Origin IGS: agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaaggcagcatgcatcgatggtttaatggaggtcgttgtcggtatcgaagcctcgccaaaacgcataccgaaacatcctcaaaagcatagcctttaatctctatctcattatatccaaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 atttggatataatgagatagagattaaaggctatgcttttgaggatgtttcggtatgcgttttggcgaggcttcgataccgacaacgacctccattaaaccatcgatgcatgctgcctttgaatcaagtcaatatacttaatcttttggcgacgtattcggatactgatttatgtactgaaaaagctgatattcggaagggttagtttgtgatttggactacaaggatcttactaaactttatttttgagaaaaggcttgaaagttccaaacacattagctacttttgccggagtaatctcttactattatttagagttctct Mask Tandem Repeat Region ================================================ agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaaggcagcatgcatcgatggtttaatggaggtcgttgtcggtatcgaagcctcgccaaaacgcataccgaaacatcctcaaaagcatagcctttaatctctatctcattatatccaaat Find is-nt database================================================ Query_seq: PG1232:PG1233|PG1232:PG1233:glutamate dehydrogenase:hypothetical protein:<-->:1309702..1310024 323 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaaggcagcatgcatcgatggtttaatggaggtcgttgtcggtatcgaagcctcgccaaaacgcataccgaaacatcctcaaaagcatagcctttaatctctatctcattatatccaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1232:PG1233|PG1232:PG1233:glutamate dehydrogenase:hypothetical protein:<-->:1309702..1310024 323 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaaggcagcatgcatcgatggtttaatggaggtcgttgtcggtatcgaagcctcgccaaaacgcataccgaaacatcctcaaaagcatagcctttaatctctatctcattatatccaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 14 Min: 207 Max: 317 Len: 111 Subject: gi|34541013|ref|NP_905492.1| ISPg1, transposase, internal deletion [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 166 Subject End: 199 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540041|ref|NP_904520.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540279|ref|NP_904758.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540363|ref|NP_904842.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540602|ref|NP_905081.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540772|ref|NP_905251.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540899|ref|NP_905378.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540911|ref|NP_905390.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34540950|ref|NP_905429.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34541119|ref|NP_905598.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34541274|ref|NP_905753.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: gi|34541511|ref|NP_905990.1| ISPg1, transposase [Porphyromonas gingivalis W83] HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: UniRef90_Q9ZNB4 Cluster: Insertion sequence IS1126-like gene; n=2; Porphyromonas gingivalis|Rep: Insertion sequence IS1126-like gene - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 166 Subject End: 199 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Subject: UniRef90_Q9ZA61 Cluster: Transposase; n=4; Porphyromonas gingivalis|Rep: Transposase - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 2.0E-6 bit: 47.4 Len: 111 Query Start:207 Query End:317 Subject Strand: null Subject Start: 316 Subject End: 349 .............................................................................................................................................................................................................. G S M H R W F N G G R C R Y R S L A K T H T E T S S K A * P L I S I S L Y ...... .............................................................................................................................................................................................................. G S I R R W F H G G R C R Y R G L A K T H T Q N I L E S - - - I A F N L Y ...... Find nr database================================================ Query_seq: PG1232:PG1233|PG1232:PG1233:glutamate dehydrogenase:hypothetical protein:<-->:1309702..1310024 323 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: - Start: 122 End: 307 ......................................................................................................................... R I D A K E T C L D T D S Y T A L L N L I N V Q N L P L M C R H N L P P R Q R Y R L R A L V C V S V D E F A Y G K I E M ................ Protein_Len: 38 Strand: - Start: 2 End: 115 . L V R F L L L L N S R C F Y S I H K S S E L R K E F I F N L L I R T T W I M ................................................................................................................................................................................................................ agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaaat 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================================================ agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1232:PG1233|PG1232:PG1233:glutamate dehydrogenase:hypothetical protein:<-->:1309702..1310024 323 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccaaat Intra-Species Hit: Count: 1 Min: 1 Max: 206 Len: 206 Subject: NC_002950_PG1232_PG1233|glutamate dehydrogenase:hypothetical protein|NEGATIVE:POSITIVE|[1309702,1310024]|323 HSP 1 e-value: 1.0E-113 bit: 408.0 Len: 206 Query Start:1 Query End:206 Subject Strand: POSITIVE Subject Start: 1 Subject End: 206 agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaa..................................................................................................................... agagaactctaaataatagtaagagattactccggcaaaagtagctaatgtgtttggaactttcaagccttttctcaaaaataaagtttagtaagatccttgtagtccaaatcacaaactaacccttccgaatatcagctttttcagtacataaatcagtatccgaatacgtcgccaaaagattaagtatattgacttgattcaaa..................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGAGAACUCUAAAUAAUAGUAAGAGAUUACUCCGGCAAAAGUAGCUAAUGUGUUUGGAACUUUCAAGCCUUUUCUCAAAAAUAAAGUUUAGUAAGAUCCUUGUAGUCCAAAUCACAAACUAACCCUUCCGAAUAUCAGCUUUUUCAGUACAUAAAUCAGUAUCCGAAUACGUCGCCAAAAGAUUAAGUAUAUUGACUUGAUUCAAA .(((((((((...........)))).)).))).(((......((((..((((((((((.((..((((..((((((.((........)).)).))))..)))).)))))))).))))........(....)......))))..(((.((((........))))..)))......)))....((((((((......)))))))).... (-31.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUGAAUCAAGUCAAUAUACUUAAUCUUUUGGCGACGUAUUCGGAUACUGAUUUAUGUACUGAAAAAGCUGAUAUUCGGAAGGGUUAGUUUGUGAUUUGGACUACAAGGAUCUUACUAAACUUUAUUUUUGAGAAAAGGCUUGAAAGUUCCAAACACAUUAGCUACUUUUGCCGGAGUAAUCUCUUACUAUUAUUUAGAGUUCUCU .((((......))))...............(((((....(((((.(((........))))))))..((((((.((((....)))).....((((.((((((((.((((..(((((..((......))..))))).....))))..)).))))))))))))))))....))))).(((....((((...........))))..))). (-39.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 879 70 21 161 112 NC_002950:PG1232|5end_glutamate_dehydrogenase_1309611..1309841_NEGATIVE 319 177 135 140 95 NC_002950:PG1645|5end_ISPg5,_transposase_Orf1_1726062..1726292_NEGATIVE 298 79 32 68 27 NC_002950:PG0332|5end_transcription_termination_factor_Rho_365619..365849_POSITIVE 295 167 123 120 77 NC_002950:PG1419|5end_ISPg5,_transposase_Orf1_1504997..1505227_POSITIVE 295 139 96 214 178 NC_002950:PG0987|5end_hypothetical_protein_1048002..1048232_POSITIVE 280 47 9 180 138 NC_002950:PG0115|5end_hexapeptide_transferase_family_protein_138038..138268_POSITIVE 279 68 25 162 123 NC_002950:PG1485|5end_conjugative_transposon_protein_TraC_1560370..1560600_NEGATIVE 279 70 21 227 164 NC_002950:PG0297|5end_hypothetical_protein_335518..335748_NEGATIVE 274 76 32 50 7 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 274 166 122 124 78 NC_002950:PG0274|5end_hypothetical_protein_306333..306563_POSITIVE 271 200 157 223 181 NC_002950:PG1368|5end_glucose-6-phosphate_isomerase_1449370..1449600_NEGATIVE 271 165 123 231 188 NC_002950:PG0214|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_250963..251193_POSITIVE 265 131 94 179 137 NC_002950:PG2173|5end_outer_membrane_lipoprotein_Omp28_2280813..2281043_NEGATIVE 264 167 124 71 29 NC_002950:PG1318|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1397768..1397998_NEGATIVE 264 182 157 160 136 NC_002950:PG1148|5end_hypothetical_protein_1231204..1231434_POSITIVE 262 180 135 229 183 NC_002950:PG0625|5end_GTP_cyclohydrolase_I_678588..678818_POSITIVE 259 67 29 56 17 NC_002950:PG1725|5end_competence/damage-inducible_protein_CinA_domain_protein_1814766..1814996_POSITIVE 258 140 91 88 34 NC_002950:PG2125|5end_transcriptional_regulator,_AraC_family_2232254..2232484_NEGATIVE 258 176 134 88 34 NC_002950:PG1762|5end_protein-export_membrane_protein_SecD/protein-export_membrane_protein_SecF_1847988..1848218_POSITIVE 257 165 122 200 161 NC_002950:PG2073|5end_hypothetical_protein_2174374..2174604_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 280 47 9 60 18 NC_002950:PG0114|3end_hypothetical_protein_137998..138148_POSITIVE 274 166 122 81 35 NC_002950:PG0273|3end_4'-phosphopantetheinyl_transferase_family_protein_306370..306520_POSITIVE 269 152 112 76 38 NC_002950:PG2212|3end_hypothetical_protein_2324483..2324633_NEGATIVE 259 67 29 56 17 NC_002950:PG1724|3end_O-sialoglycoprotein_endopeptidase_1814846..1814996_POSITIVE 257 165 122 71 32 NC_002950:PG2074|3end_hypothetical_protein_2174503..2174653_NEGATIVE 257 165 122 71 32 NC_002950:PG1670|3end_hypothetical_protein_1755695..1755845_NEGATIVE 257 165 122 71 32 NC_002950:PG1265|3end_hypothetical_protein_1345024..1345174_NEGATIVE 257 147 102 52 16 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 257 165 122 71 32 NC_002950:PG0102|3end_hypothetical_protein_121241..121391_POSITIVE 253 45 1 132 77 NC_002950:PG1684|3end_hypothetical_protein_1771483..1771633_POSITIVE 249 166 125 129 79 NC_002950:PG0269|3end_exodeoxyribonuclease_III_302872..303022_POSITIVE 247 76 34 118 70 NC_002950:PG1963|3end_Sua5/YciO/YrdC/YwlC_family_protein_2052993..2053143_POSITIVE 241 179 135 101 64 NC_002950:PG0572|3end_hypothetical_protein_627434..627584_NEGATIVE 240 79 31 97 44 NC_002950:PG1881|3end_hypothetical_protein_1978046..1978196_POSITIVE 238 70 21 127 84 NC_002950:PG0802|3end_alpha_keto_acid_dehydrogenase_complex,_E3_component,_lipoamide_dehydrogenase_858373..858523_NEGATIVE 237 69 27 80 45 NC_002950:PG1115|3end_signal_recognition_particle_protein_1188887..1189037_POSITIVE 233 76 32 106 63 NC_002950:PG2015|3end_CRISPR-associated_protein_Cas4_2105502..2105652_NEGATIVE 233 139 94 76 24 NC_002950:PG1722|3end_hypothetical_protein_1812633..1812783_NEGATIVE 233 64 22 70 10 NC_002950:PG1593|3end_shikimate_kinase_1672143..1672293_POSITIVE 232 140 99 134 90 NC_002950:PG1205|3end_DNA-binding_protein,_histone-like_family_1284503..1284653_POSITIVE