Origin IGS: tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ttatcgaatgtttttgattgcctaaaagggaagtgacgtgtactgaaaaagtttgacactcaaagagtgtctgattcgtgattaaaattacagtgtttcttctaaagtccgtatcggtttacataccttactctttaagatgactttcggttgacagctgccaaatctcctctttgccgggcagcctttttcggtacagcttgggcgagattcgagggttctttccacccggtggactccgaccagttgtcttttgaaatcaaaagcttgatgcagtgcacttaaggggagaggaacaaagcttgacctccgaaagatcatctatttaatatagtaaaccacgtgctctgaacggaacttcttacctttgtcggaaaagatgtcttcggtcacaggacaatcgcaatttaagatataatctcacctcaacataattagaagga Mask Tandem Repeat Region ================================================ tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Find is-nt database================================================ Query_seq: PG1748:PG1750|PG1748:PG1750:transketolase:alpha-1,3/4-fucosidase, putative:<-->:1835020..1835462 443 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1748:PG1750|PG1748:PG1750:transketolase:alpha-1,3/4-fucosidase, putative:<-->:1835020..1835462 443 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1748:PG1750|PG1748:PG1750:transketolase:alpha-1,3/4-fucosidase, putative:<-->:1835020..1835462 443 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 30 End: 119 ............................. M L N C D C P V T E D I F S D K G K K F R S E H V V Y Y I K .................................................................................................................................................................................................................................................................................................................................... Protein_Len: 48 Strand: + Start: 163 End: 306 .................................................................................................................................................................. M H C I K L L I S K D N W S E S T G W K E P S N L A Q A V P K K A A R Q R G D L A A V N R K S S ......................................................................................................................................... Protein_Len: 60 Strand: + Start: 123 End: 353 .......................................................................................................................... M I F R R S S F V P L P L S A L H Q A F D F K R Q L V G V H R V E R T L E S R P S C T E K G C P A K R R F G S C Q P K V .......................................................................................... Protein_Len: 30 Strand: - Start: 190 End: 279 ............................................................................................................................................................................................. F V V P R L G G P P F F G R I E G L S Y R F L S G P L S S M .................................................................................................................................................................... Protein_Len: 37 Strand: - Start: 176 End: 286 ............................................................................................................................................................................... A K S K L L C S T P T W R T S L V R S D R G L Q V S F P Q G A F L L N P M ............................................................................................................................................................. Protein_Len: 44 Strand: - Start: 162 End: 293 ................................................................................................................................................................. T C Q M L S K I E F S L Q D S D V P H F S G E F R A W A T G F F A A R C L P S K A A T M ...................................................................................................................................................... tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa 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================================================ tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -10.9 Tail_Score: -2.81815 Start: 373 End: 389 Full_Region: gtactgaaaaagttt gacactc aaa gagtgtc tgattcgtgattaaa ....................................................................................................................................................................................................................................................................................................................................................................................gacactcaaagagtgtc...................................................... Find igs database================================================ Query_seq: PG1748:PG1750|PG1748:PG1750:transketolase:alpha-1,3/4-fucosidase, putative:<-->:1835020..1835462 443 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Intra-Species Hit: Count: 2 Min: 1 Max: 443 Len: 443 Subject: NC_002950_PG1748_PG1750|transketolase:alpha-1,3/4-fucosidase, putative|NEGATIVE:POSITIVE|[1835020,1835462]|443 HSP 1 e-value: 0.0 bit: 878.0 Len: 443 Query Start:1 Query End:443 Subject Strand: POSITIVE Subject Start: 1 Subject End: 443 tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa tccttctaattatgttgaggtgagattatatcttaaattgcgattgtcctgtgaccgaagacatcttttccgacaaaggtaagaagttccgttcagagcacgtggtttactatattaaatagatgatctttcggaggtcaagctttgttcctctccccttaagtgcactgcatcaagcttttgatttcaaaagacaactggtcggagtccaccgggtggaaagaaccctcgaatctcgcccaagctgtaccgaaaaaggctgcccggcaaagaggagatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgatacggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcacttcccttttaggcaatcaaaaacattcgataa Subject: NC_002950_PG1535_PG1536|transcriptional regulator, putative:cell division protein FtsX, putative|NEGATIVE:POSITIVE|[1614582,1616501]|1920 HSP 1 e-value: 3.0E-19 bit: 97.6 Len: 136 Query Start:277 Query End:412 Subject Strand: POSITIVE Subject Start: 1253 Subject End: 1389 ....................................................................................................................................................................................................................................................................................gatttggcagctgtcaaccgaaagtcatcttaaagagtaaggtatgtaaaccgat-acggactttagaagaaacactgtaattttaatcacgaatcagacactctttgagtgtcaaactttttcagtacacgtcact............................... ....................................................................................................................................................................................................................................................................................gatttagcggctgtcaaccgaaagtcgtcttaaagagtaaggtgtgtaaacccataatggactttagagaaatctctgtaattttaatctcgaaattaacactctccgagtgtcaactcttttcagtacacgtcact............................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCUUCUAAUUAUGUUGAGGUGAGAUUAUAUCUUAAAUUGCGAUUGUCCUGUGACCGAAGACAUCUUUUCCGACAAAGGUAAGAAGUUCCGUUCAGAGCACGUGGUUUACUAUAUUAAAUAGAUGAUCUUUCGGAGGUCAAGCUUUGUUCCUCUCCCCUUAAGUGCACUGCAUCAAGCUUUUGAUUUCAAAAGACAACUGGUCGGAGUCCACCGGGUGGAAAGAACCCUCGAAUCUCGCCCAAGCUGUACCGAAAAAGGCUGCCCGGCAAAGAGGAGAUUUGGCAGCUGUCAACCGAAAGUCAUCUUAAAGAGUAAGGUAUGUAAACCGAUACGGACUUUAGAAGAAACACUGUAAUUUUAAUCACGAAUCAGACACUCUUUGAGUGUCAAACUUUUUCAGUACACGUCACUUCCCUUUUAGGCAAUCAAAAACAUUCGAUAA ............(((((((.((((((...))))))......(((((.((((...(.(((((....))))).)..(((((...(((((..(((..((((..(((((((((((((.(((...((((((.(((((((..(.((.(((..(((..(((((.(((..(((.(((.(((((..((((((....)))))).....)))).).))).))).(((((((..((....))...)).)))))..((((((((......)).)))..))).))).)))))...)))))))).)..))))))))))))).......))).))).)))))))...)))..)))).((((((....(((.((....)).))).....(((((((...)))))))....)))))).....)))..))))))))))))))))))).......))))))). (-113.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUAUCGAAUGUUUUUGAUUGCCUAAAAGGGAAGUGACGUGUACUGAAAAAGUUUGACACUCAAAGAGUGUCUGAUUCGUGAUUAAAAUUACAGUGUUUCUUCUAAAGUCCGUAUCGGUUUACAUACCUUACUCUUUAAGAUGACUUUCGGUUGACAGCUGCCAAAUCUCCUCUUUGCCGGGCAGCCUUUUUCGGUACAGCUUGGGCGAGAUUCGAGGGUUCUUUCCACCCGGUGGACUCCGACCAGUUGUCUUUUGAAAUCAAAAGCUUGAUGCAGUGCACUUAAGGGGAGAGGAACAAAGCUUGACCUCCGAAAGAUCAUCUAUUUAAUAUAGUAAACCACGUGCUCUGAACGGAACUUCUUACCUUUGUCGGAAAAGAUGUCUUCGGUCACAGGACAAUCGCAAUUUAAGAUAUAAUCUCACCUCAACAUAAUUAGAAGGA .......(((((((.((((((.......(((((.((((...........((((.(((((((...))))))).)))).(((((....)))))..)))).)))))...((((.....(((((((.((..(((.......(((((((((((((..(.(((((......(((((((((((((..(((............((((((.((..(((.((((.((((.......))))..)))))))...))))))))((((((....)))))).....))).).)))...))))))))).......))).)).)..))))))).))))))...)))..)))))))))..(((..((((..(((...((((.((......))..))))..))))))).))).))))....)))))).))))))).......((((..........).))). (-119.12) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 930 100 51 191 142 NC_002950:PG1748|5end_transketolase_1834929..1835159_NEGATIVE 424 270 224 214 163 NC_002950:PG0986|5end_hypothetical_protein_1047426..1047656_POSITIVE 420 240 192 167 117 NC_002950:PG0504|5end_lipoyl_synthase_544234..544464_POSITIVE 399 307 261 71 25 NC_002950:PG0476|5end_yngK_protein_518762..518992_NEGATIVE 392 290 244 168 125 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 389 296 259 172 127 NC_002950:PG1145|5end_long-chain-fatty-acid--CoA_ligase,_putative_1230305..1230535_NEGATIVE 373 268 225 67 14 NC_002950:PG1576|5end_L-aspartate_oxidase_1653016..1653246_POSITIVE 373 297 251 193 158 NC_002950:PG0607|5end_hypothetical_protein_662552..662782_POSITIVE 367 426 386 128 86 NC_002950:PG0942|5end_ISPg5,_transposase_Orf1_1002063..1002293_POSITIVE 367 289 241 54 8 NC_002950:PG0805|5end_prolipoprotein_diacylglyceryl_transferase_862650..862880_NEGATIVE 364 269 222 69 29 NC_002950:PG1783|5end_glycosyl_transferase,_group_2_family_protein_1871868..1872098_POSITIVE 362 288 243 169 120 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 360 297 251 60 18 NC_002950:PG1641|5end_phosphotyrosine_protein_phosphatase_1721763..1721993_NEGATIVE 358 308 265 231 187 NC_002950:PG0471|5end_hypothetical_protein_512288..512518_POSITIVE 357 90 44 153 106 NC_002950:PG2034|5end_oxidoreductase,_FAD-binding,_putative_2135701..2135931_NEGATIVE 356 278 238 48 4 NC_002950:PG1861|5end_hypothetical_protein_1960057..1960287_NEGATIVE 353 423 386 137 93 NC_002950:PG2058|5end_ISPg5,_transposase_Orf1_2156390..2156620_NEGATIVE 353 289 242 53 6 NC_002950:PG1706|5end_hypothetical_protein_1794211..1794441_NEGATIVE 352 296 252 197 152 NC_002950:PG0731|5end_hypothetical_protein_782676..782906_NEGATIVE 351 250 201 55 2 NC_002950:PG1660|5end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_1744268..1744498_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 420 240 192 64 14 NC_002950:PG0503|3end_dipeptidyl_aminopeptidase_IV_544211..544361_POSITIVE 399 307 261 81 35 NC_002950:PG0477|3end_pantoate--beta-alanine_ligase_518752..518902_NEGATIVE 398 300 251 104 44 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE 393 250 201 134 89 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 393 250 201 134 89 NC_002950:PG1972|3end_hemagglutinin_protein_HagB_2061203..2061353_POSITIVE 380 273 236 143 95 NC_002950:PG1387|3end_hypothetical_protein_1469132..1469282_NEGATIVE 378 291 252 65 25 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 364 269 222 82 42 NC_002950:PG1782|3end_hypothetical_protein_1871961..1872111_POSITIVE 362 288 243 137 88 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 356 290 244 91 43 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 348 240 197 48 1 NC_002950:PG1854|3end_5-formyltetrahydrofolate_cyclo-ligase_family_protein_1953325..1953475_NEGATIVE 347 287 243 97 54 NC_002950:PG2003|3end_deoxyguanosinetriphosphate_triphosphohydrolase_2091648..2091798_NEGATIVE 346 260 214 54 16 NC_002950:PG2132|3end_fimbrilin_2238943..2239093_POSITIVE 345 296 257 48 10 NC_002950:PG0803|3end_glucosamine-6-phosphate_deaminase_859727..859877_NEGATIVE 343 239 193 146 104 NC_002950:PG0336|3end_hypothetical_protein_370723..370873_NEGATIVE 341 289 241 83 32 NC_002950:PG1118|3end_clpB_protein_1192083..1192233_NEGATIVE 339 245 203 143 98 NC_002950:PG1954|3end_NAD_dependent_epimerase/reductase-related_protein_2045612..2045762_POSITIVE 336 296 257 49 7 NC_002950:PG2158|3end_hypothetical_protein_2264473..2264623_POSITIVE 336 180 132 50 3 NC_002950:PG0592|3end_50S_ribosomal_protein_L31_650225..650375_POSITIVE 335 253 212 146 108 NC_002950:PG1791|3end_hypothetical_protein_1880951..1881101_NEGATIVE