Origin IGS: tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa .........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 ttttagctcctatttatgtaagaaaacctttgtcattataaccaaacttagtaataaaaccgataagttttaataaaatattaactattaaatcatttactattttaatgtgttggctttttatatttaataaaaatcatatttatttataatgtaagctgtttggtgttattgaggagaaagcaaa Mask Tandem Repeat Region ================================================ tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Find is-nt database================================================ Query_seq: AA00004:AA00007|AA00004:AA00007:conserved hypothetical protein (possible methyltransferase):superoxide dismutase [Cu-Zn] precursor:->->:4356..4542 187 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00004:AA00007|AA00004:AA00007:conserved hypothetical protein (possible methyltransferase):superoxide dismutase [Cu-Zn] precursor:->->:4356..4542 187 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00004:AA00007|AA00004:AA00007:conserved hypothetical protein (possible methyltransferase):superoxide dismutase [Cu-Zn] precursor:->->:4356..4542 187 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 64 End: 171 ............................................................... M K S Q H I K I V N D L I V N I L L K L I G F I T K F G Y N D K G F L T ................ Protein_Len: 32 Strand: - Start: 39 End: 134 ...................................... L Y I H N K N F I F L W C M L I T F S K I T L I K N F S I P K M ..................................................... tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa 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: 81 Start: 79 End: 108 ..............................................................................ATTAACTATTAAATCATTTACTATTTTAAT............................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00004:AA00007|AA00004:AA00007:conserved hypothetical protein (possible methyltransferase):superoxide dismutase [Cu-Zn] precursor:->->:4356..4542 187 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Intra-Species Hit: Count: 1 Min: 1 Max: 187 Len: 187 Subject: aact_AA00004_AA00007|conserved hypothetical protein (possible methyltransferase):superoxide dismutase [Cu-Zn] precursor|POSITIVE:POSITIVE|[4356,4542]|187 HSP 1 e-value: 1.0E-102 bit: 371.0 Len: 187 Query Start:1 Query End:187 Subject Strand: POSITIVE Subject Start: 1 Subject End: 187 tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa tttgctttctcctcaataacaccaaacagcttacattataaataaatatgatttttattaaatataaaaagccaacacattaaaatagtaaatgatttaatagttaatattttattaaaacttatcggttttattactaagtttggttataatgacaaaggttttcttacataaataggagctaaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGCUUUCUCCUCAAUAACACCAAACAGCUUACAUUAUAAAUAAAUAUGAUUUUUAUUAAAUAUAAAAAGCCAACACAUUAAAAUAGUAAAUGAUUUAAUAGUUAAUAUUUUAUUAAAACUUAUCGGUUUUAUUACUAAGUUUGGUUAUAAUGACAAAGGUUUUCUUACAUAAAUAGGAGCUAAAA ........(((((.......(((((((.((((...(((((((((((.......))))))...))))).)))).............((((((.(((((....))))).........(((((((....))))))))))))).))))))).............((......))......)))))...... (-23.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUUAGCUCCUAUUUAUGUAAGAAAACCUUUGUCAUUAUAACCAAACUUAGUAAUAAAACCGAUAAGUUUUAAUAAAAUAUUAACUAUUAAAUCAUUUACUAUUUUAAUGUGUUGGCUUUUUAUAUUUAAUAAAAAUCAUAUUUAUUUAUAAUGUAAGCUGUUUGGUGUUAUUGAGGAGAAAGCAAA ......(((((....(((.(((.....)))...)))....(((((((.......((((((......)))))).........(((((((((((...........))))))).))))((((.(((((..(((............)))..)))))...)))).))))))).......)))))........ (-26.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 217 30 3 224 199 aact:AA00160|5end_pilA-like_biogenesis_protein_/_prepilin_peptidase_dependent_proteinD_112836..113066_POSITIVE 209 164 126 60 19 aact:AA00716|5end_conserved_hypothetical_protein_490973..491203_POSITIVE 208 40 1 127 92 aact:AA00900|5end_conserved_hypothetical_protein_623442..623672_POSITIVE 207 48 4 150 107 aact:AA01279|5end_phage_exclusion-related_protein_867687..867917_POSITIVE 196 149 118 189 163 aact:AA00605|5end_CDP-diglyceride_pyrophosphorylase_410930..411160_POSITIVE 195 30 1 227 199 aact:AA02947|5end_riboflavin_biosynthesis_protein_2060871..2061101_POSITIVE 191 31 4 121 95 aact:AA02226|5end_ABC_transporter_ATP-binding_protein_1514502..1514732_POSITIVE 190 54 11 82 35 aact:AA00309|5end_3-hydroxyisobutyrate_dehydrogenase;_2-hydroxy-3-oxopropionate_reductase_209285..209515_POSITIVE 187 34 1 224 187 aact:AA01827|5end_iron(III)_ABC_transporter,_periplasmic_binding_protein_1230431..1230661_POSITIVE 187 34 1 201 166 aact:AA00770|5end_outer_membrane_protein_precursor_530788..531018_POSITIVE 185 166 126 222 181 aact:AA02507|5end_penicillin-insensitive_murein_endopeptidase_A_1740058..1740288_POSITIVE 185 165 123 210 165 aact:AA00373|5end_CoA-transferase_(beta)_251013..251243_POSITIVE 184 180 134 154 108 aact:AA02271|5end_hypothetical_protein_1548623..1548853_POSITIVE 183 166 121 124 87 aact:AA02747|5end_ribose-phosphate_pyrophosphokinase;_phosphoribosylpyrophosphate_synthase_1924324..1924554_POSITIVE 183 41 3 149 110 aact:AA00533|5end_conserved_hypothetical_protein_365323..365553_POSITIVE 182 170 124 87 45 aact:AA01510|5end_ABC_transporter,_ATP-binding_protein/permease_1016430..1016660_POSITIVE 181 25 5 200 176 aact:AA00025|5end_hypothetical_protein_19235..19465_POSITIVE 178 180 132 181 131 aact:AA00076|5end_dihydroneopterin_aldolase_55653..55883_POSITIVE 174 180 141 60 24 aact:AA01398|5end_KDO_kinase_944889..945119_POSITIVE 171 53 12 95 44 aact:AA00429|5end_conserved_hypothetical_protein_290567..290797_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 210 35 5 118 84 aact:AA01690|3end_penicillin-binding_protein_1C_1149142..1149292_POSITIVE 209 164 126 57 16 aact:AA00715|3end_[2Fe-2S]_ferredoxin_491050..491200_POSITIVE 208 40 1 84 49 aact:AA00899|3end_possible_quaternary_ammonium_compound_resistance_protein_623479..623629_POSITIVE 207 48 4 108 65 aact:AA01278|3end_hypothetical_protein_867725..867875_POSITIVE 195 30 1 146 118 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE 191 31 4 131 105 aact:AA02225|3end_ABC_transporter_ATP-binding_protein_1514592..1514742_POSITIVE 184 180 134 119 73 aact:AA02270|3end_endopeptidase_La;_lon_protease;_protease_La_homolog;_ATP-dependent_protease_LA_(lon-1)_1548668..1548818_POSITIVE 183 41 3 131 92 aact:AA00531|3end_DNA_polymerase_I_365385..365535_POSITIVE 182 170 124 91 49 aact:AA01509|3end_ABC_system_transport_protein,_ATP_binding/permease_1016514..1016664_POSITIVE 178 180 132 84 34 aact:AA00075|3end_conserved_hypothetical_protein_55636..55786_POSITIVE 169 170 125 69 26 aact:AA01071|3end_RNA_methyltransferase_743001..743151_POSITIVE 168 38 1 128 91 aact:AA01948|3end_ABC_transporter_permease,_membrane_spanning_protein_1318196..1318346_POSITIVE 166 163 121 45 1 aact:AA02718|3end_spermidine/putrescine_ABC_transporter,_ATP-binding_protein_1902489..1902639_POSITIVE 163 169 122 56 15 aact:AA01988|3end_dihydrolipoamide_dehydrogenase;_lipoamide_dehydrogenase_1352018..1352168_POSITIVE 162 164 121 47 10 aact:AA02478|3end_PTS_system,_N-acetylglucosamine-specific_enzyme_IIABC_1714532..1714682_POSITIVE 162 35 1 46 11 aact:AA02407|3end_thymidine_kinase_1653240..1653390_POSITIVE 162 35 2 37 3 aact:AA01054|3end_conserved_hypothetical_protein_733940..734090_POSITIVE 160 33 4 149 113 aact:AA02043|3end_tagatose_6-phosphate_kinase_1391587..1391737_POSITIVE 159 161 126 69 37 aact:AA01839|3end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1237291..1237441_POSITIVE 159 161 122 82 36 aact:AA01295|3end_3-dehydroquinate_synthase_878437..878587_POSITIVE