Origin IGS: ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa .........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 ttcagttccttctttctttcatccattttaccactttttataggagaaggatagcgggaaggtggatttctaagttagtatcttagttttgctctatcttagaaatgaattgtattctcttgcatttgaagtaaaatctaaaaaattccaagattcactcgaaattttattccccaaacaaaaaaacccaatccgatgccccaaaatcgttccagatttttcataaacttccagnnnnnttaattaa Mask Tandem Repeat Region ================================================ ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Find is-nt database================================================ Query_seq: SMT_1862:SMT_1863|SMT_1862:SMT_1863:K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase:->->:1825521..1825767 247 ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1862:SMT_1863|SMT_1862:SMT_1863:K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase:->->:1825521..1825767 247 ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1862:SMT_1863|SMT_1862:SMT_1863:K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase:->->:1825521..1825767 247 ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict ORF larger than 30AA ================================================ Protein_Len: 46 Strand: + Start: 14 End: 151 ............. M E V Y E K S G T I L G H R I G F F C L G N K I S S E S W N F L D F T S N A R E Y N S F L R ................................................................................................ Protein_Len: 48 Strand: - Start: 25 End: 168 ........................ S F D P V I K P C R I P N K Q K P F L I E L S D Q F K K S K V E F A L S Y L E N R L Y L L V L M ............................................................................... Protein_Len: 32 Strand: - Start: 8 End: 103 ....... X X Q F N I F F R S R N Q P M P N P K K T Q P I F N R T F R P M ................................................................................................................................................ Protein_Len: 31 Strand: - Start: 3 End: 95 .. I L X X P L K H F I Q F S K P A D S Q T K K N P S Y F K S H M ........................................................................................................................................................ ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa 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================================================ ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1862:SMT_1863|SMT_1862:SMT_1863:K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase:->->:1825521..1825767 247 ttaattaannnnnctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Intra-Species Hit: Count: 2 Min: 14 Max: 247 Len: 234 Subject: smit_SMT_1862_SMT_1863|K02027 multiple sugar transport system substrate-binding protein:glutamyl aminopeptidase|POSITIVE:POSITIVE|[1825521,1825767]|247 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 234 Query Start:14 Query End:247 Subject Strand: POSITIVE Subject Start: 14 Subject End: 247 .............ctggaagtttatgaaaaatctggaacgattttggggcatcggattgggnnnnnnngtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa .............ctggaagtttatgaaaaatctggaacgattttggggcatcggattgggtttttttgtttggggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Subject: smit_SMT_1745_SMT_1746|UDP-glucose 4-epimerase:glutamyl aminopeptidase|NEGATIVE:POSITIVE|[1725632,1725924]|293 HSP 1 e-value: 4.0E-94 bit: 345.0 Len: 174 Query Start:74 Query End:247 Subject Strand: POSITIVE Subject Start: 120 Subject End: 293 .........................................................................gggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa .........................................................................gggaataaaatttcgagtgaatcttggaattttttagattttacttcaaatgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Inter-species Hit: Count: 3 Min: 123 Max: 247 Len: 125 Subject: NC_008533_SPD_1647_SPD_1648|glutamyl aminopeptidase PepA:NAD-dependent epimerase/dehydratase family protein|NEGATIVE:POSITIVE|[1662045,1662444]|400 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 125 Query Start:123 Query End:247 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 ..........................................................................................................................atgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ..........................................................................................................................atgcaagagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Subject: NC_003098_spr1682_spr1683|Glutamyl aminopeptidase:UDP-galactose 4-epimerase, truncation|NEGATIVE:POSITIVE|[1654514,1654913]|400 HSP 1 e-value: 2.0E-50 bit: 200.0 Len: 125 Query Start:123 Query End:247 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 125 ..........................................................................................................................atgcaagagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ..........................................................................................................................atgcaagagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Subject: NC_003028_SP_1865_SP_1866|glutamyl-aminopeptidase:hypothetical protein|NEGATIVE:POSITIVE|[1772988,1773106]|119 HSP 1 e-value: 6.0E-47 bit: 188.0 Len: 119 Query Start:129 Query End:247 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 119 ................................................................................................................................gagaatacaattcatttctaagatagagcaaaactaagatactaacttagaaatccaccttcccgctatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa ................................................................................................................................gagaatactatccttttctaagatagagcaggactaagatactaacttagaaatccaccttcccactatccttctcctataaaaagtggtaaaatggatgaaagaaagaaggaactgaa Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGCAAGAGAAUACAAUUCAUUUCUAAGAUAGAGCAAAACUAAGAUACUAACUUAGAAAUCCACCUUCCCGCUAUCCUUCUCCUAUAAAAAGUGGUAAAAUGGAUGAAAGAAAGAAGGAACUGAA ...................(((((((((.(((..(........)...))).)))))))))...(((((...((((((.....((((.....))))......))))...))...)))))....... (-19.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCAGUUCCUUCUUUCUUUCAUCCAUUUUACCACUUUUUAUAGGAGAAGGAUAGCGGGAAGGUGGAUUUCUAAGUUAGUAUCUUAGUUUUGCUCUAUCUUAGAAAUGAAUUGUAUUCUCUUGCAU .....(((((.((.((((((.(((..................))))))))).)).))))).....(((((((((..((((.........))))....)))))))))....((((......)))). (-26.67) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 251 95 51 82 23 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 239 109 64 138 101 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 235 110 62 130 89 smit:SMT_1616|5end_putative_ABC-type_cobalamin_Fe3+-siderophores_transport_system_ATPase_component_1603547..1603777_NEGATIVE 234 65 27 195 145 smit:SMT_1043|5end_chaperonin_GroEL_985766..985996_NEGATIVE 232 95 52 178 126 smit:SMT_349|5end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_287207..287437_POSITIVE 229 107 61 80 36 smit:SMT_939|5end_phosphomethylpyrimidine_kinase_892025..892255_NEGATIVE 228 98 62 42 14 smit:SMT_977|5end_conserved_hypothetical_protein,_Rrf2_family_protein_925689..925919_NEGATIVE 226 60 11 132 85 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 226 84 43 50 5 smit:SMT_926|5end_guanylate_kinase_880934..881164_NEGATIVE 221 85 43 116 69 smit:SMT_2027|5end_competence-specific_global_transcription_modulator_1943204..1943434_NEGATIVE 220 45 2 145 109 smit:SMT_602|5end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517192..517422_POSITIVE 219 80 33 70 23 smit:SMT_233|5end_hypothetical_protein_172656..172886_POSITIVE 216 110 61 73 4 smit:SMT_978|5end_hypothetical_protein_926607..926837_NEGATIVE 214 72 32 221 184 smit:SMT_181|5end_50S_ribosomal_protein_L24_120125..120355_POSITIVE 210 85 48 209 168 smit:SMT_1853|5end_1,4-alpha-glucan_branching_enzyme_1818064..1818294_NEGATIVE 210 72 31 178 125 smit:SMT_1210|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1171051..1171281_NEGATIVE 209 97 64 77 48 smit:SMT_520|5end_glutathione_reductase_445285..445515_NEGATIVE 208 96 60 199 161 smit:SMT_1623|5end_K03498_trk_system_potassium_uptake_protein_TrkH_1609596..1609826_POSITIVE 208 83 60 227 202 smit:SMT_1287|5end_50S_ribosomal_protein_L9_1250358..1250588_POSITIVE 208 79 35 117 74 smit:SMT_1205|5end_response_regulator_1165700..1165930_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 239 109 64 151 114 smit:SMT_1088|3end_hypothetical_protein_1024152..1024302_NEGATIVE 238 108 74 62 24 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 237 106 69 68 21 smit:SMT_330|3end_membrane-associated_phospholipid_phosphatase_266187..266337_POSITIVE 235 110 62 133 92 smit:SMT_1617|3end_K02015_iron_complex_transport_system_permease_protein_1603544..1603694_NEGATIVE 234 97 62 54 13 smit:SMT_820|3end_ABC-type_oligopeptide_transport_system,_periplasmic_component_730734..730884_NEGATIVE 229 107 61 90 46 smit:SMT_940|3end_tRNA_pseudouridine_synthase_A_892015..892165_NEGATIVE 226 60 11 51 4 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 226 88 44 109 54 smit:SMT_278|3end_tyrosine-protein_kinase_221048..221198_POSITIVE 220 45 2 128 92 smit:SMT_601|3end_hypothetical_protein_517255..517405_POSITIVE 220 95 53 55 20 smit:SMT_549|3end_hypothetical_cytosolic_protein_467367..467517_POSITIVE 219 97 65 99 71 smit:SMT_1648|3end_hypothetical_protein_1634883..1635033_POSITIVE 219 80 33 51 4 smit:SMT_232|3end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_172717..172867_POSITIVE 214 72 32 142 105 smit:SMT_180|3end_50S_ribosomal_protein_L14_120126..120276_POSITIVE 210 97 52 64 10 smit:SMT_808|3end_hypothetical_protein_predicted_by_Glimmer/Critica_717897..718047_NEGATIVE 208 79 35 120 77 smit:SMT_1206|3end_similar_to_sensor_histidine_kinase_(AgrC_from_Staphylococcus)_1165697..1165847_NEGATIVE 205 117 90 29 1 smit:SMT_2107|3end_tyrosine_recombinase_1998058..1998208_NEGATIVE 205 117 90 29 1 smit:SMT_1405|3end_tyrosine_recombinase_1382080..1382230_NEGATIVE 205 104 62 142 100 smit:SMT_963|3end_K02015_iron_complex_transport_system_permease_protein_908586..908736_NEGATIVE 204 87 57 126 93 smit:SMT_379|3end_acetyltransferase,_GNAT_family_316456..316606_POSITIVE 204 87 57 126 93 smit:SMT_370|3end_acetyltransferase,_GNAT_family_305328..305478_POSITIVE