Origin IGS: aagcgggcttgctcgctttttatactcttcaaaaatctcttccaaccacgtcagctttgtctgcaacctcaaagctgtgctttgagcaacctgtggcgagcttcctagtttgctctgtgattttcattgagtattataaaacagaagctaaaaacgttttcaaactgtactgtaatagagaataaaaacttctgagcagattcttagtaaagtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aatgataactctccttcaaatatttttaaatctactaaaaaaggtttcatatagtttttgaaaacgtttcagtaaatttttacaatactaatttatcacatttattttgactttactaagaatctgctcagaagtttttattctctattacagtacagtttgaaaacgtttttagcttctgttttataatactcaatgaaaatcacagagcaaactaggaagctcgccacaggttgctcaaagcacagctttgaggttgcagacaaagctgacgtggttggaagagatttttgaagagtataaaaagcgagcaagcccgctt Mask Tandem Repeat Region ================================================ aagcgggcttgctcgctttttatactcttcaaaaatctcttccaaccacgtcagctttgtctgcaacctcaaagctgtgctttgagcaacctgtggcgagcttcctagtttgctctgtgattttcattgagtattataaaacagaagctaaaaacgttttcaaactgtactgtaatagagaataaaaacttctgagcagattcttagtaaagtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Find is-nt database================================================ Query_seq: SMT_455:SMT_456|SMT_455:SMT_456:cation transport ATPase:pyruvate oxidase:->->:394054..394375 322 aagcgggcttgctcgctttttatactcttcaaaaatctcttccaaccacgtcagctttgtctgcaacctcaaagctgtgctttgagcaacctgtggcgagcttcctagtttgctctgtgattttcattgagtattataaaacagaagctaaaaacgttttcaaactgtactgtaatagagaataaaaacttctgagcagattcttagtaaagtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_455:SMT_456|SMT_455:SMT_456:cation transport ATPase:pyruvate oxidase:->->:394054..394375 322 aagcgggcttgctcgctttttatactcttcaaaaatctcttccaaccacgtcagctttgtctgcaacctcaaagctgtgctttgagcaacctgtggcgagcttcctagtttgctctgtgattttcattgagtattataaaacagaagctaaaaacgttttcaaactgtactgtaatagagaataaaaacttctgagcagattcttagtaaagtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_455:SMT_456|SMT_455:SMT_456:cation transport ATPase:pyruvate oxidase:->->:394054..394375 322 aagcgggcttgctcgctttttatactcttcaaaaatctcttccaaccacgtcagctttgtctgcaacctcaaagctgtgctttgagcaacctgtggcgagcttcctagtttgctctgtgattttcattgagtattataaaacagaagctaaaaacgttttcaaactgtactgtaatagagaataaaaacttctgagcagattcttagtaaagtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 6 Min: 16 Max: 211 Len: 196 Subject: UniRef90_Q04IR5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 7.0E-8 bit: 45.8 Len: 84 Query Start:44 Query End:127 Subject Strand: null Subject Start: 1 Subject End: 28 ........................................... M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ................................................................................................................................................................................................... ........................................... M K I K E Q T R K L A A G C S K H C F E V V D E T D E V ................................................................................................................................................................................................... HSP 2 e-value: 7.0E-8 bit: 32.7 Len: 48 Query Start:16 Query End:63 Subject Strand: null Subject Start: 35 Subject End: 50 ............... Q T K L T W L E E I F E E Y K K ................................................................................................................................................................................................................................................................... ............... K V K L T W F E E I F E E Y K K ................................................................................................................................................................................................................................................................... Subject: UniRef90_Q04I61 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-6 bit: 48.5 Len: 168 Query Start:44 Query End:211 Subject Strand: null Subject Start: 3 Subject End: 53 ........................................... F T K N L L R S F Y S L L Q Y S L K T F L A S V L * Y S M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ............................................................................................................... ........................................... F N V G R F T S F S T E I E S F S K I F L - - - - - Y S M K I K V Q T R K L A A G C S K H C F E V V D E T D E V ............................................................................................................... HSP 2 e-value: 2.0E-6 bit: 25.0 Len: 33 Query Start:22 Query End:54 Subject Strand: null Subject Start: 63 Subject End: 73 ..................... L T W L E E I F E E Y ............................................................................................................................................................................................................................................................................ ..................... L T W F E E I F E K Y ............................................................................................................................................................................................................................................................................ Subject: UniRef90_Q04L28 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 3.0E-6 bit: 48.9 Len: 84 Query Start:44 Query End:127 Subject Strand: null Subject Start: 1 Subject End: 28 ........................................... M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ................................................................................................................................................................................................... ........................................... M K I K E Q T R K L A A G C S K H C F E V A D K T D E V ................................................................................................................................................................................................... HSP 2 e-value: 3.0E-6 bit: 23.9 Len: 36 Query Start:19 Query End:54 Subject Strand: null Subject Start: 53 Subject End: 64 .................. L T W L E E I F E E Y K ............................................................................................................................................................................................................................................................................ .................. L T R I E E I F E E Y K ............................................................................................................................................................................................................................................................................ Subject: UniRef90_Q04LB4 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 6.0E-6 bit: 46.2 Len: 84 Query Start:44 Query End:127 Subject Strand: null Subject Start: 1 Subject End: 28 ........................................... M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ................................................................................................................................................................................................... ........................................... M K I K E Q T R K L A A G C S K H C F E V V D R T D E V ................................................................................................................................................................................................... HSP 2 e-value: 6.0E-6 bit: 25.8 Len: 33 Query Start:22 Query End:54 Subject Strand: null Subject Start: 53 Subject End: 63 ..................... L T W L E E I F E E Y ............................................................................................................................................................................................................................................................................ ..................... M T W F E E I F E E Y ............................................................................................................................................................................................................................................................................ Subject: UniRef90_Q04KB8 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 6.0E-6 bit: 43.5 Len: 84 Query Start:44 Query End:127 Subject Strand: null Subject Start: 1 Subject End: 28 ........................................... M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ................................................................................................................................................................................................... ........................................... M K I K E Q T R K L A A G Y S K H S F E V V D E T D E V ................................................................................................................................................................................................... HSP 2 e-value: 6.0E-6 bit: 28.5 Len: 36 Query Start:19 Query End:54 Subject Strand: null Subject Start: 38 Subject End: 49 .................. L T W L E E I F E E Y K ............................................................................................................................................................................................................................................................................ .................. L T W F E E I F E E Y K ............................................................................................................................................................................................................................................................................ Subject: UniRef90_Q04M07 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 1.0E-5 bit: 42.7 Len: 84 Query Start:44 Query End:127 Subject Strand: null Subject Start: 1 Subject End: 28 ........................................... M K I T E Q T R K L A T G C S K H S F E V A D K A D V V ................................................................................................................................................................................................... ........................................... M K I K E Q T R K L A A G C S K Q C F E V V D E T D E V ................................................................................................................................................................................................... HSP 2 e-value: 1.0E-5 bit: 28.5 Len: 45 Query Start:19 Query End:63 Subject Strand: null Subject Start: 35 Subject End: 49 .................. Q T K L T W L E E I F E E Y K ................................................................................................................................................................................................................................................................... .................. K A K L M W F E E I F E E Y K ................................................................................................................................................................................................................................................................... aagcgggcttgctcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Predict ORF larger than 30AA ================================================ Protein_Len: 58 Strand: + Start: 9 End: 182 ........ M L A F Y T L Q K S L P T T S A L S A T S K L C F E Q P V A S F L V C S V I F I E Y Y K T E A K N V F K L Y C N R E ............................................................................................................................................ Protein_Len: 37 Strand: - Start: 137 End: 247 ........................................................................................................................................ L V S A L F T K L S Y Q L L S Y F S R L L N K T F D F Y I H Y I L I T F M ........................................................................... Protein_Len: 32 Strand: - Start: 32 End: 127 ............................... F D R G V V D A K D A V E F S H K S C G T A L K R T Q E T I K M ................................................................................................................................................................................................... aagcgggcttgctcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt 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: 84 Start: 237 End: 266 ............................................................................................................................................................................................................................................TTTGAAAACGTTTCAGTAAATTTTTACAAT........................................................ PromScan Matrix: RpoD-17 Strand: + Score: 84 Start: 292 End: 321 ...................................................................................................................................................................................................................................................................................................ATTTAAAAATATTTGAAGGAGAGTTATCAT. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagcgggcttgctcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_455:SMT_456|SMT_455:SMT_456:cation transport ATPase:pyruvate oxidase:->->:394054..394375 322 aagcgggcttgctcgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngtcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Intra-Species Hit: Count: 1 Min: 213 Max: 322 Len: 110 Subject: smit_SMT_455_SMT_456|cation transport ATPase:pyruvate oxidase|POSITIVE:POSITIVE|[394054,394375]|322 HSP 1 e-value: 9.0E-56 bit: 218.0 Len: 110 Query Start:213 Query End:322 Subject Strand: POSITIVE Subject Start: 213 Subject End: 322 ....................................................................................................................................................................................................................tcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt ....................................................................................................................................................................................................................tcaaaataaatgtgataaattagtattgtaaaaatttactgaaacgttttcaaaaactatatgaaaccttttttagtagatttaaaaatatttgaaggagagttatcatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCAAAAUAAAUGUGAUAAAUUAGUAUUGUAAAAAUUUACUGAAACGUUUUCAAAAACUAUAUGAAACCUUUUUUAGUAGAUUUAAAAAUAUUUGAAGGAGAGUUAUCAUU ...........(((((((...((((((....(((((((((((((.(.(((((.........))))).)..)))))))))))))...))))))..........))))))). (-16.52) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUAACUCUCCUUCAAAUAUUUUUAAAUCUACUAAAAAAGGUUUCAUAUAGUUUUUGAAAACGUUUCAGUAAAUUUUUACAAUACUAAUUUAUCACAUUUAUUUUGA ..((((((......((((((.(((...((((((........)))))).....))).)))))).........((((....)))).........))))))............ (-10.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 232 108 61 154 93 smit:SMT_819|5end_hypothetical_protein_predicted_by_Glimmer/Critica_730421..730651_NEGATIVE 210 106 62 82 29 smit:SMT_978|5end_hypothetical_protein_926607..926837_NEGATIVE 200 83 57 115 88 smit:SMT_1770|5end_hypothetical_protein_1746505..1746735_NEGATIVE 194 79 36 193 156 smit:SMT_1786|5end_phenylalanyl-tRNA_synthetase_beta_chain_1763540..1763770_NEGATIVE 179 67 30 188 147 smit:SMT_1871|5end_modification_methylase,_HemK_family_1830501..1830731_NEGATIVE 177 110 67 156 117 smit:SMT_1183|5end_K02795_PTS_system,_mannose-specific_IIC_component_1141534..1141764_NEGATIVE 173 104 66 141 96 smit:SMT_1884|5end_hypothetical_protein_1838964..1839194_POSITIVE 173 104 66 141 96 smit:SMT_1875|5end_hypothetical_protein_1832965..1833195_POSITIVE 171 69 21 102 45 smit:SMT_671|5end_hypothetical_protein_580249..580479_POSITIVE 169 106 67 152 102 smit:SMT_2050|5end_K03712_MarR_family_transcriptional_regulator_1959973..1960203_NEGATIVE 169 107 68 227 180 smit:SMT_1277|5end_PcsB_protein_1240000..1240230_POSITIVE 165 105 61 134 93 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 165 77 43 201 168 smit:SMT_1393|5end_hypothetical_protein_1369106..1369336_POSITIVE 163 65 24 211 172 smit:SMT_654|5end_K06158_ATP-binding_cassette,_sub-family_F,_member_3_566058..566288_NEGATIVE 162 108 66 201 150 smit:SMT_533|5end_RNA_binding_protein_453218..453448_POSITIVE 162 108 66 59 8 smit:SMT_532|5end_30S_ribosomal_protein_S16_453076..453306_POSITIVE 162 108 66 201 150 smit:SMT_530|5end_RNA_binding_protein_452319..452549_POSITIVE 162 108 66 59 8 smit:SMT_529|5end_30S_ribosomal_protein_S16_452177..452407_POSITIVE 162 108 66 201 150 smit:SMT_526|5end_RNA_binding_protein_451149..451379_POSITIVE 162 108 66 201 150 smit:SMT_510|5end_hypothetical_protein_439038..439268_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 194 79 36 65 28 smit:SMT_1787|3end_phosphoribosylformylglycinamidine_synthase_1763668..1763818_NEGATIVE 177 110 67 129 90 smit:SMT_1184|3end_phosphotransferase_system,_mannose/fructose/N-acetylgalactosamine-specific_component_IIB_1141561..1141711_NEGATIVE 171 69 21 97 40 smit:SMT_670|3end_aminotransferase_(class_V),_putative_580324..580474_POSITIVE 169 106 67 58 8 smit:SMT_2051|3end_enoyl-CoA_hydratase_1960067..1960217_NEGATIVE 169 107 68 133 86 smit:SMT_1276|3end_rod_shape-determining_protein_MreD_1239986..1240136_POSITIVE 159 110 68 55 7 smit:SMT_1773|3end_hypothetical_protein_1749905..1750055_POSITIVE 156 103 68 56 23 smit:SMT_857|3end_endo-beta-N-acetylglucosaminidase_800881..801031_NEGATIVE 153 82 47 92 56 smit:SMT_319|3end_K02356_elongation_factor_EF-P_258304..258454_NEGATIVE 151 100 63 79 44 smit:SMT_1504|3end_topology_modulation_protein_1487808..1487958_POSITIVE 151 38 3 77 38 smit:SMT_85|3end_hypothetical_protein_predicted_by_Glimmer/Critica_16630..16780_NEGATIVE 150 104 68 33 1 smit:SMT_406|3end_hypothetical_protein_351260..351410_POSITIVE 147 102 67 78 40 smit:SMT_1571|3end_CAAX_amino_terminal_protease_family_protein_1564405..1564555_POSITIVE 147 99 56 119 73 smit:SMT_204|3end_K02012_iron(III)_transport_system_substrate-binding_protein_134925..135075_NEGATIVE 146 110 61 66 12 smit:SMT_1614|3end_K08998_hypothetical_protein_1601652..1601802_POSITIVE 146 110 68 150 106 smit:SMT_534|3end_hypothetical_protein_predicted_by_Glimmer/Critica_454190..454340_POSITIVE 144 103 65 100 70 smit:SMT_650|3end_pullulanase_557547..557697_NEGATIVE 140 104 68 57 25 smit:SMT_1026|3end_sucrose_phosphorylase_960873..961023_NEGATIVE 140 80 40 81 38 smit:SMT_354|3end_hypothetical_protein_291671..291821_POSITIVE 139 108 68 54 23 smit:SMT_1408|3end_GTP-binding_protein_1386296..1386446_NEGATIVE 139 103 66 69 29 smit:SMT_1361|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1338730..1338880_NEGATIVE