Origin IGS: agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc .........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 gggttgatattcctcgccctctttcagttctcggaaggcgttttcaggaagttcaatgttttgtttttctttattttccatatccatagttgtatgttattctaaaggtaaagttttgtttcgattttgcaaattttagtttaatgcagtcgcaaagataagtaaaaaatagcaaaggttgcattagttgtcaataaaaaatgcaataattattgagct Mask Tandem Repeat Region ================================================ agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Find is-nt database================================================ Query_seq: PI1446:PI1447|PI1446:PI1447:conserved hypothetical protein:probable OPT oligopeptide transporter protein:->->:1369893..1370111 219 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1446:PI1447|PI1446:PI1447:conserved hypothetical protein:probable OPT oligopeptide transporter protein:->->:1369893..1370111 219 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1446:PI1447|PI1446:PI1447:conserved hypothetical protein:probable OPT oligopeptide transporter protein:->->:1369893..1370111 219 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 36 End: 146 ................................... M Q P L L F F T Y L C D C I K L K F A K S K Q N F T F R I T Y N Y G Y G K ......................................................................... Protein_Len: 33 Strand: - Start: 118 End: 216 ..................................................................................................................... F L M C S H I H F I F F F L V N F K R F V G E S F Q F L A L F I M ... agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc 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: 25 End: 54 ........................ATTGACAACTAATGCAACCTTTGCTATTTT..................................................................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 81 Start: 117 End: 146 ....................................................................................................................TTTTCCATATCCATAGTTGTATGTTATTCT......................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1446:PI1447|PI1446:PI1447:conserved hypothetical protein:probable OPT oligopeptide transporter protein:->->:1369893..1370111 219 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Intra-Species Hit: Count: 1 Min: 1 Max: 219 Len: 219 Subject: pint_PI1446_PI1447|conserved hypothetical protein:probable OPT oligopeptide transporter protein|POSITIVE:POSITIVE|[1369893,1370111]|219 HSP 1 e-value: 1.0E-121 bit: 434.0 Len: 219 Query Start:1 Query End:219 Subject Strand: POSITIVE Subject Start: 1 Subject End: 219 agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc agctcaataattattgcattttttattgacaactaatgcaacctttgctattttttacttatctttgcgactgcattaaactaaaatttgcaaaatcgaaacaaaactttacctttagaataacatacaactatggatatggaaaataaagaaaaacaaaacattgaacttcctgaaaacgccttccgagaactgaaagagggcgaggaatatcaaccc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCUCAAUAAUUAUUGCAUUUUUUAUUGACAACUAAUGCAACCUUUGCUAUUUUUUACUUAUCUUUGCGACUGCAUUAAACUAAAAUUUGCAAAAUCGAAACAAAACUUUACCUUUAGAAUAACAUACAACUAUGGAUAUGGAAAAUAAAGAAAAACAAAACAUUGAACUUCCUGAAAACGCCUUCCGAGAACUGAAAGAGGGCGAGGAAUAUCAACCC ...(((((.....(((((..(((((........(((((((....((((..................)))).)))))))...)))))..))))).............(((((..(((...(((.((((....))))..))).)))..)))))...........)))))..(((((.....(((((((............))))))))))))......... (-33.27) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGGUUGAUAUUCCUCGCCCUCUUUCAGUUCUCGGAAGGCGUUUUCAGGAAGUUCAAUGUUUUGUUUUUCUUUAUUUUCCAUAUCCAUAGUUGUAUGUUAUUCUAAAGGUAAAGUUUUGUUUCGAUUUUGCAAAUUUUAGUUUAAUGCAGUCGCAAAGAUAAGUAAAAAAUAGCAAAGGUUGCAUUAGUUGUCAAUAAAAAAUGCAAUAAUUAUUGAGCU .........(((((((((.(((..........))).)))).....)))))((((((((.((((((.((.((((((.....((((....(((((..((((..(((((.((((((((.......))))))))....)))))..)))))))).).....)))))))))).)).)))))).((((((((..(((....)))..))))))))...)))))))). (-41.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 363 209 162 84 36 pint:PI0148|5end_mannose-1-phosphate_guanylyltransferase_141423..141653_POSITIVE 305 208 169 183 140 pint:PI1223|5end_conserved_hypothetical_protein_1143537..1143767_POSITIVE 301 82 42 220 170 pint:PI1518|5end_outer_membrane_protein_oprM_precursor,_multidrug_resistance_protein_1438922..1439152_POSITIVE 292 209 180 58 32 pint:PI0265|5end_conjugative_transposon_protein,_TraO_257296..257526_POSITIVE 289 209 163 84 25 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 281 209 180 172 146 pint:PI0735|5end_ABC_transporter,_ATP-binding_/_permease_668793..669023_POSITIVE 276 210 182 224 193 pint:PI2068|5end_hypothetical_protein_2028328..2028558_POSITIVE 266 205 180 148 118 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 265 209 172 40 4 pint:PI0268|5end_lysozyme-related_protein_259198..259428_POSITIVE 255 107 65 53 14 pint:PI0864|5end_dihydrodipicolinate_synthase_800527..800757_POSITIVE 253 68 26 214 174 pint:PI0820|5end_hypothetical_protein_759694..759924_POSITIVE 251 206 163 60 14 pint:PI1832|5end_conserved_hypothetical_protein_1773161..1773391_POSITIVE 249 210 161 83 40 pint:PI0374|5end_MbpB_protein_344571..344801_POSITIVE 248 208 161 88 43 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 246 201 168 200 172 pint:PI2115|5end_hypothetical_protein_2064966..2065196_POSITIVE 246 205 163 154 118 pint:PI0687|5end_hypothetical_protein_624256..624486_POSITIVE 245 207 161 151 103 pint:PI1770|5end_4-alpha-glucanotransferase_1697336..1697566_POSITIVE 243 210 163 173 128 pint:PI2014|5end_conserved_hypothetical_protein_1971471..1971701_POSITIVE 243 204 170 59 32 pint:PI0843|5end_carboxyl-terminal_protease_776145..776375_POSITIVE 241 210 181 60 27 pint:PI0317|5end_possible_kinase;_TPR_repeat?_299179..299409_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 328 209 161 95 30 pint:PI0645|3end_hypothetical_protein_586807..586957_POSITIVE 292 209 180 53 27 pint:PI0264|3end_transfer_region-related_protein,_TraN_257371..257521_POSITIVE 281 209 180 59 33 pint:PI0734|3end_ABC_transporter,_ATP-binding_/_permease_668760..668910_POSITIVE 274 207 162 95 57 pint:PI0199|3end_phosphate_acetyltransferase_190923..191073_POSITIVE 265 209 172 53 17 pint:PI0267|3end_conjugative_transposon_protein,_TraQ_259291..259441_POSITIVE 264 208 164 138 95 pint:PI0075|3end_uridine_kinase_75390..75540_POSITIVE 263 60 12 129 73 pint:PI0131|3end_conserved_hypothetical_protein_(possible_outer_membrane_lipoprotein)_124489..124639_POSITIVE 253 68 26 99 59 pint:PI0818|3end_alpha-amylase_759659..759809_POSITIVE 251 208 182 151 122 pint:PI2067|3end_hypothetical_protein_2028337..2028487_POSITIVE 246 205 163 67 31 pint:PI0686|3end_glycosyl_transferase,_group_2_family_protein_624249..624399_POSITIVE 244 208 162 97 42 pint:PI0783|3end_hypothetical_protein_723397..723547_POSITIVE 241 210 181 59 28 pint:PI0674|3end_conserved_hypothetical_protein_616154..616304_POSITIVE 239 209 164 66 13 pint:PI0982|3end_hypothetical_protein_909649..909799_POSITIVE 239 74 31 71 19 pint:PI0386|3end_integrase_354640..354790_POSITIVE 237 210 162 147 101 pint:PI0377|3end_DNA_primase/mobilizable_transposon,_excision_protein_347823..347973_POSITIVE 236 209 170 143 100 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 236 209 172 80 43 pint:PI1535|3end_response_regulator_1455501..1455651_POSITIVE 232 209 166 91 50 pint:PI0375|3end_hypothetical_protein_346082..346232_POSITIVE 231 75 43 44 9 pint:PI1637|3end_hypothetical_protein_1555284..1555434_POSITIVE 230 209 166 47 3 pint:PI1735|3end_conserved_hypothetical_protein_1654323..1654473_POSITIVE