Origin IGS: aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tcagaatcgttgtcttctttctgcaaaagtactaaaaaaaaccgacacaactaattatatacaatatcttttactttgtaaatcaatttttcaggatattgttgggttaatgaaaaaaaaggagtatttttgcaaaaaaataaattagaaaaaagtatgaaaaaatt Mask Tandem Repeat Region ================================================ aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Find is-nt database================================================ Query_seq: PI1325:PI1326|PI1325:PI1326:conserved hypothetical protein:Na+-driven multidrug efflux pump:->->:1244155..1244321 167 aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1325:PI1326|PI1325:PI1326:conserved hypothetical protein:Na+-driven multidrug efflux pump:->->:1244155..1244321 167 aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1325:PI1326|PI1325:PI1326:conserved hypothetical protein:Na+-driven multidrug efflux pump:->->:1244155..1244321 167 aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 10 End: 114 ......... M L F S N L F F C K N T P F F S L T Q Q Y P E K L I Y K V K D I V Y N ..................................................... aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga 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: 87 Start: 85 End: 114 ....................................................................................ATTTACAAAGTAAAAGATATTGTATATAAT..................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1325:PI1326|PI1325:PI1326:conserved hypothetical protein:Na+-driven multidrug efflux pump:->->:1244155..1244321 167 aattttttcatacttttttctaatttatttttttgcaaaaatactccttttttttcattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Intra-Species Hit: Count: 1 Min: 56 Max: 167 Len: 112 Subject: pint_PI1325_PI1326|conserved hypothetical protein:Na+-driven multidrug efflux pump|POSITIVE:POSITIVE|[1244155,1244321]|167 HSP 1 e-value: 6.0E-43 bit: 174.0 Len: 112 Query Start:56 Query End:167 Subject Strand: POSITIVE Subject Start: 56 Subject End: 167 .......................................................cattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggnnnnnnnnagtacttttgcagaaagaagacaacgattctga .......................................................cattaacccaacaatatcctgaaaaattgatttacaaagtaaaagatattgtatataattagttgtgtcggttttttttagtacttttgcagaaagaagacaacgattctga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAUUAACCCAACAAUAUCCUGAAAAAUUGAUUUACAAAGUAAAAGAUAUUGUAUAUAAUUAGUUGUGUCGGUUUUUUUUAGUACUUUUGCAGAAAGAAGACAACGAUUCUGA ..........((((((((........(((.....))).......))))))))........(((((((((..((((((.(((.....))).))))))..))).)))))).... (-15.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAGAAUCGUUGUCUUCUUUCUGCAAAAGUACUAAAAAAAACCGACACAACUAAUUAUAUACAAUAUCUUUUACUUUGUAAAUCAAUUUUUCAGGAUAUUGUUGGGUUAAUG ........((((..((.(((.(((....)))...))).))..)))).....(((((....((((((((((.....(((.....)))......))))))))))..)))))... (-13.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 294 106 62 179 120 pint:PI2031|5end_hypothetical_protein_1986053..1986283_POSITIVE 257 91 61 190 155 pint:PI1859|5end_conserved_hypothetical_protein_1805394..1805624_POSITIVE 241 92 56 168 126 pint:PI1748|5end_guanosine-3',5'-bis(diphosphate)_3'-pyrophosphohydrolase/possible_(p)ppgpp_synthetase_II_1668536..1668766_POSITIVE 238 104 61 216 165 pint:PI1489|5end_exodeoxyribonuclease_III_1407758..1407988_POSITIVE 238 104 61 82 31 pint:PI1487|5end_hypothetical_protein_1407624..1407854_POSITIVE 238 91 51 225 183 pint:PI0793|5end_ABC_transporter,_permease_protein_729754..729984_POSITIVE 228 107 62 75 28 pint:PI1274|5end_possible_phosphoribosylanthranilate_isomerase_1192880..1193110_POSITIVE 226 107 62 176 131 pint:PI1255|5end_conserved_hypothetical_protein_1176709..1176939_POSITIVE 225 110 62 176 132 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 223 106 68 191 143 pint:PI0002|5end_conserved_hypothetical_protein_2972..3202_POSITIVE 222 109 62 103 55 pint:PI0176|5end_hypothetical_protein_168230..168460_POSITIVE 216 105 75 211 181 pint:PI0521|5end_hypothetical_protein_478886..479116_POSITIVE 216 105 75 80 50 pint:PI0520|5end_hypothetical_protein_478755..478985_POSITIVE 213 110 61 65 5 pint:PI2174|5end_hypothetical_protein_2114245..2114475_POSITIVE 213 110 65 188 139 pint:PI0857|5end_hypothetical_protein_790697..790927_POSITIVE 210 79 36 73 21 pint:PI0237|5end_predicted_two-component_system_sensor_histidine_kinase_235979..236209_POSITIVE 204 107 61 211 151 pint:PI0670|5end_hypothetical_protein_611000..611230_POSITIVE 204 107 61 135 75 pint:PI0669|5end_hypothetical_protein_610924..611154_POSITIVE 203 108 62 69 19 pint:PI0536|5end_hypothetical_protein_492163..492393_POSITIVE 203 89 42 190 154 pint:PI0149|5end_conserved_hypothetical_protein_142735..142965_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 257 91 61 71 36 pint:PI1858|3end_conserved_hypothetical_protein_1805355..1805505_POSITIVE 241 92 56 131 89 pint:PI1747|3end_membrane-bound_lytic_murein_transglycosylase_D_1668579..1668729_POSITIVE 234 100 51 130 73 pint:PI1311|3end_large_protein_related_to_C.hutchinsonii_large_proteins_1227439..1227589_POSITIVE 229 99 51 146 102 pint:PI1395|3end_hypothetical_protein_1314407..1314557_POSITIVE 228 107 62 70 23 pint:PI1273|3end_anthranilate_synthase_component_II_1192955..1193105_POSITIVE 223 106 68 51 3 pint:PI0001|3end_possible_Ton-B_receptor_2912..3062_POSITIVE 221 91 62 147 114 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 219 110 74 46 1 pint:PI0792|3end_conserved_hypothetical_protein_729627..729777_POSITIVE 216 105 75 54 24 pint:PI0519|3end_5'-nucleotidase/2',3'-cyclic_phosphodiesterase_478809..478959_POSITIVE 210 89 42 122 68 pint:PI0487|3end_50S_ribosomal_protein_L17_446703..446853_POSITIVE 207 98 54 60 5 pint:PI0524|3end_meso-diaminopimelate_D-dehydrogenase_480849..480999_POSITIVE 204 107 61 86 26 pint:PI0668|3end_peptidyl-prolyl_cis-trans_isomerase_SlyD,_FKBP-type_(peptidylprolyl_isomerase)_610955..611105_POSITIVE 203 106 65 98 51 pint:PI1882|3end_hypothetical_protein_1826487..1826637_POSITIVE 201 110 70 128 83 pint:PI0660|3end_conserved_hypothetical_protein_603997..604147_POSITIVE 198 109 61 140 87 pint:PI1265|3end_hypothetical_protein_1185512..1185662_POSITIVE 197 107 68 137 92 pint:PI1165|3end_hypothetical_protein_1089636..1089786_POSITIVE 196 101 61 83 35 pint:PI2040|3end_conserved_hypothetical_protein;_possible_transporter_1994065..1994215_POSITIVE 196 103 71 85 48 pint:PI1238|3end_single-strand_DNA-specific_exonuclease_1163438..1163588_POSITIVE 196 100 74 84 55 pint:PI0807|3end_hydrolase,_haloacid_dehalogenase-like_hydrolase_745278..745428_POSITIVE 194 106 81 83 54 pint:PI0227|3end_ABC_transporter,_ATP-binding/permease_protein_225632..225782_POSITIVE