Origin IGS: acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 ataatcttcaatcgccacatctctctccaaaaattcgtattctcattattatagcataaaatggtctttttggcaccttcagcctcaaagattacaaaaagggcaaaagatgatatagtagtgatagtataaatgttctggaggtttgt Mask Tandem Repeat Region ================================================ acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Find is-nt database================================================ Query_seq: SSA_0574:SSA_0575|SSA_0574:SSA_0575:YdjX protein, putative:Hydrolase, HAD superfamily, putative:<-->:569518..569666 149 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_0574:SSA_0575|SSA_0574:SSA_0575:YdjX protein, putative:Hydrolase, HAD superfamily, putative:<-->:569518..569666 149 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_0574:SSA_0575|SSA_0574:SSA_0575:YdjX protein, putative:Hydrolase, HAD superfamily, putative:<-->:569518..569666 149 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Predict ORF larger than 30AA ================================================ Protein_Len: 44 Strand: + Start: 16 End: 147 ............... M Y T I T T I S S F A L F V I F E A E G A K K T I L C Y N N E N T N F W R E M W R L K I .. Protein_Len: 35 Strand: - Start: 35 End: 139 .................................. I M K Q G K Q L R Q P Q L H W F S W K I S Y Y H S Y S N K S L S T A M .......... acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat 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: 87 Start: 73 End: 102 ........................................................................GGTGCCAAAAAGACCATTTTATGCTATAAT............................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SSA_0574:SSA_0575|SSA_0574:SSA_0575:YdjX protein, putative:Hydrolase, HAD superfamily, putative:<-->:569518..569666 149 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Intra-Species Hit: Count: 1 Min: 1 Max: 149 Len: 149 Subject: NC_009009_SSA_0574_SSA_0575|YdjX protein, putative:Hydrolase, HAD superfamily, putative|NEGATIVE:POSITIVE|[569518,569666]|149 HSP 1 e-value: 2.0E-79 bit: 295.0 Len: 149 Query Start:1 Query End:149 Subject Strand: POSITIVE Subject Start: 1 Subject End: 149 acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat acaaacctccagaacatttatactatcactactatatcatcttttgccctttttgtaatctttgaggctgaaggtgccaaaaagaccattttatgctataataatgagaatacgaatttttggagagagatgtggcgattgaagattat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAAACCUCCAGAACAUUUAUACUAUCACUACUAUAUCAUCUUUUGCCCUUUUUGUAAUCUUUGAGGCUGAAGGUGCCAAAAAGACCAUUUUAUGCUAUAAUAAUGAGAAUACGAAUUUUUGGAGAGAGAUGUGGCGAUUGAAGAUUAU ......((((((((.(((..((...(((.((.((((.(((....((..(((((((..((((((......))))))..)))))))..))....))).)))).)).)))...))..)))))))))))........................ (-28.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAUCUUCAAUCGCCACAUCUCUCUCCAAAAAUUCGUAUUCUCAUUAUUAUAGCAUAAAAUGGUCUUUUUGGCACCUUCAGCCUCAAAGAUUACAAAAAGGGCAAAAGAUGAUAUAGUAGUGAUAGUAUAAAUGUUCUGGAGGUUUGU ................(((...(.(((((...(((..((((.(((((((((((.(((....((.((((((((....(((........)))....)))))))).))....))).))))))))))).))))..)))....))))))..))) (-34.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 863 90 41 181 132 NC_009009:SSA_0574|5end_YdjX_protein,_putative_569427..569657_NEGATIVE 355 88 41 105 53 NC_009009:SSA_0364|5end_Serine/threonine:Na+_symporter,_putative_356348..356578_NEGATIVE 316 87 41 50 14 NC_009009:SSA_1122|5end_Thioredoxin_family_protein,_putative_1147871..1148101_POSITIVE 302 88 41 219 168 NC_009009:SSA_1998|5end_Trigger_factor,_putative_1996331..1996561_NEGATIVE 295 77 36 128 87 NC_009009:SSA_0075|5end_ABC_sugar_transporter,_permease_protein,_putative_78963..79193_POSITIVE 282 84 41 107 64 NC_009009:SSA_0229|5end_hypothetical_protein_223535..223765_POSITIVE 280 80 37 129 88 NC_009009:SSA_2330|5end_Acetyltransferase,_putative_2333655..2333885_NEGATIVE 277 88 41 64 11 NC_009009:SSA_1573|5end_hypothetical_protein_1576536..1576766_NEGATIVE 276 79 37 59 15 NC_009009:SSA_1856|5end_hypothetical_protein_1852208..1852438_NEGATIVE 276 79 37 216 172 NC_009009:SSA_1855|5end_hypothetical_protein_1852051..1852281_NEGATIVE 270 70 23 72 25 NC_009009:SSA_0807|5end_GTP-binding_protein,_putative_789449..789679_POSITIVE 269 78 41 189 144 NC_009009:SSA_1332|5end_hypothetical_protein_1347645..1347875_NEGATIVE 266 87 46 53 3 NC_009009:SSA_1234|5end_5'-nucleotidase,_putative_1259795..1260025_NEGATIVE 265 50 7 62 13 NC_009009:SSA_1824|5end_hypothetical_protein_1812746..1812976_NEGATIVE 258 80 36 133 87 NC_009009:SSA_2302|5end_Type_IV_fimbrial_biogenesis_protein,_prepilin_cysteine_protease_(C20)_PilD,_putative_2304044..2304274_NEGATIVE 256 90 41 152 93 NC_009009:SSA_2098|5end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103617..2103847_NEGATIVE 256 99 58 67 24 NC_009009:SSA_1634|5end_Heme_utilization/adhesion_exoprotein,_putative_1637062..1637292_NEGATIVE 254 84 46 71 30 NC_009009:SSA_0584|5end_hypothetical_protein_575806..576036_POSITIVE 252 78 32 176 134 NC_009009:SSA_1017|5end_hypothetical_protein_1022072..1022302_POSITIVE 252 47 6 139 97 NC_009009:SSA_0747|5end_DD-carboxypeptidase,_putative_727936..728166_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 302 88 41 139 88 NC_009009:SSA_1999|3end_hypothetical_protein_1996411..1996561_NEGATIVE 295 87 49 35 4 NC_009009:SSA_1121|3end_Cytochrome_C-type_biogenesis_protein,_putative_1147936..1148086_POSITIVE 295 77 36 60 19 NC_009009:SSA_0074|3end_ABC_transporter_substrate-binding_protein-sugar_transport,_putative_78975..79125_POSITIVE 282 84 41 66 23 NC_009009:SSA_0228|3end_hypothetical_protein_223574..223724_POSITIVE 280 80 37 88 47 NC_009009:SSA_2331|3end_D-alanine_transfer_protein,_putative_2333696..2333846_NEGATIVE 269 78 41 141 96 NC_009009:SSA_1333|3end_hypothetical_protein_1347693..1347843_NEGATIVE 263 78 35 143 100 NC_009009:SSA_1044|3end_Homoserine_kinase,_putative_1060799..1060949_POSITIVE 258 80 36 64 18 NC_009009:SSA_2303|3end_hypothetical_protein_2304113..2304263_NEGATIVE 256 90 41 148 89 NC_009009:SSA_2099|3end_ABC-type_arginine/histidine_transporter,_permease_protein,_putative_2103621..2103771_NEGATIVE 254 87 41 54 5 NC_009009:SSA_0451|3end_Conserved_uncharacterized_protein_451636..451786_POSITIVE 249 79 36 75 31 NC_009009:SSA_1870|3end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase,_putative_1865600..1865750_NEGATIVE 248 80 39 131 81 NC_009009:SSA_0212|3end_Phenylalanyl-tRNA_synthetase,_beta_subunit,_putative_209079..209229_POSITIVE 246 79 32 137 97 NC_009009:SSA_0467|3end_Cobalt-precorrin-6A_synthase_[deacetylating],_putative_471795..471945_POSITIVE 244 78 40 144 102 NC_009009:SSA_1242|3end_Dihydroorotate_dehydrogenase_B,_putative_1266448..1266598_NEGATIVE 241 87 47 147 107 NC_009009:SSA_1631|3end_Sortase-like_protein,_putative_1631651..1631801_NEGATIVE 235 80 31 139 93 NC_009009:SSA_0858|3end_DTDP-L-rhamnose_synthase,_putative_846446..846596_POSITIVE 234 50 2 86 44 NC_009009:SSA_1672|3end_hypothetical_protein_1670291..1670441_NEGATIVE 233 80 32 123 65 NC_009009:SSA_2123|3end_Dimethyladenosine_transferase,_putative_2127664..2127814_NEGATIVE 232 69 23 145 102 NC_009009:SSA_1153|3end_HemK_protein,_putative_1182748..1182898_POSITIVE 229 77 37 127 81 NC_009009:SSA_1772|3end_hypothetical_protein_1758895..1759045_NEGATIVE