Origin IGS: agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 attgttgccctttctagaatgtcgatagtgcataacaaaaagctctactttatctagtagagcccaaagtcactgtcgaaactctattatcctcgttgaaaaactcgtcaaactagcttggagctgcctaccccaacccaagaggagcatagctttctagtttttttattttcaatgaggacaagatactagaaacctagtataaaaagagcacacaaaaagagacaaaaacaagatctactaaataaagtttctttacttgatagacttagttgttcatgtctcccttacctccgagtattagtacctctatcctatacctttcaggatattttgtcaacagaaaaccgacaattctaatct Mask Tandem Repeat Region ================================================ agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Find is-nt database================================================ Query_seq: SMT_693:SMT_694|SMT_693:SMT_694:hypothetical protein:putative ATP-binding component of a transport system:->->:604139..604501 363 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_693:SMT_694|SMT_693:SMT_694:hypothetical protein:putative ATP-binding component of a transport system:->->:604139..604501 363 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_693:SMT_694|SMT_693:SMT_694:hypothetical protein:putative ATP-binding component of a transport system:->->:604139..604501 363 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Predict ORF larger than 30AA ================================================ Protein_Len: 30 Strand: + Start: 3 End: 92 .. M R I V G F L L T K Y P E R Y R I E V L I L G G K G D M N N ............................................................................................................................................................................................................................................................................... Protein_Len: 42 Strand: - Start: 207 End: 332 .............................................................................................................................................................................................................. F A I S R K P Q P L C S W A L K V L K E V L I I S N R C H S Q A R S S L T S S K T M ............................... Protein_Len: 52 Strand: - Start: 7 End: 162 ...... F Q R N E T S L I D Q F T Y S L P V L V R L Y P L C S C S L R D L L S V K N L L D Q K Q R K K H A R K M ......................................................................................................................................................................................................... Protein_Len: 30 Strand: - Start: 2 End: 91 . I L I T P K R N V F Y G S L Y L I S T S I S P P L P S M F M ................................................................................................................................................................................................................................................................................ agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat 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: 23 End: 52 ......................GTTGACAAAATATCCTGAAAGGTATAGGAT....................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 100 HP_score: -8.8 Tail_Score: -5.19328 Start: 301 End: 322 Full_Region: CGACAGTGACTTTGG GCTCTACT AGATAA AGTAGAGC TTTTTGTTATGCACT ............................................................................................................................................................................................................................................................................................................GCTCTACTAGATAAAGTAGAGC......................................... Find igs database================================================ Query_seq: SMT_693:SMT_694|SMT_693:SMT_694:hypothetical protein:putative ATP-binding component of a transport system:->->:604139..604501 363 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Intra-Species Hit: Count: 1 Min: 1 Max: 363 Len: 363 Subject: smit_SMT_693_SMT_694|hypothetical protein:putative ATP-binding component of a transport system|POSITIVE:POSITIVE|[604139,604501]|363 HSP 1 e-value: 0.0 bit: 678.0 Len: 363 Query Start:1 Query End:363 Subject Strand: POSITIVE Subject Start: 1 Subject End: 363 agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaatnnnnnnnctagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat agattagaattgtcggttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttttatactaggtttctagtatcttgtcctcattgaaaataaaaaaactagaaagctatgctcctcttgggttggggtaggcagctccaagctagtttgacgagtttttcaacgaggataatagagtttcgacagtgactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaagggcaacaat Inter-species Hit: Count: 3 Min: 16 Max: 356 Len: 341 Subject: NC_008533_SPD_1136_SPD_1137|Uncharacterized ACR:ABC transporter, ATP-binding protein|NEGATIVE:POSITIVE|[1169744,1170468]|725 HSP 1 e-value: 7.0E-57 bit: 222.0 Len: 144 Query Start:16 Query End:159 Subject Strand: POSITIVE Subject Start: 502 Subject End: 645 ...............gttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ ...............gttttctgttgacaaaatttccttaaaggtatagtataaagatactaatactcggaggtaagggagacatgaacagctaagtctatcaaataaagaacctttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 38 Query Start:293 Query End:330 Subject Strand: POSITIVE Subject Start: 688 Subject End: 725 ....................................................................................................................................................................................................................................................................................................gactttgggctctactagataaagtagagctttttgtt................................. ....................................................................................................................................................................................................................................................................................................gactttgggctctactaggtaaagtagagctttttgtt................................. Subject: NC_003098_spr1160_spr1161|hypothetical protein:ABC transporter ATP-binding protein - unknown substrate|POSITIVE:POSITIVE|[1162699,1162970]|272 HSP 1 e-value: 7.0E-57 bit: 222.0 Len: 144 Query Start:16 Query End:159 Subject Strand: POSITIVE Subject Start: 16 Subject End: 159 ...............gttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ ...............gttttctgttgacaaaatttccttaaaggtatagtataaagatactaatactcggaggtaagggagacatgaacagctaagtctatcaaataaagaacctttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ HSP 2 e-value: 4.0E-21 bit: 103.0 Len: 64 Query Start:293 Query End:356 Subject Strand: POSITIVE Subject Start: 202 Subject End: 265 ....................................................................................................................................................................................................................................................................................................gactttgggctctactagataaagtagagctttttgttatgcactatcgacattctagaaaggg....... ....................................................................................................................................................................................................................................................................................................gactttgggctctactaggtaaagtagagctttttgttatgcactatgaacattctagaaaggg....... Subject: NC_003028_SP_1281_SP_1282|hypothetical protein:ABC transporter, ATP-binding protein|POSITIVE:POSITIVE|[1216090,1216327]|238 HSP 1 e-value: 7.0E-57 bit: 222.0 Len: 144 Query Start:16 Query End:159 Subject Strand: POSITIVE Subject Start: 16 Subject End: 159 ...............gttttctgttgacaaaatatcctgaaaggtataggatagaggtactaatactcggaggtaagggagacatgaacaactaagtctatcaagtaaagaaactttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ ...............gttttctgttgacaaaatttccttaaaggtataatataaagatactaatactcggaggtaagggagacatgaacaactaagtctatcaaataaagaacctttatttagtagatcttgtttttgtctctttttgtgtgctctttt............................................................................................................................................................................................................ HSP 2 e-value: 2.0E-10 bit: 67.9 Len: 38 Query Start:293 Query End:330 Subject Strand: POSITIVE Subject Start: 201 Subject End: 238 ....................................................................................................................................................................................................................................................................................................gactttgggctctactagataaagtagagctttttgtt................................. ....................................................................................................................................................................................................................................................................................................gactttgggctctactaggtaaagtagagctttttgtt................................. Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUUUUCUGUUGACAAAAUAUCCUGAAAGGUAUAGGAUAGAGGUACUAAUACUCGGAGGUAAGGGAGACAUGAACAACUAAGUCUAUCAAGUAAAGAAACUUUAUUUAGUAGAUCUUGUUUUUGUCUCUUUUUGUGUGCUCUUUUUAUACUAGGUUUCUAGUAUCUUGUCCUCAUUGAAAAUAAAAAAACUAGAAAGCUAUGCUCCUCUUGGGUUGGGGUAGGCAGCUCCAAGCUAGUUUGACGAGUUUUUCAACGAGGAUAAUAGAGUUUCGACAGUGACUUUGGGCUCUACUAGAUAAAGUAGAGCUUUUUGUUAUGCACUAUCGACAUUCUAGAAAGGG ..((((((.........(((((((.......)))))))..((((....)))))))))).((((((((((.((((((....((((((.((((((((...)))))))).)))))).)))))).))))))))))......(((((((.(((((((....)))))))..(((((((.(((((((.....(((((((..((((.((((((.........))))))...)))).....))))))).......))))))).))))))).((((((.((((.((((((...((((((((((......))))))))))...))....)))).)))).))))))))))))) (-104.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUUUCUAGAAUGUCGAUAGUGCAUAACAAAAAGCUCUACUUUAUCUAGUAGAGCCCAAAGUCACUGUCGAAACUCUAUUAUCCUCGUUGAAAAACUCGUCAAACUAGCUUGGAGCUGCCUACCCCAACCCAAGAGGAGCAUAGCUUUCUAGUUUUUUUAUUUUCAAUGAGGACAAGAUACUAGAAACCUAGUAUAAAAAGAGCACACAAAAAGAGACAAAAACAAGAUCUACUAAAUAAAGUUUCUUUACUUGAUAGACUUAGUUGUUCAUGUCUCCCUUACCUCCGAGUAUUAGUACCUCUAUCCUAUACCUUUCAGGAUAUUUUGUCAACAGAAAAC ...(((((......(((((((((....((.....((((((((......)))))))).....)))))))))))..((((....(((((((((((((.......(((((((...(((((((.((.((.(.......).))))..)))))))))))))).....)))))))))))))....(((((((....)))))))....))))...((((((.((((((..((((((.((((.(((.(((((...))))).))).))))))....))))..)))))).....(((..(((...(((..........)))...)))..)))...))))))....))))).. (-85.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 249 201 166 116 smit:SMT_1489|5end_K06147_ATP-binding_cassette,_subfamily_B,_bacterial_1468892..1469122_POSITIVE 336 256 220 231 197 smit:SMT_1888|5end_K02026_multiple_sugar_transport_system_permease_protein_1842088..1842318_POSITIVE 333 238 195 167 116 smit:SMT_331|5end_endo-beta-N-acetylglucosaminidase_266416..266646_POSITIVE 329 227 192 47 17 smit:SMT_435|5end_orotate_phosphoribosyltransferase_376842..377072_POSITIVE 321 246 202 138 98 smit:SMT_987|5end_N-acetylmannosamine_kinase_/_transcriptional_regulator_932224..932454_NEGATIVE 316 240 194 70 33 smit:SMT_1023|5end_hypothetical_protein_958884..959114_NEGATIVE 315 240 196 220 172 smit:SMT_1060|5end_K03977_GTP-binding_protein_998106..998336_POSITIVE 313 69 22 123 63 smit:SMT_1375|5end_putative_glucose-inhibited_division_protein_1354438..1354668_NEGATIVE 313 247 201 84 22 smit:SMT_1049|5end_hypothetical_protein_988438..988668_POSITIVE 312 240 197 69 12 smit:SMT_1822|5end_hypothetical_protein_1794452..1794682_POSITIVE 310 240 196 151 87 smit:SMT_118|5end_K02026_multiple_sugar_transport_system_permease_protein_69430..69660_POSITIVE 302 244 215 188 153 smit:SMT_131|5end_phosphatase,_putative_83663..83893_NEGATIVE 300 90 41 52 5 smit:SMT_1470|5end_K06188_aquaporin_Z_1452560..1452790_POSITIVE 299 235 197 231 196 smit:SMT_1732|5end_transcriptional_repressor_protein,_putative_1716451..1716681_POSITIVE 297 240 191 222 162 smit:SMT_1617|5end_K02015_iron_complex_transport_system_permease_protein_1604500..1604730_NEGATIVE 294 247 210 85 45 smit:SMT_878|5end_excinuclease_ABC,_subunit_C_826249..826479_NEGATIVE 293 228 200 224 190 smit:SMT_1058|5end_primosomal_protein_DnaI_996486..996716_POSITIVE 293 287 242 225 176 smit:SMT_380|5end_hypothetical_protein_316376..316606_POSITIVE 293 287 242 225 176 smit:SMT_371|5end_hypothetical_protein_305248..305478_POSITIVE 290 248 201 59 3 smit:SMT_310|5end_3-oxoacyl-_251370..251600_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 346 236 192 144 95 smit:SMT_1981|3end_K03696_ATP-dependent_Clp_protease_ATP-binding_subunit_ClpC_1912868..1913018_POSITIVE 338 227 186 59 10 smit:SMT_2109|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1999061..1999211_NEGATIVE 338 227 186 59 10 smit:SMT_1180|3end_putative_tagatose-6-phosphate_aldose/ketose_isomerase_1138036..1138186_NEGATIVE 337 250 201 126 84 smit:SMT_1649|3end_GMP_reductase_1636068..1636218_POSITIVE 321 246 202 120 80 smit:SMT_988|3end_N-acetylneuraminate_lyase_932242..932392_NEGATIVE 313 247 201 87 25 smit:SMT_1048|3end_K06518_holin-like_protein_988521..988671_POSITIVE 310 240 196 137 73 smit:SMT_117|3end_K02025_multiple_sugar_transport_system_permease_protein_69496..69646_POSITIVE 296 240 192 149 100 smit:SMT_326|3end_K02029_polar_amino_acid_transport_system_permease_protein_263217..263367_NEGATIVE 294 247 210 46 6 smit:SMT_879|3end_hypothetical_protein_826288..826438_NEGATIVE 287 227 186 59 10 smit:SMT_1809|3end_MutT/NUDIX_family_protein_1785134..1785284_POSITIVE 285 226 186 57 11 smit:SMT_1477|3end_K02077_zinc/manganese_transport_system_substrate-binding_protein_1459447..1459597_NEGATIVE 285 226 186 56 10 smit:SMT_1140|3end_glycogen_phosphorylase_1081316..1081466_NEGATIVE 281 234 197 148 107 smit:SMT_748|3end_prephenate_dehydratase_652650..652800_NEGATIVE 280 237 203 141 101 smit:SMT_1850|3end_K01421_putative_membrane_protein_1815582..1815732_POSITIVE 280 237 203 141 101 smit:SMT_81|3end_K01421_putative_membrane_protein_10988..11138_NEGATIVE 278 259 211 52 10 smit:SMT_1626|3end_undecaprenyl-diphosphatase_1615183..1615333_NEGATIVE 277 240 197 80 24 smit:SMT_1538|3end_two-component_response_regulator_YvqC_1522669..1522819_NEGATIVE 276 168 121 126 79 smit:SMT_1525|3end_pneumococcal_histidine_triad_protein_A_precursor_1505873..1506023_NEGATIVE 276 234 194 115 79 smit:SMT_339|3end_K03687_molecular_chaperone_GrpE_278490..278640_POSITIVE 274 234 203 35 4 smit:SMT_1956|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1889537..1889687_NEGATIVE