Origin IGS: ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt .........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 acagtcttctttctagtcttttttctgattgatagttcattatgattattgatccttatgaactgaatgacatcctaatcaacaactatctctcttaatcataatcaaatatcaatagaatgcaaggaaaaagtcgcattcctaaaccataaccaacatagtgagaagtctggaactttcatcccggacttttccttat Mask Tandem Repeat Region ================================================ ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Find is-nt database================================================ Query_seq: SMT_1605:SMT_1606|SMT_1605:SMT_1606:hypothetical protein:glutamate racemase:->->:1595798..1595996 199 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1605:SMT_1606|SMT_1605:SMT_1606:hypothetical protein:glutamate racemase:->->:1595798..1595996 199 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1605:SMT_1606|SMT_1605:SMT_1606:hypothetical protein:glutamate racemase:->->:1595798..1595996 199 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: - Start: 2 End: 112 . L S F D P I F T G S K E S H Q N H N L F A V K E K C E I S I Q N H N L S M ....................................................................................... ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt 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================================================ ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 46 HP_score: -3.2 Tail_Score: -3.31511 Start: 59 End: 82 Full_Region: TTGGTTATGGTTTAG GAATGCGA CTTTTTCC TTGCATTC TATTGATATTTGATT ..........................................................GAATGCGACTTTTTCCTTGCATTC..................................................................................................................... Find igs database================================================ Query_seq: SMT_1605:SMT_1606|SMT_1605:SMT_1606:hypothetical protein:glutamate racemase:->->:1595798..1595996 199 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Intra-Species Hit: Count: 1 Min: 1 Max: 199 Len: 199 Subject: smit_SMT_1605_SMT_1606|hypothetical protein:glutamate racemase|POSITIVE:POSITIVE|[1595798,1595996]|199 HSP 1 e-value: 1.0E-109 bit: 394.0 Len: 199 Query Start:1 Query End:199 Subject Strand: POSITIVE Subject Start: 1 Subject End: 199 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagagatagttgttgattaggatgtcattcagttcataaggatcaataatcataatgaactatcaatcagaaaaaagactagaaagaagactgt Inter-species Hit: Count: 3 Min: 1 Max: 199 Len: 199 Subject: NC_008533_SPD_1661_SPD_1662|glutamate racemase:hypothetical protein|NEGATIVE:NEGATIVE|[1673225,1673430]|206 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 111 Query Start:1 Query End:111 Subject Strand: NEGATIVE Subject Start: 96 Subject End: 206 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ ataaggaaaagtctgggatgaaagttccagacttctcactatgttggttatggtttagggatgagactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ HSP 2 e-value: 5.0E-16 bit: 85.7 Len: 47 Query Start:153 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 47 ........................................................................................................................................................aatcataatgaactatcaatcagaaaaaagactagaaagaagactgt ........................................................................................................................................................aatcataatgaacgatcaatcagaaaaaagactagaaagaagactgt Subject: NC_003098_spr1696_spr1697|glutamate racemase:hypothetical protein|NEGATIVE:NEGATIVE|[1665694,1665899]|206 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 111 Query Start:1 Query End:111 Subject Strand: NEGATIVE Subject Start: 96 Subject End: 206 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ ataaggaaaagtctgggatgaaagttccagacttctcactatgttggttatggtttagggatgagactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ HSP 2 e-value: 5.0E-16 bit: 85.7 Len: 47 Query Start:153 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 47 ........................................................................................................................................................aatcataatgaactatcaatcagaaaaaagactagaaagaagactgt ........................................................................................................................................................aatcataatgaacgatcaatcagaaaaaagactagaaagaagactgt Subject: NC_003028_SP_1881_SP_1882|glutamate racemase:hypothetical protein|NEGATIVE:NEGATIVE|[1784168,1784374]|207 HSP 1 e-value: 2.0E-49 bit: 196.0 Len: 111 Query Start:1 Query End:111 Subject Strand: NEGATIVE Subject Start: 97 Subject End: 207 ataaggaaaagtccgggatgaaagttccagacttctcactatgttggttatggtttaggaatgcgactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ ataaggaaaagtctgggatgaaagttccagacttctcactatgttggttatggtttagggatgagactttttccttgcattctattgatatttgattatgattaagagaga........................................................................................ HSP 2 e-value: 8.0E-12 bit: 71.9 Len: 47 Query Start:153 Query End:199 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 48 ........................................................................................................................................................aatcataatgaactatcaatcagaa-aaaagactagaaagaagactgt ........................................................................................................................................................aatcataatgaacgatcaatcagaaaaaaagactagaaagaagactgt Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAAGGAAAAGUCCGGGAUGAAAGUUCCAGACUUCUCACUAUGUUGGUUAUGGUUUAGGAAUGCGACUUUUUCCUUGCAUUCUAUUGAUAUUUGAUUAUGAUUAAGAGAGAUAGUUGUUGAUUAGGAUGUCAUUCAGUUCAUAAGGAUCAAUAAUCAUAAUGAACUAUCAAUCAGAAAAAAGACUAGAAAGAAGACUGU ...((((.(((((.(((((....))))).))))).)).))..(((..((.((((((.(((((((((........))))))))).((((((.((.((((((((((.....(((..((((.((((.((((...)))))))).))))..)))..)))))))))).)).)))))).........))))))...))..)))... (-47.80) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACAGUCUUCUUUCUAGUCUUUUUUCUGAUUGAUAGUUCAUUAUGAUUAUUGAUCCUUAUGAACUGAAUGACAUCCUAAUCAACAACUAUCUCUCUUAAUCAUAAUCAAAUAUCAAUAGAAUGCAAGGAAAAAGUCGCAUUCCUAAACCAUAACCAACAUAGUGAGAAGUCUGGAACUUUCAUCCCGGACUUUUCCUUAU ...(.(((.(((((.((.....(((((.((((((.((.((((((((((..((...........(((.((......)).)))...........)).)))))))))).)).))))))))))).)).))))).))).)......................((((.(((((((((((..........))))))))))).)))) (-37.85) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 290 44 4 214 175 smit:SMT_1263|5end_hypothetical_protein_1228104..1228334_POSITIVE 279 52 13 211 172 smit:SMT_500|5end_hypothetical_protein_432770..433000_POSITIVE 266 84 43 194 150 smit:SMT_1727|5end_uridine_kinase_1712483..1712713_POSITIVE 261 50 10 210 179 smit:SMT_2123|5end_hypothetical_protein_2008201..2008431_POSITIVE 260 120 72 209 168 smit:SMT_889|5end_K02029_polar_amino_acid_transport_system_permease_protein_836266..836496_POSITIVE 255 127 81 169 122 smit:SMT_1027|5end_K02026_multiple_sugar_transport_system_permease_protein_963474..963704_NEGATIVE 251 69 23 199 144 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 248 43 3 231 191 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 247 47 4 194 161 smit:SMT_191|5end_adenylate_kinase_125745..125975_POSITIVE 246 59 23 128 83 smit:SMT_1441|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1425570..1425800_NEGATIVE 243 60 11 113 62 smit:SMT_930|5end_ATP-dependent_RNA_helicase_884435..884665_NEGATIVE 241 77 34 181 138 smit:SMT_1214|5end_K03584_DNA_repair_protein_RecO_(recombination_protein_O)_1173422..1173652_NEGATIVE 238 36 13 102 74 smit:SMT_1396|5end_uracil-DNA_glycosylase_1372064..1372294_POSITIVE 238 60 13 62 1 smit:SMT_1093|5end_K03073_preprotein_translocase_SecE_subunit_1033926..1034156_NEGATIVE 238 60 11 61 16 smit:SMT_525|5end_30S_ribosomal_protein_S16_450875..451105_POSITIVE 238 41 11 221 187 smit:SMT_220|5end_Hypothetical_zinc_metalloprotease_151747..151977_POSITIVE 236 38 9 227 201 smit:SMT_426|5end_hypothetical_protein_368344..368574_POSITIVE 235 60 12 184 117 smit:SMT_1087|5end_K01990_ABC-2_type_transport_system_ATP-binding_protein_1024165..1024395_NEGATIVE 234 58 13 122 63 smit:SMT_1942|5end_zinc_metalloprotease_ZmpB,_truncated_1877882..1878112_POSITIVE 234 67 23 223 179 smit:SMT_1681|5end_D-alanine-activating_enzyme_1664184..1664414_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 284 50 10 49 17 smit:SMT_2067|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1974216..1974366_POSITIVE 279 52 13 61 22 smit:SMT_498|3end_hypothetical_protein_432700..432850_POSITIVE 266 84 43 84 40 smit:SMT_1726|3end_tRNA_pseudouridine_synthase_B_1712453..1712603_POSITIVE 247 47 4 44 11 smit:SMT_190|3end_preprotein_translocase,_SecY_subunit_125675..125825_POSITIVE 239 126 81 151 105 smit:SMT_1028|3end_ABC-type_sugar_transport_system,_permease_component_963491..963641_NEGATIVE 238 36 13 40 12 smit:SMT_1395|3end_K07025_putative_hydrolase_of_the_HAD_superfamily_1372082..1372232_POSITIVE 238 68 21 87 35 smit:SMT_1300|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1262614..1262764_NEGATIVE 234 67 23 132 88 smit:SMT_1680|3end_hypothetical_protein_1664173..1664323_POSITIVE 233 58 14 72 25 smit:SMT_485|3end_hypothetical_protein_420229..420379_NEGATIVE 232 41 9 69 39 smit:SMT_626|3end_1,4-alpha-glucan_branching_enzyme_531789..531939_POSITIVE 224 40 2 95 58 smit:SMT_516|3end_hypothetical_protein_442527..442677_NEGATIVE 223 60 18 66 24 smit:SMT_1573|3end_MutT/NUDIX_family_protein_1566960..1567110_POSITIVE 220 47 3 60 9 smit:SMT_1008|3end_hypothetical_protein_947524..947674_NEGATIVE 220 77 31 106 66 smit:SMT_554|3end_K09013_Fe-S_cluster_assembly_ATP-binding_protein_472323..472473_POSITIVE 217 80 32 143 97 smit:SMT_1653|3end_hydrolase_1642226..1642376_POSITIVE 217 68 23 92 51 smit:SMT_1066|3end_holo-(acyl_carrier_protein)_synthase_1005859..1006009_POSITIVE 217 60 11 140 86 smit:SMT_994|3end_nicotinate-nucleotide_adenylyltransferase_935476..935626_NEGATIVE 217 79 32 113 67 smit:SMT_315|3end_acetyl-coenzyme_A_carboxylase_carboxyl_transferase_subunit_beta_256627..256777_POSITIVE 216 147 104 67 13 smit:SMT_1505|3end_purine-nucleoside_phosphorylase_1487805..1487955_NEGATIVE 216 79 31 148 105 smit:SMT_895|3end_cysteinyl-tRNA_synthetase_841694..841844_NEGATIVE