Origin IGS: aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga .........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 tcttggtgagaatgtacaaacaaaaaaagaatcaggtttatcacctgattcttttggctctttgtcaaatagtgttgatgaagaacctaatgaaaaaagaatccaacaaaaattggactacctgtctccggttgaataccgaagacggtagccctagggtgtttttattaaattctcactttttggggtcagtccctaagcctgatagtaattttttgttcatactattcccct Mask Tandem Repeat Region ================================================ aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Find is-nt database================================================ Query_seq: SMT_241:SMT_242|SMT_241:SMT_242:hypothetical protein predicted by Glimmer/Critica:PTS system, mannose-specific IID component:-><-:179019..179252 234 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_241:SMT_242|SMT_241:SMT_242:hypothetical protein predicted by Glimmer/Critica:PTS system, mannose-specific IID component:-><-:179019..179252 234 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_241:SMT_242|SMT_241:SMT_242:hypothetical protein predicted by Glimmer/Critica:PTS system, mannose-specific IID component:-><-:179019..179252 234 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 133 End: 234 .................................................................................................................................... M L F S L G S S S T L F D K E P K E S G D K P D S F F V C T F S P R Protein_Len: 60 Strand: - Start: 2 End: 232 . F H S N L L F V R P S G D E T N L R L C T T W N K N S E K K M L N K M L V I Q C L A L L I L H Y V Q N K K Q K Y M R V M .. aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga 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================================================ aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -13.3 Tail_Score: -5.14645 Start: 79 End: 122 Full_Region: TTAATAAAAACACCC TAGGGCTACCGTCTTCGGT ATTCA ACCGGAGACAGGTAGTCCAA TTTTTGTTGGATTCT ..............................................................................TAGGGCTACCGTCTTCGGTATTCAACCGGAGACAGGTAGTCCAA................................................................................................................ TransTerm Strand: + Conf: 100 HP_score: -15.9 Tail_Score: -2.79212 Start: 81 End: 120 Full_Region: AATAAAAACACCCTA GGGCTACCGTCTTCGGT ATTCA ACCGGAGACAGGTAGTCC AATTTTTGTTGGATT ................................................................................GGGCTACCGTCTTCGGTATTCAACCGGAGACAGGTAGTCC.................................................................................................................. TransTerm Strand: + Conf: 100 HP_score: -10.7 Tail_Score: -6.02919 Start: 184 End: 206 Full_Region: GACAAAGAGCCAAAA GAATCAGGT GATAA ACCTGATTC TTTTTTTGTTTGTAC .......................................................................................................................................................................................GAATCAGGTGATAAACCTGATTC............................ Find igs database================================================ Query_seq: SMT_241:SMT_242|SMT_241:SMT_242:hypothetical protein predicted by Glimmer/Critica:PTS system, mannose-specific IID component:-><-:179019..179252 234 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Intra-Species Hit: Count: 1 Min: 1 Max: 234 Len: 234 Subject: smit_SMT_241_SMT_242|hypothetical protein predicted by Glimmer/Critica:PTS system, mannose-specific IID component|POSITIVE:NEGATIVE|[179019,179252]|234 HSP 1 e-value: 1.0E-117 bit: 422.0 Len: 234 Query Start:1 Query End:234 Subject Strand: POSITIVE Subject Start: 1 Subject End: 234 aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattcnnnnnnngtttgtacattctcaccaaga aggggaatagtatgaacaaaaaattactatcaggcttagggactgaccccaaaaagtgagaatttaataaaaacaccctagggctaccgtcttcggtattcaaccggagacaggtagtccaatttttgttggattcttttttcattaggttcttcatcaacactatttgacaaagagccaaaagaatcaggtgataaacctgattctttttttgtttgtacattctcaccaaga Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGGGGAAUAGUAUGAACAAAAAAUUACUAUCAGGCUUAGGGACUGACCCCAAAAAGUGAGAAUUUAAUAAAAACACCCUAGGGCUACCGUCUUCGGUAUUCAACCGGAGACAGGUAGUCCAAUUUUUGUUGGAUUCUUUUUUCAUUAGGUUCUUCAUCAACACUAUUUGACAAAGAGCCAAAAGAAUCAGGUGAUAAACCUGAUUCUUUUUUUGUUUGUACAUUCUCACCAAGA ..((((((.(((..((((((((................(((......))).......((((((((((((((((.......(((((((((((((((((.....))))))))).))))))))..)))))))))))))))).........(((((((..((((......))))..)))))))..(((((((((((.....)))))))))))))))))))..)))))))))....... (-88.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCUUGGUGAGAAUGUACAAACAAAAAAAGAAUCAGGUUUAUCACCUGAUUCUUUUGGCUCUUUGUCAAAUAGUGUUGAUGAAGAACCUAAUGAAAAAAGAAUCCAACAAAAAUUGGACUACCUGUCUCCGGUUGAAUACCGAAGACGGUAGCCCUAGGGUGUUUUUAUUAAAUUCUCACUUUUUGGGGUCAGUCCCUAAGCCUGAUAGUAAUUUUUUGUUCAUACUAUUCCCCU ....(((((((((...........(((((((((((((.....)))))))))))))((.((((..((((......))))..)))).)).((((((((....((((..........((.(((((.((((.((((.....)))).))))))))).))..)))).))))))))..))))))))).(((((((.....)))))))...(((((((............)))))))..... (-72.70) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 321 118 75 75 24 smit:SMT_944|5end_PhnA_protein_895106..895336_NEGATIVE 313 119 74 196 160 smit:SMT_1626|5end_undecaprenyl-diphosphatase_1616028..1616258_NEGATIVE 307 127 81 97 46 smit:SMT_816|5end_SWF/SNF_family_helicase_727440..727670_NEGATIVE 306 115 76 74 27 smit:SMT_1934|5end_homoserine_dehydrogenase_1872402..1872632_POSITIVE 304 113 75 96 54 smit:SMT_1797|5end_threonine_dehydratase_1772684..1772914_NEGATIVE 296 114 75 216 171 smit:SMT_447|5end_ABC-type_cobalt_transport_system,_permease_component_CbiQ_related_transporter_386257..386487_POSITIVE 293 140 94 191 139 smit:SMT_1083|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1020829..1021059_POSITIVE 293 120 76 100 44 smit:SMT_847|5end_thioredoxin_reductase_792800..793030_POSITIVE 292 201 162 81 45 smit:SMT_226|5end_putative_L-glutamine-D-fructose-6-phosphate_amidotransferase_163630..163860_POSITIVE 290 117 75 178 134 smit:SMT_2052|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1961591..1961821_NEGATIVE 288 120 82 205 155 smit:SMT_1358|5end_dihydroorotate_dehydrogenase_B_1337192..1337422_NEGATIVE 284 61 26 59 18 smit:SMT_2053|5end_hypothetical_membrane_associated_protein_1964422..1964652_NEGATIVE 275 115 76 213 166 smit:SMT_485|5end_hypothetical_protein_421401..421631_NEGATIVE 274 114 71 214 162 smit:SMT_2110|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999163..1999393_POSITIVE 273 115 74 224 179 smit:SMT_690|5end_pyrimidine_regulatory_protein_602168..602398_NEGATIVE 271 115 72 119 77 smit:SMT_2109|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1999099..1999329_NEGATIVE 269 120 80 109 54 smit:SMT_1901|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1850537..1850767_POSITIVE 269 150 106 213 173 smit:SMT_1590|5end_DNA-entry_nuclease_1578565..1578795_POSITIVE 266 119 80 224 196 smit:SMT_1307|5end_glycerol_uptake_facilitator_protein_1271664..1271894_POSITIVE 265 111 74 201 165 smit:SMT_624|5end_K07584_hypothetical_protein_529870..530100_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 483 179 137 107 65 smit:SMT_238|3end_hypothetical_protein_predicted_by_Glimmer/Critica_176945..177095_NEGATIVE 360 179 135 51 1 smit:SMT_1157|3end_septation_ring_formation_regulator_EzrA_1100202..1100352_NEGATIVE 313 119 74 135 99 smit:SMT_1627|3end_hypothetical_protein_1616089..1616239_NEGATIVE 306 61 28 83 46 smit:SMT_735|3end_putative_transposase,_ISSmu1_641395..641545_POSITIVE 288 186 145 51 7 smit:SMT_865|3end_50S_ribosomal_protein_L1_815022..815172_NEGATIVE 272 119 77 41 5 smit:SMT_1695|3end_ribulose-phosphate_3-epimerase_1678299..1678449_POSITIVE 271 120 76 60 10 smit:SMT_1946|3end_sucrose-6-phosphate_hydrolase_1881205..1881355_POSITIVE 270 122 89 135 103 smit:SMT_1082|3end_Cof_family_protein_1020877..1021027_POSITIVE 269 120 80 112 57 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 269 115 72 148 95 smit:SMT_1633|3end_formate--tetrahydrofolate_ligase_1620990..1621140_POSITIVE 265 111 74 63 27 smit:SMT_623|3end_50S_ribosomal_protein_L21_529812..529962_POSITIVE 264 120 75 49 5 smit:SMT_606|3end_cytochrome_c-type_biogenesis_protein_CcdA_520147..520297_POSITIVE 262 120 80 40 1 smit:SMT_842|3end_hypothetical_protein_788414..788564_NEGATIVE 255 120 76 128 83 smit:SMT_260|3end_phage_transcriptional_repressor_200236..200386_POSITIVE 252 116 77 64 19 smit:SMT_1588|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1578425..1578575_POSITIVE 251 215 176 99 61 smit:SMT_1104|3end_K06346_spoIIIJ-associated_protein_1045795..1045945_NEGATIVE 249 138 92 60 6 smit:SMT_1258|3end_acetolactate_synthase_large_subunit_1223166..1223316_NEGATIVE 249 120 76 62 8 smit:SMT_1212|3end_acyl_carrier_protein,_putative_1171424..1171574_NEGATIVE 248 130 82 133 81 smit:SMT_1160|3end_K03152_4-methyl-5(b-hydroxyethyl)-thiazole_monophosphate_biosynthesis_1104620..1104770_NEGATIVE 245 129 94 57 15 smit:SMT_1353|3end_GTP-binding_protein_1330690..1330840_NEGATIVE