Origin IGS: aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgatactcaatgaaaatcaaagtgcaaactaggaagctagccgcaggttactcaaagcacagttttgaggttgcagataaagctgacgtggtttgaagagattttcgaagagtatgggaaaaataatatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact .........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 agttcttctcctaaaatagtatcttatcctttattatatcacaaaatatagtccagtacatattatttttcccatactcttcgaaaatctcttcaaaccacgtcagctttatctgcaacctcaaaactgtgctttgagtaacctgcggctagcttcctagtttgcactttgattttcattgagtatcagtgtctattgtagccctgcttaaactagtaagaaagaactcctatatccacaagtgacataggagtttattttgtatt Mask Tandem Repeat Region ================================================ aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgatactcaatgaaaatcaaagtgcaaactaggaagctagccgcaggttactcaaagcacagttttgaggttgcagataaagctgacgtggtttgaagagattttcgaagagtatgggaaaaataatatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Find is-nt database================================================ Query_seq: SMT_1591:SMT_1592|SMT_1591:SMT_1592:DNA-entry nuclease:putative hemolysin:->->:1579529..1579794 266 aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgatactcaatgaaaatcaaagtgcaaactaggaagctagccgcaggttactcaaagcacagttttgaggttgcagataaagctgacgtggtttgaagagattttcgaagagtatgggaaaaataatatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1591:SMT_1592|SMT_1591:SMT_1592:DNA-entry nuclease:putative hemolysin:->->:1579529..1579794 266 aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgatactcaatgaaaatcaaagtgcaaactaggaagctagccgcaggttactcaaagcacagttttgaggttgcagataaagctgacgtggtttgaagagattttcgaagagtatgggaaaaataatatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1591:SMT_1592|SMT_1591:SMT_1592:DNA-entry nuclease:putative hemolysin:->->:1579529..1579794 266 aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgatactcaatgaaaatcaaagtgcaaactaggaagctagccgcaggttactcaaagcacagttttgaggttgcagataaagctgacgtggtttgaagagattttcgaagagtatgggaaaaataatatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 4 Min: 82 Max: 205 Len: 124 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: 2.0E-7 bit: 48.1 Len: 84 Query Start:88 Query End:171 Subject Strand: null Subject Start: 1 Subject End: 28 ....................................................................................... M K I K V Q T R K L A A G Y 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: 2.0E-7 bit: 28.9 Len: 33 Query Start:161 Query End:193 Subject Strand: null Subject Start: 38 Subject End: 48 ................................................................................................................................................................ L T W F E E I F E E Y ......................................................................... ................................................................................................................................................................ L T W F E E I F E E Y ......................................................................... 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: 2.0E-7 bit: 42.7 Len: 84 Query Start:88 Query End:171 Subject Strand: null Subject Start: 1 Subject End: 28 ....................................................................................... M K I K V Q T R K L A A G Y 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: 2.0E-7 bit: 34.3 Len: 54 Query Start:152 Query End:205 Subject Strand: null Subject Start: 35 Subject End: 52 ....................................................................................................................................................... Q I K L T W F E E I F E E Y G K N N ............................................................. ....................................................................................................................................................... K V K L T W F E E I F E E Y K K S S ............................................................. 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-7 bit: 49.3 Len: 90 Query Start:82 Query End:171 Subject Strand: null Subject Start: 24 Subject End: 53 ................................................................................. Y S M K I K V Q T R K L A A G Y S K H S F E V A D K A D V V ............................................................................................... ................................................................................. 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-7 bit: 27.3 Len: 33 Query Start:161 Query End:193 Subject Strand: null Subject Start: 63 Subject End: 73 ................................................................................................................................................................ L T W F E E I F E E Y ......................................................................... ................................................................................................................................................................ L T W F E E I F E K Y ......................................................................... 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: 1.0E-5 bit: 43.1 Len: 84 Query Start:88 Query End:171 Subject Strand: null Subject Start: 1 Subject End: 28 ....................................................................................... M K I K V Q T R K L A A G Y 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: 1.0E-5 bit: 28.1 Len: 33 Query Start:161 Query End:193 Subject Strand: null Subject Start: 53 Subject End: 63 ................................................................................................................................................................ L T W F E E I F E E Y ......................................................................... ................................................................................................................................................................ M T W F E E I F E E Y ......................................................................... aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 143 End: 253 .............................................................................................................................................. M R L Q I K L T W F E E I F E E Y G K N N M Y W T I F C D I I K D K I L F ............. Protein_Len: 38 Strand: - Start: 133 End: 246 .................................................................................................................................... L V T K L N C I F S V H N S S I K S S Y P F F L I Y Q V I N Q S I I F S L M .................... Protein_Len: 44 Strand: - Start: 110 End: 241 ............................................................................................................. S A L R L N S L A C N Q P Q L Y L Q R P K F L N E F L I P F I I H V P S Y K T I Y Y L M ......................... aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact 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================================================ aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1591:SMT_1592|SMT_1591:SMT_1592:DNA-entry nuclease:putative hemolysin:->->:1579529..1579794 266 aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactgannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Intra-Species Hit: Count: 1 Min: 1 Max: 266 Len: 266 Subject: smit_SMT_1591_SMT_1592|DNA-entry nuclease:putative hemolysin|POSITIVE:POSITIVE|[1579529,1579794]|266 HSP 1 e-value: 1.0E-38 bit: 161.0 Len: 81 Query Start:1 Query End:81 Subject Strand: POSITIVE Subject Start: 1 Subject End: 81 aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactga......................................................................................................................................................................................... aatacaaaataaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggctacaatagacactga......................................................................................................................................................................................... HSP 2 e-value: 1.0E-26 bit: 121.0 Len: 61 Query Start:206 Query End:266 Subject Strand: POSITIVE Subject Start: 206 Subject End: 266 .............................................................................................................................................................................................................atgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact .............................................................................................................................................................................................................atgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact Inter-species Hit: Count: 3 Min: 10 Max: 266 Len: 257 Subject: NC_008533_SPD_1761_SPD_1762|CBS domain membrane protein:DNA-entry nuclease|NEGATIVE:NEGATIVE|[1761180,1761407]|228 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 61 Query Start:206 Query End:266 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 61 .............................................................................................................................................................................................................atgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact .............................................................................................................................................................................................................atgtattggattaaattttgtgatataataaaggataagatactattttaggagaagaact HSP 2 e-value: 7.0E-16 bit: 85.7 Len: 59 Query Start:10 Query End:68 Subject Strand: NEGATIVE Subject Start: 161 Subject End: 218 .........taaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggcta...................................................................................................................................................................................................... .........taaactcctatgtcacttatggatgtaggagttcttt-ttactagtttaagcagggcta...................................................................................................................................................................................................... Subject: NC_003098_spr1778_spr1779|Hemolysin:DNA-entry nuclease (competence-specific nuclease)|NEGATIVE:NEGATIVE|[1753648,1753875]|228 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 61 Query Start:206 Query End:266 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 61 .............................................................................................................................................................................................................atgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact .............................................................................................................................................................................................................atgtattggattaaattttgtgatataataaaggataagatactattttaggagaagaact HSP 2 e-value: 7.0E-16 bit: 85.7 Len: 59 Query Start:10 Query End:68 Subject Strand: NEGATIVE Subject Start: 161 Subject End: 218 .........taaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagggcta...................................................................................................................................................................................................... .........taaactcctatgtcacttatggatgtaggagttcttt-ttactagtttaagcagggcta...................................................................................................................................................................................................... Subject: NC_003028_SP_1963_SP_1964|CBS domain protein:DNA-entry nuclease|NEGATIVE:NEGATIVE|[1871982,1872209]|228 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 61 Query Start:206 Query End:266 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 61 .............................................................................................................................................................................................................atgtactggactatattttgtgatataataaaggataagatactattttaggagaagaact .............................................................................................................................................................................................................atgtattggattaaattttgtgatataataaaggataagatactattttaggagaagaact HSP 2 e-value: 2.0E-13 bit: 77.8 Len: 55 Query Start:10 Query End:64 Subject Strand: NEGATIVE Subject Start: 165 Subject End: 218 .........taaactcctatgtcacttgtggatataggagttctttcttactagtttaagcagg.......................................................................................................................................................................................................... .........taaactcctatgtcacttatggatgtaggagttcttt-ttactagtttaagcagg.......................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAACUCCUAUGUCACUUGUGGAUAUAGGAGUUCUUUCUUACUAGUUUAAGCAGGGCUACAAUAGACACUGAUACUCAAUGAAAAUCAAAGUGCAAACUAGGAAGCUAGCCGCAGGUUACUCAAAGCACAGUUUUGAGGUUGCAGAUAAAGCUGACGUGGUUUGAAGAGAUUUUCGAAGAGUAUGGGAAAAAUAAUAUGUACUGGACUAUAUUUUGUGAUAUAAUAAAGGAUAAGAUACUAUUUUAGGAGAAGAACU ..((((((((((((.(....))))))))))))).((((((.((((..((..(((..(...........((.((((((..((((((((......((((((((..((((..(.((((....((((((((...)))))))).)))).)....))))..).)))))))....))))))))..)))))).))...........)..)))...(((.((((((......)))))).)))......))..)))))))))).... (-67.85) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUCUUCUCCUAAAAUAGUAUCUUAUCCUUUAUUAUAUCACAAAAUAUAGUCCAGUACAUAUUAUUUUUCCCAUACUCUUCGAAAAUCUCUUCAAACCACGUCAGCUUUAUCUGCAACCUCAAAACUGUGCUUUGAGUAACCUGCGGCUAGCUUCCUAGUUUGCACUUUGAUUUUCAUUGAGUAUCAGUGUCUAUUGUAGCCCUGCUUAAACUAGUAAGAAAGAACUCCUAUAUCCACAAGUGACAUAGGAGUUUA ..(((((((...((((((((((......((..(((((((......)))))))..))...))))))))))....((((((...(((((((....(((((...(..((((....(((((..((((((.......)))))).....)))))..))))..)..)))))......)))))))...))))))(((.((........)).)))........)).))))).((((((((((.(((....).)).)))))))))). (-50.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 804 180 131 221 171 smit:SMT_163|5end_cardiolipin_synthetase_107309..107539_POSITIVE 795 180 131 61 11 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 772 118 72 198 152 smit:SMT_1810|5end_hypothetical_protein_1785219..1785449_POSITIVE 772 118 72 150 104 smit:SMT_483|5end_transcriptional_activator_TipA,_putative_418827..419057_POSITIVE 763 129 81 229 181 smit:SMT_1379|5end_thymidylate_kinase_1357438..1357668_NEGATIVE 749 148 101 223 176 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 741 118 72 212 166 smit:SMT_1138|5end_hypothetical_protein_1079547..1079777_NEGATIVE 741 118 72 189 143 smit:SMT_833|5end_hypothetical_protein_predicted_by_Glimmer/Critica_775362..775592_NEGATIVE 741 118 72 173 127 smit:SMT_130|5end_capsular_polysaccharide_biosynthesis_protein_80995..81225_POSITIVE 720 118 72 163 117 smit:SMT_1963|5end_ribonuclease_BN,_putative_1896462..1896692_NEGATIVE 720 140 93 173 126 smit:SMT_1200|5end_K06148_ATP-binding_cassette,_subfamily_C,_bacterial_1163235..1163465_NEGATIVE 717 118 71 164 114 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 716 118 72 215 169 smit:SMT_1179|5end_aldose_1-epimerase_1137854..1138084_NEGATIVE 715 118 71 176 126 smit:SMT_1488|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1467157..1467387_POSITIVE 688 140 93 183 136 smit:SMT_366|5end_hypothetical_protein_302085..302315_POSITIVE 659 118 71 161 109 smit:SMT_1782|5end_hypothetical_protein_1759520..1759750_POSITIVE 633 116 75 230 189 smit:SMT_443|5end_hydroxyethylthiazole_kinase_382555..382785_POSITIVE 624 140 93 192 145 smit:SMT_1544|5end_mevalonate_kinase_1528884..1529114_NEGATIVE 598 140 93 177 130 smit:SMT_775|5end_alpha-acetolactate_decarboxylase_685972..686202_NEGATIVE 588 184 142 220 177 smit:SMT_677|5end_DNA_topoisomerase_I_587318..587548_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 841 170 121 55 6 smit:SMT_455|3end_cation_transport_ATPase_393993..394143_POSITIVE 749 180 131 59 9 smit:SMT_1144|3end_K02026_multiple_sugar_transport_system_permease_protein_1089144..1089294_POSITIVE 749 148 101 141 94 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 712 189 141 52 4 smit:SMT_452|3end_phosphomethylpyrimidine_kinase_389777..389927_NEGATIVE 708 180 131 87 38 smit:SMT_1489|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1470714..1470864_POSITIVE 680 180 131 52 3 smit:SMT_1626|3end_undecaprenyl-diphosphatase_1615183..1615333_NEGATIVE 678 189 143 48 1 smit:SMT_1076|3end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_/_dihydroneopterin_aldolase_1014001..1014151_NEGATIVE 670 180 131 52 2 smit:SMT_1380|3end_pyrroline-5-carboxylate_reductase_1357667..1357817_NEGATIVE 631 185 142 48 4 smit:SMT_1872|3end_K03217_preprotein_translocase_YidC_subunit_1830883..1831033_NEGATIVE 620 188 151 90 53 smit:SMT_1536|3end_trigger_factor_1520636..1520786_NEGATIVE 620 185 149 86 50 smit:SMT_124|3end_hypothetical_protein_75590..75740_NEGATIVE 604 184 142 88 45 smit:SMT_799|3end_hypothetical_protein_707296..707446_NEGATIVE 588 184 142 91 48 smit:SMT_678|3end_K04096_DNA_processing_protein_587447..587597_NEGATIVE 569 184 142 91 48 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 567 187 142 89 43 smit:SMT_1569|3end_dihydroxy-acid_dehydratase_1563068..1563218_POSITIVE 566 189 151 75 32 smit:SMT_1815|3end_K02035_peptide/nickel_transport_system_substrate-binding_protein_1788899..1789049_NEGATIVE 566 121 86 38 1 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 566 121 86 38 1 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 565 184 151 79 46 smit:SMT_1357|3end_endo-beta-N-acetylglucosaminidase_1334450..1334600_NEGATIVE 565 184 151 91 58 smit:SMT_915|3end_sucrose_operon_repressor_868619..868769_POSITIVE