Origin IGS: tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taagatttatctgtggaattgccaacgtattgtttctcttgaagcaatagcgttgcaatgccacagacattaaattctattctgtcatgagacctctgtaaaatccaaccaaaacggcaaaatgacaaatataatgttgtca Mask Tandem Repeat Region ================================================ tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Find is-nt database================================================ Query_seq: PI1567:PI1568|PI1567:PI1568:hypothetical protein:OmpA family protein:->->:1489582..1489723 142 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1567:PI1568|PI1567:PI1568:hypothetical protein:OmpA family protein:->->:1489582..1489723 142 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1567:PI1568|PI1567:PI1568:hypothetical protein:OmpA family protein:->->:1489582..1489723 142 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Predict ORF larger than 30AA ================================================ Protein_Len: 42 Strand: + Start: 15 End: 140 .............. M S F C R F G W I L Q R S H D R I E F N V C G I A T L L L Q E K Q Y V G N S T D K S .. tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta 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: 40 End: 69 .......................................TTTTACAGAGGTCTCATGACAGAATAGAAT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1567:PI1568|PI1567:PI1568:hypothetical protein:OmpA family protein:->->:1489582..1489723 142 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Intra-Species Hit: Count: 1 Min: 1 Max: 142 Len: 142 Subject: pint_PI1567_PI1568|hypothetical protein:OmpA family protein|POSITIVE:POSITIVE|[1489582,1489723]|142 HSP 1 e-value: 3.0E-75 bit: 281.0 Len: 142 Query Start:1 Query End:142 Subject Strand: POSITIVE Subject Start: 1 Subject End: 142 tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta tgacaacattatatttgtcattttgccgttttggttggattttacagaggtctcatgacagaatagaatttaatgtctgtggcattgcaacgctattgcttcaagagaaacaatacgttggcaattccacagataaatctta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAACAUUAUAUUUGUCAUUUUGCCGUUUUGGUUGGAUUUUACAGAGGUCUCAUGACAGAAUAGAAUUUAAUGUCUGUGGCAUUGCAACGCUAUUGCUUCAAGAGAAACAAUACGUUGGCAAUUCCACAGAUAAAUCUUA ((((((........))))))....(((.....)))(((((((((.....(((....)))....))))))))).(((((((((.(((((((((.(((((.(((....))).))))))))).))))).)))))))))....... (-41.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAUUUAUCUGUGGAAUUGCCAACGUAUUGUUUCUCUUGAAGCAAUAGCGUUGCAAUGCCACAGACAUUAAAUUCUAUUCUGUCAUGAGACCUCUGUAAAAUCCAACCAAAACGGCAAAAUGACAAAUAUAAUGUUGUCA ...(((...(((((((.(((((.(((((((((((((....)))))))).)))))))))).)))))))......(((.((((.((((((.......((((..............))))....)))))))))).)))...))). (-38.94) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 70 21 178 125 pint:PI0600|5end_bifunctional_purine_biosynthesis_protein,_5-aminoimidazole-4-carboxamide_ribonucleotide(AICAR)_transformylase/IMP_cyclohydrolase_547482..547712_POSITIVE 324 70 21 72 19 pint:PI0599|5end_hypothetical_protein_547376..547606_POSITIVE 297 130 85 55 13 pint:PI1184|5end_conserved_hypothetical_protein_1105784..1106014_POSITIVE 292 108 61 54 15 pint:PI0500|5end_mobilizable_transposon,_tnpC_protein_460674..460904_POSITIVE 284 93 55 156 106 pint:PI1419|5end_conserved_hypothetical_protein;_membrane_protease_subunits,_stomatin/prohibitin_homologs_1339136..1339366_POSITIVE 277 107 70 64 31 pint:PI0620|5end_hypothetical_protein_569729..569959_POSITIVE 272 100 55 208 156 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 272 100 55 143 91 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 269 118 87 121 88 pint:PI0936|5end_conserved_hypothetical_protein_868329..868559_POSITIVE 268 107 75 227 203 pint:PI0782|5end_beta-lactamase_induction_signal_transducer,_AmpG_protein_720573..720803_POSITIVE 267 62 23 73 39 pint:PI0016|5end_magnesium_chelatase,_subunit_ChlI_20191..20421_POSITIVE 266 128 82 83 40 pint:PI1425|5end_conserved_hypothetical_protein_1344488..1344718_POSITIVE 261 109 77 84 51 pint:PI2150|5end_acyl_carrier_protein_2096972..2097202_POSITIVE 260 119 78 74 34 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 258 125 81 92 40 pint:PI0397|5end_conserved_hypothetical_protein_362406..362636_POSITIVE 257 100 52 193 137 pint:PI0831|5end_hypothetical_protein_768129..768359_POSITIVE 256 127 82 79 35 pint:PI0822|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_761028..761258_POSITIVE 256 120 74 186 147 pint:PI0310|5end_outer_membrane_protein_291657..291887_POSITIVE 254 120 74 214 169 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 250 120 72 109 44 pint:PI1224|5end_sensor_histidine_kinase_and_response_regulator_1144574..1144804_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 93 55 141 91 pint:PI1418|3end_UDP-N-acetylglucosamine_2-epimerase_1339201..1339351_POSITIVE 273 130 89 38 5 pint:PI1183|3end_conserved_hypothetical_protein_1105847..1105997_POSITIVE 272 100 55 143 91 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 265 50 1 133 71 pint:PI1567|3end_hypothetical_protein_1489521..1489671_POSITIVE 257 127 81 67 32 pint:PI0570|3end_exsB_protein;_possible_aluminum_resistance_protein_515395..515545_POSITIVE 256 120 74 51 12 pint:PI0308|3end_conserved_hypothetical_protein_291602..291752_POSITIVE 255 130 82 146 76 pint:PI0797|3end_tRNA_pseudouridine_synthase_A_(pseudouridylate_synthase)_735752..735902_POSITIVE 247 126 81 62 14 pint:PI1362|3end_60Kd_inner_membrane_protein_1281813..1281963_POSITIVE 246 128 81 127 76 pint:PI1784|3end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1717195..1717345_POSITIVE 243 55 14 148 116 pint:PI2060|3end_conserved_hypothetical_protein;_possible_metalloprotease_2018358..2018508_POSITIVE 243 50 11 52 13 pint:PI2036|3end_hypothetical_protein_1989516..1989666_POSITIVE 242 108 69 75 30 pint:PI0655|3end_Na+/H+_anitporter_599541..599691_POSITIVE 240 128 83 101 49 pint:PI0743|3end_hypothetical_protein_673026..673176_POSITIVE 238 118 78 81 22 pint:PI1818|3end_hypothetical_protein_1757270..1757420_POSITIVE 238 101 73 117 85 pint:PI0049|3end_outer_membrane_receptor_protein_(iron_transport)_51090..51240_POSITIVE 237 50 3 144 83 pint:PI1009|3end_cytochrome_c_nitrite_reductase,_large_subunit_930840..930990_POSITIVE 236 99 55 83 40 pint:PI0125|3end_undecaprenyl_pyrophosphate_synthase_117890..118040_POSITIVE 235 116 76 114 60 pint:PI1027|3end_hypothetical_protein_943399..943549_POSITIVE 235 68 22 151 106 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 234 129 82 81 31 pint:PI0033|3end_peptidylprolyl_isomerase_37101..37251_POSITIVE