Origin IGS: tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt .........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 aaatatctcattactagtcagatttcttaacagataaaaattaagaattcactgcaaatttgctatctgtaagaagctttacatgaacaagttcattaatagcttctaagatcatttcactcaaacacagcaagatttgctcggttcattttatttaatttttatcttaaaatctggaatgtaacttacttatttttatatttaatttaatgttatggtataggaggaaaaaatgaaaaaatttttagttttaattattggagttttaatgtca Mask Tandem Repeat Region ================================================ tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Find is-nt database================================================ Query_seq: FN1808:FN1809|FN1808:FN1809:hypothetical protein:Iron/zinc/copper-binding protein:<-<-:289996..290269 274 tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: FN1808:FN1809|FN1808:FN1809:hypothetical protein:Iron/zinc/copper-binding protein:<-<-:289996..290269 274 tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: FN1808:FN1809|FN1808:FN1809:hypothetical protein:Iron/zinc/copper-binding protein:<-<-:289996..290269 274 tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 139 End: 231 .......................................................................................................................................... M L L C L S E M I L E A I N E L V H V K L L T D S K F A V N S ........................................... tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt 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: 81 Start: 102 End: 131 .....................................................................................................GTTCATTTTATTTAATTTTTATCTTAAAAT............................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: FN1808:FN1809|FN1808:FN1809:hypothetical protein:Iron/zinc/copper-binding protein:<-<-:289996..290269 274 tgacattaaaactccaataattaaaactaaaaattttttcattttttcctcctataccataacattaaattaaatataaaaataagtaagttacattccagattttaagataaaaattaaataaaatgaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt Intra-Species Hit: Count: 4 Min: 1 Max: 274 Len: 274 Subject: NC_003454_FN1808_FN1809|hypothetical protein:Iron/zinc/copper-binding protein|NEGATIVE:NEGATIVE|[289996,290269]|274 HSP 1 e-value: 6.0E-78 bit: 291.0 Len: 147 Query Start:128 Query End:274 Subject Strand: POSITIVE Subject Start: 128 Subject End: 274 ...............................................................................................................................gaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt ...............................................................................................................................gaaccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatgagatattt HSP 2 e-value: 7.0E-10 bit: 65.9 Len: 33 Query Start:1 Query End:33 Subject Strand: POSITIVE Subject Start: 1 Subject End: 33 tgacattaaaactccaataattaaaactaaaaa................................................................................................................................................................................................................................................. tgacattaaaactccaataattaaaactaaaaa................................................................................................................................................................................................................................................. Subject: NC_003454_FN0358_FN0359|ATP synthase subunit B:ATP synthase gamma chain, sodium ion specific|NEGATIVE:NEGATIVE|[989765,990084]|320 HSP 1 e-value: 1.0E-26 bit: 121.0 Len: 137 Query Start:131 Query End:267 Subject Strand: POSITIVE Subject Start: 140 Subject End: 275 ..................................................................................................................................ccgagcaaatcttgctgtgtttgagtgaaatgatcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaatga....... ..................................................................................................................................ccgagcaaatctcgctatgtttgaacgaagtgatcttagaagcacttaatgaacttgttcatttagagcttcttacagatagcgaatttgcagcaaattcttgatttttatc-attaagaaatttagctagtaatga....... Subject: NC_003454_FN0084_FN0085|Acetaldehyde dehydrogenase [acetylating]:Ethanolamine utilization cobalamin adenosyltransferase|POSITIVE:POSITIVE|[723155, 723409]|255 HSP 1 e-value: 8.0E-25 bit: 115.0 Len: 102 Query Start:163 Query End:264 Subject Strand: NEGATIVE Subject Start: 18 Subject End: 119 ..................................................................................................................................................................atcttagaagctattaatgaacttgttcatgtaaagcttcttacagatagcaaatttgcagtgaattcttaatttttatctgttaagaaatctgactagtaa.......... ..................................................................................................................................................................atcttagaagcttttaatgaacttgttcatttagagcttcttacagatgccaaaattacagcgaattcttaatttttatccgttaagaaatttggctagtaa.......... Subject: NC_003454_FN0906_FN0907|Glycerol-3-phosphate dehydrogenase [NAD(P)+]:Ribosomal RNA small subunit methyltransferase C|NEGATIVE:NEGATIVE|[1565222,1565413]|192 HSP 1 e-value: 4.0E-14 bit: 79.8 Len: 44 Query Start:221 Query End:264 Subject Strand: POSITIVE Subject Start: 140 Subject End: 183 ............................................................................................................................................................................................................................cagtgaattcttaatttttatctgttaagaaatctgactagtaa.......... ............................................................................................................................................................................................................................cagtgaattcttaatttttatctgttaagaaatttgactagtaa.......... HSP 2 e-value: 3.0E-6 bit: 54.0 Len: 27 Query Start:134 Query End:160 Subject Strand: POSITIVE Subject Start: 97 Subject End: 123 .....................................................................................................................................agcaaatcttgctgtgtttgagtgaaa.................................................................................................................. .....................................................................................................................................agcaaatcttgctgtgtttgagtgaaa.................................................................................................................. Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UGACAUUAAAACUCCAAUAAUUAAAACUAAAAAUUUUUUCAUUUUUUCCUCCUAUACCAUAACAUUAAAUUAAAUAUAAAAAUAAGUAAGUUACAUUCCAGAUUUUAAGAUAAAAAUUAAAUAAAAUGAACCGAGCAAAUCUUGCUGUGUUUGAGUGAAAUGAUCUUAGAAGCUAUUAAUGAACUUGUUCAUGUAAAGCUUCUUACAGAUAGCAAAUUUGCAGUGAAUUCUUAAUUUUUAUCUGUUAAGAAAUCUGACUAGUAAUGAGAUAUUU ...........(((..................((((((..((((...........................))))..))))))......(((((....((((((((.(((((((((((((....(((..((...((((((.(((((((...((((.........))))((((((....(((((....)))))....))))))......))))))))))))).))..))).))))))))))))).....))))))))....))))))))...... (-45.83) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAUAUCUCAUUACUAGUCAGAUUUCUUAACAGAUAAAAAUUAAGAAUUCACUGCAAAUUUGCUAUCUGUAAGAAGCUUUACAUGAACAAGUUCAUUAAUAGCUUCUAAGAUCAUUUCACUCAAACACAGCAAGAUUUGCUCGGUUCAUUUUAUUUAAUUUUUAUCUUAAAAUCUGGAAUGUAACUUACUUAUUUUUAUAUUUAAUUUAAUGUUAUGGUAUAGGAGGAAAAAAUGAAAAAAUUUUUAGUUUUAAUUAUUGGAGUUUUAAUGUCA ......(((.((((...((((((((......(((((((((((((((((..((((((((((((((.......(((((((....(((((....)))))....)))))))..((.....))..........))).))))))))..)))..))))...)))))))))))))..))))))))...))))........((((((((((((((.....)))).))))))))))..((((((......))))))..............)))........... (-51.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 666 140 91 231 182 NC_003454:FN1808|5end_hypothetical_protein_289905..290135_NEGATIVE 619 140 91 205 156 NC_003454:FN1819|5end_Export_ABC_transporter_307519..307749_POSITIVE 607 160 111 214 165 NC_003454:FN0906|5end_Glycerol-3-phosphate_dehydrogenase_[NAD(P)+]_1565131..1565361_NEGATIVE 589 160 112 226 178 NC_003454:FN0070|5end_Glycyl-tRNA_synthetase_beta_chain_708902..709132_POSITIVE 569 159 112 205 158 NC_003454:FN2006|5end_Cobalt_transport_protein_cbiQ_506079..506309_POSITIVE 520 150 101 214 165 NC_003454:FN1486|5end_Integral_membrane_protein_with_CBS_domains_2169299..2169529_NEGATIVE 514 140 91 200 151 NC_003454:FN0392|5end_Oxygen-independent_coproporphyrinogen_III_oxidase_1029624..1029854_POSITIVE 501 139 91 217 169 NC_003454:FN0117|5end_O6-methylguanine-DNA_methyltransferase_750338..750568_POSITIVE 483 159 112 222 175 NC_003454:FN1217|5end_Holliday_junction_DNA_helicase_ruvB_1877597..1877827_NEGATIVE 481 259 213 82 37 NC_003454:FN0171|5end_Hypothetical_cytosolic_protein_796548..796778_POSITIVE 481 140 91 186 137 NC_003454:FN2095|5end_General_secretion_pathway_protein_E_606080..606310_NEGATIVE 481 267 222 163 118 NC_003454:FN1821|5end_Hypothetical_cytosolic_protein_311031..311261_POSITIVE 451 140 95 205 160 NC_003454:FN1835|5end_hypothetical_protein_323680..323910_NEGATIVE 439 129 81 187 139 NC_003454:FN0085|5end_Ethanolamine_utilization_cobalamin_adenosyltransferase_723270..723500_POSITIVE 418 267 221 94 48 NC_003454:FN0797|5end_hypothetical_protein_1455799..1456029_NEGATIVE 417 140 91 188 139 NC_003454:FN1822|5end_Flavodoxin_311148..311378_POSITIVE 400 147 101 218 171 NC_003454:FN0988|5end_phosphoribosylaminoimidazole-succinocarboxamide_synthase_1640968..1641198_NEGATIVE 396 118 79 166 127 NC_003454:FN1614|5end_MG(2+)_chelatase_family_protein_125002..125232_NEGATIVE 374 140 95 224 179 NC_003454:FN1459|5end_Phospho-N-acetylmuramoyl-pentapeptide-_transferase_2141360..2141590_NEGATIVE 373 129 81 229 181 NC_003454:FN0484|5end_Lipase_1129470..1129700_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 600 260 213 66 19 NC_003454:FN1836|3end_Tetratricopeptide_repeat_family_protein_323904..324054_NEGATIVE 585 267 221 84 38 NC_003454:FN0907|3end_Ribosomal_RNA_small_subunit_methyltransferase_C_1565324..1565474_NEGATIVE 570 260 215 76 31 NC_003454:FN2096|3end_hypothetical_protein_606267..606417_NEGATIVE 569 268 221 76 29 NC_003454:FN0483|3end_Uracil_phosphoribosyltransferase_1129301..1129451_POSITIVE 536 250 201 59 10 NC_003454:FN0084|3end_Acetaldehyde_dehydrogenase_[acetylating]_723094..723244_POSITIVE 502 267 221 73 27 NC_003454:FN1461|3end_Histidinol-phosphatase_2141603..2141753_NEGATIVE 481 259 213 67 22 NC_003454:FN0170|3end_GTP-binding_protein_796613..796763_POSITIVE 481 267 222 68 23 NC_003454:FN1820|3end_Export_ABC_transporter_311016..311166_POSITIVE 464 268 223 76 31 NC_003454:FN1487|3end_hypothetical_protein_2169559..2169709_NEGATIVE 454 267 221 83 37 NC_003454:FN0391|3end_Hydrolase_(HAD_superfamily)_1029496..1029646_POSITIVE 404 260 211 62 13 NC_003454:FN0069|3end_glycyl-tRNA_synthetase_alpha_subunit_708761..708911_POSITIVE 387 120 76 149 105 NC_003454:FN1821|3end_Hypothetical_cytosolic_protein_311209..311359_POSITIVE 371 267 222 71 26 NC_003454:FN0989|3end_phosphoribosylaminoimidazole_carboxylase_catalytic_subunit_1641194..1641344_NEGATIVE 367 154 112 147 105 NC_003454:FN0797|3end_hypothetical_protein_1455668..1455818_NEGATIVE 351 267 228 40 1 NC_003454:FN0116|3end_Chaperone_protein_dnaK_750156..750306_POSITIVE 321 268 221 73 26 NC_003454:FN1811|3end_Manganese_transport_system_ATP-binding_protein_mntA_292161..292311_NEGATIVE 316 267 221 86 41 NC_003454:FN2005|3end_Cobalt_transport_ATP-binding_protein_cbiO_505976..506126_POSITIVE 284 268 235 82 50 NC_003454:FN2081|3end_ABC_transporter_substrate-binding_protein_592075..592225_NEGATIVE 283 267 222 45 1 NC_003454:FN0359|3end_ATP_synthase_gamma_chain,_sodium_ion_specific_989995..990145_NEGATIVE 281 55 28 91 64 NC_003454:FN0913|3end_Cobinamide_kinase_1570172..1570322_NEGATIVE