Origin IGS: taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agttttttcttgttctaagtgcttacaaatatagtgcttttctttttatctgcgatggttttaaactgttttttagcacgctgccctgcataaaccaaatgggaaacaatgttcctttcggttcattgtttcccatttttatttcttttcctatcaggattgatta Mask Tandem Repeat Region ================================================ taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Find is-nt database================================================ Query_seq: PI0602:PI0603|PI0602:PI0603:conserved hypothetical protein:3-dehydroquinate synthase:->->:549692..549857 166 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0602:PI0603|PI0602:PI0603:conserved hypothetical protein:3-dehydroquinate synthase:->->:549692..549857 166 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0602:PI0603|PI0602:PI0603:conserved hypothetical protein:3-dehydroquinate synthase:->->:549692..549857 166 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 7 End: 141 ...... M L I G K E I K M G N N E P K G T L F P I W F M Q G S V L K N S L K P S Q I K R K A L Y L ......................... Protein_Len: 31 Strand: + Start: 57 End: 149 ........................................................ M V S H L V Y A G Q R A K K Q F K T I A D K K K S T I F V S T ................. Protein_Len: 39 Strand: - Start: 3 End: 119 .. D I R I P F S I F I P F L S G F P V N N G M Q N I C P L T S F F L K F G D C M ............................................... taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact 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================================================ taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -13.4 Tail_Score: -5.59962 Start: 32 End: 67 Full_Region: cctgcataaaccaaa tgggaaacaatgttcc tttc ggttcattgtttccca tttttatttcttttc ...............................tgggaaacaatgttcctttcggttcattgtttccca................................................................................................... Find igs database================================================ Query_seq: PI0602:PI0603|PI0602:PI0603:conserved hypothetical protein:3-dehydroquinate synthase:->->:549692..549857 166 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Intra-Species Hit: Count: 1 Min: 1 Max: 166 Len: 166 Subject: pint_PI0602_PI0603|conserved hypothetical protein:3-dehydroquinate synthase|POSITIVE:POSITIVE|[549692,549857]|166 HSP 1 e-value: 2.0E-89 bit: 329.0 Len: 166 Query Start:1 Query End:166 Subject Strand: POSITIVE Subject Start: 1 Subject End: 166 taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact taatcaatcctgataggaaaagaaataaaaatgggaaacaatgaaccgaaaggaacattgtttcccatttggtttatgcagggcagcgtgctaaaaaacagtttaaaaccatcgcagataaaaagaaaagcactatatttgtaagcacttagaacaagaaaaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCAAUCCUGAUAGGAAAAGAAAUAAAAAUGGGAAACAAUGAACCGAAAGGAACAUUGUUUCCCAUUUGGUUUAUGCAGGGCAGCGUGCUAAAAAACAGUUUAAAACCAUCGCAGAUAAAAAGAAAAGCACUAUAUUUGUAAGCACUUAGAACAAGAAAAAACU ...((..((((((((((...........(((((((((((((((..((....))..)))))))))))))))..))))).)))))....(((((........((.....))....(((((((...............))))))).)))))...))............. (-39.88) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUUUUCUUGUUCUAAGUGCUUACAAAUAUAGUGCUUUUCUUUUUAUCUGCGAUGGUUUUAAACUGUUUUUUAGCACGCUGCCCUGCAUAAACCAAAUGGGAAACAAUGUUCCUUUCGGUUCAUUGUUUCCCAUUUUUAUUUCUUUUCCUAUCAGGAUUGAUUA ((((...(((((......(((((...(((.(((((..........(((((...)))))......))))).))).))))).................(((((((((((((((..((....))..)))))))))))))))................)))))..)))). (-38.19) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 309 114 71 80 38 pint:PI1923|5end_conserved_hypothetical_protein_1865560..1865790_POSITIVE 297 90 41 123 80 pint:PI0069|5end_hypothetical_protein_67072..67302_POSITIVE 291 88 51 131 84 pint:PI1547|5end_hypothetical_protein_1465808..1466038_POSITIVE 289 89 41 213 172 pint:PI0769|5end_phosphomannomutase_704653..704883_POSITIVE 288 90 41 117 43 pint:PI0539|5end_hypothetical_protein_493406..493636_POSITIVE 286 89 45 56 10 pint:PI2113|5end_hypothetical_protein_2063794..2064024_POSITIVE 273 91 52 42 3 pint:PI0814|5end_conserved_hypothetical_protein_752946..753176_POSITIVE 272 100 52 231 182 pint:PI0913|5end_glycerate_dehydrogenase_842700..842930_POSITIVE 270 89 43 92 37 pint:PI1570|5end_succinyl-diaminopimelate_desuccinylase_1493280..1493510_POSITIVE 270 89 41 174 116 pint:PI0750|5end_zinc_protease_677746..677976_POSITIVE 267 84 42 67 24 pint:PI1879|5end_uracil_phosphoribosyltransferase_1820671..1820901_POSITIVE 265 109 62 188 147 pint:PI0720|5end_conserved_hypothetical_protein_653949..654179_POSITIVE 264 89 47 204 150 pint:PI0646|5end_hypothetical_protein_586583..586813_POSITIVE 263 118 71 67 17 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 263 92 51 83 32 pint:PI0633|5end_possible_preprotein_translocase,_YajC_subunit_579671..579901_POSITIVE 263 90 56 199 159 pint:PI0396|5end_possible_tetracycline_resistance_element_mobilization_regulatory_protein,_C-terminal_fragment_361993..362223_POSITIVE 261 93 59 171 128 pint:PI1930|5end_conserved_hypothetical_protein;_possible_ankyrin_repeat_protein_(eukaryotic-like)_1874219..1874449_POSITIVE 258 90 41 181 127 pint:PI0845|5end_peptidyl-dipeptidase_778272..778502_POSITIVE 256 92 62 157 131 pint:PI2097|5end_conserved_hypothetical_protein_2050912..2051142_POSITIVE 256 115 71 100 55 pint:PI0851|5end_hypothetical_protein_784310..784540_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 400 70 29 62 21 pint:PI0602|3end_conserved_hypothetical_protein_549631..549781_POSITIVE 330 85 41 148 101 pint:PI1372|3end_thiamine_monophosphate_kinase_1293971..1294121_POSITIVE 289 89 41 141 100 pint:PI0768|3end_conserved_hypothetical_protein;_possible_acetyltransferase_704661..704811_POSITIVE 272 100 52 143 94 pint:PI0912|3end_conserved_hypothetical_protein_842692..842842_POSITIVE 264 89 47 110 56 pint:PI0644|3end_dnaJ_protein_586569..586719_POSITIVE 263 118 71 143 93 pint:PI1541|3end_hypothetical_protein_1461884..1462034_POSITIVE 263 92 51 63 12 pint:PI0632|3end_NusB_family_protein_(N_utilization_substance_protein_B)_579731..579881_POSITIVE 261 93 59 46 3 pint:PI1929|3end_conserved_hypothetical_protein;_possible_ankyrin_repeat_protein_(eukaryotic-like)_1874174..1874324_POSITIVE 258 90 41 145 91 pint:PI0844|3end_cytidine/deoxycytidylate_deaminase_(dCMP_deaminase)_778316..778466_POSITIVE 257 90 58 37 1 pint:PI0324|3end_conserved_hypothetical_protein_305680..305830_POSITIVE 256 92 62 49 23 pint:PI2096|3end_conserved_hypothetical_protein;_possible_phosphoesterase_2050884..2051034_POSITIVE 256 90 42 117 59 pint:PI1366|3end_conserved_hypothetical_protein;_possible_hydrolase,_HAD_superfamily_1286647..1286797_POSITIVE 256 92 51 116 66 pint:PI0049|3end_outer_membrane_receptor_protein_(iron_transport)_51090..51240_POSITIVE 255 85 41 77 30 pint:PI0503|3end_mobilizable_transposon,_excision_protein_464198..464348_POSITIVE 252 116 78 101 62 pint:PI1789|3end_hypothetical_protein_1719037..1719187_POSITIVE 252 118 71 116 71 pint:PI0732|3end_conserved_hypothetical_protein_664367..664517_POSITIVE 246 115 78 136 97 pint:PI2108|3end_cell_surface_protein;_possible_cell_surface_antigen_BspA_2060625..2060775_POSITIVE 246 92 55 48 5 pint:PI0454|3end_hypothetical_protein_426963..427113_POSITIVE 245 88 44 133 86 pint:PI0760|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_695989..696139_POSITIVE 244 91 71 108 90 pint:PI0129|3end_hypothetical_protein_121941..122091_POSITIVE