Origin IGS: tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 tgctttctaatatattaaggaaaaggtggtttatcttatcatagggcttcgctataatgcacacatcaaatgacgaaacaacctcaaacaggacatcttatgaagaaacttttaaaaaccacccttttagccacattaattggtacatcatttttaggagcaaatgca Mask Tandem Repeat Region ================================================ tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Find is-nt database================================================ Query_seq: AA00976:AA00977|AA00976:AA00977:conserved hypothetical protein:transcriptional regulator (LysR family):->->:682339..682506 168 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00976:AA00977|AA00976:AA00977:conserved hypothetical protein:transcriptional regulator (LysR family):->->:682339..682506 168 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00976:AA00977|AA00976:AA00977:conserved hypothetical protein:transcriptional regulator (LysR family):->->:682339..682506 168 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 78 End: 167 ............................................................................. M F E V V S S F D V C I I A K P Y D K I N H L F L N I L E S . Protein_Len: 38 Strand: - Start: 2 End: 115 . C K S R F I I Y W N I H S F P H N K F T E E Y S T R N S T T E D N S T H M M ..................................................... Protein_Len: 33 Strand: - Start: 1 End: 99 A N A G L F S T G I L T A L L T T K L L K K M L H G T Q P Q K T M ..................................................................... tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca 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: 83 Start: 111 End: 140 ..............................................................................................................GTTTATCTTATCATAGGGCTTCGCTATAAT............................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: AA00976:AA00977|AA00976:AA00977:conserved hypothetical protein:transcriptional regulator (LysR family):->->:682339..682506 168 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: aact_AA00976_AA00977|conserved hypothetical protein:transcriptional regulator (LysR family)|POSITIVE:POSITIVE|[682339,682506]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca tgcatttgctcctaaaaatgatgtaccaattaatgtggctaaaagggtggtttttaaaagtttcttcataagatgtcctgtttgaggttgtttcgtcatttgatgtgtgcattatagcgaagccctatgataagataaaccaccttttccttaatatattagaaagca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCAUUUGCUCCUAAAAAUGAUGUACCAAUUAAUGUGGCUAAAAGGGUGGUUUUUAAAAGUUUCUUCAUAAGAUGUCCUGUUUGAGGUUGUUUCGUCAUUUGAUGUGUGCAUUAUAGCGAAGCCCUAUGAUAAGAUAAACCACCUUUUCCUUAAUAUAUUAGAAAGCA ..(((((........))))).........((((((((....((((((((((((......((((..(((((......(((.....)))..(((((((....(((((....)))))..)))))))..)))))..))))))))))))))))......))))))))...... (-36.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUUUCUAAUAUAUUAAGGAAAAGGUGGUUUAUCUUAUCAUAGGGCUUCGCUAUAAUGCACACAUCAAAUGACGAAACAACCUCAAACAGGACAUCUUAUGAAGAAACUUUUAAAAACCACCCUUUUAGCCACAUUAAUUGGUACAUCAUUUUUAGGAGCAAAUGCA (((((.((((.........((((.((((((((.(((..((((((((....((......)).....................(((.....)))...))))))))))).........)))))))).)))).((((.......)))).........)))))))))...... (-30.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 129 81 207 160 aact:AA02368|5end_conserved_hypothetical_protein_1623544..1623774_POSITIVE 293 119 71 165 110 aact:AA00689|5end_GTP-binding_protein_470433..470663_POSITIVE 274 118 74 167 117 aact:AA01839|5end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1236870..1237100_POSITIVE 273 110 64 99 55 aact:AA01557|5end_recombinase_A_1044911..1045141_POSITIVE 272 118 76 146 108 aact:AA01088|5end_rare_lipoprotein_B_precursor_752903..753133_POSITIVE 270 109 63 178 116 aact:AA02904|5end_50S_ribosomal_protein_L31_2032290..2032520_POSITIVE 270 120 77 228 179 aact:AA02066|5end_hypothetical_protein_1405115..1405345_POSITIVE 269 111 76 131 99 aact:AA00340|5end_NADP(H)_oxidoreductase_(NAD(P)H_dehydrogenase_(quinone))_228797..229027_POSITIVE 265 118 71 132 93 aact:AA00313|5end_hypothetical_protein_212822..213052_POSITIVE 260 140 91 125 65 aact:AA01375|5end_hypothetical_protein_931020..931250_POSITIVE 260 120 71 210 151 aact:AA00809|5end_possible_oxidoreductase_553211..553441_POSITIVE 258 111 73 168 133 aact:AA01773|5end_hypothetical_protein_1194877..1195107_POSITIVE 256 89 45 99 38 aact:AA00167|5end_possible_amino-acid_transporter_(sodium-alanine_symporters)_118239..118469_POSITIVE 255 48 1 108 60 aact:AA02218|5end_deoxyribose-phosphate_aldolase_(fragment?)_1509758..1509988_POSITIVE 254 120 74 46 8 aact:AA01513|5end_hydrogen_peroxide-inducible_activator_1018835..1019065_POSITIVE 253 89 72 113 96 aact:AA00096|5end_L-asparaginase_II_precursor_71280..71510_POSITIVE 252 56 31 138 113 aact:AA00709|5end_metallocluster_assembly_(NifU_protein)_487378..487608_POSITIVE 249 55 14 107 62 aact:AA02289|5end_cell_division_protein_H,_a_metalloprotease_1559223..1559453_POSITIVE 249 125 89 66 22 aact:AA01376|5end_hypothetical_protein_931163..931393_POSITIVE 245 122 86 141 92 aact:AA02603|5end_possible_thioredoxin_trxA_homolog_1814635..1814865_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 272 150 103 143 91 aact:AA01662|3end_molybdopterin_biosynthesis_protein_1127422..1127572_POSITIVE 272 118 76 143 105 aact:AA01087|3end_DNA_polymerase_III,_delta_subunit_752980..753130_POSITIVE 269 111 76 116 84 aact:AA00339|3end_hypothetical_protein_228862..229012_POSITIVE 268 130 81 76 17 aact:AA02169|3end_hypothetical_protein_1484664..1484814_POSITIVE 264 119 73 143 90 aact:AA00329|3end_molybdopterin-guanine_dinucleotide_biosynthesis_protein_223347..223497_POSITIVE 260 140 91 122 62 aact:AA01374|3end_tRNA/rRNA_methyltransferase_931097..931247_POSITIVE 260 120 71 107 48 aact:AA00807|3end_fumarate_reductase_13_kD_hydrophobic_protein_553188..553338_POSITIVE 255 48 1 105 57 aact:AA02217|3end_deoxyribose-phosphate_aldolase_1509835..1509985_POSITIVE 252 56 31 75 50 aact:AA00708|3end_cysteine_desulfurase_487395..487545_POSITIVE 250 119 74 110 69 aact:AA01155|3end_hypothetical_protein_791411..791561_POSITIVE 249 96 58 150 104 aact:AA01841|3end_conserved_hypothetical_protein_1237863..1238013_POSITIVE 248 110 62 110 61 aact:AA02476|3end_conserved_hypothetical_protein_1712817..1712967_POSITIVE 243 120 73 79 28 aact:AA00674|3end_nicotinate-nucleotide-dimethylbenzimidazole_phosphoribosyltransferase_462585..462735_POSITIVE 242 120 71 110 65 aact:AA02698|3end_formate_dehydrogenase_H,_selenopolypeptide_subunit_1881425..1881575_POSITIVE 241 129 81 93 39 aact:AA01739|3end_conserved_hypothetical_protein_1176512..1176662_POSITIVE 239 55 18 132 91 aact:AA01216|3end_conserved_hypothetical_protein_832709..832859_POSITIVE 238 140 92 62 8 aact:AA01747|3end_single-stranded-DNA-specific_exonuclease_1183130..1183280_POSITIVE 238 50 1 115 54 aact:AA01474|3end_hypothetical_protein_990431..990581_POSITIVE 237 119 76 131 74 aact:AA00602|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_410251..410401_POSITIVE 236 126 83 142 83 aact:AA01642|3end_possible_iron(III)_ABC_transporter_1112075..1112225_POSITIVE