Origin IGS: gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta .........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 taggaagaagttggaaaactttaacaaatttaacagttatagtgcctcaagtgtataatatagaaaaattatgctttatttatatcaagtgcgaacgaagtgagcttttagcggatatttcccgctatagtggtattctagataataatttattattatctagaacggaatttttgagacattctggctcaaaaattagggatgaaattacgaagtgagttgctcccgtccgcacttttcagggaaatatcagaattacaaaagaaaaatcaacctatagtcttttctaataacaagtcatagtcacttataagaattactaataacacgtttgaagagcctaactgcaatagagctataaaacaagatatacaaaggatttgaggcatgtgtctcaagtctttttcttttgtctaaaatagaggtatagtttcaaactatatcaaagcctaattttttacaattatacagatgatttcttttctgttaagatagtttcaacaacaaattttggaggacacatc Mask Tandem Repeat Region ================================================ gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Find is-nt database================================================ Query_seq: SMT_900:SMT_901|SMT_900:SMT_901:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase:hypothetical protein:<-<-:850707..851230 524 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_900:SMT_901|SMT_900:SMT_901:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase:hypothetical protein:<-<-:850707..851230 524 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_900:SMT_901|SMT_900:SMT_901:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase:hypothetical protein:<-<-:850707..851230 524 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 105 End: 218 ........................................................................................................ M L D K R K R L E T H A S N P L Y I L F Y S S I A V R L F K R V I S N S Y K .................................................................................................................................................................................................................................................................................................................. Protein_Len: 42 Strand: + Start: 127 End: 252 .............................................................................................................................. M R H M P Q I L C I S C F I A L L Q L G S S N V L L V I L I S D Y D L L L E K T I G ................................................................................................................................................................................................................................................................................ Protein_Len: 36 Strand: + Start: 290 End: 397 ................................................................................................................................................................................................................................................................................................. M R T G A T H F V I S S L I F E P E C L K N S V L D N N K L L S R I P L ............................................................................................................................... Protein_Len: 59 Strand: - Start: 310 End: 486 ..................................................................................................................................................................................................................................................................................................................... K T I E D R I K S G S H R L F E T R S L L L N N D L I G S Y R S I D A L L E S R E C K I Y I F C L K E I N Y V Q P V M ...................................... Protein_Len: 40 Strand: - Start: 225 End: 344 ................................................................................................................................................................................................................................ S K N N S F V I P Q N K K Q L E S I E R F L A S P L L E S R L K M G L K Q A L M .................................................................................................................................................................................... gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta 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: 81 Start: 32 End: 61 ...............................TTATACAGATGATTTCTTTTCTGTTAAGAT............................................................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -8.2 Tail_Score: -5.58522 Start: 124 End: 147 Full_Region: acaagatatacaaag gatttgaggc atgt gtctcaagtc tttttcttttgtcta ...........................................................................................................................gatttgaggcatgtgtctcaagtc......................................................................................................................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 74 HP_score: -8.7 Tail_Score: -3.24245 Start: 330 End: 354 Full_Region: TAATTTCATCCCTAA TTTTTGAGCCA GAA TGTCTCAAAAA TTCCGTTCTAGATAA .........................................................................................................................................................................................................................................................................................................................................TTTTTGAGCCAGAATGTCTCAAAAA.......................................................................................................................................................................... Find igs database================================================ Query_seq: SMT_900:SMT_901|SMT_900:SMT_901:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase:hypothetical protein:<-<-:850707..851230 524 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Intra-Species Hit: Count: 1 Min: 1 Max: 524 Len: 524 Subject: smit_SMT_900_SMT_901|5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase:hypothetical protein|NEGATIVE:NEGATIVE|[850707,851230]|524 HSP 1 e-value: 0.0 bit: 1039.0 Len: 524 Query Start:1 Query End:524 Subject Strand: POSITIVE Subject Start: 1 Subject End: 524 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactataggttgatttttcttttgtaattctgatatttccctgaaaagtgcggacgggagcaactcacttcgtaatttcatccctaatttttgagccagaatgtctcaaaaattccgttctagataataataaattattatctagaataccactatagcgggaaatatccgctaaaagctcacttcgttcgcacttgatataaataaagcataatttttctatattatacacttgaggcactataactgttaaatttgttaaagttttccaacttcttccta Inter-species Hit: Count: 3 Min: 1 Max: 249 Len: 249 Subject: NC_008533_SPD_0509_SPD_0510|hypothetical protein:5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase|POSITIVE:POSITIVE|[519216, 519475]|260 HSP 1 e-value: 9.0E-91 bit: 335.0 Len: 249 Query Start:1 Query End:249 Subject Strand: NEGATIVE Subject Start: 12 Subject End: 260 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactata................................................................................................................................................................................................................................................................................... gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaagcgtctgtataattgtaaaaaattaggctttgatatagtttgaaactatatatctgtttcggacaaaagaaaaagacttgaagcaaacgtctcaaatcctttgtatagcttgttttatagctttatttcagttagacggttcaaacgcgttattagtaattcttataagtgactatggcttgttattagaaaagactata................................................................................................................................................................................................................................................................................... Subject: NC_003028_SP_0584_SP_0585|transcriptional regulator, putative:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase|POSITIVE:POSITIVE|[553839,554098]|260 HSP 1 e-value: 1.0E-71 bit: 272.0 Len: 249 Query Start:1 Query End:249 Subject Strand: NEGATIVE Subject Start: 12 Subject End: 260 gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaatcatctgtataattgtaaaaaattaggctttgatatagtttgaaactatacctctattttagacaaaagaaaaagacttgagacacatgcctcaaatcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactata................................................................................................................................................................................................................................................................................... gatgtgtcctccaaaatttgttgttgaaactatcttaacagaaaagaaagcgtctgtataattgtaaaaaattagggtttgatatagtttgaaactatatatctgtttcggacaaaagaaaaagacttgaagcaaacgtctcaaatcctttgtaattcttactttacagctatattccaattagaatactaaaacatgttattagtaattcttataagtgactatgacctgttattagaaaagactata................................................................................................................................................................................................................................................................................... Subject: NC_003098_spr0513_spr0514|hypothetical protein:5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase|POSITIVE:POSITIVE|[511686,511801]|116 HSP 1 e-value: 2.0E-33 bit: 145.0 Len: 105 Query Start:145 Query End:249 Subject Strand: NEGATIVE Subject Start: 12 Subject End: 116 ................................................................................................................................................atcctttgtatatcttgttttatagctctattgcagttaggctcttcaaacgtgttattagtaattcttataagtgactatgacttgttattagaaaagactata................................................................................................................................................................................................................................................................................... ................................................................................................................................................atcctttgtatagcttgttttatagctttatttcagttagacggttcaaacgcgttattagtaattcttataagtgactatggcttgttattagaaaagactata................................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GAUGUGUCCUCCAAAAUUUGUUGUUGAAACUAUCUUAACAGAAAAGAAAUCAUCUGUAUAAUUGUAAAAAAUUAGGCUUUGAUAUAGUUUGAAACUAUACCUCUAUUUUAGACAAAAGAAAAAGACUUGAGACACAUGCCUCAAAUCCUUUGUAUAUCUUGUUUUAUAGCUCUAUUGCAGUUAGGCUCUUCAAACGUGUUAUUAGUAAUUCUUAUAAGUGACUAUGACUUGUUAUUAGAAAAGACUAUA .(((((((.((........(((.....)))..((((.(((((..(....)..)))))....((((..(((((.(((......((((((.....)))))))))..)))))..))))......))))...)))))))))((((........(((((......(((....))).....)))))..))))................((((..((((.((((((.......))))))....))))...)))).. (-36.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAGUCUUUUCUAAUAACAAGUCAUAGUCACUUAUAAGAAUUACUAAUAACACGUUUGAAGAGCCUAACUGCAAUAGAGCUAUAAAACAAGAUAUACAAAGGAUUUGAGGCAUGUGUCUCAAGUCUUUUUCUUUUGUCUAAAAUAGAGGUAUAGUUUCAAACUAUAUCAAAGCCUAAUUUUUUACAAUUAUACAGAUGAUUUCUUUUCUGUUAAGAUAGUUUCAACAACAAAUUUUGGAGGACACAUC ....(((((((....(((((......((((((((((((......(((.......((((....((((((.......))).)))...)))).(((((...((((((((((((((....)))))))))))))).....)))))....))).((((((((.....))))))))...................))))).)).))))).......))))).((.....)).............)))))))..... (-48.52) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 793 140 91 231 182 smit:SMT_900|5end_5-methyltetrahydropteroyltriglutamate--_homocysteine_methyltransferase_850616..850846_NEGATIVE 264 199 166 159 121 smit:SMT_1931|5end_23S_rRNA_methyltransferase_1870978..1871208_NEGATIVE 257 187 146 137 100 smit:SMT_1492|5end_DNA-directed_RNA_polymerase_beta_chain_1472093..1472323_POSITIVE 243 189 141 122 72 smit:SMT_1077|5end_GTP_cyclohydrolase_I_1015410..1015640_NEGATIVE 240 116 73 49 7 smit:SMT_1510|5end_ribose_5-phosphate_isomerase_1493488..1493718_NEGATIVE 240 187 141 231 191 smit:SMT_876|5end_hypothetical_protein_predicted_by_Glimmer/Critica_823502..823732_NEGATIVE 239 127 81 133 87 smit:SMT_482|5end_hypothetical_protein_predicted_by_Glimmer/Critica_418536..418766_NEGATIVE 236 37 2 90 47 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 236 37 2 90 47 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 236 191 168 226 206 smit:SMT_1685|5end_phenylalanyl-tRNA_synthetase_alpha_chain_1668845..1669075_NEGATIVE 234 229 184 67 13 smit:SMT_1181|5end_phosphotransferase_system,_mannose/fructose-specific_component_IIA_1139817..1140047_NEGATIVE 231 199 157 116 78 smit:SMT_993|5end_hypothetical_protein_935476..935706_NEGATIVE 229 153 121 191 159 smit:SMT_486|5end_hypothetical_protein_422305..422535_NEGATIVE 229 191 156 76 51 smit:SMT_103|5end_adenylosuccinate_synthetase_40766..40996_POSITIVE 227 143 101 173 129 smit:SMT_1079|5end_dihydropteroate_synthase_1017659..1017889_NEGATIVE 226 238 204 196 162 smit:SMT_869|5end_hypothetical_protein_817698..817928_NEGATIVE 224 167 121 220 164 smit:SMT_746|5end_LPS_biosynthesis_protein_651222..651452_NEGATIVE 222 194 158 40 4 smit:SMT_1120|5end_hypothetical_protein_1057063..1057293_NEGATIVE 221 174 133 198 147 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 220 199 159 181 145 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 255 36 1 122 84 smit:SMT_159|3end_hypothetical_protein_104615..104765_POSITIVE 243 189 141 141 91 smit:SMT_1078|3end_folylpolyglutamate_synthase_1015391..1015541_NEGATIVE 237 230 183 145 88 smit:SMT_2122|3end_cell_surface_protein_precursor_2007319..2007469_NEGATIVE 236 37 2 93 50 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 235 102 61 118 85 smit:SMT_561|3end_putative_translation_elongation_factor_EF-Tu_480687..480837_POSITIVE 234 229 184 63 9 smit:SMT_1182|3end_K02796_PTS_system,_mannose-specific_IID_component_1139821..1139971_NEGATIVE 231 199 157 116 78 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 227 143 101 49 5 smit:SMT_1080|3end_CAAX_amino_terminal_protease_family_protein_1017783..1017933_NEGATIVE 224 167 121 99 43 smit:SMT_747|3end_transcriptional_regulator,_LytR_family_651343..651493_NEGATIVE 216 166 126 107 57 smit:SMT_1362|3end_chaperone_protein_hscC_1341414..1341564_NEGATIVE 213 195 156 97 46 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 210 200 159 60 8 smit:SMT_1191|3end_phosphoribosylamine--glycine_ligase_1148475..1148625_NEGATIVE 210 210 166 67 14 smit:SMT_199|3end_K07166_ACT_domain-containing_protein_129817..129967_POSITIVE 209 176 137 109 66 smit:SMT_1379|3end_thymidylate_kinase_1356800..1356950_NEGATIVE 209 158 112 92 50 smit:SMT_206|3end_K07720_two-component_system,_response_regulator_YesN_137467..137617_NEGATIVE 208 188 148 37 3 smit:SMT_1738|3end_peptidyl-prolyl_cis-trans_isomerase_1721341..1721491_POSITIVE 206 143 101 80 31 smit:SMT_107|3end_ribose-phosphate_pyrophosphokinase_53450..53600_POSITIVE 204 199 155 122 87 smit:SMT_1475|3end_K02004_1458661..1458811_POSITIVE 204 198 172 53 30 smit:SMT_1099|3end_protein_tyrosine_phosphatase_1042044..1042194_NEGATIVE 204 169 127 64 20 smit:SMT_1069|3end_acetyl_xylan_esterase,_putative_1009595..1009745_POSITIVE