Origin IGS: tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact .........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 agtagggtgttttttgattttccacggacaaaggtattcgattaggtcatacaagctgtatggaacctttactttctttcttataccatgtattataatgaataatccttgccttggatataaacgataggaggaaaaaaatgtaaaaaaggacaaaatgtcagtctttaggcgttggcatggatgttggattttgtctggtaacaacaaacacagca Mask Tandem Repeat Region ================================================ tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Find is-nt database================================================ Query_seq: PG1118:PG1119|PG1118:PG1119:clpB protein:flavodoxin, putative:<-->:1194765..1194982 218 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1118:PG1119|PG1118:PG1119:clpB protein:flavodoxin, putative:<-->:1194765..1194982 218 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1118:PG1119|PG1118:PG1119:clpB protein:flavodoxin, putative:<-->:1194765..1194982 218 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 77 End: 169 ............................................................................ M F F L L S F I S K A R I I H Y N T W Y K K E S K G S I Q L V ................................................. Protein_Len: 60 Strand: + Start: 3 End: 218 .. M C L L L P D K I Q H P C Q R L K T D I L S F F T F F S S Y R L Y P R Q G L F I I I H G I R K K V K V P Y S L Y D L I E Protein_Len: 38 Strand: - Start: 92 End: 205 ........................................................................................... R K Y G L C P N N M I I C P I L F F T F T G Y L K Y S R I S Y R Q G H F I M ............. tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact 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: 123 End: 152 ..........................................................................................................................CTTTACTTTCTTTCTTATACCATGTATTAT.................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ PromScan Matrix: RpoN Strand: - Score: 83 Start: 28 End: 44 ...........................TTGGCATGGATGTTGGA.............................................................................................................................................................................. tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1118:PG1119|PG1118:PG1119:clpB protein:flavodoxin, putative:<-->:1194765..1194982 218 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtccttttttacatttttttcctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact Intra-Species Hit: Count: 1 Min: 1 Max: 218 Len: 218 Subject: NC_002950_PG1118_PG1119|clpB protein:flavodoxin, putative|NEGATIVE:POSITIVE|[1194765,1194982]|218 HSP 1 e-value: 3.0E-70 bit: 266.0 Len: 134 Query Start:85 Query End:218 Subject Strand: POSITIVE Subject Start: 85 Subject End: 218 ....................................................................................cctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact ....................................................................................cctcctatcgtttatatccaaggcaaggattattcattataatacatggtataagaaagaaagtaaaggttccatacagcttgtatgacctaatcgaatacctttgtccgtggaaaatcaaaaaacaccctact HSP 2 e-value: 7.0E-31 bit: 135.0 Len: 68 Query Start:1 Query End:68 Subject Strand: POSITIVE Subject Start: 1 Subject End: 68 tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtcc...................................................................................................................................................... tgctgtgtttgttgttaccagacaaaatccaacatccatgccaacgcctaaagactgacattttgtcc...................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGCUGUGUUUGUUGUUACCAGACAAAAUCCAACAUCCAUGCCAACGCCUAAAGACUGACAUUUUGUCCUUUUUUACAUUUUUUUCCUCCUAUCGUUUAUAUCCAAGGCAAGGAUUAUUCAUUAUAAUACAUGGUAUAAGAAAGAAAGUAAAGGUUCCAUACAGCUUGUAUGACCUAAUCGAAUACCUUUGUCCGUGGAAAAUCAAAAAACACCCUACU ....((((((.(((...(((((((((.......((((.((((......((((((..(((.....)))..))))))..................(........)..)))).))))(((((.(((((........)))))............((((..(((((.....)))))))))....)))))..))))))..))).....))).))))))...... (-37.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUAGGGUGUUUUUUGAUUUUCCACGGACAAAGGUAUUCGAUUAGGUCAUACAAGCUGUAUGGAACCUUUACUUUCUUUCUUAUACCAUGUAUUAUAAUGAAUAAUCCUUGCCUUGGAUAUAAACGAUAGGAGGAAAAAAAUGUAAAAAAGGACAAAAUGUCAGUCUUUAGGCGUUGGCAUGGAUGUUGGAUUUUGUCUGGUAACAACAAACACAGCA .((...((((((.(((.((.....((((((((...(((((((.(((((((((.....)))))..)))).................((((((..............(((((...(((........)))...)))))....(((((....((((((.........))))))..))))).))))))..)))))))))))))))..))))).)))))).)). (-47.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 918 50 1 141 92 NC_002950:PG1118|5end_clpB_protein_1194674..1194904_NEGATIVE 352 69 27 83 50 NC_002950:PG0070|5end_UDP-N-acetylglucosamine_acyltransferase_84734..84964_NEGATIVE 327 48 1 65 17 NC_002950:PG1230|5end_hypothetical_protein_1308068..1308298_NEGATIVE 290 49 2 98 59 NC_002950:PG0979|5end_hypothetical_protein_1040752..1040982_POSITIVE 277 78 33 42 1 NC_002950:PG0658|5end_phosphatase,_YrbI_family_708319..708549_NEGATIVE 276 97 51 221 172 NC_002950:PG0333|5end_hypothetical_protein_367823..368053_POSITIVE 271 48 1 206 166 NC_002950:PG1851|5end_phosphopantothenoylcysteine_decarboxylase/phosphopantothenate--cysteine_ligase_1951168..1951398_NEGATIVE 270 195 151 190 151 NC_002950:PG2092|5end_hypothetical_protein_2192910..2193140_NEGATIVE 270 50 1 222 162 NC_002950:PG1155|5end_ADP-heptose--LPS_heptosyltransferase,_putative_1235861..1236091_POSITIVE 266 197 156 44 4 NC_002950:PG1314|5end_chorismate_synthase_1395468..1395698_NEGATIVE 265 194 151 136 80 NC_002950:PG1189|5end_hypothetical_protein_1269992..1270222_POSITIVE 265 198 160 187 145 NC_002950:PG0248|5end_translation_initation_factor_SUI1,_putative_281842..282072_NEGATIVE 265 47 1 198 146 NC_002950:PG0030|5end_cytidine_deaminase_35846..36076_POSITIVE 264 80 31 126 71 NC_002950:PG1093|5end_hypothetical_protein_1158121..1158351_POSITIVE 261 197 163 168 128 NC_002950:PG0954|5end_TPR_domain_protein_1013186..1013416_POSITIVE 260 90 41 105 50 NC_002950:PG0441|5end_hypothetical_protein_478734..478964_POSITIVE 259 180 131 184 127 NC_002950:PG1353|5end_orotate_phosphoribosyltransferase_1433833..1434063_NEGATIVE 257 169 129 142 89 NC_002950:PG0316|5end_seryl-tRNA_synthetase_348437..348667_POSITIVE 255 75 33 90 49 NC_002950:PG1381|5end_ABC_transporter,_permease_protein_1460622..1460852_POSITIVE 255 49 4 181 132 NC_002950:PG0452|5end_hypothetical_protein_492879..493109_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 352 69 27 86 53 NC_002950:PG0071|3end_UDP-3-O-acyl-GlcNAc_deacetylase/beta-hydroxyacyl-[acyl_carrier_protein]_dehydratase_FabZ_84731..84881_NEGATIVE 290 49 2 128 89 NC_002950:PG0978|3end_shikimate_5-dehydrogenase_1040862..1041012_POSITIVE 271 197 152 143 100 NC_002950:PG0522|3end_tRNA_delta(2)-isopentenylpyrophosphate_transferase_565993..566143_NEGATIVE 265 198 160 90 48 NC_002950:PG0249|3end_oxaloacetate_decarboxylase,_putative_281939..282089_NEGATIVE 262 45 2 48 1 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 261 197 163 140 100 NC_002950:PG0953|3end_deoxyuridine_5'-triphosphate_nucleotidohydrolase_1013238..1013388_POSITIVE 260 200 165 121 79 NC_002950:PG2106|3end_hypothetical_protein_2215457..2215607_POSITIVE 260 90 41 101 46 NC_002950:PG0439|3end_hypothetical_protein_478810..478960_POSITIVE 259 180 131 73 16 NC_002950:PG1354|3end_hydrolase,_carbon-nitrogen_family_1433944..1434094_NEGATIVE 255 75 33 93 52 NC_002950:PG1380|3end_ABC_transporter,_ATP-binding_protein_1460705..1460855_POSITIVE 255 49 4 74 25 NC_002950:PG0451|3end_CBS_domain_protein_492852..493002_POSITIVE 252 47 2 148 98 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 252 120 85 142 109 NC_002950:PG0492|3end_hypothetical_protein_534408..534558_NEGATIVE 251 199 152 64 14 NC_002950:PG1429|3end_hypothetical_protein_1515003..1515153_NEGATIVE 250 49 1 118 66 NC_002950:PG0443|3end_hemagglutinin-related_protein_483147..483297_POSITIVE 249 76 33 94 40 NC_002950:PG0780|3end_hypothetical_protein_832589..832739_NEGATIVE 248 76 34 64 8 NC_002950:PG1592|3end_HDIG_domain_protein_1671535..1671685_POSITIVE 247 103 64 143 102 NC_002950:PG1103|3end_ATPase,_AAA_family_1174989..1175139_POSITIVE 246 88 41 131 67 NC_002950:PG1701|3end_glutamine_amidotransferase,_class_II/dipeptidase_1786145..1786295_NEGATIVE 245 96 55 118 77 NC_002950:PG1105|3end_RNA_polymerase_sigma-54_factor_1175716..1175866_NEGATIVE