Origin IGS: cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat .........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 atcaaaaattttttgaaatttgtttcaagcgagaaaaatgattgacaatctttctaaagaggagtatagtaagagtgaaaaatcggtaggtgaggctaccataaggatacggatgactaccgcaaagcagtggagacactactcgttggtcaacagtcctgatcgccaaggtcaagactaagctcatttcatcgccttatggagttaaagcttgaacggtaaatgcttgctttatctgtgcataaaacaatgaagcgaataacctgacatgcaaacaaccctgccgagaattggcagggtattcttttttgctgaaaatatttcaagagagtaaatagttgattggcctgcctcttaagaaaaaagaaggaggaatagtg Mask Tandem Repeat Region ================================================ cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Find is-nt database================================================ Query_seq: SSA_1735:SSA_1736|SSA_1735:SSA_1736:UreX, putative:L-cysteine desulfhydrase, putative:<-<-:1721163..1721542 380 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SSA_1735:SSA_1736|SSA_1735:SSA_1736:UreX, putative:L-cysteine desulfhydrase, putative:<-<-:1721163..1721542 380 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SSA_1735:SSA_1736|SSA_1735:SSA_1736:UreX, putative:L-cysteine desulfhydrase, putative:<-<-:1721163..1721542 380 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Predict ORF larger than 30AA ================================================ Protein_Len: 34 Strand: + Start: 45 End: 146 ............................................ M Y S L E I F S A K K N T L P I L G R V V C M S G Y S L H C F M H R .......................................................................................................................................................................................................................................... Protein_Len: 40 Strand: + Start: 62 End: 181 ............................................................. M F S K K E Y P A N S R Q G C L H V R L F A S L F Y A Q I K Q A F T V Q A L T P ....................................................................................................................................................................................................... Protein_Len: 45 Strand: + Start: 55 End: 189 ...................................................... M K Y F Q Q K R I P C Q F S A G L F A C Q V I R F I V L C T D K A S I Y R S S F N S I R R ............................................................................................................................................................................................... Protein_Len: 60 Strand: + Start: 194 End: 376 ................................................................................................................................................................................................. M S L V L T L A I R T V D Q R V V S P L L C G S H P Y P Y G S L T Y R F F T L T I L L F R K I V N H F S R L K Q I S K N .... Protein_Len: 53 Strand: - Start: 203 End: 361 .......................................................................................................................................................................................................... D Q G Q R D P S N V L S Y H R W Q K A T T M R I R I T A E G V S K E S K S Y E E K S L N D I M K R A Q F M ................... cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat 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: 87 Start: 311 End: 340 ......................................................................................................................................................................................................................................................................................................................ATTGACAATCTTTCTAAAGAGGAGTATAGT........................................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 76 HP_score: -4.6 Tail_Score: -5.14965 Start: 77 End: 107 Full_Region: ataacctgacatgca aacaaccctgccga gaa ttggcagggtattc ttttttgctgaaaat ............................................................................aacaaccctgccgagaattggcagggtattc................................................................................................................................................................................................................................................................................. TransTerm Strand: - Conf: 93 HP_score: -10.7 Tail_Score: -4.67552 Start: 80 End: 104 Full_Region: acctgacatgcaaac aaccctgccga gaa ttggcagggta ttcttttttgctgaa ...............................................................................aaccctgccgagaattggcagggta.................................................................................................................................................................................................................................................................................... TransTerm Strand: + Conf: 88 HP_score: -11.1 Tail_Score: -3.98913 Start: 82 End: 102 Full_Region: CAGCAAAAAAGAATA CCCTGCCAA TTC TCGGCAGGG TTGTTTGCATGTCAG .................................................................................CCCTGCCAATTCTCGGCAGGG...................................................................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 100 HP_score: -13.3 Tail_Score: -3.93875 Start: 82 End: 102 Full_Region: ctgacatgcaaacaa ccctgccga gaa ttggcaggg tattcttttttgctg .................................................................................ccctgccgagaattggcaggg...................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: SSA_1735:SSA_1736|SSA_1735:SSA_1736:UreX, putative:L-cysteine desulfhydrase, putative:<-<-:1721163..1721542 380 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Intra-Species Hit: Count: 1 Min: 1 Max: 380 Len: 380 Subject: NC_009009_SSA_1735_SSA_1736|UreX, putative:L-cysteine desulfhydrase, putative|NEGATIVE:NEGATIVE|[1721163,1721542]|380 HSP 1 e-value: 0.0 bit: 753.0 Len: 380 Query Start:1 Query End:380 Subject Strand: POSITIVE Subject Start: 1 Subject End: 380 cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat cactattcctccttcttttttcttaagaggcaggccaatcaactatttactctcttgaaatattttcagcaaaaaagaataccctgccaattctcggcagggttgtttgcatgtcaggttattcgcttcattgttttatgcacagataaagcaagcatttaccgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccgatttttcactcttactatactcctctttagaaagattgtcaatcatttttctcgcttgaaacaaatttcaaaaaatttttgat Inter-species Hit: Count: 2 Min: 163 Max: 297 Len: 135 Subject: smit_SMT_1708_SMT_1709|magnesium-translocating P-type ATPase:aminopeptidase P|NEGATIVE:NEGATIVE|[1694644,1695045]|402 HSP 1 e-value: 7.0E-54 bit: 212.0 Len: 135 Query Start:163 Query End:297 Subject Strand: POSITIVE Subject Start: 207 Subject End: 341 ..................................................................................................................................................................cgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccg................................................................................... ..................................................................................................................................................................cgttcaagctttaactccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccctatggtagcctcacctaccg................................................................................... Subject: smit_SMT_1710_SMT_1711|magnesium-translocating P-type ATPase:Xaa-Pro dipeptidase|NEGATIVE:NEGATIVE|[1696121,1696522]|402 HSP 1 e-value: 2.0E-51 bit: 204.0 Len: 135 Query Start:163 Query End:297 Subject Strand: POSITIVE Subject Start: 207 Subject End: 341 ..................................................................................................................................................................cgttcaagctttaactccataaggcgatgaaatgagcttagtcttgaccttggcgatcaggactgttgaccaacgagtagtgtctccactgctttgcggtagtcatccgtatccttatggtagcctcacctaccg................................................................................... ..................................................................................................................................................................cgttcaagctttaacyccatagggcaatgtaatgagcttagtcttggccttcgcgaccaggactgttgaccaacgagtagtgtctccactgctttgcggyagtcatccgtatccctatggtagcctcacctaccg................................................................................... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGUUCAAGCUUUAACUCCAUAAGGCGAUGAAAUGAGCUUAGUCUUGACCUUGGCGAUCAGGACUGUUGACCAACGAGUAGUGUCUCCACUGCUUUGCGGUAGUCAUCCGUAUCCUUAUGGUAGCCUCACCUACCG .......(((......((((((((.(((((........(((((((((.(.....).)))))))))...(((...((((((((....))))))))...)))..))))).....)))))))).)))........... (-38.50) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGGUAGGUGAGGCUACCAUAAGGAUACGGAUGACUACCGCAAAGCAGUGGAGACACUACUCGUUGGUCAACAGUCCUGAUCGCCAAGGUCAAGACUAAGCUCAUUUCAUCGCCUUAUGGAGUUAAAGCUUGAACG ...(((((..((((.((((((((.......((((((.((...((.((((....)))).)))).))))))..((((.(((((.....))))).))))...............))))))))))))...))))).... (-43.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 380 130 82 184 131 NC_009009:SSA_0580|5end_Isochorismatase_family_protein,_putative_572816..573046_POSITIVE 363 97 51 209 167 NC_009009:SSA_0653|5end_UDP-N-acetylglucosamine--N-acetylmuramyl-_(pentapeptide)_pyrophosphoryl-undecaprenol_N-acetylglucosamine_transferase,_putative_636390..636620_POSITIVE 353 118 74 104 47 NC_009009:SSA_1413|5end_GufA-like_protein,_putative_1424919..1425149_NEGATIVE 351 107 61 224 167 NC_009009:SSA_1463|5end_Shikimate_kinase,_putative_1470240..1470470_NEGATIVE 351 102 64 204 161 NC_009009:SSA_0287|5end_Glycerol_dehydrogenase,_NAD+_dependent,_putative_279528..279758_POSITIVE 351 67 21 222 171 NC_009009:SSA_0190|5end_hypothetical_protein_191481..191711_POSITIVE 350 98 55 62 17 NC_009009:SSA_0592|5end_hypothetical_protein_583626..583856_POSITIVE 345 110 62 229 179 NC_009009:SSA_1806|5end_Replication_initiation/membrane_attachment_protein_DnaB,_putative_1790749..1790979_NEGATIVE 340 129 81 120 62 NC_009009:SSA_1859|5end_Penicillin-binding_protein-like_factor_A/_recombinase,_putative_1853704..1853934_POSITIVE 336 126 88 60 16 NC_009009:SSA_2345|5end_hypothetical_protein_2346919..2347149_POSITIVE 331 95 51 203 156 NC_009009:SSA_0251|5end_D-tyrosyl-tRNA(Tyr)_deacylase,_putative_244455..244685_POSITIVE 327 70 21 58 11 NC_009009:SSA_0652|5end_UDP-N-acetylmuramoylalanine--D-glutamate_ligase,_putative_635036..635266_POSITIVE 327 130 83 58 17 NC_009009:SSA_0629|5end_hypothetical_protein_618967..619197_POSITIVE 320 109 63 52 8 NC_009009:SSA_0490|5end_Cobalamin_5'-phosphate_synthase,_putative_490236..490466_POSITIVE 313 90 43 68 17 NC_009009:SSA_1433|5end_tRNA_delta(2)-isopentenylpyrophosphate_transferase,_putative_1440817..1441047_NEGATIVE 311 85 43 199 147 NC_009009:SSA_0047|5end_NAD(P)H_dehydrogenase_(Quinone),_putative_52850..53080_NEGATIVE 310 69 23 218 159 NC_009009:SSA_0810|5end_P-loop_ATPase,_putative_791582..791812_POSITIVE 310 110 68 188 133 NC_009009:SSA_0397|5end_hypothetical_protein_394657..394887_NEGATIVE 309 89 42 64 6 NC_009009:SSA_1072|5end_Glutamate_5-kinase,_putative_1089755..1089985_POSITIVE 307 110 61 70 23 NC_009009:SSA_1576|5end_Catabolite_control_protein_A,_putative_1580181..1580411_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 353 118 74 81 24 NC_009009:SSA_1414|3end_hypothetical_protein_1424942..1425092_NEGATIVE 352 108 63 140 88 NC_009009:SSA_0613|3end_Glucosyltransferase,_putative_606633..606783_POSITIVE 350 98 55 50 5 NC_009009:SSA_0591|3end_Conserved_uncharacterized_protein_583694..583844_POSITIVE 331 95 51 134 87 NC_009009:SSA_0250|3end_GTP_pyrophosphokinase,_putative_244466..244616_POSITIVE 327 130 83 71 30 NC_009009:SSA_0628|3end_Fe-S-cluster_redox_enzyme/radical_SAM_enzyme,_Cfr_family,_putative_619060..619210_POSITIVE 320 109 63 55 11 NC_009009:SSA_0489|3end_Adenosylcobinamide_kinase_/_adenosylcobinamide_phosphate_guanyltransferase,_putative_490319..490469_POSITIVE 307 130 82 70 9 NC_009009:SSA_0469|3end_Precorrin-6B_methylase_2,putative_472959..473109_POSITIVE 298 107 74 151 113 NC_009009:SSA_1176|3end_Acetoin_dehydrogenase,_E1_component,_beta_subunit,_putative_1204437..1204587_NEGATIVE 298 90 41 71 18 NC_009009:SSA_1008|3end_Galactokinase,_putative_1011114..1011264_POSITIVE 295 94 55 75 30 NC_009009:SSA_0553|3end_hypothetical_protein_549341..549491_POSITIVE 292 78 36 78 29 NC_009009:SSA_1026|3end_ABC-type_multidrug_transporter,_ATPase_component,_putative_1043617..1043767_POSITIVE 289 118 72 52 5 NC_009009:SSA_2281|3end_hypothetical_protein_2281912..2282062_NEGATIVE 286 130 81 150 96 NC_009009:SSA_0896|3end_Two-component_system_transcriptional_regulator_(CheY_domain_and_HTH-like_DNA-binding_domain),_putative_888441..888591_POSITIVE 284 130 93 136 95 NC_009009:SSA_1852|3end_Metal_dependent_phosphohydrolase_(HD_motif),_putative_1846869..1847019_NEGATIVE 284 99 52 124 74 NC_009009:SSA_1770|3end_hypothetical_protein_1757484..1757634_NEGATIVE 284 100 54 139 102 NC_009009:SSA_0133|3end_50S_ribosomal_protein_L17,_putative_122562..122712_POSITIVE 283 85 42 129 68 NC_009009:SSA_2105|3end_hypothetical_protein_2106756..2106906_NEGATIVE 282 109 62 98 33 NC_009009:SSA_1607|3end_Formamidopyrimidine-DNA_glycosylase,_putative_1612431..1612581_NEGATIVE 281 75 33 149 113 NC_009009:SSA_2199|3end_ATP-dependent_Clp_protease,_ATP-binding_subunit,_putative_2198679..2198829_NEGATIVE 281 62 22 144 107 NC_009009:SSA_1157|3end_PvaA-like_protein,_putative_1186218..1186368_POSITIVE