Origin IGS: taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata .........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 tataacctaaattggaaatatattaactaactggttaatttaaaacacaaaaatgtttattcttgtattttttcttagtcaccactcgaaggtgattactgaatctatcggcattatgagccagtttcacaaagtctgatagacgactaaataccttgactcaaattaaatgcctttccgagataatcttgtgaaaggcatttcttagggtggatctttttta Mask Tandem Repeat Region ================================================ taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Find is-nt database================================================ Query_seq: AA00020:AA00021|AA00020:AA00021:conserved hypothetical protein:DNA helicase IV:->->:14547..14769 223 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA00020:AA00021|AA00020:AA00021:conserved hypothetical protein:DNA helicase IV:->->:14547..14769 223 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA00020:AA00021|AA00020:AA00021:conserved hypothetical protein:DNA helicase IV:->->:14547..14769 223 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 94 End: 186 ............................................................................................. M K L A H N A D R F S N H L R V V T K K K Y K N K H F C V L N ..................................... taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata 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================================================ taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -10.9 Tail_Score: -4.18488 Start: 24 End: 53 Full_Region: ttgactcaaattaaa tgcctttccgaga taa tcttgtgaaaggca tttcttagggtggat .......................tgcctttccgagataatcttgtgaaaggca.......................................................................................................................................................................... Find igs database================================================ Query_seq: AA00020:AA00021|AA00020:AA00021:conserved hypothetical protein:DNA helicase IV:->->:14547..14769 223 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Intra-Species Hit: Count: 1 Min: 1 Max: 223 Len: 223 Subject: aact_AA00020_AA00021|conserved hypothetical protein:DNA helicase IV|POSITIVE:POSITIVE|[14547,14769]|223 HSP 1 e-value: 1.0E-123 bit: 442.0 Len: 223 Query Start:1 Query End:223 Subject Strand: POSITIVE Subject Start: 1 Subject End: 223 taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata taaaaaagatccaccctaagaaatgcctttcacaagattatctcggaaaggcatttaatttgagtcaaggtatttagtcgtctatcagactttgtgaaactggctcataatgccgatagattcagtaatcaccttcgagtggtgactaagaaaaaatacaagaataaacatttttgtgttttaaattaaccagttagttaatatatttccaatttaggttata Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAAGAUCCACCCUAAGAAAUGCCUUUCACAAGAUUAUCUCGGAAAGGCAUUUAAUUUGAGUCAAGGUAUUUAGUCGUCUAUCAGACUUUGUGAAACUGGCUCAUAAUGCCGAUAGAUUCAGUAAUCACCUUCGAGUGGUGACUAAGAAAAAAUACAAGAAUAAACAUUUUUGUGUUUUAAAUUAACCAGUUAGUUAAUAUAUUUCCAAUUUAGGUUAUA ...........((((((...(((((((((((.(.((.....)).))))))))))))..........(((((..(((.(.(((((((.(...((((((.......))))))..).)))))))..).)))..)))))..)).)))).(((((..(((((((((((((....)))))))))))))..((((((......))))))..........)))))...... (-53.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAACCUAAAUUGGAAAUAUAUUAACUAACUGGUUAAUUUAAAACACAAAAAUGUUUAUUCUUGUAUUUUUUCUUAGUCACCACUCGAAGGUGAUUACUGAAUCUAUCGGCAUUAUGAGCCAGUUUCACAAAGUCUGAUAGACGACUAAAUACCUUGACUCAAAUUAAAUGCCUUUCCGAGAUAAUCUUGUGAAAGGCAUUUCUUAGGGUGGAUCUUUUUUA .....((......))...((.(((((((....))))))).))......(((((.(((((((((.((((((..((.((((((((.......)))))))).....(((((((((.((.((((.....)))).)).).)))))))).))..)))))).............(((((((((((((((.....)))).)))))))))))...))))))))).))))).. (-54.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 319 146 101 229 188 aact:AA01756|5end_cobalt_membrane_transport_protein_1186475..1186705_POSITIVE 304 140 91 149 95 aact:AA01978|5end_hypothetical_protein_1337055..1337285_POSITIVE 294 149 101 55 10 aact:AA00652|5end_arginyl-tRNA_synthetase_(arginine--tRNA_ligase)_445718..445948_POSITIVE 291 117 72 171 132 aact:AA00553|5end_NapD_component_of_periplasmic_nitrate_reductase_379851..380081_POSITIVE 288 147 102 200 158 aact:AA01154|5end_sec-independent_protein_translocase_protein_790832..791062_POSITIVE 287 145 103 109 74 aact:AA01066|5end_conserved_hypothetical_protein_738380..738610_POSITIVE 282 134 96 86 38 aact:AA00310|5end_conserved_hypothetical_protein_210193..210423_POSITIVE 276 115 78 56 24 aact:AA01963|5end_dnaK_suppressor_protein_1328924..1329154_POSITIVE 276 138 94 189 147 aact:AA01730|5end_conserved_hypothetical_protein_(possible_transcriptional_regulator)_1168725..1168955_POSITIVE 276 138 94 49 7 aact:AA01729|5end_hypothetical_protein_1168585..1168815_POSITIVE 276 144 102 62 21 aact:AA01141|5end_conserved_hypothetical_protein_(possible_component_of_anaerobic_dehydrogenase/oxidoreductase)_782497..782727_POSITIVE 275 64 24 205 175 aact:AA01446|5end_conserved_hypothetical_protein_970151..970381_POSITIVE 274 124 81 207 166 aact:AA01845|5end_gamma-glutamyltranspeptidase_precursor_1239841..1240071_POSITIVE 270 150 111 44 1 aact:AA02103|5end_D-alanyl-D-alanine-endopeptidase;_penicillin-binding_protein_7_1431105..1431335_POSITIVE 270 76 32 72 22 aact:AA01682|5end_molybdate_ABC_transporter_protein_1135568..1135798_POSITIVE 268 147 103 178 136 aact:AA00533|5end_conserved_hypothetical_protein_365323..365553_POSITIVE 267 145 101 171 123 aact:AA02514|5end_esterase/lipase_1747501..1747731_POSITIVE 265 146 112 180 145 aact:AA02524|5end_orotidine_5'-phosphate_decarboxylase_1753313..1753543_POSITIVE 261 118 77 147 111 aact:AA00887|5end_hypothetical_protein_616739..616969_POSITIVE 260 138 93 69 22 aact:AA02955|5end_trigger_factor_2067022..2067252_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 304 140 91 146 92 aact:AA01976|3end_colicin_V_production_protein_1337132..1337282_POSITIVE 293 56 21 70 35 aact:AA00020|3end_conserved_hypothetical_protein_14486..14636_POSITIVE 291 117 72 134 95 aact:AA00552|3end_periplasmic_nitrate_reductase_precursor_379894..380044_POSITIVE 287 145 103 41 6 aact:AA01064|3end_conserved_hypothetical_protein_(possible_aminomethyltransferase)_738392..738542_POSITIVE 282 134 96 80 32 aact:AA00309|3end_3-hydroxyisobutyrate_dehydrogenase;_2-hydroxy-3-oxopropionate_reductase_210267..210417_POSITIVE 279 124 90 51 20 aact:AA01127|3end_energy_transducer_protein_773520..773670_POSITIVE 276 138 94 49 7 aact:AA01728|3end_conserved_hypothetical_protein(related_to_HipA_protein)_1168665..1168815_POSITIVE 275 64 24 81 51 aact:AA01445|3end_hypothetical_protein_970107..970257_POSITIVE 274 124 81 116 75 aact:AA01843|3end_sensor_protein;_probable_two-component_system_sensor_histidine_kinase_1239830..1239980_POSITIVE 270 150 111 47 4 aact:AA02101|3end_penicillin-binding_protein_7_1431188..1431338_POSITIVE 270 76 32 94 44 aact:AA01681|3end_molybdate-binding_periplasmic_protein_1135670..1135820_POSITIVE 267 145 101 84 36 aact:AA02513|3end_seqA_protein_1747494..1747644_POSITIVE 258 150 109 142 102 aact:AA01598|3end_conserved_hypothetical_protein_1079966..1080116_POSITIVE 256 144 103 93 56 aact:AA02421|3end_conserved_hypothetical_protein_1667300..1667450_POSITIVE 249 144 103 143 97 aact:AA01193|3end_AMP-binding_enzyme_819672..819822_POSITIVE 249 119 77 112 70 aact:AA00475|3end_conserved_hypothetical_protein_(possible_N6-adenine-specific_methylase)_332282..332432_POSITIVE 247 150 101 149 98 aact:AA00234|3end_collagen_adhesin_168641..168791_POSITIVE 246 115 79 127 94 aact:AA01611|3end_anthranilate_synthase_component_II_1089619..1089769_POSITIVE 245 87 43 55 3 aact:AA00601|3end_hypothetical_protein_409119..409269_POSITIVE 244 145 101 149 102 aact:AA00931|3end_elongation_factor_Tu_(tufA)_643181..643331_POSITIVE