Origin IGS: taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta .........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 taaatcatctctgtgcgttgaaaaaaaatattttcatttgcaatgggcgctattctagcaaaaaacgaaaacatttgcgcaaaaaaattatgcgctcaaaaaagcgcccttttgatcaaatgatccaaaggacgttactatcccattgttatatttataaatatggaaaattcgaggctta Mask Tandem Repeat Region ================================================ taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Find is-nt database================================================ Query_seq: AA01974:AA01976|AA01974:AA01976:conserved hypothetical protein:colicin V production protein:->->:1336472..1336652 181 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: AA01974:AA01976|AA01974:AA01976:conserved hypothetical protein:colicin V production protein:->->:1336472..1336652 181 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: AA01974:AA01976|AA01974:AA01976:conserved hypothetical protein:colicin V production protein:->->:1336472..1336652 181 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: - Start: 62 End: 154 ............................................................. K I L L A S K Q A C L K K A C I N E N K A L I A G M A F S F M ........................... Protein_Len: 54 Strand: - Start: 3 End: 164 .. A E F K G Y K Y I Y C H S L L T R Q I M Q D F P R K K S R M I K K R L H K R K K S S Y R G N C I F I N K K M ................. taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta 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================================================ taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 91 HP_score: -8.0 Tail_Score: -5.0133 Start: 47 End: 78 Full_Region: AACAATGGGATAGTA ACGTCCTTTGGATC ATTT GATCAAAAGGGCGC TTTTTTGAGCGCATA ..............................................ACGTCCTTTGGATCATTTGATCAAAAGGGCGC....................................................................................................... TransTerm Strand: + Conf: 93 HP_score: -11.5 Tail_Score: -3.60316 Start: 48 End: 77 Full_Region: ACAATGGGATAGTAA CGTCCTTTGGATC ATTT GATCAAAAGGGCG CTTTTTTGAGCGCAT ...............................................CGTCCTTTGGATCATTTGATCAAAAGGGCG........................................................................................................ TransTerm Strand: - Conf: 77 HP_score: -9.3 Tail_Score: -3.28261 Start: 48 End: 77 Full_Region: atgcgctcaaaaaag cgcccttttgatc aaat gatccaaaggacg ttactatcccattgt ...............................................cgcccttttgatcaaatgatccaaaggacg........................................................................................................ Find igs database================================================ Query_seq: AA01974:AA01976|AA01974:AA01976:conserved hypothetical protein:colicin V production protein:->->:1336472..1336652 181 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgcttttttgagcgcataatttttttgcgcaaatgttttcgttttttgctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Intra-Species Hit: Count: 1 Min: 1 Max: 181 Len: 181 Subject: aact_AA01974_AA01976|conserved hypothetical protein:colicin V production protein|POSITIVE:POSITIVE|[1336472,1336652]|181 HSP 1 e-value: 6.0E-37 bit: 155.0 Len: 78 Query Start:1 Query End:78 Subject Strand: POSITIVE Subject Start: 1 Subject End: 78 taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgc....................................................................................................... taagcctcgaattttccatatttataaatataacaatgggatagtaacgtcctttggatcatttgatcaaaagggcgc....................................................................................................... HSP 2 e-value: 3.0E-11 bit: 69.9 Len: 59 Query Start:123 Query End:181 Subject Strand: POSITIVE Subject Start: 123 Subject End: 181 ..........................................................................................................................gctagaatagcgcccattgcaaatgaaaatannnnnnnncaacgcacagagatgattta ..........................................................................................................................gctagaatagcgcccattgcaaatgaaaatattttttttcaacgcacagagatgattta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCUCGAAUUUUCCAUAUUUAUAAAUAUAACAAUGGGAUAGUAACGUCCUUUGGAUCAUUUGAUCAAAAGGGCGCUUUUUUGAGCGCAUAAUUUUUUUGCGCAAAUGUUUUCGUUUUUUGCUAGAAUAGCGCCCAUUGCAAAUGAAAAUAUUUUUUUUCAACGCACAGAGAUGAUUUA ...((((((((..((((((..((((....))))..))))))......((((((((.((((....)))).))))))))....)))))).))...((((((.((((.(((((((((((((...(((................))))))))))))))))........)))).))))))...... (-44.69) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUCAUCUCUGUGCGUUGAAAAAAAAUAUUUUCAUUUGCAAUGGGCGCUAUUCUAGCAAAAAACGAAAACAUUUGCGCAAAAAAAUUAUGCGCUCAAAAAAGCGCCCUUUUGAUCAAAUGAUCCAAAGGACGUUACUAUCCCAUUGUUAUAUUUAUAAAUAUGGAAAAUUCGAGGCUUA ..............((.(((((.....((((((......((((((((.((((...)))).................(((((.........))))).......((((.(((((.((((....)))).))))).)))).....)))))))).........))))))......))))).))... (-42.36) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 78 33 211 166 aact:AA02785|5end_ribose_ABC_transporter,_permease_1951808..1952038_POSITIVE 325 90 44 214 170 aact:AA00684|5end_adenylosuccinate_synthase_467486..467716_POSITIVE 317 88 51 173 138 aact:AA01286|5end_5,10-methylenetetrahydrofolate_dehydrogenase_(bifunctional_protein)_870309..870539_POSITIVE 287 88 48 146 99 aact:AA00894|5end_selenium_transferase_(Cysteinyl-tRNA(Sec)_selenium_transferase)_619879..620109_POSITIVE 283 110 62 209 152 aact:AA01590|5end_hypothetical_protein_1070766..1070996_POSITIVE 282 120 71 81 36 aact:AA00581|5end_thiosulfate_sulfurtransferase_(rhodanese)_397605..397835_POSITIVE 279 104 62 183 145 aact:AA00759|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_I_520603..520833_POSITIVE 279 104 62 65 27 aact:AA00758|5end_hypothetical_protein_520485..520715_POSITIVE 279 144 103 144 98 aact:AA00382|5end_hypothetical_protein_258593..258823_POSITIVE 276 110 68 45 1 aact:AA01879|5end_glutamyl-tRNA_reductase_1265717..1265947_POSITIVE 273 137 91 105 46 aact:AA01779|5end_molybdenum_ABC_transporter,_ATP-binding_protein_1200036..1200266_POSITIVE 273 142 101 123 85 aact:AA00603|5end_undecaprenyl_pyrophosphate_synthetase_(UPPS)_410283..410513_POSITIVE 271 90 41 170 125 aact:AA01097|5end_conserved_hypothetical_protein_757189..757419_POSITIVE 269 110 64 110 67 aact:AA00425|5end_N-terminal_region_of_competence_protein_M_287295..287525_POSITIVE 268 116 75 74 40 aact:AA02662|5end_hypothetical_protein_1853283..1853513_POSITIVE 268 136 95 221 177 aact:AA00109|5end_conserved_hypothetical_protein_78582..78812_POSITIVE 266 116 78 83 43 aact:AA00458|5end_nickel-binding_periplasmic_protein_319374..319604_POSITIVE 265 142 104 37 3 aact:AA01599|5end_phosphocarrier_protein_HPr_1080110..1080340_POSITIVE 265 92 52 63 16 aact:AA01270|5end_hydrolase_(possible_2-haloalkanoic_acid_dehalogenase_I)_863317..863547_POSITIVE 263 142 101 150 100 aact:AA00449|5end_conserved_hypothetical_protein_312996..313226_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 387 78 33 122 77 aact:AA02784|3end_NAD+_dependent_acetaldehyde-alcohol_dehydrogenase,_iron-containing_1951799..1951949_POSITIVE 357 150 101 75 24 aact:AA01873|3end_mannose-6-phosphate_isomerase_1261940..1262090_POSITIVE 325 90 44 123 79 aact:AA00682|3end_S-adenosylmethionine-dependent_methyltransferase_467475..467625_POSITIVE 317 88 51 78 43 aact:AA01284|3end_heat_shock_protein_(hsp60)_870294..870444_POSITIVE 314 137 98 135 99 aact:AA01146|3end_conserved_hypothetical_protein_784770..784920_POSITIVE 287 88 48 146 99 aact:AA00892|3end_selenocysteine-specific_elongation_factor_(SelB_translation_factor)_619959..620109_POSITIVE 284 77 48 43 14 aact:AA01974|3end_conserved_hypothetical_protein_1336411..1336561_POSITIVE 279 104 62 39 1 aact:AA00757|3end_aerobic_respiration_sensor-response_protein_520539..520689_POSITIVE 278 89 41 97 50 aact:AA01962|3end_recombination_protein_rec2_1328706..1328856_POSITIVE 276 125 81 146 106 aact:AA00168|3end_possible_sigma_54_modulation_protein_120240..120390_POSITIVE 272 143 103 132 89 aact:AA00398|3end_protein-tyrosine-phosphatase_(PTPase)_268018..268168_POSITIVE 269 110 64 138 95 aact:AA00424|3end_hypothetical_protein_287403..287553_POSITIVE 268 116 75 58 24 aact:AA02659|3end_conserved_hypothetical_protein_1853347..1853497_POSITIVE 265 92 52 79 32 aact:AA01269|3end_hypothetical_protein_863413..863563_POSITIVE 263 142 101 132 82 aact:AA00448|3end_C-terminal_region_of_competence_protein_M_313058..313208_POSITIVE 261 106 70 150 119 aact:AA00574|3end_regulatory_protein_392381..392531_POSITIVE 260 145 102 148 106 aact:AA02119|3end_hypothetical_protein_1446580..1446730_POSITIVE 258 133 101 140 104 aact:AA01597|3end_oligoribonuclease_1078936..1079086_POSITIVE 257 77 32 105 50 aact:AA02666|3end_DNA_helicase_II_1856583..1856733_POSITIVE 256 138 96 104 64 aact:AA02338|3end_conserved_hypothetical_protein;_possible_integral_membrane_protein_1598885..1599035_POSITIVE