Origin IGS: gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct .........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 agatttgtctcctacacattatgatctgatgtttttgttttgacggcgtgtcataatgagcaatttgctgcgttgcctgcgacattcggcttcagtcacgtacttcagtacgttcctttcagactctgttttagcacctttgtgctccaaaagaattttgacactgctccatctttattgcaaatgtcatcattttgtcgacatttttaccatatatttcgccgtttcaaaaagtataacccttgatttcaggaaattcatc Mask Tandem Repeat Region ================================================ gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Find is-nt database================================================ Query_seq: PG1407:PG1408|PG1407:PG1408:nitroimidazole resistance protein, putative:heavy metal efflux pump, CzcD family:<-->:1491739..1492000 262 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1407:PG1408|PG1407:PG1408:nitroimidazole resistance protein, putative:heavy metal efflux pump, CzcD family:<-->:1491739..1492000 262 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1407:PG1408|PG1407:PG1408:nitroimidazole resistance protein, putative:heavy metal efflux pump, CzcD family:<-->:1491739..1492000 262 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 107 End: 241 .......................................................................................................... M L L E H K G A K T E S E R N V L K Y V T E A E C R R Q R S K L L I M T R R Q N K N I R S ..................... Protein_Len: 60 Strand: - Start: 20 End: 223 ................... F I H Y F H R C F S S M Q L L S P A T D F N K Q L V F T S F C L R F P V Y Q L V H S F G F T A P L A A F Q E N H C A T M ....................................... Protein_Len: 60 Strand: - Start: 1 End: 210 K S V A F Y I T F I D V F H H C K C Y L H L L T L I R K S C L P A L V S D S L F T S F Y T V S A S H R L C R L L N S M M .................................................... gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct 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================================================ gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1407:PG1408|PG1407:PG1408:nitroimidazole resistance protein, putative:heavy metal efflux pump, CzcD family:<-->:1491739..1492000 262 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Intra-Species Hit: Count: 1 Min: 1 Max: 262 Len: 262 Subject: NC_002950_PG1407_PG1408|nitroimidazole resistance protein, putative:heavy metal efflux pump, CzcD family|NEGATIVE:POSITIVE|[1491739,1492000]|262 HSP 1 e-value: 1.0E-146 bit: 519.0 Len: 262 Query Start:1 Query End:262 Subject Strand: POSITIVE Subject Start: 1 Subject End: 262 gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct gatgaatttcctgaaatcaagggttatactttttgaaacggcgaaatatatggtaaaaatgtcgacaaaatgatgacatttgcaataaagatggagcagtgtcaaaattcttttggagcacaaaggtgctaaaacagagtctgaaaggaacgtactgaagtacgtgactgaagccgaatgtcgcaggcaacgcagcaaattgctcattatgacacgccgtcaaaacaaaaacatcagatcataatgtgtaggagacaaatct Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGAAUUUCCUGAAAUCAAGGGUUAUACUUUUUGAAACGGCGAAAUAUAUGGUAAAAAUGUCGACAAAAUGAUGACAUUUGCAAUAAAGAUGGAGCAGUGUCAAAAUUCUUUUGGAGCACAAAGGUGCUAAAACAGAGUCUGAAAGGAACGUACUGAAGUACGUGACUGAAGCCGAAUGUCGCAGGCAACGCAGCAAAUUGCUCAUUAUGACACGCCGUCAAAACAAAAACAUCAGAUCAUAAUGUGUAGGAGACAAAUCU (((...(((((((........((((....((((((..((((((.....(((.((((..((((((.(.....).)))))))))).)))......(((((((......(((((.((..(((((....)))))..)).)))))(((..((..((((((....))))))..))...(((..........)))....)))...))))))).........)))))).....)))))).....))))........)))))))...))). (-65.79) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAUUUGUCUCCUACACAUUAUGAUCUGAUGUUUUUGUUUUGACGGCGUGUCAUAAUGAGCAAUUUGCUGCGUUGCCUGCGACAUUCGGCUUCAGUCACGUACUUCAGUACGUUCCUUUCAGACUCUGUUUUAGCACCUUUGUGCUCCAAAAGAAUUUUGACACUGCUCCAUCUUUAUUGCAAAUGUCAUCAUUUUGUCGACAUUUUUACCAUAUAUUUCGCCGUUUCAAAAAGUAUAACCCUUGAUUUCAGGAAAUUCAUC .(((..((.((((..((((((.....))))))(((((....(((((((....(((..(((((....((((.((((....))))...))))...((..((((((....))))))..)).(((((.(((.....(((((....))))).....)))..)))))...)))))............(((((((..(.....)..)))))))......)))....))))))).)))))..................)))).))..))) (-57.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 878 130 81 221 172 NC_002950:PG1407|5end_nitroimidazole_resistance_protein,_putative_1491648..1491878_NEGATIVE 626 220 175 186 141 NC_002950:PG1117|5end_MATE_efflux_family_protein_1190010..1190240_POSITIVE 369 204 163 65 17 NC_002950:PG1427|5end_thiol_protease/hemagglutinin_PrtT_precursor,_putative_1514396..1514626_NEGATIVE 350 205 161 56 2 NC_002950:PG1992|5end_glucose-inhibited_division_protein_A_2081410..2081640_POSITIVE 349 206 163 51 1 NC_002950:PG1022|5end_hypothetical_protein_1083537..1083767_POSITIVE 335 219 171 213 166 NC_002950:PG1487|5end_hypothetical_protein_1561468..1561698_POSITIVE 333 198 151 224 177 NC_002950:PG1927|5end_50S_ribosomal_protein_L24_2019557..2019787_NEGATIVE 333 198 155 108 71 NC_002950:PG0458|5end_ISPg5,_transposase_Orf2_501463..501693_NEGATIVE 324 205 163 58 27 NC_002950:PG1198|5end_hypothetical_protein_1276650..1276880_POSITIVE 324 199 155 71 15 NC_002950:PG0171|5end_5'-nucleotidase_family_protein_191724..191954_POSITIVE 322 195 155 52 1 NC_002950:PG1582|5end_batA_protein_1659321..1659551_POSITIVE 317 190 147 45 7 NC_002950:PG0322|5end_serine/threonine_transporter_355708..355938_POSITIVE 313 206 163 78 29 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 311 192 151 47 13 NC_002950:PG1751|5end_aminotransferase,_class_V_1837280..1837510_POSITIVE 310 206 163 50 4 NC_002950:PG1770|5end_hypothetical_protein_1857284..1857514_POSITIVE 308 220 172 91 44 NC_002950:PG1145|5end_long-chain-fatty-acid--CoA_ligase,_putative_1230305..1230535_NEGATIVE 307 204 163 57 12 NC_002950:PG0195|5end_rubrerythrin_232046..232276_POSITIVE 306 219 171 196 140 NC_002950:PG1592|5end_HDIG_domain_protein_1669383..1669613_POSITIVE 305 188 146 69 25 NC_002950:PG1964|5end_bacterial_sugar_transferase_2052910..2053140_POSITIVE 305 189 141 231 180 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 348 198 155 63 12 NC_002950:PG2063|3end_hypothetical_protein_2160390..2160540_NEGATIVE 333 198 155 54 17 NC_002950:PG0459|3end_ISPg5,_transposase_Orf1_501517..501667_NEGATIVE 324 196 151 50 8 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 322 195 155 55 4 NC_002950:PG1581|3end_hypothetical_protein_1659404..1659554_POSITIVE 311 196 151 147 101 NC_002950:PG1594|3end_ComEC/Rec2-related_protein_1672052..1672202_NEGATIVE 306 216 172 119 83 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 305 188 146 72 28 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 304 209 163 128 82 NC_002950:PG0003|3end_hypothetical_protein_1919..2069_NEGATIVE 303 188 141 147 104 NC_002950:PG1608|3end_methylmalonyl-CoA_decarboxylase,_beta_subunit_1688685..1688835_NEGATIVE 302 219 176 128 82 NC_002950:PG0524|3end_hypothetical_protein_568963..569113_POSITIVE 299 205 161 54 6 NC_002950:PG1945|3end_hypothetical_protein_2032220..2032370_POSITIVE 298 188 141 89 31 NC_002950:PG0594|3end_RNA_polymerase_sigma-70_factor_652991..653141_POSITIVE 298 220 175 66 1 NC_002950:PG0170|3end_methionyl-tRNA_synthetase_191774..191924_POSITIVE 297 218 172 145 80 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE 296 218 172 106 56 NC_002950:PG1759|3end_adhesion_protein,_putative_1846597..1846747_POSITIVE 296 196 151 77 13 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 295 197 151 136 95 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 293 197 151 134 86 NC_002950:PG1726|3end_PDZ_domain_protein_1816779..1816929_POSITIVE 293 218 171 130 80 NC_002950:PG1578|3end_quinolinate_synthetase_1656472..1656622_POSITIVE 288 197 151 140 97 NC_002950:PG1998|3end_polyprenyl_synthetase_2087151..2087301_NEGATIVE