Origin IGS: taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctactatagtctaatactcttcgaaaatctcttcaaaccacgtcagctctatctgccacctcaaaacagtgttttgagcaacctgcggctagcttcctagtttgctttttgattttcattgagtctaatatctacaatgtaaaaaactctagctatcagttcattgatagttagagtttttt .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 aaaaaactctaactatcaatgaactgatagctagagttttttacattgtagatattagactcaatgaaaatcaaaaagcaaactaggaagctagccgcaggttgctcaaaacactgttttgaggtggcagatagagctgacgtggtttgaagagattttcgaagagtattagactatagtagattgaagctagagtaatacgccgcgacttctaaaccttttctagaaattaatttgactttcctaatcgagttgttcagattttatttcatctcactataattcaatgattttctaagaattctatttctttcgaaaattctttcaaagttttttcaaatcagtccaacaaaaaaggtttataatttccataaaagttgacatggaaattataaaaccatta Mask Tandem Repeat Region ================================================ taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctactatagtctaatactcttcgaaaatctcttcaaaccacgtcagctctatctgccacctcaaaacagtgttttgagcaacctgcggctagcttcctagtttgctttttgattttcattgagtctaatatctacaatgtaaaaaactctagctatcagttcattgatagttagagtttttt Find is-nt database================================================ Query_seq: SMT_1597:SMT_1598|SMT_1597:SMT_1598:K02032 peptide/nickel transport system ATP-binding protein:malolactic regulator, LysR family:-><-:1588048..1588450 403 taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctactatagtctaatactcttcgaaaatctcttcaaaccacgtcagctctatctgccacctcaaaacagtgttttgagcaacctgcggctagcttcctagtttgctttttgattttcattgagtctaatatctacaatgtaaaaaactctagctatcagttcattgatagttagagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1597:SMT_1598|SMT_1597:SMT_1598:K02032 peptide/nickel transport system ATP-binding protein:malolactic regulator, LysR family:-><-:1588048..1588450 403 taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctactatagtctaatactcttcgaaaatctcttcaaaccacgtcagctctatctgccacctcaaaacagtgttttgagcaacctgcggctagcttcctagtttgctttttgattttcattgagtctaatatctacaatgtaaaaaactctagctatcagttcattgatagttagagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1597:SMT_1598|SMT_1597:SMT_1598:K02032 peptide/nickel transport system ATP-binding protein:malolactic regulator, LysR family:-><-:1588048..1588450 403 taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctactatagtctaatactcttcgaaaatctcttcaaaccacgtcagctctatctgccacctcaaaacagtgttttgagcaacctgcggctagcttcctagtttgctttttgattttcattgagtctaatatctacaatgtaaaaaactctagctatcagttcattgatagttagagtttttt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 4 Min: 226 Max: 373 Len: 148 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: 5.0E-7 bit: 44.7 Len: 60 Query Start:281 Query End:340 Subject Strand: null Subject Start: 1 Subject End: 20 ........................................................................................................................................................................................................................................................................................ M K I K K Q T R K L A A G C S K H C F E ............................................................... ........................................................................................................................................................................................................................................................................................ M K I K E Q T R K L A A G C S K H C F E ............................................................... HSP 2 e-value: 5.0E-7 bit: 30.8 Len: 42 Query Start:235 Query End:276 Subject Strand: null Subject Start: 35 Subject End: 48 .......................................................................................................................................................................................................................................... Q I E L T W F E E I F E E Y ............................................................................................................................... .......................................................................................................................................................................................................................................... K V K L T W F E E I F E E Y ............................................................................................................................... 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: 7.0E-7 bit: 47.8 Len: 93 Query Start:281 Query End:373 Subject Strand: null Subject Start: 15 Subject End: 45 ........................................................................................................................................................................................................................................................................................ L E F F T L * I L D S M K I K K Q T R K L A A G C S K H C F 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 .............................. HSP 2 e-value: 7.0E-7 bit: 27.3 Len: 33 Query Start:235 Query End:267 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: 3.0E-6 bit: 44.7 Len: 60 Query Start:281 Query End:340 Subject Strand: null Subject Start: 1 Subject End: 20 ........................................................................................................................................................................................................................................................................................ M K I K K Q T R K L A A G C S K H C F E ............................................................... ........................................................................................................................................................................................................................................................................................ M K I K E Q T R K L A A G C S K H C F E ............................................................... HSP 2 e-value: 3.0E-6 bit: 28.1 Len: 33 Query Start:235 Query End:267 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 ........................................................................................................................................ Subject: UniRef90_O05164 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae|Rep: Hypothetical protein - Streptococcus pneumoniae HSP 1 e-value: 7.0E-6 bit: 39.3 Len: 81 Query Start:291 Query End:371 Subject Strand: null Subject Start: 26 Subject End: 49 .................................................................................................................................................................................................................................................................................................. C F E Q P A A S F L V C F L I F I E S N I Y N V K N S ................................ .................................................................................................................................................................................................................................................................................................. C F E Q P A A S F L V C S L I F I E - - - Y K N K N T ................................ HSP 2 e-value: 7.0E-6 bit: 32.3 Len: 45 Query Start:226 Query End:270 Subject Strand: null Subject Start: 4 Subject End: 18 ................................................................................................................................................................................................................................. Y S L I L F E N L F K P R Q L ..................................................................................................................................... ................................................................................................................................................................................................................................. Y D L I L F E N L F K P R Q L ..................................................................................................................................... taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctatcagttcattgatagttagagtttttt Predict ORF larger than 30AA ================================================ Protein_Len: 38 Strand: + Start: 205 End: 318 ............................................................................................................................................................................................................ M T L A S I Y Y S L I L F E N L F K P R Q L Y L P P Q N S V L S N L R L A S ..................................................................................... Protein_Len: 32 Strand: - Start: 257 End: 352 ................................................................................................................................................................................................................................................................ V V D A R D A V E F C H K S C G A A L K R T Q K K I K M S D L M ................................................... taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctatcagttcattgatagttagagtttttt 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================================================ taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctatcagttcattgatagttagagtttttt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1597:SMT_1598|SMT_1597:SMT_1598:K02032 peptide/nickel transport system ATP-binding protein:malolactic regulator, LysR family:-><-:1588048..1588450 403 taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnctatcagttcattgatagttagagtttttt Intra-Species Hit: Count: 1 Min: 1 Max: 403 Len: 403 Subject: smit_SMT_1597_SMT_1598|K02032 peptide/nickel transport system ATP-binding protein:malolactic regulator, LysR family|POSITIVE:NEGATIVE|[1588048,1588450]|403 HSP 1 e-value: 1.0E-124 bit: 446.0 Len: 225 Query Start:1 Query End:225 Subject Strand: POSITIVE Subject Start: 1 Subject End: 225 taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctac.................................................................................................................................................................................. taatggttttataatttccatgtcaacttttatggaaattataaaccttttttgttggactgatttgaaaaaactttgaaagaattttcgaaagaaatagaattcttagaaaatcattgaattatagtgagatgaaataaaatctgaacaactcgattaggaaagtcaaattaatttctagaaaaggtttagaagtcgcggcgtattactctagcttcaatctac.................................................................................................................................................................................. HSP 2 e-value: 6.0E-8 bit: 60.0 Len: 30 Query Start:374 Query End:403 Subject Strand: POSITIVE Subject Start: 374 Subject End: 403 .....................................................................................................................................................................................................................................................................................................................................................................................ctatcagttcattgatagttagagtttttt .....................................................................................................................................................................................................................................................................................................................................................................................ctatcagttcattgatagttagagtttttt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAUGGUUUUAUAAUUUCCAUGUCAACUUUUAUGGAAAUUAUAAACCUUUUUUGUUGGACUGAUUUGAAAAAACUUUGAAAGAAUUUUCGAAAGAAAUAGAAUUCUUAGAAAAUCAUUGAAUUAUAGUGAGAUGAAAUAAAAUCUGAACAACUCGAUUAGGAAAGUCAAAUUAAUUUCUAGAAAAGGUUUAGAAGUCGCGGCGUAUUACUCUAGCUUCAAUCUACUAUAGUCUAAUACUCUUCGAAAAUCUCUUCAAACCACGUCAGCUCUAUCUGCCACCUCAAAACAGUGUUUUGAGCAACCUGCGGCUAGCUUCCUAGUUUGCUUUUUGAUUUUCAUUGAGUCUAAUAUCUACAAUGUAAAAAACUCUAGCUAUCAGUUCAUUGAUAGUUAGAGUUUUUU ....(((((.((((((((((((........))))))))))))))))).....(((((((((.(................((((((((((....))....)))))))).((((((((..((......((.((((........))))..)).....(((((((((.................((...(((((.(((((((.((.((((((..(((..............)))..)))))).)).)))......)))))))))...))....(((.((((...((((((((...))))))))......)))).))).)))))))))...))..))))))))..).)))))))))..........(((((((((((((((((((....))))))))))))))))))) (-106.94) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAAACUCUAACUAUCAAUGAACUGAUAGCUAGAGUUUUUUACAUUGUAGAUAUUAGACUCAAUGAAAAUCAAAAAGCAAACUAGGAAGCUAGCCGCAGGUUGCUCAAAACACUGUUUUGAGGUGGCAGAUAGAGCUGACGUGGUUUGAAGAGAUUUUCGAAGAGUAUUAGACUAUAGUAGAUUGAAGCUAGAGUAAUACGCCGCGACUUCUAAACCUUUUCUAGAAAUUAAUUUGACUUUCCUAAUCGAGUUGUUCAGAUUUUAUUUCAUCUCACUAUAAUUCAAUGAUUUUCUAAGAAUUCUAUUUCUUUCGAAAAUUCUUUCAAAGUUUUUUCAAAUCAGUCCAACAAAAAAGGUUUAUAAUUUCCAUAAAAGUUGACAUGGAAAUUAUAAAACCAUUA (((((((((((.((((((......)))))).)))))))))))...((((.......((.(((...............((...((((....))))..))..((..((((((((...))))))).)..)).....)))))(((.(((((((((((((((((.(((((.((((..(.((((((((((.((((.((((((.............(((((.........)))))..((((((((.........)))))))).....)))))))))))))).)))))).)..)))).(((((.(((((......)))))..))))).))))).))))))))))))))))))))..))))....((((((((((((((((..........))))))))))).))))).... (-101.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 867 330 281 81 32 smit:SMT_123|5end_hypothetical_protein_75391..75621_POSITIVE 769 340 291 91 42 smit:SMT_1494|5end_nucleoside_diphosphate_kinase_1479500..1479730_POSITIVE 760 277 232 166 120 smit:SMT_1783|5end_peptide_methionine_sulfoxide_reductase_1759756..1759986_POSITIVE 758 345 303 225 183 smit:SMT_1535|5end_exodeoxyribonuclease_V_alpha_chain_1518067..1518297_POSITIVE 743 340 291 91 42 smit:SMT_1911|5end_hypothetical_protein_1857614..1857844_POSITIVE 735 298 253 231 186 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 731 310 262 61 13 smit:SMT_2086|5end_hypothetical_protein_1983696..1983926_NEGATIVE 722 348 303 208 165 smit:SMT_2133|5end_hypothetical_protein_2014007..2014237_NEGATIVE 722 348 303 208 165 smit:SMT_872|5end_hypothetical_protein_820618..820848_NEGATIVE 722 348 303 208 165 smit:SMT_385|5end_hypothetical_protein_319895..320125_POSITIVE 719 288 241 218 171 smit:SMT_1592|5end_putative_hemolysin_1579655..1579885_POSITIVE 718 309 261 231 183 smit:SMT_1026|5end_sucrose_phosphorylase_962324..962554_NEGATIVE 677 319 271 231 183 smit:SMT_604|5end_DNA_polymerase_III,_epsilon_chain_518693..518923_POSITIVE 664 340 291 91 42 smit:SMT_867|5end_hypothetical_protein_816316..816546_POSITIVE 638 340 296 194 150 smit:SMT_740|5end_50S_ribosomal_protein_L10_644116..644346_NEGATIVE 531 278 232 215 167 smit:SMT_1139|5end_rRNA_(guanine-N1-)-methyltransferase_1079755..1079985_POSITIVE 507 278 235 196 152 smit:SMT_236|5end_ribosomal_small_subunit_pseudouridine_synthase_A_174625..174855_POSITIVE 500 268 223 230 185 smit:SMT_496|5end_superoxide_dismutase,_manganese-dependent_430433..430663_POSITIVE 499 334 303 231 200 smit:SMT_662|5end_A/G-specific_adenine_glycosylase_573827..574057_NEGATIVE 488 269 234 231 195 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 849 310 262 54 6 smit:SMT_1625|3end_DNA_polymerase_IV_1615066..1615216_POSITIVE 844 340 291 80 31 smit:SMT_451|3end_thiamine-phosphate_pyrophosphorylase_389647..389797_POSITIVE 838 330 282 74 26 smit:SMT_1075|3end_hypothetical_protein_1013870..1014020_POSITIVE 785 330 281 60 11 smit:SMT_235|3end_hypothetical_protein_174391..174541_POSITIVE 760 277 232 70 24 smit:SMT_1782|3end_hypothetical_protein_1759740..1759890_POSITIVE 757 340 293 50 3 smit:SMT_1217|3end_hypothetical_protein_1176166..1176316_NEGATIVE 743 340 291 51 2 smit:SMT_1910|3end_pyruvate-formate_lyase_activating_enzyme_1857654..1857804_POSITIVE 722 348 303 93 50 smit:SMT_2134|3end_hypothetical_protein_2014122..2014272_NEGATIVE 722 348 303 93 50 smit:SMT_873|3end_hypothetical_protein_820733..820883_NEGATIVE 722 348 303 93 50 smit:SMT_384|3end_hypothetical_protein_319860..320010_POSITIVE 696 345 305 89 49 smit:SMT_1670|3end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_1659295..1659445_POSITIVE 696 345 305 68 28 smit:SMT_1068|3end_ATP-dependent_DNA_helicase_RecG_1008986..1009136_POSITIVE 696 345 305 51 11 smit:SMT_916|3end_3-hydroxy-3-methylglutaryl-CoA_reductase_868730..868880_NEGATIVE 679 345 303 53 11 smit:SMT_663|3end_phosphate_acetyltransferase_574016..574166_NEGATIVE 672 345 303 89 47 smit:SMT_1689|3end_PTS_enzyme,_maltose-and_glucose-specific,_factor_II_homologue_1673139..1673289_POSITIVE 645 345 307 39 1 smit:SMT_1356|3end_fibronectin-binding_protein-like_protein_A_1334269..1334419_POSITIVE 645 310 262 54 6 smit:SMT_951|3end_oxidoreductase,_DadA_family_protein/D-amino_acid_oxidase_898995..899145_NEGATIVE 625 278 235 139 100 smit:SMT_123|3end_hypothetical_protein_75623..75773_POSITIVE 617 345 306 44 1 smit:SMT_1535|3end_exodeoxyribonuclease_V_alpha_chain_1520513..1520663_POSITIVE 422 278 235 74 35 smit:SMT_131|3end_phosphatase,_putative_83031..83181_NEGATIVE