Origin IGS: tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgatagctgcatttagctatcactttttttatgccgctgaaacagaaaacaacaaaatacagattcttccaacaacatttttaaagagctgttattgccgttctcccatactcaaaacacagtaatatttctca Mask Tandem Repeat Region ================================================ tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Find is-nt database================================================ Query_seq: PI0119:PI0120|PI0119:PI0120:hypothetical protein:glutamate racemase:->->:111784..111917 134 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0119:PI0120|PI0119:PI0120:hypothetical protein:glutamate racemase:->->:111784..111917 134 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0119:PI0120|PI0119:PI0120:hypothetical protein:glutamate racemase:->->:111784..111917 134 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: - Start: 13 End: 132 ............ Q T K L I P S R C Y C S K L F T T P L I Q I K N N E T E A A Y F F H Y S F A A M .. tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0119:PI0120|PI0119:PI0120:hypothetical protein:glutamate racemase:->->:111784..111917 134 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Intra-Species Hit: Count: 1 Min: 1 Max: 134 Len: 134 Subject: pint_PI0119_PI0120|hypothetical protein:glutamate racemase|POSITIVE:POSITIVE|[111784,111917]|134 HSP 1 e-value: 6.0E-58 bit: 224.0 Len: 134 Query Start:1 Query End:134 Subject Strand: POSITIVE Subject Start: 1 Subject End: 134 tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcatnnnnnnngtgatagctaaatgcagctatca tgagaaatattactgtgttttgagtatgggagaacggcaataacagctctttaaaaatgttgttggaagaatctgtattttgttgttttctgtttcagcggcataaaaaaagtgatagctaaatgcagctatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAGAAAUAUUACUGUGUUUUGAGUAUGGGAGAACGGCAAUAACAGCUCUUUAAAAAUGUUGUUGGAAGAAUCUGUAUUUUGUUGUUUUCUGUUUCAGCGGCAUAAAAAAAGUGAUAGCUAAAUGCAGCUAUCA .............(((((((((((....((((((((((((..((((.(((((...(((...))).)))))..))))...))))))))))))..))))).)))))).......((((((((......)))))))) (-33.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUAGCUGCAUUUAGCUAUCACUUUUUUUAUGCCGCUGAAACAGAAAACAACAAAAUACAGAUUCUUCCAACAACAUUUUUAAAGAGCUGUUAUUGCCGUUCUCCCAUACUCAAAACACAGUAAUAUUUCUCA (((((((((....)))))))))................((((..((.(((..(((...((((.(((((...............)))))))))..)))..))).))...((((........))))...))))... (-19.56) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 41 4 136 99 pint:PI0689|5end_hypothetical_protein_625624..625854_POSITIVE 302 128 81 216 176 pint:PI1721|5end_peptidyl-prolyl_cis-trans_isomerase,_PPIC-type_1638086..1638316_POSITIVE 296 69 23 141 98 pint:PI2076|5end_hypothetical_protein_2035403..2035633_POSITIVE 289 114 78 204 165 pint:PI1796|5end_2-hydroxyhepta-2,4-diene-1,7-dioate_isomerase,_fumarylacetoacetate_hydrolase_family_protein_1730452..1730682_POSITIVE 285 83 46 107 74 pint:PI1377|5end_cAMP-binding_domain_protein_(cyclic_nucleotide-binding_domain)_1299289..1299519_POSITIVE 279 130 92 79 34 pint:PI1150|5end_30S_ribosomal_protein_S6_1075683..1075913_POSITIVE 271 129 81 208 153 pint:PI2085|5end_conserved_hypothetical_protein_2041100..2041330_POSITIVE 258 67 38 161 130 pint:PI0132|5end_hypothetical_protein_123783..124013_POSITIVE 255 66 21 124 70 pint:PI1580|5end_conserved_hypothetical_protein_1507833..1508063_POSITIVE 253 49 12 196 160 pint:PI0531|5end_ABC_transporter,_ATP-binding_protein;_possible_gliding_motility_related_484696..484926_POSITIVE 251 101 61 137 89 pint:PI1020|5end_hypothetical_protein_938469..938699_POSITIVE 240 117 72 102 48 pint:PI0695|5end_xanthine/uracil_permease_family_protein_631413..631643_POSITIVE 236 76 31 153 105 pint:PI1468|5end_conserved_hypothetical_protein;_probable_TPR_domain_protein_1393900..1394130_POSITIVE 236 50 8 159 118 pint:PI0308|5end_conserved_hypothetical_protein_290587..290817_POSITIVE 235 66 26 146 113 pint:PI2008|5end__ABC_transporter,_ATP-binding_protein_1967123..1967353_POSITIVE 234 89 41 185 127 pint:PI1118|5end_glycosyl_transferases,_group_1_1042496..1042726_POSITIVE 232 130 81 110 67 pint:PI1391|5end_hypothetical_protein_1311420..1311650_POSITIVE 231 100 58 208 153 pint:PI2144|5end_hypothetical_protein_2091954..2092184_POSITIVE 231 70 23 223 176 pint:PI0432|5end_hypothetical_protein_404781..405011_POSITIVE 231 70 23 166 119 pint:PI0433|5end_hypothetical_protein_404724..404954_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 41 4 84 47 pint:PI0687|3end_hypothetical_protein_625652..625802_POSITIVE 302 128 81 42 2 pint:PI1720|3end_conserved_hypothetical_protein_1637992..1638142_POSITIVE 285 83 46 57 24 pint:PI1376|3end_outer_membrane_protein_1299319..1299469_POSITIVE 280 66 21 109 56 pint:PI0432|3end_hypothetical_protein_405037..405187_POSITIVE 280 66 21 145 92 pint:PI0433|3end_hypothetical_protein_405073..405223_POSITIVE 279 130 92 73 28 pint:PI1149|3end_30S_ribosomal_protein_S18_1075757..1075907_POSITIVE 271 129 81 97 42 pint:PI2084|3end_hypothetical_protein_2041069..2041219_POSITIVE 260 107 78 151 119 pint:PI1795|3end_conserved_hypothetical_protein_1730486..1730636_POSITIVE 258 67 23 150 111 pint:PI0524|3end_meso-diaminopimelate_D-dehydrogenase_480849..480999_POSITIVE 255 66 21 124 70 pint:PI1579|3end_penicillin-binding_protein_2_1507913..1508063_POSITIVE 253 130 88 44 4 pint:PI0017|3end_thiol-disulfide_isomerase;_thioredoxin_22835..22985_POSITIVE 240 102 61 62 8 pint:PI0528|3end_hypothetical_protein_483122..483272_POSITIVE 236 76 31 82 34 pint:PI1467|3end_conserved_hypothetical_protein_1393909..1394059_POSITIVE 234 75 33 56 6 pint:PI1455|3end_hypothetical_protein_1378963..1379113_POSITIVE 231 100 58 148 93 pint:PI2143|3end_DNA_mismatch_repair_protein_2091974..2092124_POSITIVE 231 38 1 149 111 pint:PI0104|3end_hypothetical_protein_99346..99496_POSITIVE 230 47 12 139 95 pint:PI1739|3end_Na+-driven_multidrug_efflux_pump,_MATE_efflux_family_protein_1661645..1661795_POSITIVE 229 44 10 57 20 pint:PI2053|3end_conserved_hypothetical_protein;_possible_outer_membrane_receptor_protein_2012876..2013026_POSITIVE 223 130 83 124 81 pint:PI1349|3end_polysaccharide_export_protein_1265720..1265870_POSITIVE 222 106 71 150 111 pint:PI1500|3end_hypothetical_protein_1421392..1421542_POSITIVE