Origin IGS: tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc .........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 gagttaaacaactcaaatgattgacttttaaattttaaaggtttatactgaaaaacgaaaacggtaggtgaggctaccatagggatacggatgactaccgcaaagcagtggagacactactcgttggtcaacagtcctggtcgcgaaggccaagactaagctcattacattgccctatggagttaaagcttgaacgaaaaacagataattagttttttaatcctgccattttatggtgggattttctactgtttaaatcaaagaaaggagatagacgatgcaaattgacgatcatccggaaccgcacatacacagccaatcgctgatttgtgtcattctgcccttataaagtgattggtctctgtgtatgaaacacatcattcatacagataggagaaacca Mask Tandem Repeat Region ================================================ tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Find is-nt database================================================ Query_seq: SMT_1708:SMT_1709|SMT_1708:SMT_1709:magnesium-translocating P-type ATPase:aminopeptidase P:<-<-:1694644..1695045 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1708:SMT_1709|SMT_1708:SMT_1709:magnesium-translocating P-type ATPase:aminopeptidase P:<-<-:1694644..1695045 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1708:SMT_1709|SMT_1708:SMT_1709:magnesium-translocating P-type ATPase:aminopeptidase P:<-<-:1694644..1695045 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Predict ORF larger than 30AA ================================================ Protein_Len: 36 Strand: + Start: 84 End: 191 ................................................................................... M A V Y V R F R M I V N L H R L S P F F D L N S R K S H H K M A G L K N ................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 238 End: 357 ............................................................................................................................................................................................................................................. M S L V L A F A T R T V D Q R V V S P L L C G S H P Y P Y G S L T Y R F R F S V ............................................. Protein_Len: 30 Strand: + Start: 311 End: 400 ...................................................................................................................................................................................................................................................................................................................... M R I P M V A S P T V F V F Q Y K P L K F K S Q S F E L F N .. Protein_Len: 34 Strand: - Start: 194 End: 295 ................................................................................................................................................................................................. N D T K R E L K L E M P C H L S S L R P R R S W S Q Q G V L L T E M ........................................................................................................... Protein_Len: 32 Strand: - Start: 118 End: 213 ..................................................................................................................... N A D D I E K R Q N L C Y F I G G Y F P L I L F S I I Q K E N M ............................................................................................................................................................................................. Protein_Len: 32 Strand: - Start: 80 End: 175 ............................................................................... R N A T Y T R N R I I T L K C R R D G K K S K F L L F D W W L M ................................................................................................................................................................................................................................... tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc 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: 86 Start: 354 End: 383 .................................................................................................................................................................................................................................................................................................................................................................ATTGACTTTTAAATTTTAAAGGTTTATACT................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -8.3 Tail_Score: -4.58303 Start: 162 End: 182 Full_Region: taattagttttttaa tcctgccat ttt atggtggga ttttctactgtttaa .................................................................................................................................................................tcctgccattttatggtggga............................................................................................................................................................................................................................ Find igs database================================================ Query_seq: SMT_1708:SMT_1709|SMT_1708:SMT_1709:magnesium-translocating P-type ATPase:aminopeptidase P:<-<-:1694644..1695045 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Intra-Species Hit: Count: 2 Min: 1 Max: 402 Len: 402 Subject: smit_SMT_1708_SMT_1709|magnesium-translocating P-type ATPase:aminopeptidase P|NEGATIVE:NEGATIVE|[1694644,1695045]|402 HSP 1 e-value: 0.0 bit: 797.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Subject: smit_SMT_1710_SMT_1711|magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase|NEGATIVE:NEGATIVE|[1696121,1696522]|402 HSP 1 e-value: 0.0 bit: 789.0 Len: 402 Query Start:1 Query End:402 Subject Strand: POSITIVE Subject Start: 1 Subject End: 402 tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc tggtttctcctatctgtatgaatgatgtgtttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctttgatttaaacagtagaaaatcccaccataaaatggcaggattaaaaaactaattatctgtttttcgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccgttttcgtttttcagtataaacctttaaaatttaaaagtcaatcatttgagttgtttaactc Inter-species Hit: Count: 2 Min: 30 Max: 341 Len: 312 Subject: NC_009009_SSA_1735_SSA_1736|UreX, putative:L-cysteine desulfhydrase, putative|NEGATIVE:NEGATIVE|[1721163,1721542]|380 HSP 1 e-value: 7.0E-54 bit: 212.0 Len: 135 Query Start:207 Query End:341 Subject Strand: POSITIVE Subject Start: 163 Subject End: 297 ..............................................................................................................................................................................................................cgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccg............................................................. ..............................................................................................................................................................................................................cgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccg............................................................. Subject: NC_009009_SSA_1734_SSA_1735|Cation (Mg/Ni uptake) transport ATPase, putative:UreX, putative|NEGATIVE:NEGATIVE|[1720394,1720550]|157 HSP 1 e-value: 2.0E-38 bit: 161.0 Len: 113 Query Start:30 Query End:142 Subject Strand: POSITIVE Subject Start: 30 Subject End: 142 .............................tttcatacacagagaccaatcactttataagggcagaatgacacaaatcagcgattggctgtgtatgtgcggttccggatgatcgtcaatttgcatcgtctatctcctttctt.................................................................................................................................................................................................................................................................... .............................tttcatacacagggaccaatcactttatgaggacagaacgacacaaatcagcgattggctgtgtatgtgcggttccggataatcgtcaatttgcatcgcatgtctcctttctt.................................................................................................................................................................................................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUCAUACACAGAGACCAAUCACUUUAUAAGGGCAGAAUGACACAAAUCAGCGAUUGGCUGUGUAUGUGCGGUUCCGGAUGAUCGUCAAUUUGCAUCGUCUAUCUCCUUUCUUUGAUUUAAACAGUAGAAAAUCCCACCAUAAAAUGGCAGGAUUAAAAAACUAAUUAUCUGUUUUUCGUUCAAGCUUUAACUCCAUAGGGCAAUGUAAUGAGCUUAGUCUUGGCCUUCGCGACCAGGACUGUUGACCAACGAGUAGUGUCUCCACUGCUUUGCGGUAGUCAUCCGUAUCCCUAUGGUAGCCUCACCUACCG ...(((((((((...((((((.((.......(.........).......)).)))))))))))))))...((...((((((((..((..........(((...(((......((((...(((((((((..(((((..((((...))))..)))))......))).....)))))).....))))((((((......))))))........)))..(((((((((.(.....).)))))))))..)))....((((((((....))))))))...))..))))))))...))....(((((......))))). (-80.64) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUAGGUGAGGCUACCAUAGGGAUACGGAUGACUACCGCAAAGCAGUGGAGACACUACUCGUUGGUCAACAGUCCUGGUCGCGAAGGCCAAGACUAAGCUCAUUACAUUGCCCUAUGGAGUUAAAGCUUGAACGAAAAACAGAUAAUUAGUUUUUUAAUCCUGCCAUUUUAUGGUGGGAUUUUCUACUGUUUAAAUCAAAGAAAGGAGAUAGACGAUGCAAAUUGACGAUCAUCCGGAACCGCACAUACACAGCCAAUCGCUGAUUUGUGUCAUUCUGCCCUUAUAAAGUGAUUGGUCUCUGUGUAUGAAA ((((((((..((((.((((((((.......((((((.((...((.((((....)))).)))).))))))..((((.(((((.....))))).))))...............))))))))))))...)))).......((((((.....(((......(((((..((((...))))..)))))..)))))))))............((((((...((((....))))...))).)))...))))..((((((((((((((((((.....(.((......)).)......)))))))))...)))))))))... (-97.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1014 80 31 200 151 smit:SMT_1710|5end_magnesium-translocating_P-type_ATPase_1696030..1696260_NEGATIVE 1014 80 31 200 151 smit:SMT_1708|5end_magnesium-translocating_P-type_ATPase_1694553..1694783_NEGATIVE 359 76 31 63 16 smit:SMT_1213|5end_fatty_acid/phospholipid_synthesis_protein_PlsX_1172655..1172885_NEGATIVE 342 258 212 64 10 smit:SMT_302|5end_K07444_putative_N6-adenine-specific_DNA_methylase_244808..245038_POSITIVE 337 257 211 221 156 smit:SMT_2051|5end_enoyl-CoA_hydratase_1960639..1960869_NEGATIVE 336 299 256 150 98 smit:SMT_217|5end_hypothetical_protein_149236..149466_POSITIVE 329 278 231 122 66 smit:SMT_712|5end_alcohol_dehydrogenase,_zinc-containing_620381..620611_NEGATIVE 326 308 262 84 30 smit:SMT_749|5end_shikimate_kinase_653971..654201_NEGATIVE 325 303 263 66 21 smit:SMT_2134|5end_hypothetical_protein_2014700..2014930_NEGATIVE 325 96 51 222 158 smit:SMT_1825|5end_ATP_synthase_F1,_gamma_subunit_1796927..1797157_POSITIVE 325 308 261 139 86 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 325 303 263 66 21 smit:SMT_873|5end_hypothetical_protein_821311..821541_NEGATIVE 320 250 205 207 155 smit:SMT_1840|5end_6-phosphogluconate_dehydrogenase,_decarboxylating_1806285..1806515_NEGATIVE 318 310 269 102 61 smit:SMT_1838|5end_response_regulator_1805400..1805630_NEGATIVE 318 283 255 91 56 smit:SMT_479|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_416656..416886_NEGATIVE 318 283 255 91 56 smit:SMT_462|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_401658..401888_NEGATIVE 316 278 237 219 169 smit:SMT_540|5end_DNA_gyrase,_B_subunit_456358..456588_POSITIVE 314 304 262 185 145 smit:SMT_877|5end_hypothetical_protein_824412..824642_NEGATIVE 311 260 214 219 169 smit:SMT_382|5end_valyl-tRNA_synthetase_317706..317936_POSITIVE 307 303 265 112 74 smit:SMT_885|5end_single-stranded-DNA-specific_exonuclease_RecJ_832660..832890_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 520 310 284 27 1 smit:SMT_1711|3end_Xaa-Pro_dipeptidase_1696433..1696583_NEGATIVE 359 76 31 66 19 smit:SMT_1214|3end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1172652..1172802_NEGATIVE 337 270 221 130 78 smit:SMT_494|3end_K04767_acetoin_utilization_protein_AcuB_428891..429041_POSITIVE 337 240 197 84 37 smit:SMT_362|3end_K02519_translation_initiation_factor_IF-2_297950..298100_POSITIVE 334 99 57 39 1 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 326 308 262 91 37 smit:SMT_750|3end_3-phosphoshikimate_1-carboxyvinyltransferase_653964..654114_NEGATIVE 325 308 261 142 89 smit:SMT_1644|3end_3-isopropylmalate_dehydrogenase_1631821..1631971_POSITIVE 320 250 205 131 79 smit:SMT_1841|3end_hypothetical_protein_1806361..1806511_NEGATIVE 320 250 205 131 79 smit:SMT_303|3end_hypothetical_protein_245758..245908_POSITIVE 318 310 269 90 49 smit:SMT_1839|3end_6-phosphogluconate_dehydrogenase,_decarboxylating_1805412..1805562_NEGATIVE 314 268 221 118 65 smit:SMT_2081|3end_glycosyltransferase_1981336..1981486_POSITIVE 312 100 51 61 4 smit:SMT_1941|3end_hypothetical_protein_1877663..1877813_POSITIVE 311 80 31 64 4 smit:SMT_325|3end_K02029_polar_amino_acid_transport_system_permease_protein_262247..262397_NEGATIVE 310 291 256 150 117 smit:SMT_216|3end_Holliday_junction_DNA_helicase_RuvB_149335..149485_POSITIVE 308 237 197 149 106 smit:SMT_1958|3end_tryptophan_synthase,_beta_subunit_1892052..1892202_POSITIVE 306 288 241 86 42 smit:SMT_1751|3end_indole-3-glycerol_phosphate_synthase_1729865..1730015_POSITIVE 306 115 71 112 59 smit:SMT_771|3end_spermidine/putrescine_transport_system_permease_protein_PotB_681356..681506_NEGATIVE 302 307 261 55 2 smit:SMT_2015|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1932839..1932989_POSITIVE 301 86 49 36 1 smit:SMT_2025|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1940995..1941145_NEGATIVE 301 307 261 112 64 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE