Origin IGS: cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cataaaggcaaaggctgggcaaccagtctttttcgatgtttatagactagtcaggcaagtaagctaggataggaatctttttggcgctaagattttaagagaagagactgcaagaaggggtagatttatgataaaatagaagtctaagaagcgaatgaagagagtaag Mask Tandem Repeat Region ================================================ cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Find is-nt database================================================ Query_seq: SMT_1619:SMT_1620|SMT_1619:SMT_1620:K02006 cobalt transport system ATP-binding protein:hypothetical protein:<-<-:1606617..1606784 168 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1619:SMT_1620|SMT_1619:SMT_1620:K02006 cobalt transport system ATP-binding protein:hypothetical protein:<-<-:1606617..1606784 168 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1619:SMT_1620|SMT_1619:SMT_1620:K02006 cobalt transport system ATP-binding protein:hypothetical protein:<-<-:1606617..1606784 168 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 13 End: 102 ............ M R F L D F Y F I I N L P L L A V S S L K I L A P K R F L S .................................................................. cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg 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================================================ cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1619:SMT_1620|SMT_1619:SMT_1620:K02006 cobalt transport system ATP-binding protein:hypothetical protein:<-<-:1606617..1606784 168 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Intra-Species Hit: Count: 1 Min: 1 Max: 168 Len: 168 Subject: smit_SMT_1619_SMT_1620|K02006 cobalt transport system ATP-binding protein:hypothetical protein|NEGATIVE:NEGATIVE|[1606617,1606784]|168 HSP 1 e-value: 1.0E-90 bit: 333.0 Len: 168 Query Start:1 Query End:168 Subject Strand: POSITIVE Subject Start: 1 Subject End: 168 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctttgcctttatg Inter-species Hit: Count: 3 Min: 1 Max: 158 Len: 158 Subject: NC_003098_spr0429_spr0430|hypothetical protein:ABC transporter ATP-binding protein - cobalt transport|POSITIVE:POSITIVE|[429872,430191]|320 HSP 1 e-value: 9.0E-73 bit: 274.0 Len: 158 Query Start:1 Query End:158 Subject Strand: NEGATIVE Subject Start: 163 Subject End: 320 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctt.......... cttactctcttcattcgcttcttagacttctattttatcataaatcaagcccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctaactaatctataaacatcgaaaaagactagttgcccagcctt.......... Subject: NC_003028_SP_0482_SP_0483|hypothetical protein:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[463540,463904]|365 HSP 1 e-value: 2.0E-70 bit: 266.0 Len: 158 Query Start:1 Query End:158 Subject Strand: NEGATIVE Subject Start: 208 Subject End: 365 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctgactagtctataaacatcgaaaaagactggttgcccagcctt.......... cttactctcttcattcgcttcttagacttctattttatcataaatcaagcccttcttgcagtctctcctcttaaaatcttagcgccaaaaagattcctatcctagcttacttgcctaactaatctataaacatcgaaaaagactagttgcccagcctt.......... Subject: NC_008533_SPD_0433_SPD_0434|hypothetical protein:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[437621,437721]|101 HSP 1 e-value: 6.0E-46 bit: 184.0 Len: 101 Query Start:1 Query End:101 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 101 cttactctcttcattcgcttcttagacttctattttatcataaatctaccccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatc................................................................... cttactctcttcattcgcttcttagacttctattttatcataaatcaagcccttcttgcagtctcttctcttaaaatcttagcgccaaaaagattcctatc................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUACUCUCUUCAUUCGCUUCUUAGACUUCUAUUUUAUCAUAAAUCUACCCCUUCUUGCAGUCUCUUCUCUUAAAAUCUUAGCGCCAAAAAGAUUCCUAUCCUAGCUUACUUGCCUGACUAGUCUAUAAACAUCGAAAAAGACUGGUUGCCCAGCCUU .............((((.((..(((((....((((......))))..............((((...........((((((.........)))))).........((......))..)))).)))))..))...)))).(((.((((....)))).))) (-16.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGGCUGGGCAACCAGUCUUUUUCGAUGUUUAUAGACUAGUCAGGCAAGUAAGCUAGGAUAGGAAUCUUUUUGGCGCUAAGAUUUUAAGAGAAGAGACUGCAAGAAGGGGUAGAUUUAUGAUAAAAUAGAAGUCUAAGAAGCGAAUGAAGAGAGUAAG ((((((((....))))))))................(((..(.(((......))).)..)))...(((((((..((((.(((((((........(((((((........)))).)))...........)))))))....))))...)))))))..... (-35.11) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 894 130 81 221 172 smit:SMT_1619|5end_K02006_cobalt_transport_system_ATP-binding_protein_1606526..1606756_NEGATIVE 321 48 1 62 21 smit:SMT_1667|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1657567..1657797_NEGATIVE 321 48 1 162 121 smit:SMT_1666|5end_hypothetical_protein_1657467..1657697_NEGATIVE 310 70 21 128 75 smit:SMT_908|5end_hypothetical_protein_857230..857460_NEGATIVE 307 74 34 140 87 smit:SMT_2024|5end_hypothetical_protein_1940359..1940589_POSITIVE 307 74 34 140 87 smit:SMT_724|5end_hypothetical_protein_630060..630290_NEGATIVE 296 150 101 177 127 smit:SMT_1826|5end_ATP_synthase_beta_chain_1797408..1797638_POSITIVE 296 150 101 177 127 smit:SMT_586|5end_ATP_synthase_F1,_beta_subunit_502533..502763_POSITIVE 288 62 21 122 79 smit:SMT_1072|5end_Cof_family_protein_1011193..1011423_NEGATIVE 282 97 58 147 108 smit:SMT_495|5end_bacterial_peptide_chain_release_factor_2_(RF-2)_429038..429268_POSITIVE 277 120 80 69 21 smit:SMT_929|5end_hypothetical_protein_883342..883572_NEGATIVE 277 120 80 193 145 smit:SMT_928|5end_hypothetical_protein_883218..883448_NEGATIVE 274 109 62 120 56 smit:SMT_1050|5end_transcriptional_regulator_PlcR,_putative_990380..990610_NEGATIVE 267 60 11 126 76 smit:SMT_651|5end_DNA_ligase_561944..562174_NEGATIVE 260 147 105 79 26 smit:SMT_1167|5end_aminopeptidase_N_1115076..1115306_NEGATIVE 259 97 52 190 147 smit:SMT_219|5end_phosphatidate_cytidylyltransferase_150922..151152_POSITIVE 258 63 29 134 98 smit:SMT_266|5end_S-adenosyl-methyltransferase_204190..204420_POSITIVE 257 150 104 151 107 smit:SMT_2032|5end_hydrolase,_alpha/beta_fold_family_1946421..1946651_NEGATIVE 256 150 102 231 186 smit:SMT_514|5end_tRNA_(guanine-N(1)-)-methyltransferase_441377..441607_POSITIVE 254 109 64 166 100 smit:SMT_189|5end_50S_ribosomal_protein_L15_123832..124062_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 310 70 21 135 82 smit:SMT_909|3end_type_I_restriction_enzyme_M_protein_857223..857373_NEGATIVE 307 74 34 150 97 smit:SMT_725|3end_hypothetical_protein_630050..630200_NEGATIVE 296 150 101 91 41 smit:SMT_1825|3end_ATP_synthase_F1,_gamma_subunit_1797402..1797552_POSITIVE 296 150 101 91 41 smit:SMT_585|3end_ATP_synthase_gamma_chain_502527..502677_POSITIVE 265 60 18 50 1 smit:SMT_1177|3end_immunoglobulin_A1_protease_1129193..1129343_NEGATIVE 250 42 6 44 8 smit:SMT_1541|3end_isopentenyl-diphosphate_delta-isomerase_1525083..1525233_NEGATIVE 247 91 51 60 16 smit:SMT_629|3end_glycogen_synthase_535480..535630_POSITIVE 245 123 84 102 59 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 244 60 30 33 3 smit:SMT_652|3end_transporter,_putative_562037..562187_NEGATIVE 244 133 91 134 93 smit:SMT_309|3end_acyl-carrier-protein_S-malonyltransferase_251406..251556_POSITIVE 242 128 83 50 8 smit:SMT_2083|3end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1983006..1983156_POSITIVE 242 60 11 113 60 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 239 86 42 106 43 smit:SMT_1934|3end_homoserine_dehydrogenase_1873150..1873300_POSITIVE 239 60 27 78 48 smit:SMT_565|3end_polypeptide_deformylase_482762..482912_NEGATIVE 237 64 27 138 105 smit:SMT_1317|3end_glycosyltransferase_1283587..1283737_POSITIVE 237 114 77 150 116 smit:SMT_798|3end_hypothetical_protein_707106..707256_POSITIVE 237 125 86 47 11 smit:SMT_726|3end_ImpB/MucB/SamB_family_protein_630412..630562_NEGATIVE 236 118 73 58 4 smit:SMT_814|3end_UDP-N-acetyl_muramate-alanine_ligase_722332..722482_NEGATIVE 234 101 69 148 124 smit:SMT_399|3end_cytochrome_c-type_biogenesis_protein_CcdA_329156..329306_POSITIVE 233 38 1 126 90 smit:SMT_1723|3end_hypothetical_protein_1709724..1709874_POSITIVE