Origin IGS: tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa .........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 ttgcttgtattttattgctcttttgcttctatgttattgttcttttgcttaataaacgaatgcaaagatagaactttttttcgttttaatggcattaaaaaactattaagccagacttttttagtacttttgcatttaagtataaacgacacggttcattctttgcggttacgctttagagtgcccgataaacaacaaaagagaca Mask Tandem Repeat Region ================================================ tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Find is-nt database================================================ Query_seq: PI0792:PI0793|PI0792:PI0793:conserved hypothetical protein:ABC transporter, permease protein:->->:729688..729893 206 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0792:PI0793|PI0792:PI0793:conserved hypothetical protein:ABC transporter, permease protein:->->:729688..729893 206 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0792:PI0793|PI0792:PI0793:conserved hypothetical protein:ABC transporter, permease protein:->->:729688..729893 206 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 55 End: 192 ...................................................... M S F I L K C K S T K K V W L N S F L M P L K R K K V L S L H S F I K Q K N N N I E A K E Q .............. Protein_Len: 60 Strand: - Start: 3 End: 206 .. R F R L R L S H V T D N I S L H L L V L F T Q S L L K K I G N F R F F T R D K C E N I L C F F L L M S A F S C Y F V L M tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa 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================================================ tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0792:PI0793|PI0792:PI0793:conserved hypothetical protein:ABC transporter, permease protein:->->:729688..729893 206 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: pint_PI0792_PI0793|conserved hypothetical protein:ABC transporter, permease protein|POSITIVE:POSITIVE|[729688,729893]|206 HSP 1 e-value: 1.0E-100 bit: 367.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgnnnnnnngttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa tgtctcttttgttgtttatcgggcactctaaagcgtaaccgcaaagaatgaaccgtgtcgtttatacttaaatgcaaaagtactaaaaaagtctggcttaatagttttttaatgccattaaaacgaaaaaaagttctatctttgcattcgtttattaagcaaaagaacaataacatagaagcaaaagagcaataaaatacaagcaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGUCUCUUUUGUUGUUUAUCGGGCACUCUAAAGCGUAACCGCAAAGAAUGAACCGUGUCGUUUAUACUUAAAUGCAAAAGUACUAAAAAAGUCUGGCUUAAUAGUUUUUUAAUGCCAUUAAAACGAAAAAAAGUUCUAUCUUUGCAUUCGUUUAUUAAGCAAAAGAACAAUAACAUAGAAGCAAAAGAGCAAUAAAAUACAAGCAA ((.((((((((((((((.....((......(((((.....(((((((..((((..(.((((((.(((((........)))))...........((((((((.......)))).))))...))))))...)..))))..)))))))...))))).....))....)))))...........)))))))))))............... (-41.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUGCUUGUAUUUUAUUGCUCUUUUGCUUCUAUGUUAUUGUUCUUUUGCUUAAUAAACGAAUGCAAAGAUAGAACUUUUUUUCGUUUUAAUGGCAUUAAAAAACUAUUAAGCCAGACUUUUUUAGUACUUUUGCAUUUAAGUAUAAACGACACGGUUCAUUCUUUGCGGUUACGCUUUAGAGUGCCCGAUAAACAACAAAAGAGACA ...............((((((((((...........(((((....(((((((.......((((((((.((((((........)))))).((((.((((.......))))))))..............)))))))))))))))..)))))..(((..((((((..(((....)))...)))))).)))........)))))))).)) (-43.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 324 60 12 77 33 pint:PI0950|5end_50S_ribosomal_protein_L31_883327..883557_POSITIVE 303 44 2 104 64 pint:PI0916|5end_hypothetical_protein_845617..845847_POSITIVE 291 166 133 95 67 pint:PI0596|5end_hypothetical_protein_546400..546630_POSITIVE 290 170 122 174 135 pint:PI0912|5end_conserved_hypothetical_protein_842034..842264_POSITIVE 289 60 12 178 118 pint:PI1507|5end_tRNA_pseudouridine_synthase_B_1426554..1426784_POSITIVE 288 77 34 69 25 pint:PI1609|5end_Na+/H+_anti-porter_1536058..1536288_POSITIVE 278 77 33 66 9 pint:PI1443|5end_conserved_hypotehtical_protein;_possible_tonB-dependent_outer_membrane_receptor_1364560..1364790_POSITIVE 273 54 22 194 159 pint:PI0981|5end_outer_membrane_protein,_TonB_dependent_receptor_906968..907198_POSITIVE 268 97 53 137 88 pint:PI1326|5end_Na+-driven_multidrug_efflux_pump_1244182..1244412_POSITIVE 267 61 23 229 192 pint:PI0235|5end_hypothetical_protein_234938..235168_POSITIVE 260 60 11 214 151 pint:PI0699|5end_conserved_hypothetical_protein_636647..636877_POSITIVE 260 99 53 44 1 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 258 60 11 56 5 pint:PI1586|5end_possible_HesA/MoeB/ThiF_family_protein_1514372..1514602_POSITIVE 257 42 10 37 7 pint:PI1646|5end_hypothetical_protein_1561954..1562184_POSITIVE 257 62 21 46 17 pint:PI0341|5end_conserved_hypothetical_protein_317038..317268_POSITIVE 256 60 17 172 139 pint:PI2079|5end_conserved_hypothetical_protein;_possible_ATPase_2036715..2036945_POSITIVE 256 50 1 86 25 pint:PI1935|5end_possible__internalin-related_protein_1883324..1883554_POSITIVE 256 57 20 211 177 pint:PI1644|5end_hypothetical_protein_1560372..1560602_POSITIVE 255 75 31 109 62 pint:PI0362|5end_hypothetical_protein_333397..333627_POSITIVE 254 56 11 58 11 pint:PI1566|5end_predicted_TPR-repeat-containing_protein_1487570..1487800_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 293 60 11 69 6 pint:PI0583|3end_hypothetical_protein_526276..526426_POSITIVE 289 60 12 106 46 pint:PI1506|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_(queuine_synthetase)_1426562..1426712_POSITIVE 278 77 33 75 18 pint:PI1442|3end_radical-activating_enzyme_(pyruvate-formate_lyase-activating_enzyme)_1364649..1364799_POSITIVE 272 60 13 108 43 pint:PI0857|3end_hypothetical_protein_790986..791136_POSITIVE 267 42 1 135 92 pint:PI1873|3end_hypothetical_protein_1818419..1818569_POSITIVE 257 42 10 32 2 pint:PI1643|3end_conserved_hypothetical_protein_1562029..1562179_POSITIVE 255 75 31 58 11 pint:PI0361|3end_hypothetical_protein_333426..333576_POSITIVE 255 75 31 104 57 pint:PI0360|3end_conserved_hypothetical_protein_333472..333622_POSITIVE 251 48 10 141 95 pint:PI1858|3end_conserved_hypothetical_protein_1805355..1805505_POSITIVE 251 60 20 58 11 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 247 57 11 111 56 pint:PI0805|3end_conserved_hypothetical_protein_743807..743957_POSITIVE 241 59 20 40 1 pint:PI1531|3end_biotin--acetyl-CoA-carboxylase_ligase_1451734..1451884_POSITIVE 240 45 3 134 78 pint:PI1250|3end_RNA_polymerase_ECF-type_sigma_70_factor_1174781..1174931_POSITIVE 240 57 13 99 60 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 239 42 5 51 10 pint:PI0166|3end_hypothetical_protein_161258..161408_POSITIVE 237 42 10 32 2 pint:PI0350|3end_conserved_hypothetical_protein_324835..324985_POSITIVE 233 70 21 76 3 pint:PI0284|3end_flavoprotein_A_270157..270307_POSITIVE 232 61 23 143 110 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 231 66 32 82 48 pint:PI1066|3end_dihydrofolate_reductase_983932..984082_POSITIVE 230 61 21 101 68 pint:PI0758|3end_hypothetical_protein_690506..690656_POSITIVE