Origin IGS: taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat .........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 attgatttcaatataattgctgaactccttttgtccaacatagcgaatgatatacgatttacctatctgtcgtgctccatctatcaggagtatcttgtcatcagacgattgtagatggctttttataaacttttctatctttctatacagcataaatacactttttcaatgtttctgttgtggcaaaaatacacttttcttttgaaataagcaagcataaatacacttttcctataaaattagagctttaaaaatacacttttctattgatacttttgtttcaatactttaagattaatcattatttccaataaatttcggtcgtgttcactatggtatactgtcaaagaaagatagggtattatgttgtataagcgcataaaaaaactctgtgcaaagctgcacagagtttttaaagctttatgtatgataaggttttcgcctta Mask Tandem Repeat Region ================================================ taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Find is-nt database================================================ Query_seq: PI1837:PI1838|PI1837:PI1838:aspartate ammonia-lyase:conserved hypothetical protein:->->:1780467..1780912 446 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1837:PI1838|PI1837:PI1838:aspartate ammonia-lyase:conserved hypothetical protein:->->:1780467..1780912 446 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1837:PI1838|PI1837:PI1838:aspartate ammonia-lyase:conserved hypothetical protein:->->:1780467..1780912 446 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Predict ORF larger than 30AA ================================================ Protein_Len: 55 Strand: + Start: 16 End: 180 ............... M I H K A L K T L C S F A Q S F F M R L Y N I I P Y L S L T V Y H S E H D R N L L E I M I N L K V L K Q K Y Q .......................................................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 212 End: 301 ................................................................................................................................................................................................................... M G K V Y L C L L I S K E K C I F A T T E T L K K C I Y A V ................................................................................................................................................. Protein_Len: 51 Strand: + Start: 294 End: 446 ..................................................................................................................................................................................................................................................................................................... M L Y R K I E K F I K S H L Q S S D D K I L L I D G A R Q I G K S Y I I R Y V G Q K E F S N Y I E I N Protein_Len: 37 Strand: - Start: 336 End: 446 ............................................................................................................................................................................................................................................................................................................................................... L R R I V L Y E Q Y I S C S L Y T F R I D N A I N S L L L E A I I N F D M Protein_Len: 52 Strand: - Start: 245 End: 400 .................................................................................................................................................................................................................................................... F F L T N K G C C F C Q F L T N I S Y L F I S F N I F L W R C D D S S L I S R I S P A R C I P L D Y I M .............................................. Protein_Len: 31 Strand: - Start: 240 End: 332 ............................................................................................................................................................................................................................................... K L L F T Y K Q W L L F M S F T Y K H Q I S L Y F L K Y F A M .................................................................................................................. Protein_Len: 31 Strand: - Start: 199 End: 291 ...................................................................................................................................................................................................... L E L K I P F T Y K H K S I E F S F H I K A V V S V N F F H M ........................................................................................................................................................... taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat 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: 85 Start: 152 End: 181 .......................................................................................................................................................ATTGATACTTTTGTTTCAATACTTTAAGAT......................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.1 Tail_Score: -4.6526 Start: 38 End: 59 Full_Region: aagcgcataaaaaaa ctctgtgca aagc tgcacagag tttttaaagctttat .....................................ctctgtgcaaagctgcacagag................................................................................................................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PI1837:PI1838|PI1837:PI1838:aspartate ammonia-lyase:conserved hypothetical protein:->->:1780467..1780912 446 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Intra-Species Hit: Count: 1 Min: 1 Max: 446 Len: 446 Subject: pint_PI1837_PI1838|aspartate ammonia-lyase:conserved hypothetical protein|POSITIVE:POSITIVE|[1780467,1780912]|446 HSP 1 e-value: 0.0 bit: 842.0 Len: 446 Query Start:1 Query End:446 Subject Strand: POSITIVE Subject Start: 1 Subject End: 446 taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagnnnnnnnatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat taaggcgaaaaccttatcatacataaagctttaaaaactctgtgcagctttgcacagagtttttttatgcgcttatacaacataataccctatctttctttgacagtataccatagtgaacacgaccgaaatttattggaaataatgattaatcttaaagtattgaaacaaaagtatcaatagaaaagtgtatttttaaagctctaattttataggaaaagtgtatttatgcttgcttatttcaaaagaaaagtgtatttttgccacaacagaaacattgaaaaagtgtatttatgctgtatagaaagatagaaaagtttataaaaagccatctacaatcgtctgatgacaagatactcctgatagatggagcacgacagataggtaaatcgtatatcattcgctatgttggacaaaaggagttcagcaattatattgaaatcaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGGCGAAAACCUUAUCAUACAUAAAGCUUUAAAAACUCUGUGCAGCUUUGCACAGAGUUUUUUUAUGCGCUUAUACAACAUAAUACCCUAUCUUUCUUUGACAGUAUACCAUAGUGAACACGACCGAAAUUUAUUGGAAAUAAUGAUUAAUCUUAAAGUAUUGAAACAAAAGUAUCAAUAGAAAAGUGUAUUUUUAAAGCUCUAAUUUUAUAGGAAAAGUGUAUUUAUGCUUGCUUAUUUCAAAAGAAAAGUGUAUUUUUGCCACAACAGAAACAUUGAAAAAGUGUAUUUAUGCUGUAUAGAAAGAUAGAAAAGUUUAUAAAAAGCCAUCUACAAUCGUCUGAUGACAAGAUACUCCUGAUAGAUGGAGCACGACAGAUAGGUAAAUCGUAUAUCAUUCGCUAUGUUGGACAAAAGGAGUUCAGCAAUUAUAUUGAAAUCAAU ...((((((..................((...(((((((((((((......)))))))))))))....))...(((((...........((((((((((...((((((((.....(((.((((..((((......)))).............(((((...((((((.((....)).))))))....((.((.........)).)).......)))))...))))...(((((((.(((.......)))..))))))).......))).......(((((.....)))))...))))))))..))))))))))...............(((((((......(((....)))......((((........))))......)))).))).....)))))...)))))).((((((((.......)))))))).....((((....)))) (-101.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUGAUUUCAAUAUAAUUGCUGAACUCCUUUUGUCCAACAUAGCGAAUGAUAUACGAUUUACCUAUCUGUCGUGCUCCAUCUAUCAGGAGUAUCUUGUCAUCAGACGAUUGUAGAUGGCUUUUUAUAAACUUUUCUAUCUUUCUAUACAGCAUAAAUACACUUUUUCAAUGUUUCUGUUGUGGCAAAAAUACACUUUUCUUUUGAAAUAAGCAAGCAUAAAUACACUUUUCCUAUAAAAUUAGAGCUUUAAAAAUACACUUUUCUAUUGAUACUUUUGUUUCAAUACUUUAAGAUUAAUCAUUAUUUCCAAUAAAUUUCGGUCGUGUUCACUAUGGUAUACUGUCAAAGAAAGAUAGGGUAUUAUGUUGUAUAAGCGCAUAAAAAAACUCUGUGCAAAGCUGCACAGAGUUUUUAAAGCUUUAUGUAUGAUAAGGUUUUCGCCUUA ((((....))))......((.(((..(((..((((..((((((((.....((((((((....(((((((..(((((((........))))))).(((((....)))))...)))))))..............((((((((((((..((((((.(((((...........))))).))))))((((...((((...((((....))))........((((...((((.....(((......)))...............(((...((((((.((....)).))))))....)))..............................))))....))))))))..))))..))))))))))))......))))))))..)))....((((((((((((((....)))))))))))))).......)))))..)))))))..))))).... (-95.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 307 340 292 67 21 pint:PI1094|5end_recombination_protein_1019236..1019466_POSITIVE 304 78 37 86 33 pint:PI1676|5end_phosphatidate_cytidylyltransferase_1590896..1591126_POSITIVE 289 397 351 63 5 pint:PI0105|5end_possible_sulfatase_99403..99633_POSITIVE 280 400 358 108 55 pint:PI0611|5end_hypothetical_protein_559387..559617_POSITIVE 273 377 336 117 73 pint:PI2131|5end_hypothetical_protein_2080678..2080908_POSITIVE 272 380 332 214 167 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 268 264 221 210 166 pint:PI2038|5end_conserved_hypothetical_protein;_possible_internalin-related_protein_1990463..1990693_POSITIVE 267 379 337 217 185 pint:PI0029|5end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_32593..32823_POSITIVE 266 387 343 114 63 pint:PI1677|5end_cell_division_protein_FtsH_1591766..1591996_POSITIVE 263 75 42 200 164 pint:PI0609|5end_conserved_hypothetical_protein_556519..556749_POSITIVE 259 74 40 231 194 pint:PI1064|5end_hypothetical_protein_983071..983301_POSITIVE 258 376 337 178 133 pint:PI1743|5end_stationary-phase_survival_protein_1663948..1664178_POSITIVE 257 72 39 226 188 pint:PI1565|5end_conserved_hypothetical_protein;_possible_surface_antigen_1485460..1485690_POSITIVE 256 429 387 41 6 pint:PI0732|5end_conserved_hypothetical_protein_663598..663828_POSITIVE 254 407 367 223 171 pint:PI1038|5end_hypothetical_protein_958685..958915_POSITIVE 253 73 47 227 201 pint:PI2065|5end_hypothetical_protein_2026877..2027107_POSITIVE 251 380 331 110 71 pint:PI0030|5end_transcriptional_regulator,_AsnC_family_34509..34739_POSITIVE 250 417 371 91 35 pint:PI1153|5end_histidine_kinase_sensor_protein_1077116..1077346_POSITIVE 250 70 27 73 26 pint:PI0522|5end_50S_ribosomal_protein_L19_479004..479234_POSITIVE 249 405 368 225 191 pint:PI2062|5end_type_I_restriction-modification_system_2021658..2021888_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 69 22 69 22 pint:PI1837|3end_aspartate_ammonia-lyase_1780406..1780556_POSITIVE 301 74 43 149 121 pint:PI1586|3end_possible_HesA/MoeB/ThiF_family_protein_1515183..1515333_POSITIVE 300 73 39 53 13 pint:PI0111|3end_hypothetical_protein_108265..108415_POSITIVE 273 377 336 70 26 pint:PI2130|3end_DNA_polymerase_I_2080711..2080861_POSITIVE 261 379 340 147 91 pint:PI1920|3end_hypothetical_protein_1865203..1865353_POSITIVE 260 368 326 151 109 pint:PI1957|3end_calcium-transporting_ATPase_1916574..1916724_POSITIVE 258 238 198 58 14 pint:PI0057|3end_conserved_hypothetical_protein_56512..56662_POSITIVE 256 429 387 36 1 pint:PI0731|3end_conserved_hypothetical_protein_663673..663823_POSITIVE 255 381 347 46 8 pint:PI1921|3end_conserved_hypothetical_protein_1865100..1865250_POSITIVE 255 379 332 71 5 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 253 388 345 70 17 pint:PI0540|3end_conserved_hypothetical_protein_493865..494015_POSITIVE 251 380 331 59 20 pint:PI0029|3end_glutamine_amidotransferase_(GMP_synthase_(glutamine-hydrolyzing))_34538..34688_POSITIVE 250 70 27 50 3 pint:PI0521|3end_hypothetical_protein_479061..479211_POSITIVE 249 405 368 134 100 pint:PI2061|3end_type_I_restriction_enzyme_restriction_subunit_2021647..2021797_POSITIVE 244 428 383 129 81 pint:PI0385|3end_hypothetical_protein_354449..354599_POSITIVE 242 386 344 89 51 pint:PI2027|3end_arginine_decarboxylase_1982130..1982280_POSITIVE 241 430 383 100 52 pint:PI0245|3end_possible_mobilization_protein_244258..244408_POSITIVE 241 72 38 95 69 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 240 407 365 65 13 pint:PI1676|3end_phosphatidate_cytidylyltransferase_1591773..1591923_POSITIVE 238 411 371 82 32 pint:PI2166|3end_hypothetical_protein_2112073..2112223_POSITIVE