Origin IGS: aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt .........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 acggcgtttcctattttatttcttgcaaaaataataataatagttgggaattaaggtgtattgacggctctttttcagccaaagcaatataaaaaatgaaactatttggtattttatccaattatcttttgtatttttgtatcaaatataagagttatcttagaaacgaggaaacataaaccaggaacataccttataattatatttatattggtt Mask Tandem Repeat Region ================================================ aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Find is-nt database================================================ Query_seq: PI1172:PI1173|PI1172:PI1173:sensor histidine kinase:transcription regulatory protein, LacI family:->->:1094975..1095190 216 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1172:PI1173|PI1172:PI1173:sensor histidine kinase:transcription regulatory protein, LacI family:->->:1094975..1095190 216 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1172:PI1173|PI1172:PI1173:sensor histidine kinase:transcription regulatory protein, LacI family:->->:1094975..1095190 216 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 8 End: 100 ....... M N I I I R Y V P G L C F L V S K I T L I F D T K I Q K I I G .................................................................................................................... Protein_Len: 33 Strand: + Start: 100 End: 198 ................................................................................................... M K Y Q I V S F F I L L W L K K S R Q Y T L I P N Y Y Y Y F C K K .................. Protein_Len: 36 Strand: + Start: 96 End: 203 ............................................................................................... M D K I P N S F I F Y I A L A E K E P S I H L N S Q L L L L F L Q E I K ............. Protein_Len: 37 Strand: - Start: 1 End: 111 V L I F I I I L Y T G P K H K R T E L I V R I N S V F I C F I I P Y F V M ......................................................................................................... aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt 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================================================ aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1172:PI1173|PI1172:PI1173:sensor histidine kinase:transcription regulatory protein, LacI family:->->:1094975..1095190 216 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Intra-Species Hit: Count: 1 Min: 1 Max: 216 Len: 216 Subject: pint_PI1172_PI1173|sensor histidine kinase:transcription regulatory protein, LacI family|POSITIVE:POSITIVE|[1094975,1095190]|216 HSP 1 e-value: 1.0E-119 bit: 428.0 Len: 216 Query Start:1 Query End:216 Subject Strand: POSITIVE Subject Start: 1 Subject End: 216 aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt aaccaatataaatataattataaggtatgttcctggtttatgtttcctcgtttctaagataactcttatatttgatacaaaaatacaaaagataattggataaaataccaaatagtttcattttttatattgctttggctgaaaaagagccgtcaatacaccttaattcccaactattattattatttttgcaagaaataaaataggaaacgccgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACCAAUAUAAAUAUAAUUAUAAGGUAUGUUCCUGGUUUAUGUUUCCUCGUUUCUAAGAUAACUCUUAUAUUUGAUACAAAAAUACAAAAGAUAAUUGGAUAAAAUACCAAAUAGUUUCAUUUUUUAUAUUGCUUUGGCUGAAAAAGAGCCGUCAAUACACCUUAAUUCCCAACUAUUAUUAUUAUUUUUGCAAGAAAUAAAAUAGGAAACGCCGU .......................(((...((((((.(((.((((((.(((..(.(((((....))))).)..)))..((((((((..((.((((.((((...((((........)))).........(((((...(((((.......))))).)))))...........)))).)))).))..))))))))...)))))))))))))))..))).. (-33.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGGCGUUUCCUAUUUUAUUUCUUGCAAAAAUAAUAAUAAUAGUUGGGAAUUAAGGUGUAUUGACGGCUCUUUUUCAGCCAAAGCAAUAUAAAAAAUGAAACUAUUUGGUAUUUUAUCCAAUUAUCUUUUGUAUUUUUGUAUCAAAUAUAAGAGUUAUCUUAGAAACGAGGAAACAUAAACCAGGAACAUACCUUAUAAUUAUAUUUAUAUUGGUU .....(((((((....(((((..((((((((((..((..(((((((((........(((((((..((((.......))))....))))))).((((((...(.....).)))))).)))))))))..))..))))))))))..)))))(((((....)))))......)))))))...((((.((......)).(((((......)))))..)))) (-44.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 153 115 76 30 pint:PI1471|5end_conserved_hypothetical_protein_1395050..1395280_POSITIVE 269 160 118 51 12 pint:PI1845|5end_hypothetical_protein_1791457..1791687_POSITIVE 257 173 132 41 6 pint:PI1447|5end_probable_OPT_oligopeptide_transporter_protein_1369972..1370202_POSITIVE 257 180 131 148 89 pint:PI0791|5end_conserved_hypothetical_protein_728361..728591_POSITIVE 244 66 29 223 174 pint:PI1262|5end_ISPg3-related_transposase,_C-terminal_region_1183967..1184197_POSITIVE 240 150 108 194 145 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 239 170 130 215 185 pint:PI1862|5end_hypothetical_protein_1806189..1806419_POSITIVE 238 172 133 147 105 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 232 178 137 182 139 pint:PI0365|5end_hypothetical_protein_335721..335951_POSITIVE 229 53 27 229 200 pint:PI0603|5end_3-dehydroquinate_synthase_549718..549948_POSITIVE 227 88 41 178 131 pint:PI0501|5end_excisionase_461430..461660_POSITIVE 226 153 129 115 94 pint:PI0123|5end_outer_membrane_protein,_ompH_family_113906..114136_POSITIVE 225 151 115 179 142 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 219 172 131 71 20 pint:PI0351|5end_hypothetical_protein_324317..324547_POSITIVE 218 164 127 54 23 pint:PI1045|5end_cytidine/deoxycytidylate_deaminase_family_protein_965104..965334_POSITIVE 218 153 111 165 117 pint:PI0220|5end_conserved_hypothetical_protein_211980..212210_POSITIVE 216 163 130 195 163 pint:PI1891|5end_hypothetical_protein_1835196..1835426_POSITIVE 216 162 130 68 33 pint:PI0932|5end_conserved_hypothetical_protein;_possible_hemin_receptor_863854..864084_POSITIVE 212 153 120 42 1 pint:PI1469|5end_hypothetical_protein_1395016..1395246_POSITIVE 210 159 128 75 50 pint:PI0064|5end_hypothetical_protein_63622..63852_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 292 153 115 68 22 pint:PI1470|3end_hypothetical_protein_1395122..1395272_POSITIVE 257 180 131 92 33 pint:PI0789|3end_NAD-utilizing_dehydrogenase_728385..728535_POSITIVE 239 170 130 60 30 pint:PI1861|3end_hypothetical_protein_1806114..1806264_POSITIVE 236 154 122 120 85 pint:PI1229|3end_conserved_hypothetical_protein_1151669..1151819_POSITIVE 229 53 27 62 33 pint:PI0602|3end_conserved_hypothetical_protein_549631..549781_POSITIVE 229 140 108 148 114 pint:PI0113|3end_arginyl-tRNA_synthetase_110082..110232_POSITIVE 227 88 41 75 28 pint:PI0500|3end_mobilizable_transposon,_tnpC_protein_461407..461557_POSITIVE 226 153 129 28 7 pint:PI0122|3end_outer_membrane_protein,_ompH_family_113899..114049_POSITIVE 218 153 111 142 94 pint:PI0219|3end_conserved_hypothetical_protein_212037..212187_POSITIVE 211 139 97 62 17 pint:PI0391|3end_conserved_hypothetical_protein_358216..358366_POSITIVE 204 180 133 144 89 pint:PI2039|3end_hypothetical_protein_1992991..1993141_POSITIVE 203 172 131 81 30 pint:PI0605|3end_chloromuconate_cycloisomerase_553026..553176_POSITIVE 203 176 131 90 43 pint:PI0026|3end_two-component_system_response_regulator_30537..30687_POSITIVE 201 154 117 135 106 pint:PI1492|3end_triosephosphate_isomerase_1412310..1412460_POSITIVE 201 141 114 30 1 pint:PI0599|3end_hypothetical_protein_547545..547695_POSITIVE 198 153 130 88 64 pint:PI0924|3end_possible_glycosyl_hydrolase_855953..856103_POSITIVE 197 160 113 64 15 pint:PI1513|3end_conserved_hypothetical_protein_1432502..1432652_POSITIVE 197 170 130 57 17 pint:PI1505|3end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1425409..1425559_POSITIVE 195 151 119 142 110 pint:PI0666|3end_chorismate_synthase_610171..610321_POSITIVE 194 152 112 132 80 pint:PI2011|3end_hypothetical_protein_1970730..1970880_POSITIVE