA00169|AA00168:AA00169:possible sigma 54 modulation protein:conserved hypothetical protein:->->:120301..120451 151 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 48 End: 140 ............................................... N E G G E Q G K R Y V F W K D I S L K N S S Y L K A K K L N M ........... Protein_Len: 38 Strand: - Start: 2 End: 115 . F F V R S F S R V K S T R N R I K E G K K D K G I F L G N I L L Y S I A L M .................................... taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga 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: 86 End: 115 .....................................................................................ATTTATCAATAGATAACTTATTGCTAGAAT.................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -7.1 Tail_Score: -4.11773 Start: 20 End: 44 Full_Region: gggggagaaaattag aaaccgcactt cta aagtgcggtca ttttcacgggtgttt ...................aaaccgcacttctaaagtgcggtca........................................................................................................... TransTerm Strand: - Conf: 93 HP_score: -13.2 Tail_Score: -3.08508 Start: 23 End: 41 Full_Region: ggagaaaattagaaa ccgcactt cta aagtgcgg tcattttcacgggtg ......................ccgcacttctaaagtgcgg.............................................................................................................. Find igs database================================================ Query_seq: AA00168:AA00169|AA00168:AA00169:possible sigma 54 modulation protein:conserved hypothetical protein:->->:120301..120451 151 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Intra-Species Hit: Count: 1 Min: 1 Max: 151 Len: 151 Subject: aact_AA00168_AA00169|possible sigma 54 modulation protein:conserved hypothetical protein|POSITIVE:POSITIVE|[120301,120451]|151 HSP 1 e-value: 1.0E-80 bit: 299.0 Len: 151 Query Start:1 Query End:151 Subject Strand: POSITIVE Subject Start: 1 Subject End: 151 taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga taaaaaacacccgtgaaaatgaccgcactttagaagtgcggtttctaattttctcccccttcttgtcctttcctataaacaaaccatttatcaatagataacttattgctagaatacagcttcgctttctttaaattcataaggctaagga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAACACCCGUGAAAAUGACCGCACUUUAGAAGUGCGGUUUCUAAUUUUCUCCCCCUUCUUGUCCUUUCCUAUAAACAAACCAUUUAUCAAUAGAUAACUUAUUGCUAGAAUACAGCUUCGCUUUCUUUAAAUUCAUAAGGCUAAGGA ............(.(((((((((((((((.....)))))))))....)))))).)..........(((((.(((............((((.((((((.....)))))).))))....(((...)))...............)))..))))) (-27.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUAGCCUUAUGAAUUUAAAGAAAGCGAAGCUGUAUUCUAGCAAUAAGUUAUCUAUUGAUAAAUGGUUUGUUUAUAGGAAAGGACAAGAAGGGGGAGAAAAUUAGAAACCGCACUUCUAAAGUGCGGUCAUUUUCACGGGUGUUUUUUA (((((..((((.......((((.(((.((..((((.....))))......(((((....))))).)).))).)))).....)))).....)))))...((((((.....((((((((.....)))))))).)))))).............. (-32.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 494 42 3 150 108 aact:AA01027|5end_Na(+)-translocating_NADH-quinone_reductase_subunit_F_717676..717906_POSITIVE 465 42 1 145 92 aact:AA01603|5end_oligopeptidase_A_1082898..1083128_POSITIVE 423 48 3 164 104 aact:AA00075|5end_conserved_hypothetical_protein_54963..55193_POSITIVE 418 43 3 139 93 aact:AA02137|5end_transcriptional_regulators_(TetR/AcrR_family)_1460453..1460683_POSITIVE 403 44 3 150 97 aact:AA01692|5end_hexulose-6-phosphate_synthase_1149178..1149408_POSITIVE 400 44 1 136 92 aact:AA00988|5end_conserved_hypothetical_protein_690898..691128_POSITIVE 399 42 4 226 185 aact:AA00347|5end_50S_ribosomal_protein_L11_232137..232367_POSITIVE 396 44 3 153 106 aact:AA02963|5end_opacity_associated_protein_B_2072302..2072532_POSITIVE 393 46 3 144 94 aact:AA01315|5end_DNA/pantothenate_metabolism_flavoprotein_890091..890321_POSITIVE 393 46 3 74 24 aact:AA01314|5end_hypothetical_protein_890021..890251_POSITIVE 393 42 1 56 9 aact:AA01041|5end_hypothetical_protein_724853..725083_POSITIVE 390 47 1 160 103 aact:AA00454|5end_conserved_hypothetical_protein_318020..318250_POSITIVE 388 46 16 137 100 aact:AA00705|5end_Inositol-1-monophosphatase_(IMPase);_extragenic_suppressor_483827..484057_POSITIVE 377 44 2 137 94 aact:AA00401|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_slyD_(PPiase)_268361..268591_POSITIVE 374 39 2 176 140 aact:AA01918|5end_anaerobic_C4-dicarboxylate_transporter_1290931..1291161_POSITIVE 364 42 1 191 144 aact:AA03011|5end_inner_membrane_protein,_60_kDa_2102585..2102815_POSITIVE 360 43 12 158 130 aact:AA02084|5end_conserved_hypothetical_protein_1417843..1418073_POSITIVE 360 43 12 136 101 aact:AA01090|5end_leucyl-tRNA_synthetase,_leucyl-tRNA_ligase_753548..753778_POSITIVE 359 42 3 138 98 aact:AA00757|5end_aerobic_respiration_sensor-response_protein_518615..518845_POSITIVE 357 43 3 140 93 aact:AA01024|5end_thiamine_biosynthesis_lipoprotein_precursor_716437..716667_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 423 48 3 68 8 aact:AA00072|3end_conserved_hypothetical_protein_54947..55097_POSITIVE 418 43 3 82 36 aact:AA02136|3end_aspartate_aminotransferase_1460476..1460626_POSITIVE 399 40 3 68 33 aact:AA01945|3end_selenophosphate_synthase_1316022..1316172_POSITIVE 399 42 4 67 26 aact:AA00345|3end_transcription_antitermination_protein_232058..232208_POSITIVE 396 44 3 56 9 aact:AA02962|3end_recombination_associated_protein_2072285..2072435_POSITIVE 393 46 3 72 22 aact:AA01313|3end_deoxyuridinetriphosphatase;_deoxyuridine_5'-triphosphate_nucleotidohydrolase_890099..890249_POSITIVE 393 42 1 69 22 aact:AA01040|3end_possible_lipoprotein_724946..725096_POSITIVE 390 47 1 69 12 aact:AA00453|3end_phosphoglyceromutase_318009..318159_POSITIVE 388 46 16 78 41 aact:AA00702|3end_conserved_hypothetical_protein_483848..483998_POSITIVE 378 40 2 56 11 aact:AA02491|3end_topoisomerase_IV,_subunit_A_1729159..1729309_POSITIVE 377 44 2 59 16 aact:AA00399|3end_conserved_hypothetical_protein_268363..268513_POSITIVE 364 42 1 60 13 aact:AA03010|3end_thiophene_and_furan_oxidation_protein_2102534..2102684_POSITIVE 361 46 12 72 24 aact:AA00223|3end_catalase_(hydroperoxidase;_iron_heme_axial_ligand)_155808..155958_POSITIVE 360 43 12 83 55 aact:AA02082|3end_glutaminyl-tRNA_synthetase_1417848..1417998_POSITIVE 360 43 12 105 70 aact:AA01089|3end_hypothetical_protein_753597..753747_POSITIVE 359 42 3 58 18 aact:AA00753|3end_galactoside_ABC_transporter,_permease_protein_518615..518765_POSITIVE 357 43 3 58 11 aact:AA01023|3end_conserved_hypothetical_protein_716435..716585_POSITIVE 351 48 12 140 94 aact:AA01492|3end_glucose_inhibited_division_protein_B_1003566..1003716_POSITIVE 351 44 1 61 4 aact:AA00790|3end_recombination_DNA_repair_protein_543134..543284_POSITIVE 345 33 3 91 61 aact:AA02105|3end_killing_protein_1433290..1433440_POSITIVE