Origin IGS: cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cctttccctccttatcgttttcttttcattataccattttttaaacgattcccaaaacaattcttctttttgcttgacaagttttttgttttgttgtattatttaattaagacaaaaggataaaagaaaggagaccaag Mask Tandem Repeat Region ================================================ cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Find is-nt database================================================ Query_seq: SMT_1055:SMT_1056|SMT_1055:SMT_1056:transcriptional regulator, GntR family:K07738 ATP-cone domain protein:<-->:994843..994981 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1055:SMT_1056|SMT_1055:SMT_1056:transcriptional regulator, GntR family:K07738 ATP-cone domain protein:<-->:994843..994981 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1055:SMT_1056|SMT_1055:SMT_1056:transcriptional regulator, GntR family:K07738 ATP-cone domain protein:<-->:994843..994981 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 38 End: 139 ..................................... M I Q Q N K K L V K Q K E E L F W E S F K K W Y N E K K T I R R E R Protein_Len: 30 Strand: - Start: 37 End: 126 .................................... I I C C F L F S T L C F S S N N Q S D N L F H Y L S F F V M ............. Protein_Len: 31 Strand: - Start: 20 End: 112 ................... G K T K I L Y Y L L V F F K D L L F F F Q K P F R K F F P I M ........................... cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg 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: 91 Start: 38 End: 67 .....................................CTTGACAAGTTTTTTGTTTTGTTGTATTAT........................................................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1055:SMT_1056|SMT_1055:SMT_1056:transcriptional regulator, GntR family:K07738 ATP-cone domain protein:<-->:994843..994981 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Intra-Species Hit: Count: 1 Min: 1 Max: 139 Len: 139 Subject: smit_SMT_1055_SMT_1056|transcriptional regulator, GntR family:K07738 ATP-cone domain protein|NEGATIVE:POSITIVE|[994843,994981]|139 HSP 1 e-value: 2.0E-73 bit: 276.0 Len: 139 Query Start:1 Query End:139 Subject Strand: POSITIVE Subject Start: 1 Subject End: 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Inter-species Hit: Count: 2 Min: 1 Max: 139 Len: 139 Subject: NC_008533_SPD_1523_SPD_1524|transcriptional regulator, NrdR family protein:transcriptional regulator, GntR family protein|NEGATIVE:POSITIVE|[1546263,1546401]|139 HSP 1 e-value: 3.0E-66 bit: 252.0 Len: 139 Query Start:1 Query End:139 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 139 cttggtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg cttggtctcctttctcttacccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgcttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Subject: NC_003028_SP_1713_SP_1714|hypothetical protein:transcriptional regulator, GntR family|NEGATIVE:POSITIVE|[1617326,1617464]|139 HSP 1 e-value: 2.0E-61 bit: 236.0 Len: 135 Query Start:5 Query End:139 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 135 ....gtctcctttcttttatccttttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgtttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg ....gtctcctttcttttaccttgttgtcttaattaaataatacaacaaaacaaaaaacttgtcaagcaaaaagaagaattgttttgggaatcgcttaaaaaatggtataatgaaaagaaaacgataaggagggaaagg Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUUGGUCUCCUUUCUUUUAUCCUUUUGUCUUAAUUAAAUAAUACAACAAAACAAAAAACUUGUCAAGCAAAAAGAAGAAUUGUUUUGGGAAUCGUUUAAAAAAUGGUAUAAUGAAAAGAAAACGAUAAGGAGGGAAAGG ........(((((((....((((((((((((.((((..........((((((((....(((..........))).....))))))))...((((((.....)))))).))))...))))...))).))))).))))))) (-22.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCUUUCCCUCCUUAUCGUUUUCUUUUCAUUAUACCAUUUUUUAAACGAUUCCCAAAACAAUUCUUCUUUUUGCUUGACAAGUUUUUUGUUUUGUUGUAUUAUUUAAUUAAGACAAAAGGAUAAAAGAAAGGAGACCAAG ................((((((((((..((((.((.................((((((((.....(((.((....)).)))....))))))))((((.(((......))).))))..))))))..)))))))))).... (-20.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 724 110 61 201 152 smit:SMT_1055|5end_transcriptional_regulator,_GntR_family_994752..994982_NEGATIVE 249 120 71 225 184 smit:SMT_588|5end_hypothetical_protein_505477..505707_NEGATIVE 223 29 8 105 83 smit:SMT_420|5end_hypothetical_protein_predicted_by_Glimmer/Critica_362795..363025_POSITIVE 212 67 22 173 126 smit:SMT_827|5end_hypothetical_protein_750389..750619_POSITIVE 209 95 61 198 163 smit:SMT_619|5end_riboflavin_kinase_/_FMN_adenylyltransferase_527812..528042_POSITIVE 209 20 3 111 94 smit:SMT_516|5end_hypothetical_protein_442847..443077_NEGATIVE 207 90 41 210 149 smit:SMT_1556|5end_phosphoglycerate_mutase_1541194..1541424_POSITIVE 199 42 2 117 81 smit:SMT_1613|5end_ribosomal_large_subunit_pseudouridine_synthase_B_1600608..1600838_POSITIVE 196 119 72 202 157 smit:SMT_958|5end_hypothetical_protein_predicted_by_Glimmer/Critica_905052..905282_POSITIVE 191 28 1 153 121 smit:SMT_1645|5end_hypothetical_protein_1631738..1631968_POSITIVE 191 28 6 124 96 smit:SMT_195|5end_30S_ribosomal_protein_S13_126877..127107_POSITIVE 190 29 6 126 98 smit:SMT_1374|5end_uridylate_kinase_1353020..1353250_NEGATIVE 187 95 58 91 65 smit:SMT_1745|5end_UDP-glucose_4-epimerase_1725541..1725771_NEGATIVE 186 44 5 128 92 smit:SMT_1403|5end_dihydrolipoamide_dehydrogenase_1379204..1379434_POSITIVE 185 31 1 227 195 smit:SMT_1694|5end_GTPase_1676674..1676904_POSITIVE 182 31 6 123 92 smit:SMT_1070|5end_hypothetical_protein_1009946..1010176_NEGATIVE 178 110 61 62 10 smit:SMT_1098|5end_hypothetical_protein_1041992..1042222_NEGATIVE 178 94 51 174 132 smit:SMT_857|5end_endo-beta-N-acetylglucosaminidase_802491..802721_NEGATIVE 177 24 1 119 93 smit:SMT_1347|5end_SsrA-binding_protein_1325185..1325415_NEGATIVE 177 109 65 54 18 smit:SMT_988|5end_N-acetylneuraminate_lyase_932889..933119_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 199 42 2 130 94 smit:SMT_1612|3end_K06024_segregation_and_condensation_protein_B_1600701..1600851_POSITIVE 191 28 6 106 78 smit:SMT_193|3end_50S_ribosomal_protein_L36_126939..127089_POSITIVE 190 29 6 42 14 smit:SMT_1375|3end_putative_glucose-inhibited_division_protein_1353104..1353254_NEGATIVE 186 44 5 82 46 smit:SMT_1402|3end_pyruvate_dehydrogenase_E2_component_(dihydrolipoamide_acetyltransferase)_1379238..1379388_POSITIVE 178 94 51 140 98 smit:SMT_858|3end_triosephosphate_isomerase_802525..802675_NEGATIVE 175 31 1 42 13 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 174 26 1 121 100 smit:SMT_126|3end_hypothetical_membrane_associated_protein_77657..77807_NEGATIVE 173 96 58 92 52 smit:SMT_406|3end_hypothetical_protein_351260..351410_POSITIVE 170 96 61 135 108 smit:SMT_1795|3end_DNA_polymerase_III,_delta_subunit_1769185..1769335_NEGATIVE 170 30 4 43 12 smit:SMT_380|3end_hypothetical_protein_316944..317094_POSITIVE 168 31 3 146 116 smit:SMT_1783|3end_peptide_methionine_sulfoxide_reductase_1760774..1760924_POSITIVE 168 96 67 35 3 smit:SMT_183|3end_30S_ribosomal_protein_S14_121279..121429_POSITIVE 167 26 4 100 76 smit:SMT_1410|3end_exonuclease_RexA_1388532..1388682_NEGATIVE 164 30 1 96 68 smit:SMT_1529|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1512776..1512926_NEGATIVE 164 24 3 77 52 smit:SMT_192|3end_translation_initiation_factor_IF-1_126798..126948_POSITIVE 163 32 1 59 28 smit:SMT_166|3end_hypothetical_protein_113207..113357_POSITIVE 162 95 55 131 93 smit:SMT_1895|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1847402..1847552_POSITIVE 162 16 1 144 130 smit:SMT_1348|3end_exoribonuclease_II_1325148..1325298_NEGATIVE 162 33 2 94 59 smit:SMT_1131|3end_threonine_synthase_1065271..1065421_NEGATIVE 162 97 58 100 63 smit:SMT_308|3end_trans-2-enoyl-ACP_reductase_II_250493..250643_POSITIVE