Origin IGS: aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct .........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 aggcgcctcctagttcattttaatgatacctattctacccaaaaaggcctcaaatttgaagcctttttgtttgtttttaggtatgatttttagggatgtgagataaaacgtgctgtcggtaaaagcaagcccctaccgatacaacctaaaaacactcttcacaactatctccccgtgttttattgactattctagtatagcacacttttagaattaagaaaagacttt Mask Tandem Repeat Region ================================================ aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Find is-nt database================================================ Query_seq: SMT_1804:SMT_1805|SMT_1804:SMT_1805:hypothetical protein:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:->->:1780375..1780602 228 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1804:SMT_1805|SMT_1804:SMT_1805:hypothetical protein:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:->->:1780375..1780602 228 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1804:SMT_1805|SMT_1804:SMT_1805:hypothetical protein:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:->->:1780375..1780602 228 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Predict ORF larger than 30AA ================================================ Protein_Len: 33 Strand: - Start: 21 End: 119 .................... F H A I S S Y D I F C P S I T T F L T K L N Y R Y P S A K V S L M ............................................................................................................. aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct 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: 168 End: 197 .......................................................................................................................................................................CTTCAAATTTGAGGCCTTTTTGGGTAGAAT............................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -12.3 Tail_Score: -4.89966 Start: 160 End: 189 Full_Region: gatacctattctacc caaaaaggcctca aatt tgaagcctttttg tttgtttttaggtat ...............................................................................................................................................................caaaaaggcctcaaatttgaagcctttttg....................................... TransTerm Strand: - Conf: 88 HP_score: -5.5 Tail_Score: -5.63012 Start: 166 End: 183 Full_Region: tattctacccaaaaa ggcctca aatt tgaagcc tttttgtttgttttt .....................................................................................................................................................................ggcctcaaatttgaagcc............................................. Find igs database================================================ Query_seq: SMT_1804:SMT_1805|SMT_1804:SMT_1805:hypothetical protein:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:->->:1780375..1780602 228 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Intra-Species Hit: Count: 1 Min: 1 Max: 228 Len: 228 Subject: smit_SMT_1804_SMT_1805|hypothetical protein:2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative|POSITIVE:POSITIVE|[1780375,1780602]|228 HSP 1 e-value: 1.0E-126 bit: 452.0 Len: 228 Query Start:1 Query End:228 Subject Strand: POSITIVE Subject Start: 1 Subject End: 228 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggcgcct Inter-species Hit: Count: 3 Min: 1 Max: 224 Len: 224 Subject: NC_008533_SPD_1923_SPD_1924|2,3,4, 5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:hypothetical protein|NEGATIVE:NEGATIVE|[1892363,1892591]|229 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 224 Query Start:1 Query End:224 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 229 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatcccta-aaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggc.... aaagtcttttcttaattctaaaagtgtgctatactggaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaaatcatacctaaaaacagacaaaaaggtttcaaatttgaggccttttttggtagaataggtatcattataacgaaccaggaggc.... Subject: NC_003098_spr1907_spr1908|2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase-related protein:hypothetical protein|NEGATIVE:NEGATIVE|[1884831,1885059]|229 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 224 Query Start:1 Query End:224 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 229 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatcccta-aaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggc.... aaagtcttttcttaattctaaaagtgtgctatactggaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaaatcatacctaaaaacagacaaaaaggtttcaaatttgaggccttttttggtagaataggtatcattataacgaaccaggaggc.... Subject: NC_003028_SP_2097_SP_2098|2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, putative:membrane protein|NEGATIVE:NEGATIVE|[2005496,2005724]|229 HSP 1 e-value: 1.0E-103 bit: 375.0 Len: 224 Query Start:1 Query End:224 Subject Strand: NEGATIVE Subject Start: 5 Subject End: 229 aaagtcttttcttaattctaaaagtgtgctatactagaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatcccta-aaaatcatacctaaaaacaaacaaaaaggcttcaaatttgaggcctttttgggtagaataggtatcattaaaatgaactaggaggc.... aaagtcttttcttaattctaaaagtgtgctatactggaatagtcaataaaacacggggagatagttgtgaagagtgtttttaggttgtatcggtaggggcttgcttttaccgacagcacgttttatctcacatccctaaaaaatcatacctaaaaacagacaaaaaggtttcaaatttgaggccttttttggtagaataggtatcattataacgaaccaggaggc.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAGUCUUUUCUUAAUUCUAAAAGUGUGCUAUACUAGAAUAGUCAAUAAAACACGGGGAGAUAGUUGUGAAGAGUGUUUUUAGGUUGUAUCGGUAGGGGCUUGCUUUUACCGACAGCACGUUUUAUCUCACAUCCCUAAAAAUCAUACCUAAAAACAAACAAAAAGGCUUCAAAUUUGAGGCCUUUUUGGGUAGAAUAGGUAUCAUUAAAAUGAACUAGGAGGC .......(((((((.(((.....(((((((((......))))).......)))).((((......(((((.((..........((((..((((((((((....))))))))))))))........)))))))))))....(((.(((((((...((...(((((((((((((....))))))))))))).))....))))))).))).....))).))))))). (-62.18) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GCCUCCUAGUUCAUUUUAAUGAUACCUAUUCUACCCAAAAAGGCCUCAAAUUUGAAGCCUUUUUGUUUGUUUUUAGGUAUGAUUUUUAGGGAUGUGAGAUAAAACGUGCUGUCGGUAAAAGCAAGCCCCUACCGAUACAACCUAAAAACACUCUUCACAACUAUCUCCCCGUGUUUUAUUGACUAUUCUAGUAUAGCACACUUUUAGAAUUAAGAAAAGACUUU ...((.((((((.....(((.(((((((...((..(((((((((.(((....))).)))))))))..))....))))))).)))....(((((((((((.......((.((((((((...(....)...))))))))))............)).)))))......)))).(((((.(((((.......))))).))))).......)))))).))......... (-51.51) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 334 100 53 176 121 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 303 99 52 231 184 smit:SMT_422|5end_K02004_363781..364011_POSITIVE 298 218 171 83 40 smit:SMT_1332|5end_hypothetical_protein_1307576..1307806_NEGATIVE 290 117 71 225 185 smit:SMT_1285|5end_ribosomal_subunit_interface_protein_1247704..1247934_POSITIVE 289 122 86 191 157 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 289 139 93 59 19 smit:SMT_1531|5end_hypothetical_protein_1515997..1516227_NEGATIVE 289 100 51 82 36 smit:SMT_149|5end_hypothetical_protein_predicted_by_Glimmer/Critica_98592..98822_POSITIVE 288 100 52 106 49 smit:SMT_1896|5end_lysine_decarboxylase_1848735..1848965_NEGATIVE 286 137 93 54 1 smit:SMT_2126|5end_indole-3-glycerol_phosphate_synthase_2009107..2009337_POSITIVE 286 137 93 54 1 smit:SMT_1751|5end_indole-3-glycerol_phosphate_synthase_1729012..1729242_POSITIVE 285 94 51 63 14 smit:SMT_830|5end_hypothetical_protein_772623..772853_NEGATIVE 282 100 52 194 133 smit:SMT_1073|5end_L-asparaginase_1011209..1011439_POSITIVE 282 124 83 80 47 smit:SMT_151|5end_K02073_D-methionine_transport_system_substrate-binding_protein_99474..99704_POSITIVE 281 138 92 71 13 smit:SMT_1345|5end_K06198_competence_protein_CoiA_1323770..1324000_NEGATIVE 279 118 76 178 126 smit:SMT_615|5end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_524884..525114_POSITIVE 278 129 82 63 20 smit:SMT_2016|5end_tyrosine_recombinase_1933425..1933655_NEGATIVE 278 120 73 230 195 smit:SMT_225|5end_pullulanase_163529..163759_NEGATIVE 276 127 91 219 182 smit:SMT_1487|5end_hypothetical_protein_1466361..1466591_POSITIVE 275 100 53 228 172 smit:SMT_150|5end_K02030_polar_amino_acid_transport_system_substrate-binding_protein_98787..99017_POSITIVE 274 120 72 230 164 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 312 99 55 110 72 smit:SMT_1216|3end_hypothetical_protein_1175969..1176119_POSITIVE 306 100 54 144 97 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 298 218 171 67 24 smit:SMT_1333|3end_glycosyltransferase_1307592..1307742_NEGATIVE 290 117 71 145 105 smit:SMT_1284|3end_predicted_amidophosphoribosyltransferase_1247704..1247854_POSITIVE 289 139 93 62 22 smit:SMT_1532|3end_hypothetical_protein_1515994..1516144_NEGATIVE 288 100 52 75 18 smit:SMT_1897|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1848766..1848916_NEGATIVE 286 137 93 57 4 smit:SMT_1750|3end_anthranilate_phosphoribosyltransferase_1729095..1729245_POSITIVE 281 100 55 148 104 smit:SMT_594|3end_lysyl-tRNA_synthetase_510348..510498_NEGATIVE 275 100 53 146 90 smit:SMT_149|3end_hypothetical_protein_predicted_by_Glimmer/Critica_98785..98935_POSITIVE 271 100 54 129 92 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 271 128 82 118 55 smit:SMT_1729|3end_exodeoxyribonuclease_VII_small_subunit_1714858..1715008_POSITIVE 271 120 71 61 1 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 270 97 51 141 97 smit:SMT_75|3end_hypothetical_protein_2754..2904_POSITIVE 268 119 76 140 94 smit:SMT_1426|3end_K03095_SprT-like_protein_1410864..1411014_NEGATIVE 266 117 71 113 68 smit:SMT_1806|3end_aminoacylase/N-acyl-L-amino_acid_amidohydrolase/hippurate_hydrolase_1781644..1781794_POSITIVE 265 117 71 147 97 smit:SMT_121|3end_hypothetical_protein_74414..74564_POSITIVE 264 98 54 151 92 smit:SMT_1942|3end_zinc_metalloprotease_ZmpB,_truncated_1878384..1878534_POSITIVE 264 136 91 104 63 smit:SMT_446|3end_ABC-type_cobalt_transport_system,_ATPase_component_386335..386485_POSITIVE 261 100 54 147 97 smit:SMT_713|3end_heat_shock_protein_HtpX_620505..620655_NEGATIVE 257 117 73 130 93 smit:SMT_316|3end_acetyl-CoA_carboxylase_carboxyl_transferase_subunit_alpha_257391..257541_POSITIVE