Origin IGS: agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gctgttctcttgggaagtatgtgaaaattcctttagtggttctccatcggcttgcgcgaaattctctatctttgatagattgttgatcttgagaccataagtttttgtggctctgtgcatcgacgacttcgatcatcaataacaataaacgatcagtagcact Mask Tandem Repeat Region ================================================ agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Find is-nt database================================================ Query_seq: PG1885:PG1886|PG1885:PG1886:polyphosphate kinase:GTP-binding protein HflX:<-<-:1983243..1983405 163 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1885:PG1886|PG1885:PG1886:polyphosphate kinase:GTP-binding protein HflX:<-<-:1983243..1983405 163 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1885:PG1886|PG1885:PG1886:polyphosphate kinase:GTP-binding protein HflX:<-<-:1983243..1983405 163 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 19 End: 162 .................. M L L M I E V V D A Q S H K N L W S Q D Q Q S I K D R E F R A S R W R T T K G I F T Y F P R E Q . Protein_Len: 40 Strand: + Start: 44 End: 163 ........................................... M H R A T K T Y G L K I N N L S K I E N F A Q A D G E P L K E F S H T S Q E N S Protein_Len: 32 Strand: - Start: 67 End: 162 .................................................................. P R L I L L R D F I S F K A C A S P S G S F S N E C V E W S F M . agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc 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================================================ agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 71 HP_score: -7.2 Tail_Score: -3.82084 Start: 85 End: 99 Full_Region: gcttgcgcgaaattc tctatc ttt gataga ttgttgatcttgaga ....................................................................................tctatctttgataga................................................................ Find igs database================================================ Query_seq: PG1885:PG1886|PG1885:PG1886:polyphosphate kinase:GTP-binding protein HflX:<-<-:1983243..1983405 163 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Intra-Species Hit: Count: 1 Min: 1 Max: 163 Len: 163 Subject: NC_002950_PG1885_PG1886|polyphosphate kinase:GTP-binding protein HflX|NEGATIVE:NEGATIVE|[1983243,1983405]|163 HSP 1 e-value: 1.0E-87 bit: 323.0 Len: 163 Query Start:1 Query End:163 Subject Strand: POSITIVE Subject Start: 1 Subject End: 163 agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc agtgctactgatcgtttattgttattgatgatcgaagtcgtcgatgcacagagccacaaaaacttatggtctcaagatcaacaatctatcaaagatagagaatttcgcgcaagccgatggagaaccactaaaggaattttcacatacttcccaagagaacagc Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUGCUACUGAUCGUUUAUUGUUAUUGAUGAUCGAAGUCGUCGAUGCACAGAGCCACAAAAACUUAUGGUCUCAAGAUCAACAAUCUAUCAAAGAUAGAGAAUUUCGCGCAAGCCGAUGGAGAACCACUAAAGGAAUUUUCACAUACUUCCCAAGAGAACAGC .((((...(((((......(((((((((((((....)))))))))).)))((((((.((....)).))).)))..)))))....((((((...)))))).......))))......((((((((((......))..))))).))).................. (-35.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCUGUUCUCUUGGGAAGUAUGUGAAAAUUCCUUUAGUGGUUCUCCAUCGGCUUGCGCGAAAUUCUCUAUCUUUGAUAGAUUGUUGAUCUUGAGACCAUAAGUUUUUGUGGCUCUGUGCAUCGACGACUUCGAUCAUCAAUAACAAUAAACGAUCAGUAGCACU ((((.((....(((((...((((...(..((....((((....)))).))..).))))...)))))......((((.(((((((((((..(((.((((((....)))))))))...).))))))))..)).))))...............)).))))...... (-35.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 926 80 31 171 122 NC_002950:PG1885|5end_polyphosphate_kinase_1983152..1983382_NEGATIVE 403 80 31 90 33 NC_002950:PG0362|5end_hypothetical_protein_395301..395531_POSITIVE 316 128 81 55 8 NC_002950:PG2219|5end_potassium_uptake_protein_TrkH_2332947..2333177_POSITIVE 309 135 97 187 148 NC_002950:PG1196|5end_hypothetical_protein_1275127..1275357_POSITIVE 305 127 92 188 148 NC_002950:PG0445|5end_peptidase_T_485252..485482_POSITIVE 297 56 11 182 128 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 290 79 33 68 29 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 284 126 90 180 137 NC_002950:PG0668|5end_TonB-dependent_receptor_717451..717681_POSITIVE 283 53 11 225 186 NC_002950:PG0614|5end_hypothetical_protein_665847..666077_POSITIVE 282 144 106 74 27 NC_002950:PG0661|5end_hypothetical_protein_709853..710083_NEGATIVE 278 57 12 65 9 NC_002950:PG0374|5end_hypothetical_protein_405564..405794_NEGATIVE 275 74 36 157 117 NC_002950:PG1079|5end_enoyl-CoA_hydratase/isomerase_family_protein_1146549..1146779_POSITIVE 273 124 84 214 163 NC_002950:PG1388|5end_hypothetical_protein_1470889..1471119_NEGATIVE 273 72 31 160 119 NC_002950:PG1159|5end_cobalamin_biosynthesis_protein_CbiB_1238967..1239197_NEGATIVE 272 55 12 230 184 NC_002950:PG0010|5end_ATP-dependent_Clp_protease,_ATP-binding_subunit_ClpC_8775..9005_POSITIVE 271 70 23 57 13 NC_002950:PG0950|5end_glycine_cleavage_system_protein_H_1009861..1010091_POSITIVE 270 80 33 69 30 NC_002950:PG0747|5end_sigma-54_dependent_DNA-binding_response_regulator_795294..795524_NEGATIVE 269 57 12 160 111 NC_002950:PG0223|5end_exonuclease_257610..257840_NEGATIVE 266 46 1 176 117 NC_002950:PG1076|5end_acyl-CoA_dehydrogenase,_short-chain_specific_1143485..1143715_POSITIVE 265 143 106 231 185 NC_002950:PG0660|5end_nitroreductase_family_protein_709695..709925_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 296 47 4 62 17 NC_002950:PG2047|3end_helicase,_putative_2145758..2145908_NEGATIVE 290 79 33 64 25 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 281 41 2 112 73 NC_002950:PG0344|3end_purple_acid_phosphatase_378543..378693_NEGATIVE 275 74 36 53 13 NC_002950:PG1078|3end_electron_transfer_flavoprotein,_alpha_subunit_1146525..1146675_POSITIVE 273 72 31 146 105 NC_002950:PG1160|3end_L-threonine-O-3-phosphate_decarboxylase,_putative_1238981..1239131_NEGATIVE 266 46 1 131 72 NC_002950:PG1075|3end_coenzyme_A_transferase,_beta_subunit_1143520..1143670_POSITIVE 265 148 104 95 42 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 263 149 109 54 19 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 261 58 12 131 85 NC_002950:PG1853|3end_DNA_polymerase_III,_beta_subunit_1951986..1952136_NEGATIVE 258 124 89 119 74 NC_002950:PG2219|3end_potassium_uptake_protein_TrkH_2334490..2334640_POSITIVE 257 90 41 150 91 NC_002950:PG1918|3end_preprotein_translocase_SecY_2014490..2014640_NEGATIVE 255 120 90 76 45 NC_002950:PG0838|3end_integrase_896855..897005_POSITIVE 253 73 31 150 99 NC_002950:PG0166|3end_peptidyl-tRNA_hydrolase_187813..187963_NEGATIVE 251 74 31 151 103 NC_002950:PG0352|3end_sialidase,_putative_388847..388997_POSITIVE 247 50 6 127 63 NC_002950:PG2103|3end_hypothetical_protein_2213226..2213376_NEGATIVE 247 142 104 93 59 NC_002950:PG1361|3end_dipeptidyl_aminopeptidase_IV,_putative_1439910..1440060_NEGATIVE 247 49 4 120 68 NC_002950:PG0872|3end_mobilizable_transposon,_xis_protein_934846..934996_NEGATIVE 247 48 2 48 4 NC_002950:PG0086|3end_ATP-dependent_RNA_helicase,_DEAD/DEAH_box_family_100545..100695_NEGATIVE 245 159 114 109 54 NC_002950:PG1363|3end_hypothetical_protein_1444159..1444309_POSITIVE 245 48 2 146 102 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE