Origin IGS: acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 ctgcttgtaaaaattttaacgattttatattatcggatgatttgtttattttcaaacaattacataggatttgctaaaaaagcatcacgccacaaaatacagacaaggttttacgcaatcaggattgattggaataaagtaatgtagattaacaataacagtgccgtttaaagccgtaaaaaaagaatttatagcggaaatatcgaaataaatgcttaattttgcagctgttttggtgatacgtcggtcattctgccgttcgcataaaagggaatccggtcggagtccggaacagtgcccgctactgtggaacccgtgaagaggaaaagcaaacttacaccactgtcgtcattgacgggaaggtcgcttttcggggtgtagtcaggaaacctgccaagcataaaagacgaacatgttctcgggggcaagaacagcgtgattggaatcgaatgattttttagtttcgaccatagggtgagaagcctgcaagtagccatgctgctttgcaggt Mask Tandem Repeat Region ================================================ acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Find is-nt database================================================ Query_seq: TF0045:TF0046|TF0045:TF0046:outer membrane protein, TonB dependent receptor:thiamin biosynthesis lipoprotein, ApbE:->->:52151..52661 511 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0045:TF0046|TF0045:TF0046:outer membrane protein, TonB dependent receptor:thiamin biosynthesis lipoprotein, ApbE:->->:52151..52661 511 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0045:TF0046|TF0045:TF0046:outer membrane protein, TonB dependent receptor:thiamin biosynthesis lipoprotein, ApbE:->->:52151..52661 511 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Predict ORF larger than 30AA ================================================ Protein_Len: 35 Strand: + Start: 23 End: 127 ...................... M Q A S H P M V E T K K S F D S N H A V L A P E N M F V F Y A W Q V S ................................................................................................................................................................................................................................................................................................................................................................................................ Protein_Len: 39 Strand: + Start: 58 End: 174 ......................................................... M I R F Q S R C S C P R E H V R L L C L A G F L T T P R K A T F P S M T T V V ................................................................................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 3 End: 293 .. M Q S S M A T C R L L T L W S K L K N H S I P I T L F L P P R T C S S F M L G R F P D Y T P K S D L P V N D D S G V S L .......................................................................................................................................................................................................................... Protein_Len: 51 Strand: + Start: 272 End: 424 ............................................................................................................................................................................................................................................................................... M T K T A A K L S I Y F D I S A I N S F F T A L N G T V I V N L H Y F I P I N P D C V K P C L Y F V A ....................................................................................... Protein_Len: 48 Strand: - Start: 368 End: 511 ............................................................................................................................................................................................................................................................................................................................................................................... M V K N W D I R I A Y F R T Q I K H R S A K K A F G I Y N N S F L C I M R Y Y L I T L I K V L M Protein_Len: 35 Strand: - Start: 196 End: 300 ................................................................................................................................................................................................... P N W L L P C Q E P S R G S E R K H S R C F S R R I V L V A A F N L M ................................................................................................................................................................................................................... Protein_Len: 35 Strand: - Start: 134 End: 238 ..................................................................................................................................... V G F L S R G T L S S L P T L K S K R K V P E V T A P V T G S E S R M ................................................................................................................................................................................................................................................................................. Protein_Len: 60 Strand: - Start: 54 End: 248 ..................................................... W D R Q E Q G R S C T R R K H K A P K R V V G R F A V K G D I V V T T Y T Q K E E E R T G C Y R A S N R V G V P N G K M ....................................................................................................................................................................................................................................................................... acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 456 End: 485 .......................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTTGAAAATAAACAAATCATCCGATAATAT.......................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 479 End: 508 ..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTTGTAAAAATTTTAACGATTTTATATTAT... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF0045:TF0046|TF0045:TF0046:outer membrane protein, TonB dependent receptor:thiamin biosynthesis lipoprotein, ApbE:->->:52151..52661 511 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Intra-Species Hit: Count: 1 Min: 1 Max: 511 Len: 511 Subject: tfor_TF0045_TF0046|outer membrane protein, TonB dependent receptor:thiamin biosynthesis lipoprotein, ApbE|POSITIVE:POSITIVE|[52151,52661]|511 HSP 1 e-value: 0.0 bit: 971.0 Len: 511 Query Start:1 Query End:511 Subject Strand: POSITIVE Subject Start: 1 Subject End: 511 acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattcnnnnnnnacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag acctgcaaagcagcatggctacttgcaggcttctcaccctatggtcgaaactaaaaaatcattcgattccaatcacgctgttcttgcccccgagaacatgttcgtcttttatgcttggcaggtttcctgactacaccccgaaaagcgaccttcccgtcaatgacgacagtggtgtaagtttgcttttcctcttcacgggttccacagtagcgggcactgttccggactccgaccggattcccttttatgcgaacggcagaatgaccgacgtatcaccaaaacagctgcaaaattaagcatttatttcgatatttccgctataaattctttttttacggctttaaacggcactgttattgttaatctacattactttattccaatcaatcctgattgcgtaaaaccttgtctgtattttgtggcgtgatgcttttttagcaaatcctatgtaattgtttgaaaataaacaaatcatccgataatataaaatcgttaaaatttttacaagcag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACCUGCAAAGCAGCAUGGCUACUUGCAGGCUUCUCACCCUAUGGUCGAAACUAAAAAAUCAUUCGAUUCCAAUCACGCUGUUCUUGCCCCCGAGAACAUGUUCGUCUUUUAUGCUUGGCAGGUUUCCUGACUACACCCCGAAAAGCGACCUUCCCGUCAAUGACGACAGUGGUGUAAGUUUGCUUUUCCUCUUCACGGGUUCCACAGUAGCGGGCACUGUUCCGGACUCCGACCGGAUUCCCUUUUAUGCGAACGGCAGAAUGACCGACGUAUCACCAAAACAGCUGCAAAAUUAAGCAUUUAUUUCGAUAUUUCCGCUAUAAAUUCUUUUUUUACGGCUUUAAACGGCACUGUUAUUGUUAAUCUACAUUACUUUAUUCCAAUCAAUCCUGAUUGCGUAAAACCUUGUCUGUAUUUUGUGGCGUGAUGCUUUUUUAGCAAAUCCUAUGUAAUUGUUUGAAAAUAAACAAAUCAUCCGAUAAUAUAAAAUCGUUAAAAUUUUUACAAGCAG ..((((.(((((.((((.((((.(((((((.....((((..(((((((((((......................(((.((((((((....)))))))))))..(((..........))).))))))..)))))......(((((((((.(((((((((......)))...)).).))).)))))))))........))))...((((((((((...(((((..(((.(((....))).))).....(((((..((((.....).))).))))).........(((((.((((..(((.((((((..((.......))..)))))).))).)))).)))))...)))))..)))))))))).............(((((..((((((....)))))).))))).....)))))))....)))))))).)))))(((((((......(((((.((((..(((...........)))..)))).))))).....))))))).........)))) (-121.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGCUUGUAAAAAUUUUAACGAUUUUAUAUUAUCGGAUGAUUUGUUUAUUUUCAAACAAUUACAUAGGAUUUGCUAAAAAAGCAUCACGCCACAAAAUACAGACAAGGUUUUACGCAAUCAGGAUUGAUUGGAAUAAAGUAAUGUAGAUUAACAAUAACAGUGCCGUUUAAAGCCGUAAAAAAAGAAUUUAUAGCGGAAAUAUCGAAAUAAAUGCUUAAUUUUGCAGCUGUUUUGGUGAUACGUCGGUCAUUCUGCCGUUCGCAUAAAAGGGAAUCCGGUCGGAGUCCGGAACAGUGCCCGCUACUGUGGAACCCGUGAAGAGGAAAAGCAAACUUACACCACUGUCGUCAUUGACGGGAAGGUCGCUUUUCGGGGUGUAGUCAGGAAACCUGCCAAGCAUAAAAGACGAACAUGUUCUCGGGGGCAAGAACAGCGUGAUUGGAAUCGAAUGAUUUUUUAGUUUCGACCAUAGGGUGAGAAGCCUGCAAGUAGCCAUGCUGCUUUGCAGGU ..(((...(((((((....((((((((....(((..(((..((((((......))))))...)))..))).((((.....))))((((((.......(((((....(((((((..(((((......))))).......(((.(((............))).)))....)))))))................((((((...((((((((((..(((........)))..)))))))))).(((.((((..((((((((((((.(......).)))..))).))))))))))....))).)))))))))))(..((((.(((...(((((((...(((......((((((....)))))).)))...)))))))...((((.(((.(....).(((...))).....)))..)))).))).))))..).......)))))).))))))))...))))))).)))(((.(((....))))))..(((((((((((((...))))).)))))))) (-134.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 450 255 211 45 4 tfor:TF1145|5end_anaerobic_C4-dicarboxylate_membrane_transporter_1225799..1226029_POSITIVE 432 255 211 231 189 tfor:TF1598|5end_conserved_hypothetical_protein_1713358..1713588_POSITIVE 417 244 207 70 30 tfor:TF2752|5end_endonuclease_III_2936781..2937011_POSITIVE 399 200 151 99 55 tfor:TF2128|5end_3-oxoacyl-(acyl-carrier_protein)_synthase_2304258..2304488_POSITIVE 399 270 221 132 78 tfor:TF1720|5end_conserved_hypothetical_protein_1843679..1843909_POSITIVE 398 236 196 83 45 tfor:TF1485|5end_conserved_hypothetical_protein_1581871..1582101_POSITIVE 395 169 122 78 24 tfor:TF2793|5end_possible_L-lysine_2,3-aminomutase_2977661..2977891_POSITIVE 394 230 187 53 10 tfor:TF2267|5end_lysozyme-related_protein_2434869..2435099_POSITIVE 393 122 84 218 185 tfor:TF0077|5end_hypothetical_protein_84241..84471_POSITIVE 390 259 213 205 155 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 386 236 196 88 46 tfor:TF2126|5end_S-adenosylhomocysteine_hydrolase_2302501..2302731_POSITIVE 385 260 211 78 31 tfor:TF1240|5end_conserved_hypothetical_protein_1324304..1324534_POSITIVE 385 238 191 136 96 tfor:TF1040|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_1101253..1101483_POSITIVE 382 279 231 54 8 tfor:TF2310|5end_dehydrogenase,_possible_3-oxoacyl-[acyl-carrier-protein]_reductase_2470481..2470711_POSITIVE 382 260 211 212 147 tfor:TF0692|5end_conserved_hypothetical_protein_736379..736609_POSITIVE 378 225 181 104 43 tfor:TF2159|5end_conserved_hypothetical_protein_2334446..2334676_POSITIVE 377 156 111 81 34 tfor:TF1035|5end_iron(III)_ABC_transporter,_periplasmic-binding_protein_1095910..1096140_POSITIVE 376 172 131 35 6 tfor:TF1600|5end_uroporphyrinogen-III_synthase_1713964..1714194_POSITIVE 375 231 191 177 126 tfor:TF2261|5end_transfer_region-related_protein,_TraM_2430496..2430726_POSITIVE 372 236 197 229 175 tfor:TF0587|5end_outer_membrane_protein_618319..618549_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 399 200 151 67 23 tfor:TF2127|3end_hypothetical_protein_2304306..2304456_POSITIVE 394 230 187 53 10 tfor:TF2266|3end_transfer_region-related_protein,_TraQ_2434949..2435099_POSITIVE 385 238 191 105 65 tfor:TF1039|3end_conserved_hypothetical_protein_1101302..1101452_POSITIVE 376 172 131 45 16 tfor:TF1599|3end_ribonuclease_P_protein_component_1714054..1714204_POSITIVE 369 246 204 142 93 tfor:TF2336|3end_conserved_hypothetical_protein_2498159..2498309_POSITIVE 367 268 221 131 81 tfor:TF2924|3end_DNA-binding_response_regulator/sensor_histidine_kinase_3125618..3125768_POSITIVE 365 255 211 77 30 tfor:TF3107|3end_hypothetical_protein_3338736..3338886_POSITIVE 361 240 192 151 98 tfor:TF1684|3end_zinc_protease_1800331..1800481_POSITIVE 360 237 195 79 26 tfor:TF1066|3end_hypothetical_protein_1136858..1137008_POSITIVE 358 157 115 77 14 tfor:TF2978|3end_conserved_hypothetical_protein_3190862..3191012_POSITIVE 356 240 191 138 73 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 355 228 182 60 18 tfor:TF1169|3end_lipoprotein_ABC_transporter,_permease_component_1251573..1251723_POSITIVE 352 260 214 61 10 tfor:TF1382|3end_hypothetical_protein_1457777..1457927_POSITIVE 352 260 214 57 6 tfor:TF1383|3end_hypothetical_protein_1457773..1457923_POSITIVE 351 236 197 138 93 tfor:TF2358|3end_possible_small-conductance_mechanosensitive_channel_2524850..2525000_POSITIVE 347 246 204 79 37 tfor:TF1034|3end_conserved_hypothetical_protein_1095901..1096051_POSITIVE 346 260 211 64 12 tfor:TF3009|3end_RNA_polymerase_ECF-type_sigma_factor_3229709..3229859_POSITIVE 346 260 211 88 27 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 345 230 181 70 3 tfor:TF1794|3end_possible_glucose-1-phosphatase_1935816..1935966_POSITIVE 344 257 212 55 17 tfor:TF1734|3end_conserved_hypothetical_protein_1860118..1860268_POSITIVE