Origin IGS: gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta .........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.........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 taaaagaccctgacaaaaataatgctttttgaacgttggctttgtcggcggagtcgaggatacaagtaaatcttcaagatttatgagtaagaaattaaccgcacttttagagtagaacatcaaatcagaaagccgaattcatttcgatgagttcggttttttattgcccgtaattagggtatttcttcttcgataaaatattcaaataaaaataattcttttttgtagcataaaatgtaaatatacctctttatagttatatatttctgcttcatttaattttcccctttaatgatatttttatactaataaataggtagttgatacattttaggagaaattttcatgctacaaaatttcactaaaatagaaaattaaattggaaaaattgatcaaaaacaagaaaatgtaaaataaccatggaatgagcgcggatatttggttatgttaaactcgtttaacccccttttataccttatatcgcattgtttttcatgataaaagttatcatttttatgatgcgggcggtatagacatttccttaacaaaactacagttaacctgattggagtgattatc Mask Tandem Repeat Region ================================================ gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Find is-nt database================================================ Query_seq: AA00047:AA00048|AA00047:AA00048:formate dependent nitrite reductase, cytochrome c552:conserved hypothetical protein:->->:38414..38992 579 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00047:AA00048|AA00047:AA00048:formate dependent nitrite reductase, cytochrome c552:conserved hypothetical protein:->->:38414..38992 579 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00047:AA00048|AA00047:AA00048:formate dependent nitrite reductase, cytochrome c552:conserved hypothetical protein:->->:38414..38992 579 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 2 End: 184 . M I T P I R L T V V L L R K C L Y R P H H K N D N F Y H E K Q C D I R Y K R G L N E F N I T K Y P R S F H G Y F T F S C ........................................................................................................................................................................................................................................................................................................................................................................................................... Protein_Len: 33 Strand: + Start: 305 End: 403 ................................................................................................................................................................................................................................................................................................................ M K Q K Y I T I K R Y I Y I L C Y K K E L F L F E Y F I E E E I P ................................................................................................................................................................................ Protein_Len: 46 Strand: + Start: 442 End: 579 ......................................................................................................................................................................................................................................................................................................................................................................................................................................................... M R L S D L M F Y S K S A V N F L L I N L E D L L V S S T P P T K P T F K K H Y F C Q G L L gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta 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: 60 End: 89 ...........................................................TTTCATGATAAAAGTTATCATTTTTATGAT.......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -5.8 Tail_Score: -4.91109 Start: 70 End: 84 Full_Region: tcgcattgtttttca tgataa aag ttatca tttttatgatgcggg .....................................................................tgataaaagttatca............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 70 HP_score: -8.2 Tail_Score: -3.08782 Start: 424 End: 447 Full_Region: ACGGGCAATAAAAAA CCGAACTCAT CGAA ATGAATTCGG CTTTCTGATTTGATG .......................................................................................................................................................................................................................................................................................................................................................................................................................................CCGAACTCATCGAAATGAATTCGG.................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -10.4 Tail_Score: -5.45652 Start: 424 End: 447 Full_Region: catcaaatcagaaag ccgaattcat ttcg atgagttcgg ttttttattgcccgt .......................................................................................................................................................................................................................................................................................................................................................................................................................................ccgaattcatttcgatgagttcgg.................................................................................................................................... Find igs database================================================ Query_seq: AA00047:AA00048|AA00047:AA00048:formate dependent nitrite reductase, cytochrome c552:conserved hypothetical protein:->->:38414..38992 579 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggttattttacattttcttgtttttgatcaatttttccaatttaattttctattttagtgaaattttgtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta Intra-Species Hit: Count: 1 Min: 1 Max: 579 Len: 579 Subject: aact_AA00047_AA00048|formate dependent nitrite reductase, cytochrome c552:conserved hypothetical protein|POSITIVE:POSITIVE|[38414,38992]|579 HSP 1 e-value: 0.0 bit: 698.0 Len: 352 Query Start:228 Query End:579 Subject Strand: POSITIVE Subject Start: 228 Subject End: 579 ...................................................................................................................................................................................................................................gtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta ...................................................................................................................................................................................................................................gtagcatgaaaatttctcctaaaatgtatcaactacctatttattagtataaaaatatcattaaaggggaaaattaaatgaagcagaaatatataactataaagaggtatatttacattttatgctacaaaaaagaattatttttatttgaatattttatcgaagaagaaataccctaattacgggcaataaaaaaccgaactcatcgaaatgaattcggctttctgatttgatgttctactctaaaagtgcggttaatttcttactcataaatcttgaagatttacttgtatcctcgactccgccgacaaagccaacgttcaaaaagcattatttttgtcagggtctttta HSP 2 e-value: 1.0E-87 bit: 325.0 Len: 164 Query Start:1 Query End:164 Subject Strand: POSITIVE Subject Start: 1 Subject End: 164 gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggtt............................................................................................................................................................................................................................................................................................................................................................................................................................... gataatcactccaatcaggttaactgtagttttgttaaggaaatgtctataccgcccgcatcataaaaatgataacttttatcatgaaaaacaatgcgatataaggtataaaagggggttaaacgagtttaacataaccaaatatccgcgctcattccatggtt............................................................................................................................................................................................................................................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUAAUCACUCCAAUCAGGUUAACUGUAGUUUUGUUAAGGAAAUGUCUAUACCGCCCGCAUCAUAAAAAUGAUAACUUUUAUCAUGAAAAACAAUGCGAUAUAAGGUAUAAAAGGGGGUUAAACGAGUUUAACAUAACCAAAUAUCCGCGCUCAUUCCAUGGUUAUUUUACAUUUUCUUGUUUUUGAUCAAUUUUUCCAAUUUAAUUUUCUAUUUUAGUGAAAUUUUGUAGCAUGAAAAUUUCUCCUAAAAUGUAUCAACUACCUAUUUAUUAGUAUAAAAAUAUCAUUAAAGGGGAAAAUUAAAUGAAGCAGAAAUAUAUAACUAUAAAGAGGUAUAUUUACAUUUUAUGCUACAAAAAAGAAUUAUUUUUAUUUGAAUAUUUUAUCGAAGAAGAAAUACCCUAAUUACGGGCAAUAAAAAACCGAACUCAUCGAAAUGAAUUCGGCUUUCUGAUUUGAUGUUCUACUCUAAAAGUGCGGUUAAUUUCUUACUCAUAAAUCUUGAAGAUUUACUUGUAUCCUCGACUCCGCCGACAAAGCCAACGUUCAAAAAGCAUUAUUUUUGUCAGGGUCUUUUA .........(((...(((.....)))..((((((((..(((......((((((...(((((.......((((((.....))))))........)))))......))))))...((((((...(((((...............((.((((((........((((((....(((......)))...))))))......................((((((.(...(((((((((((((((.((((((((..(((((((.......(((.....))).......))).))))..))))))))..............((((((((..((....))..))))))))...))))))))))))))).................(((((((..(((..(((((.....(((.......)))..........(((((.((((....)))).))))).))))))))..)))))))..).)))))))))))).))............((((((.....)))))))))))))))))...)))...)))))))).......((((((......))))))...)))....... (-118.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAGACCCUGACAAAAAUAAUGCUUUUUGAACGUUGGCUUUGUCGGCGGAGUCGAGGAUACAAGUAAAUCUUCAAGAUUUAUGAGUAAGAAAUUAACCGCACUUUUAGAGUAGAACAUCAAAUCAGAAAGCCGAAUUCAUUUCGAUGAGUUCGGUUUUUUAUUGCCCGUAAUUAGGGUAUUUCUUCUUCGAUAAAAUAUUCAAAUAAAAAUAAUUCUUUUUUGUAGCAUAAAAUGUAAAUAUACCUCUUUAUAGUUAUAUAUUUCUGCUUCAUUUAAUUUUCCCCUUUAAUGAUAUUUUUAUACUAAUAAAUAGGUAGUUGAUACAUUUUAGGAGAAAUUUUCAUGCUACAAAAUUUCACUAAAAUAGAAAAUUAAAUUGGAAAAAUUGAUCAAAAACAAGAAAAUGUAAAAUAACCAUGGAAUGAGCGCGGAUAUUUGGUUAUGUUAAACUCGUUUAACCCCCUUUUAUACCUUAUAUCGCAUUGUUUUUCAUGAUAAAAGUUAUCAUUUUUAUGAUGCGGGCGGUAUAGACAUUUCCUUAACAAAACUACAGUUAACCUGAUUGGAGUGAUUAUC .......((((((((((..(((((.........)))))..)))))))).)).((..(((((((..(((((((.....)))))))..))).........((((.(((...(((((....(((.....((((((((((((((((....))))))))))))))))..(((((.......)))))..........)))....)))))...............((((((((.(((.(((((((((.((((......)))).)))))).))).)))((((((((((((((.(((..((((.((((....((((........))))...))))))))..))).((((((((........)))))))).........)))))))))).))))..............))))))))....................))).))))......((....((((((....))))))..)).((((((((.....((((((..(.....((((((.....))))))....)..))))))..))))))))....))))..))...(((.(((((.....))))).)))....... (-129.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 418 556 511 184 127 aact:AA00054|5end_cytochrome_c_biogenesis_protein_41393..41623_POSITIVE 393 567 521 219 168 aact:AA02220|5end_ABC_transport_system_permease_protein_1511155..1511385_POSITIVE 356 559 515 170 122 aact:AA01079|5end_conserved_hypothetical_protein_747404..747634_POSITIVE 351 542 501 148 101 aact:AA00993|5end_possible_D-tyrosyl-tRNA(Tyr)_deacylase_694488..694718_POSITIVE 344 485 446 156 119 aact:AA02092|5end_glycogen_synthase_1424674..1424904_POSITIVE 332 557 513 170 114 aact:AA02595|5end_cytochrome_c_peroxidase_1805741..1805971_POSITIVE 322 555 520 45 8 aact:AA00311|5end_L-fuculose-phosphate_aldolase_211434..211664_POSITIVE 321 567 521 75 24 aact:AA01953|5end_hypothetical_protein_1320132..1320362_POSITIVE 313 497 460 177 144 aact:AA00914|5end_aminoacyl-histidine_dipeptidase;_Beta-alanyl-histidine_dipeptidase_628038..628268_POSITIVE 306 484 445 117 70 aact:AA00343|5end_conserved_hypothetical_protein_(possible_cytosolic_protein)_229908..230138_POSITIVE 300 489 443 109 62 aact:AA02081|5end_periplasmic_protein_1414698..1414928_POSITIVE 298 553 514 169 132 aact:AA02728|5end_conserved_hypothetical_protein_(possible_ATPase)_1910145..1910375_POSITIVE 297 548 514 80 42 aact:AA02075|5end_conserved_hypothetical_protein_1409654..1409884_POSITIVE 297 59 11 212 162 aact:AA01522|5end_conserved_hypothetical_protein_1022840..1023070_POSITIVE 297 553 515 194 152 aact:AA01502|5end_serine_acetyltransferase_1010014..1010244_POSITIVE 292 185 146 63 18 aact:AA01818|5end_high-affinity_zinc_uptake_system_membrane_protein_1224306..1224536_POSITIVE 292 448 402 82 42 aact:AA01039|5end_transcriptional_regulator_(possible_murein_gene_regulator)_723864..724094_POSITIVE 288 546 504 198 163 aact:AA01634|5end_hypothetical_protein_1104324..1104554_POSITIVE 285 480 433 169 127 aact:AA02743|5end_outer_membrane_lipoprotein_precursor/glutamyl-tRNA_reductase_subunit_1922650..1922880_POSITIVE 284 485 441 64 22 aact:AA02989|5end_conserved_hypothetical_protein_2089118..2089348_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 356 559 515 139 91 aact:AA01078|3end_transcriptional_regulator_(probable_MerR_family)_747453..747603_POSITIVE 351 542 501 148 101 aact:AA00992|3end_ribonuclease_BN_694568..694718_POSITIVE 344 485 446 69 32 aact:AA02091|3end_hypothetical_protein_1424667..1424817_POSITIVE 322 555 520 45 8 aact:AA00310|3end_conserved_hypothetical_protein_211514..211664_POSITIVE 320 569 522 64 9 aact:AA01880|3end_N-acetylglucosamine_repressor_1268383..1268533_POSITIVE 314 568 526 54 2 aact:AA01167|3end_glucose-6-phosphate_1-dehydrogenase_801067..801217_POSITIVE 313 497 460 91 58 aact:AA00912|3end_short-chain_dehydrogenase_628032..628182_POSITIVE 311 536 491 148 105 aact:AA01722|3end_conserved_hypothetical_protein_1163639..1163789_POSITIVE 306 484 445 68 21 aact:AA00342|3end_hypothetical_protein_229939..230089_POSITIVE 300 489 443 125 78 aact:AA02080|3end_ABC_transporter,_ATP-binding/permease_1414794..1414944_POSITIVE 297 553 515 140 98 aact:AA01501|3end_hypothetical_protein_1010040..1010190_POSITIVE 294 568 526 138 98 aact:AA01113|3end_transcriptional_regulator_(merR_family)_765249..765399_POSITIVE 292 185 146 77 32 aact:AA01817|3end_hypothetical_protein_1224400..1224550_POSITIVE 292 448 402 50 10 aact:AA01037|3end_hypothetical_protein_723912..724062_POSITIVE 289 545 505 117 76 aact:AA01750|3end_MTA/SAH_nucleosidase_[Includes:_5'-methylthioadenosine_nucleosidase;_S-adenosylhomocysteine_nucleosidase]_1184519..1184669_POSITIVE 288 546 504 127 92 aact:AA01633|3end_probable_ferredoxin-like_protein_1104333..1104483_POSITIVE 285 480 433 137 95 aact:AA02742|3end_tRNA_nucleotidyltransferase_1922698..1922848_POSITIVE 284 485 441 60 18 aact:AA02987|3end_histidine_triad_protein_homolog_2089194..2089344_POSITIVE 283 450 407 89 46 aact:AA01221|3end_transformation_locus_protein_orfG_homolog_834239..834389_POSITIVE 281 546 502 151 104 aact:AA02946|3end_virulence_factor_protein_2060870..2061020_POSITIVE