Origin IGS: aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta .........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 tagtttgaagatattaaggattaacagtttttcgtatagtgcgagatgttaatccttaatattttgttttgtgaataaaagtcgcaaaaagtaaagaattatactaaaatttggaaaattagctatttatgcttatctttgcatagatataatgtatgtattggcgaaatggtagaatgtagattttgccgagcttacaatgctttaaatagaaatatattaaataattgtctttatgaaggacttttttaagaatgtctttgccacttttgttggcgtattcctttttggtttagtaacgttgttgttaggtctcgtttgtatatttggaatgatattgtcgagcgatgaaacggcagaagtaaaagataattctgtattggtagtagacttgtcaggagtactgaacgaacgttccaagaaagatgtt Mask Tandem Repeat Region ================================================ aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Find is-nt database================================================ Query_seq: PI1375:PI1376|PI1375:PI1376:protease IV family, clan S (peptidase family S49):outer membrane protein:->->:1297675..1298104 430 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1375:PI1376|PI1375:PI1376:protease IV family, clan S (peptidase family S49):outer membrane protein:->->:1297675..1298104 430 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1375:PI1376|PI1375:PI1376:protease IV family, clan S (peptidase family S49):outer membrane protein:->->:1297675..1298104 430 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Predict ORF larger than 30AA ================================================ Protein_Len: 49 Strand: + Start: 33 End: 179 ................................ M T S L L P I Q N Y L L L L P F H R S T I S F Q I Y K R D L T T T L L N Q K G I R Q Q K W Q R H S ........................................................................................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 11 End: 208 .......... M E R S F S T P D K S T T N T E L S F T S A V S S L D N I I P N I Q T R P N N N V T K P K R N T P T K V A K T F L K K S .............................................................................................................................................................................................................................. Protein_Len: 45 Strand: + Start: 175 End: 309 .............................................................................................................................................................................. M L K K V L H K D N Y L I Y F Y L K H C K L G K I Y I L P F R Q Y I H Y I Y A K I S I N S ......................................................................................................................... Protein_Len: 47 Strand: - Start: 182 End: 322 ..................................................................................................................................................................................... F L G E Y L C N N L I N R N L A N Y A R C F R C E V M E G I C V N Y R H L S L C L Y S I K W M ............................................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 207 V G S L D V V L V S N D K V E A T E D S S L I M G F I C V L G L L L T V L G F L F V G V F T A F V N K F F D K M F V I M ............................................................................................................................................................................................................................... aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta 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: 83 Start: 292 End: 321 ...................................................................................................................................................................................................................................................................................................TTTGGAAAATTAGCTATTTATGCTTATCTT............................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 43 HP_score: -2.6 Tail_Score: -3.17229 Start: 54 End: 74 Full_Region: cgagcgatgaaacgg cagaagta aaaga taattctg tattggtagtagact .....................................................cagaagtaaaagataattctg.................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -5.0 Tail_Score: -5.04385 Start: 187 End: 201 Full_Region: atatattaaataatt gtcttt atg aaggac ttttttaagaatgtc ..........................................................................................................................................................................................gtctttatgaaggac..................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 41 HP_score: -2.7 Tail_Score: -2.76055 Start: 282 End: 307 Full_Region: atttggaaaattagc tatttatgc ttatcttt gcatagata taatgtatgtattgg .........................................................................................................................................................................................................................................................................................tatttatgcttatctttgcatagata........................................................................................................................... TransTerm Strand: - Conf: 82 HP_score: -6.1 Tail_Score: -5.19275 Start: 370 End: 419 Full_Region: tagtttgaaga tattaaggattaacagtttttcgt ata gtgcgagatgttaatccttaata ttttgttttgtgaat .................................................................................................................................................................................................................................................................................................................................................................................tattaaggattaacagtttttcgtatagtgcgagatgttaatccttaata........... Find igs database================================================ Query_seq: PI1375:PI1376|PI1375:PI1376:protease IV family, clan S (peptidase family S49):outer membrane protein:->->:1297675..1298104 430 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Intra-Species Hit: Count: 1 Min: 1 Max: 430 Len: 430 Subject: pint_PI1375_PI1376|protease IV family, clan S (peptidase family S49):outer membrane protein|POSITIVE:POSITIVE|[1297675,1298104]|430 HSP 1 e-value: 0.0 bit: 852.0 Len: 430 Query Start:1 Query End:430 Subject Strand: POSITIVE Subject Start: 1 Subject End: 430 aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta aacatctttcttggaacgttcgttcagtactcctgacaagtctactaccaatacagaattatcttttacttctgccgtttcatcgctcgacaatatcattccaaatatacaaacgagacctaacaacaacgttactaaaccaaaaaggaatacgccaacaaaagtggcaaagacattcttaaaaaagtccttcataaagacaattatttaatatatttctatttaaagcattgtaagctcggcaaaatctacattctaccatttcgccaatacatacattatatctatgcaaagataagcataaatagctaattttccaaattttagtataattctttactttttgcgacttttattcacaaaacaaaatattaaggattaacatctcgcactatacgaaaaactgttaatccttaatatcttcaaacta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACAUCUUUCUUGGAACGUUCGUUCAGUACUCCUGACAAGUCUACUACCAAUACAGAAUUAUCUUUUACUUCUGCCGUUUCAUCGCUCGACAAUAUCAUUCCAAAUAUACAAACGAGACCUAACAACAACGUUACUAAACCAAAAAGGAAUACGCCAACAAAAGUGGCAAAGACAUUCUUAAAAAAGUCCUUCAUAAAGACAAUUAUUUAAUAUAUUUCUAUUUAAAGCAUUGUAAGCUCGGCAAAAUCUACAUUCUACCAUUUCGCCAAUACAUACAUUAUAUCUAUGCAAAGAUAAGCAUAAAUAGCUAAUUUUCCAAAUUUUAGUAUAAUUCUUUACUUUUUGCGACUUUUAUUCACAAAACAAAAUAUUAAGGAUUAACAUCUCGCACUAUACGAAAAACUGUUAAUCCUUAAUAUCUUCAAACUA ....(((((.((((..((((.((((((.....))))...(((...........(((((.((.....)).))))).((......))...))).................)).)))).....((((......)))).....)))).)))))..........((((((.(((((((.............(((.........)))......................(((((.((((((.....(((.((((............)))).))).............(((.(((((........))))).)))....................)))))).))))).))))))).))))))..............((((((((((((((((..(((.......))).....)))))))))))))))).......... (-66.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGUUUGAAGAUAUUAAGGAUUAACAGUUUUUCGUAUAGUGCGAGAUGUUAAUCCUUAAUAUUUUGUUUUGUGAAUAAAAGUCGCAAAAAGUAAAGAAUUAUACUAAAAUUUGGAAAAUUAGCUAUUUAUGCUUAUCUUUGCAUAGAUAUAAUGUAUGUAUUGGCGAAAUGGUAGAAUGUAGAUUUUGCCGAGCUUACAAUGCUUUAAAUAGAAAUAUAUUAAAUAAUUGUCUUUAUGAAGGACUUUUUUAAGAAUGUCUUUGCCACUUUUGUUGGCGUAUUCCUUUUUGGUUUAGUAACGUUGUUGUUAGGUCUCGUUUGUAUAUUUGGAAUGAUAUUGUCGAGCGAUGAAACGGCAGAAGUAAAAGAUAAUUCUGUAUUGGUAGUAGACUUGUCAGGAGUACUGAACGAACGUUCCAAGAAAGAUGUU ((((((.(((((((((((((((((((...((((((.....))))))))))))))))))))))))).((((((((.......))))))))......))))))........(((((((.......(((((((((........)))))))))....((((...(((((((...((((((((....))))))))..(((..((((((.....(((....))).......((((((((((...((((((.(((....))).))))))...((((((((((...((..((.....))..)).(((((....)))))..(((((((((.(((((......)))))...))))))).))..)))))))))).))))))))))..))))))..)))....)))))))..))))..........)))))))......... (-110.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 291 268 226 231 187 pint:PI2155|5end_hypothetical_protein_2100664..2100894_POSITIVE 290 267 225 228 178 pint:PI0334|5end_hypothetical_protein_313234..313464_POSITIVE 283 278 235 165 120 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 280 40 5 201 164 pint:PI2150|5end_acyl_carrier_protein_2096972..2097202_POSITIVE 280 90 44 98 60 pint:PI0250|5end_hypothetical_protein_246946..247176_POSITIVE 270 266 229 68 33 pint:PI2135|5end_conserved_hypothetical_protein_2082754..2082984_POSITIVE 263 87 51 226 185 pint:PI2058|5end_riboflavin_biosynthesis_protein_2015800..2016030_POSITIVE 263 269 222 59 26 pint:PI1401|5end_TPR-repeat-containing_protein_1322027..1322257_POSITIVE 259 116 71 126 84 pint:PI0967|5end_conserved_hypothetical_protein_895424..895654_POSITIVE 259 99 55 214 174 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 257 49 3 107 65 pint:PI1550|5end_conserved_hypothetical_protein_1467360..1467590_POSITIVE 256 89 41 215 149 pint:PI1279|5end_RNA_polymerase_sigma_factor/ECF_subfamily_(sigma-70)_1195215..1195445_POSITIVE 256 109 63 52 1 pint:PI0580|5end_Holliday_junction_DNA_helicase_524178..524408_POSITIVE 256 77 31 74 27 pint:PI0235|5end_hypothetical_protein_234938..235168_POSITIVE 252 190 143 119 69 pint:PI1052|5end_fructose-1,6-bisphosphatase_970492..970722_POSITIVE 251 92 69 222 197 pint:PI0751|5end_conserved_hypothetical_protein_680623..680853_POSITIVE 250 50 3 146 94 pint:PI0985|5end_aspartyl-tRNA_synthetase_910174..910404_POSITIVE 249 104 62 190 150 pint:PI0889|5end_pyruvate_kinase_818758..818988_POSITIVE 248 87 62 178 148 pint:PI0384|5end_probable_radical_SAM_domain_protein_352884..353114_POSITIVE 247 160 114 90 41 pint:PI1834|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1774861..1775091_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 90 44 98 60 pint:PI0249|3end_conserved_hypothetical_protein_247026..247176_POSITIVE 270 266 229 74 39 pint:PI2136|3end_hypothetical_protein_2082840..2082990_POSITIVE 270 266 229 44 9 pint:PI2134|3end_hypothetical_protein_2082810..2082960_POSITIVE 258 49 10 97 48 pint:PI1547|3end_hypothetical_protein_1466226..1466376_POSITIVE 257 49 3 49 7 pint:PI1549|3end_conserved_hypothetical_protein_1467382..1467532_POSITIVE 248 87 62 115 85 pint:PI0383|3end_conserved_hypothetical_protein;_possible_Zn-dependent_hydrolase_352901..353051_POSITIVE 247 43 5 100 60 pint:PI1626|3end_hypothetical_protein_1550522..1550672_POSITIVE 247 270 228 57 19 pint:PI0783|3end_hypothetical_protein_723397..723547_POSITIVE 244 176 145 86 39 pint:PI1832|3end_conserved_hypothetical_protein_1774023..1774173_POSITIVE 243 92 69 150 127 pint:PI0750|3end_zinc_protease_680633..680783_POSITIVE 243 87 43 46 4 pint:PI0469|3end_30S_ribosomal_protein_S17_437445..437595_POSITIVE 243 102 72 125 100 pint:PI0349|3end_hypothetical_protein_323802..323952_POSITIVE 242 87 47 123 78 pint:PI0396|3end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_362396..362546_POSITIVE 242 50 3 118 71 pint:PI0265|3end_conjugative_transposon_protein,_TraO_257957..258107_POSITIVE 240 89 52 121 89 pint:PI0875|3end_conserved_hypothetical_protein_811437..811587_POSITIVE 236 119 71 71 21 pint:PI2030|3end_hypothetical_protein_1986127..1986277_POSITIVE 235 266 227 139 98 pint:PI1933|3end_hypothetical_protein_1880463..1880613_POSITIVE 233 120 72 75 10 pint:PI0789|3end_NAD-utilizing_dehydrogenase_728385..728535_POSITIVE 233 98 69 119 93 pint:PI0336|3end_hypothetical_protein_314806..314956_POSITIVE 231 275 231 143 108 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE