Origin IGS: ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 atgtagaaaagccgatagattgatatcggtttttttctatatttgtcaaaatgctgattttaaggtataatagttgctgttcgagaaattttgattttcaaagaatagtgaatgatgataaggagaaacc Mask Tandem Repeat Region ================================================ ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Find is-nt database================================================ Query_seq: SMT_944:SMT_945|SMT_944:SMT_945:PhnA protein:cytidylate kinase:<-<-:895197..895326 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_944:SMT_945|SMT_944:SMT_945:PhnA protein:cytidylate kinase:<-<-:895197..895326 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_944:SMT_945|SMT_944:SMT_945:PhnA protein:cytidylate kinase:<-<-:895197..895326 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: - Start: 3 End: 92 .. K E K D D N V I R Q F D F N R S C C S N Y R L I L M K V F M ...................................... ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat 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: 92 Start: 60 End: 89 ...........................................................TTTGTCAAAATGCTGATTTTAAGGTATAAT......................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_944:SMT_945|SMT_944:SMT_945:PhnA protein:cytidylate kinase:<-<-:895197..895326 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Intra-Species Hit: Count: 1 Min: 1 Max: 130 Len: 130 Subject: smit_SMT_944_SMT_945|PhnA protein:cytidylate kinase|NEGATIVE:NEGATIVE|[895197,895326]|130 HSP 1 e-value: 1.0E-55 bit: 216.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagnnnnnnnccgatatcaatctatcggcttttctacat ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagaaaaaaaccgatatcaatctatcggcttttctacat Inter-species Hit: Count: 3 Min: 1 Max: 130 Len: 130 Subject: NC_008533_SPD_1427_SPD_1428|PhnA protein:cytidylate kinase|NEGATIVE:NEGATIVE|[1445697,1445826]|130 HSP 1 e-value: 8.0E-51 bit: 200.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagnnnnnnnccgatatcaatctatcggcttttctacat ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccctaaaatcagcattttgacaaatttagaaaaaaaccgatatcaatctatcggcttttctacat Subject: NC_003098_spr1455_spr1456|Required for expression of the phosphonate utilization phenotype in E. coli:cytidylate kinase|NEGATIVE:NEGATIVE|[1438166,1438295]|130 HSP 1 e-value: 8.0E-51 bit: 200.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagnnnnnnnccgatatcaatctatcggcttttctacat ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccctaaaatcagcattttgacaaatttagaaaaaaaccgatatcaatctatcggcttttctacat Subject: NC_003028_SP_1602_SP_1603|phnA protein:cytidylate kinase|NEGATIVE:NEGATIVE|[1505865,1505994]|130 HSP 1 e-value: 8.0E-51 bit: 200.0 Len: 130 Query Start:1 Query End:130 Subject Strand: POSITIVE Subject Start: 1 Subject End: 130 ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccttaaaatcagcattttgacaaatatagnnnnnnnccgatatcaatctatcggcttttctacat ggtttctccttatcatcattcactattctttgaaaatcaaaatttctcgaacagcaactattataccctaaaatcagcattttgacaaatttagaaaaaaaccgatatcaatctatcggcttttctacat Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GGUUUCUCCUUAUCAUCAUUCACUAUUCUUUGAAAAUCAAAAUUUCUCGAACAGCAACUAUUAUACCUUAAAAUCAGCAUUUUGACAAAUAUAGAAAAAAACCGAUAUCAAUCUAUCGGCUUUUCUACAU ((.....)).........((((........)))).......((((.(((((..((.....(((.....))).....))..))))).)))).(((((((...((((((......)))))).)))))))... (-14.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGUAGAAAAGCCGAUAGAUUGAUAUCGGUUUUUUUCUAUAUUUGUCAAAAUGCUGAUUUUAAGGUAUAAUAGUUGCUGUUCGAGAAAUUUUGAUUUUCAAAGAAUAGUGAAUGAUGAUAAGGAGAAACC (((((((((((((((((......)))))))..))))))))))((((((..(((((........))))).....(..((((((..((((.......))))...))))))..)....))))))......... (-33.30) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 760 120 71 211 162 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 230 87 42 196 145 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 226 70 24 217 168 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 217 50 2 142 94 smit:SMT_919|5end_hypothetical_protein_872499..872729_NEGATIVE 209 53 15 60 26 smit:SMT_1356|5end_fibronectin-binding_protein-like_protein_A_1332534..1332764_POSITIVE 209 105 67 195 158 smit:SMT_431|5end_UDP-N-acetylmuramoyl-L-alanyl-D-glutamate_synthetase_372199..372429_POSITIVE 206 79 36 71 27 smit:SMT_841|5end_dihydrodipicolinate_reductase_788025..788255_NEGATIVE 204 68 24 171 124 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 202 50 1 139 93 smit:SMT_789|5end_hypothetical_protein_701072..701302_NEGATIVE 202 127 81 228 185 smit:SMT_741|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_645618..645848_NEGATIVE 199 30 1 101 69 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 198 67 25 67 24 smit:SMT_1850|5end_K01421_putative_membrane_protein_1815062..1815292_POSITIVE 197 86 42 97 53 smit:SMT_303|5end_hypothetical_protein_245364..245594_POSITIVE 196 85 46 57 15 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 196 50 1 179 133 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 193 48 1 89 37 smit:SMT_1529|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1512880..1513110_NEGATIVE 193 50 5 55 4 smit:SMT_642|5end_beta-glucoside_operon_antiterminator_547979..548209_NEGATIVE 192 41 1 133 93 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 191 55 15 61 17 smit:SMT_860|5end_homoserine_O-succinyltransferase_805011..805241_NEGATIVE 189 70 25 127 76 smit:SMT_1609|5end_hypothetical_protein_1598113..1598343_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 243 50 3 49 1 smit:SMT_1782|3end_hypothetical_protein_1759740..1759890_POSITIVE 234 49 5 123 71 smit:SMT_1494|3end_nucleoside_diphosphate_kinase_1480221..1480371_POSITIVE 217 50 2 53 5 smit:SMT_920|3end_serine/threonine_protein_kinase_872588..872738_NEGATIVE 216 50 6 112 59 smit:SMT_1204|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1164595..1164745_NEGATIVE 209 105 67 80 43 smit:SMT_430|3end_hypothetical_protein_372164..372314_POSITIVE 202 50 1 118 72 smit:SMT_790|3end_hypothetical_protein_701093..701243_NEGATIVE 202 127 81 62 19 smit:SMT_742|3end_hypothetical_protein_645784..645934_NEGATIVE 201 61 26 94 57 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 191 107 61 80 40 smit:SMT_693|3end_hypothetical_protein_604078..604228_POSITIVE 189 70 25 130 79 smit:SMT_1608|3end_hypothetical_protein_1598196..1598346_POSITIVE 189 55 19 133 97 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 186 50 7 151 102 smit:SMT_1051|3end_K01990_ABC-2_type_transport_system_ATP-binding_protein_991920..992070_POSITIVE 186 50 1 125 65 smit:SMT_312|3end_acetyl-CoA_carboxylase,_biotin_carboxyl_carrier_protein_253926..254076_POSITIVE 184 37 1 105 70 smit:SMT_132|3end_L-serine_dehydratase_alpha_subunit_83685..83835_NEGATIVE 183 43 3 150 115 smit:SMT_1231|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1193034..1193184_POSITIVE 177 70 29 151 117 smit:SMT_1510|3end_ribose_5-phosphate_isomerase_1492805..1492955_NEGATIVE 173 128 106 107 89 smit:SMT_1497|3end_acetyltransferase,_GNAT_family_1482030..1482180_POSITIVE 170 47 1 118 67 smit:SMT_1151|3end_histidyl-tRNA_synthetase_1095002..1095152_NEGATIVE 169 53 24 119 95 smit:SMT_1911|3end_hypothetical_protein_1857840..1857990_POSITIVE 169 53 24 119 95 smit:SMT_867|3end_hypothetical_protein_816542..816692_POSITIVE