Origin IGS: taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca .........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 tgatgatgttatctgtggggttatctgaaagcttccacctgtttccatagacaattcaatacgagggggggagaattttctctcctccccccccaaaaaaaaatggatacaaaggttcagggtttttactcggtttcttctttgtcataccggactgtccgtgcattgtttgatggcacggacagcatggctgtcgtgcttttcggtcatgagatta Mask Tandem Repeat Region ================================================ taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Find is-nt database================================================ Query_seq: TF0655:TF0656|TF0655:TF0656:outer membrane protein:acetyltransferase, possible GNAT family:->->:701968..702184 217 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0655:TF0656|TF0655:TF0656:outer membrane protein:acetyltransferase, possible GNAT family:->->:701968..702184 217 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0655:TF0656|TF0655:TF0656:outer membrane protein:acetyltransferase, possible GNAT family:->->:701968..702184 217 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 52 End: 159 ................................................... M H G Q S G M T K K K P S K N P E P L Y P F F F G G G G E K I L P P S Y .......................................................... Protein_Len: 40 Strand: + Start: 98 End: 217 ................................................................................................. M N L C I H F F L G G E E R K F S P P R I E L S M E T G G S F Q I T P Q I T S S Protein_Len: 39 Strand: - Start: 48 End: 164 ............................................... V I C P C D P I V F F F G L L F G S G K Y G N K K P P P P S F I R G G E Y Q M ..................................................... Protein_Len: 60 Strand: - Start: 2 End: 205 . A M S D T G D F L A R V T R Y S L S S V S Y F G Q V K T D M K K Q P P L L S F E G G R T N F Q R H F C T S A K L Y G W M ............ Protein_Len: 57 Strand: - Start: 1 End: 171 L R M V S F C S L W A T R A M L C H V S L G T H C L L F R T F V R F R Q I W K K K P P S S L F N E G G R I S N D M .............................................. taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca 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================================================ taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 95 HP_score: -11.8 Tail_Score: -4.21194 Start: 19 End: 42 Full_Region: gtgcattgtttgatg gcacggacagc atg gctgtcgtgc ttttcggtcatgaga ..................gcacggacagcatggctgtcgtgc............................................................................................................................................................................... TransTerm Strand: + Conf: 68 HP_score: -8.9 Tail_Score: -3.19913 Start: 123 End: 156 Full_Region: GTATCCATTTTTTTT TGGGGGGGGAGGA GAGAAAA TTCTCCCCCCCTCG TATTGAATTGTCTAT ..........................................................................................................................TGGGGGGGGAGGAGAGAAAATTCTCCCCCCCTCG............................................................. TransTerm Strand: + Conf: 84 HP_score: -13.9 Tail_Score: -2.78505 Start: 125 End: 153 Full_Region: ATCCATTTTTTTTTG GGGGGGGAGGA GAGAAAA TTCTCCCCCCC TCGTATTGAATTGTC ............................................................................................................................GGGGGGGAGGAGAGAAAATTCTCCCCCCC................................................................ TransTerm Strand: + Conf: 76 HP_score: -12.1 Tail_Score: -2.51225 Start: 126 End: 155 Full_Region: TCCATTTTTTTTTGG GGGGGGAGGAGAG AAAA TTCTCCCCCCCTC GTATTGAATTGTCTA .............................................................................................................................GGGGGGAGGAGAGAAAATTCTCCCCCCCTC.............................................................. Find igs database================================================ Query_seq: TF0655:TF0656|TF0655:TF0656:outer membrane protein:acetyltransferase, possible GNAT family:->->:701968..702184 217 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatccatttttttttggggggggaggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Intra-Species Hit: Count: 1 Min: 1 Max: 217 Len: 217 Subject: tfor_TF0655_TF0656|outer membrane protein:acetyltransferase, possible GNAT family|POSITIVE:POSITIVE|[701968,702184]|217 HSP 1 e-value: 2.0E-58 bit: 226.0 Len: 114 Query Start:1 Query End:114 Subject Strand: POSITIVE Subject Start: 1 Subject End: 114 taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatcca....................................................................................................... taatctcatgaccgaaaagcacgacagccatgctgtccgtgccatcaaacaatgcacggacagtccggtatgacaaagaagaaaccgagtaaaaaccctgaacctttgtatcca....................................................................................................... HSP 2 e-value: 4.0E-29 bit: 129.0 Len: 86 Query Start:132 Query End:217 Subject Strand: POSITIVE Subject Start: 132 Subject End: 217 ...................................................................................................................................aggagagaaaattctnnnnnnntcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca ...................................................................................................................................aggagagaaaattctccccccctcgtattgaattgtctatggaaacaggtggaagctttcagataaccccacagataacatcatca Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUCUCAUGACCGAAAAGCACGACAGCCAUGCUGUCCGUGCCAUCAAACAAUGCACGGACAGUCCGGUAUGACAAAGAAGAAACCGAGUAAAAACCCUGAACCUUUGUAUCCAUUUUUUUUUGGGGGGGGAGGAGAGAAAAUUCUCCCCCCCUCGUAUUGAAUUGUCUAUGGAAACAGGUGGAAGCUUUCAGAUAACCCCACAGAUAACAUCAUCA .....(((((.(((....((......))...(((((((((((...........))))))))))).))))))))........................((((((((((((.(((((...(((.(((((((((((((.......))))))))))).))....)))......))))).))))).)).....)))))...........(((......))). (-64.10) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGAUGAUGUUAUCUGUGGGGUUAUCUGAAAGCUUCCACCUGUUUCCAUAGACAAUUCAAUACGAGGGGGGGAGAAUUUUCUCUCCUCCCCCCCCAAAAAAAAAUGGAUACAAAGGUUCAGGGUUUUUACUCGGUUUCUUCUUUGUCAUACCGGACUGUCCGUGCAUUGUUUGAUGGCACGGACAGCAUGGCUGUCGUGCUUUUCGGUCAUGAGAUUA .((((((.(((....))).)))))).((((((((..((((((.(((((.((....)).....(.(((((((((...........))))))))))........))))).))..))))...))))))))...((((..(......)....))))..(((((((((((((....))).))))))))))((((((((..........))))))))...... (-70.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 391 80 32 75 33 tfor:TF1019|5end_N-acetylmuramoyl-L-alanine_amidase_1075367..1075597_POSITIVE 380 60 13 64 7 tfor:TF1462|5end_erythronate-4-phosphate_dehydrogenase_1552184..1552414_POSITIVE 371 158 122 56 22 tfor:TF2946|5end_conserved_hypothetical_protein;_possible_ATPase_3151750..3151980_POSITIVE 370 59 11 222 181 tfor:TF1322|5end_conserved_hypothetical_protein;_possible_surface_protein_1401864..1402094_POSITIVE 360 48 6 220 175 tfor:TF0970|5end_2-keto-3-deoxygluconate_kinase_1020396..1020626_POSITIVE 359 69 22 161 114 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 357 69 21 109 66 tfor:TF2017|5end_conserved_hypothetical_protein_2173504..2173734_POSITIVE 353 60 11 56 11 tfor:TF0329|5end_membrane-bound_lytic_murein_transglycosylase_D_355189..355419_POSITIVE 352 67 24 218 156 tfor:TF2381|5end_muramidase/hemagglutinin_2545757..2545987_POSITIVE 352 56 13 62 19 tfor:TF1402|5end_cation_efflux_system_protein_1477922..1478152_POSITIVE 346 69 23 49 9 tfor:TF0763|5end_chromate_transport_protein_809675..809905_POSITIVE 342 68 21 225 177 tfor:TF2443|5end_amidophosphoribosyl-transferase_2620287..2620517_POSITIVE 342 70 22 201 147 tfor:TF0088|5end_ABC_transporter,_permease_component_94299..94529_POSITIVE 340 68 26 71 10 tfor:TF2675|5end_conserved_hypothetical_protein_2848864..2849094_POSITIVE 340 70 21 228 170 tfor:TF1300|5end_conserved_hypothetical_protein_1382389..1382619_POSITIVE 339 70 22 191 138 tfor:TF2533|5end_adenylosuccinate_synthetase_2715666..2715896_POSITIVE 339 46 3 148 99 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 339 188 143 51 1 tfor:TF2045|5end_aminoacyl-histidine_dipeptidase_2206114..2206344_POSITIVE 338 67 27 72 36 tfor:TF2342|5end_glutathione_peroxidase_2505963..2506193_POSITIVE 335 42 1 166 124 tfor:TF1181|5end_methylated-DNA--[protein]-cysteine_S-methyltransferase_1267522..1267752_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 450 139 96 67 22 tfor:TF1514|3end_hypothetical_protein_1626094..1626244_POSITIVE 406 139 97 66 20 tfor:TF1519|3end_hypothetical_protein_1628022..1628172_POSITIVE 366 68 25 61 11 tfor:TF1461|3end_DNA-damage-inducible_protein_F_1552253..1552403_POSITIVE 362 186 141 58 9 tfor:TF2687|3end_iron-regulated_ABC-type_transporter_membrane_component_2864962..2865112_POSITIVE 358 68 22 42 1 tfor:TF1834|3end_3-isopropylmalate_dehydrogenase_1984311..1984461_POSITIVE 353 60 11 53 8 tfor:TF0328|3end_conserved_hypothetical_protein_355266..355416_POSITIVE 352 56 13 85 42 tfor:TF1403|3end_hypothetical_protein_1478025..1478175_POSITIVE 347 159 111 103 52 tfor:TF0779|3end_possible_outer_membrane_protein_831874..832024_POSITIVE 346 69 23 49 9 tfor:TF0762|3end_chromate_transport_protein_809755..809905_POSITIVE 343 70 25 97 55 tfor:TF1740|3end_hypothetical_protein_1869192..1869342_POSITIVE 342 68 21 129 81 tfor:TF2442|3end_heat_shock_protein_60_2620271..2620421_POSITIVE 339 46 3 135 86 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 338 67 27 56 20 tfor:TF2341|3end_hypothetical_protein_2506027..2506177_POSITIVE 333 69 21 75 18 tfor:TF2846|3end_cobyric_acid_synthase_3036469..3036619_POSITIVE 333 68 21 150 84 tfor:TF0833|3end_conserved_hypothetical_protein_889052..889202_POSITIVE 327 140 96 72 37 tfor:TF2305|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_2462693..2462843_POSITIVE 326 67 22 151 100 tfor:TF2532|3end_ferric-uptake_regulator_2715708..2715858_POSITIVE 326 157 122 70 22 tfor:TF0625|3end_hypothetical_protein_661945..662095_POSITIVE 325 155 113 79 36 tfor:TF1597|3end_TatD_family_protein_1713418..1713568_POSITIVE 323 68 25 63 19 tfor:TF0655|3end_outer_membrane_protein_701907..702057_POSITIVE