Origin IGS: ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattttctccgcactctgtgcattgccattgattgtgtctctaacttcttgtgggaagaagaaagacgagccgaaccaaccctccacacccgaagcagtaaccaaaaccgtaactatcgatgcttcgaaatacgaaacgtggcagtatttctctttttccaaaggtgaagtcgtaaatgttaccgactataagaacgatttgaactgggac .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 gtcccagttcaaatcgttcttatagtcggtaacatttacgacttcacctttggaaaaagagaaatactgccacgtttcgtatttcgaagcatcgatagttacggttttggttactgcttcgggtgtggagggttggttcggctcgtctttcttcttcccacaagaagttagagacacaatcaatggcaatgcacagagtgcggagaaaatgatttttttcataattatctgaccttacttttaataggtttcatccggctgcaaagttgagatgttcacaaaaaacgagcaatcccaatttgtaggtatttaatgtcggatttatactaaataagtggtattgggaatactggaattgcacatgaaaaagccctcgatacataggtgcttttattcatttattatttgtgtatcagccgattattccgtgtgtttatggtatgatcaatgacacaaagctatggcacgacaaggaaaatcatctaatgaggcctttgaaaaagagaaggttatcgcttaggttgcaacttatacaaaggg Mask Tandem Repeat Region ================================================ ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattttctccgcactctgtgcattgccattgattgtgtctctaacttcttgtgggaagaagaaagacgagccgaaccaaccctccacacccgaagcagtaaccaaaaccgtaactatcgatgcttcgaaatacgaaacgtggcagtatttctctttttccaaaggtgaagtcgtaaatgttaccgactataagaacgatttgaactgggac Find is-nt database================================================ Query_seq: PG1549:PG1551|PG1549:PG1551:hypothetical protein:hmuY protein:<-->:1628038..1628577 540 ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattttctccgcactctgtgcattgccattgattgtgtctctaacttcttgtgggaagaagaaagacgagccgaaccaaccctccacacccgaagcagtaaccaaaaccgtaactatcgatgcttcgaaatacgaaacgtggcagtatttctctttttccaaaggtgaagtcgtaaatgttaccgactataagaacgatttgaactgggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1549:PG1551|PG1549:PG1551:hypothetical protein:hmuY protein:<-->:1628038..1628577 540 ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattttctccgcactctgtgcattgccattgattgtgtctctaacttcttgtgggaagaagaaagacgagccgaaccaaccctccacacccgaagcagtaaccaaaaccgtaactatcgatgcttcgaaatacgaaacgtggcagtatttctctttttccaaaggtgaagtcgtaaatgttaccgactataagaacgatttgaactgggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1549:PG1551|PG1549:PG1551:hypothetical protein:hmuY protein:<-->:1628038..1628577 540 ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattttctccgcactctgtgcattgccattgattgtgtctctaacttcttgtgggaagaagaaagacgagccgaaccaaccctccacacccgaagcagtaaccaaaaccgtaactatcgatgcttcgaaatacgaaacgtggcagtatttctctttttccaaaggtgaagtcgtaaatgttaccgactataagaacgatttgaactgggac Intra-Species Hit: Count: 0 Inter-species Hit: Count: 1 Min: 334 Max: 540 Len: 207 Subject: UniRef90_A2BCY7 Cluster: Hemin-binding protein; n=5; Porphyromonas gingivalis|Rep: Hemin-binding protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 3.0E-34 bit: 146.0 Len: 207 Query Start:334 Query End:540 Subject Strand: null Subject Start: 6 Subject End: 74 ............................................................................................................................................................................................................................................................................................................................................. F S A L C A L P L I V S L T S C G K K K D E P N Q P S T P E A V T K T V T I D A S K Y E T W Q Y F S F S K G E V V N V T D Y K N D L N W D ............................................................................................................................................................................................................................................................................................................................................. F S A L C A L P L I V S L T S C G K K K D E P N Q P S T P E A V T K T V T I D A S K Y E T W Q Y F S F S K G E V V N V T D Y K N D L N W D ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict ORF larger than 30AA ================================================ Protein_Len: 47 Strand: + Start: 147 End: 287 .................................................................................................................................................. M K A P M Y R G L F H V Q F Q Y S Q Y H L F S I N P T L N T Y K L G L L V F C E H L N F A A G ............................................................................................................................................................................................................................................................. Protein_Len: 50 Strand: + Start: 345 End: 494 ........................................................................................................................................................................................................................................................................................................................................................ M C I A I D C V S N F L W E E E R R A E P T L H T R S S N Q N R N Y R C F E I R N V A V F L F F Q R .............................................. Protein_Len: 60 Strand: + Start: 313 End: 540 ........................................................................................................................................................................................................................................................................................................................ M I M K K I I F S A L C A L P L I V S L T S C G K K K D E P N Q P S T P E A V T K T V T I D A S K Y E T W Q Y F S F S K Protein_Len: 52 Strand: - Start: 373 End: 528 .................................................................................................................................................................................................................................................................................................................................................................................... S R T P L L F V L R V L G G C G F C Y G F G Y S D I S R F V F R P L I E R K G F T F D Y I N G V I L V M ............ Protein_Len: 32 Strand: - Start: 332 End: 427 ........................................................................................................................................................................................................................................................................................................................................... K R R V R H M A M S Q T E L K K H S S S L R A S G V R W V R L M ................................................................................................................. Protein_Len: 60 Strand: - Start: 312 End: 491 ....................................................................................................................................................................................................................................................................................................................... I I I F F I M K E A S Q A N G N I T D R V E Q P F F F S S G F W G E V G S A T V L V T V I S A E F Y S V H C Y K E K E M ................................................. Protein_Len: 38 Strand: - Start: 93 End: 206 ............................................................................................ Q D Y W L C V S Y D A S V C I I F S Y F C R H I S P K K M H L E L I G L V M .............................................................................................................................................................................................................................................................................................................................................. Protein_Len: 53 Strand: - Start: 2 End: 160 . R Q I L Q L R L S L R R K K L P R M L H N E K D H W L K T D N I M G Y V C P I I P Q Y V F L L H I F A G M ............................................................................................................................................................................................................................................................................................................................................................................................ ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 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: 82 Start: 92 End: 121 ...........................................................................................ATTGATCATACCATAAACACACGGAATAAT................................................................................................................................................................................................................................................................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG1549:PG1551|PG1549:PG1551:hypothetical protein:hmuY protein:<-->:1628038..1628577 540 ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcattnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Intra-Species Hit: Count: 1 Min: 1 Max: 333 Len: 333 Subject: NC_002950_PG1549_PG1551|hypothetical protein:hmuY protein|NEGATIVE:POSITIVE|[1628038,1628577]|540 HSP 1 e-value: 0.0 bit: 660.0 Len: 333 Query Start:1 Query End:333 Subject Strand: POSITIVE Subject Start: 1 Subject End: 333 ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcatt............................................................................................................................................................................................................... ccctttgtataagttgcaacctaagcgataaccttctctttttcaaaggcctcattagatgattttccttgtcgtgccatagctttgtgtcattgatcataccataaacacacggaataatcggctgatacacaaataataaatgaataaaagcacctatgtatcgagggctttttcatgtgcaattccagtattcccaataccacttatttagtataaatccgacattaaatacctacaaattgggattgctcgttttttgtgaacatctcaactttgcagccggatgaaacctattaaaagtaaggtcagataattatgaaaaaaatcatt............................................................................................................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCUUUGUAUAAGUUGCAACCUAAGCGAUAACCUUCUCUUUUUCAAAGGCCUCAUUAGAUGAUUUUCCUUGUCGUGCCAUAGCUUUGUGUCAUUGAUCAUACCAUAAACACACGGAAUAAUCGGCUGAUACACAAAUAAUAAAUGAAUAAAAGCACCUAUGUAUCGAGGGCUUUUUCAUGUGCAAUUCCAGUAUUCCCAAUACCACUUAUUUAGUAUAAAUCCGACAUUAAAUACCUACAAAUUGGGAUUGCUCGUUUUUUGUGAACAUCUCAACUUUGCAGCCGGAUGAAACCUAUUAAAAGUAAGGUCAGAUAAUUAUGAAAAAAAUCAUU .((((((...(((((((.......)))).........)))...))))))........(((..(((((.(((((..(((....((.(((((...((.......))...))))).)).....(((((((...((((((.(((..(((((..(((((.(((........)))))))))))))..........((((.(((((((......((((((((...........)))))))).......))))))).)))).))).))))))..((.........)))))))))....................)))..)))))....)))))..)))... (-65.22) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUGAUUUUUUUCAUAAUUAUCUGACCUUACUUUUAAUAGGUUUCAUCCGGCUGCAAAGUUGAGAUGUUCACAAAAAACGAGCAAUCCCAAUUUGUAGGUAUUUAAUGUCGGAUUUAUACUAAAUAAGUGGUAUUGGGAAUACUGGAAUUGCACAUGAAAAAGCCCUCGAUACAUAGGUGCUUUUAUUCAUUUAUUAUUUGUGUAUCAGCCGAUUAUUCCGUGUGUUUAUGGUAUGAUCAAUGACACAAAGCUAUGGCACGACAAGGAAAAUCAUCUAAUGAGGCCUUUGAAAAAGAGAAGGUUAUCGCUUAGGUUGCAACUUAUACAAAGGG .((((......)))).......(((((((.(((((...(((((((((....(((((((.(((.(((((((.........)))).))).))))))))))...(((..(((((................(((.((((((..((((((.....(((((((((.((...((.((((((((((((...............))))))))))))))....)).)).)))))))...))))))..)))))).)))...((....)).)))))..))).........)))))))))....)))))..)))))))..(..(((((....)))))..)...... (-77.06) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 879 90 41 181 132 NC_002950:PG1549|5end_hypothetical_protein_1627947..1628177_NEGATIVE 325 198 151 101 34 NC_002950:PG0133|5end_hypothetical_protein_155764..155994_NEGATIVE 313 84 47 38 3 NC_002950:PG2209|5end_hypothetical_protein_2320928..2321158_NEGATIVE 302 58 11 52 9 NC_002950:PG0287|5end_hypothetical_protein_320457..320687_POSITIVE 301 118 71 178 140 NC_002950:PG1306|5end_metallo-beta-lactamase_family_protein_1387187..1387417_NEGATIVE 296 104 62 56 9 NC_002950:PG1311|5end_hypothetical_protein_1389709..1389939_POSITIVE 296 204 161 123 67 NC_002950:PG1301|5end_hypothetical_protein_1379921..1380151_NEGATIVE 295 198 152 189 126 NC_002950:PG1072|5end_MutS_family_protein_1138976..1139206_POSITIVE 291 80 31 91 44 NC_002950:PG0785|5end_tonB_protein,_putative_837592..837822_NEGATIVE 290 199 161 181 148 NC_002950:PG0216|5end_hypothetical_protein_251956..252186_POSITIVE 289 287 242 151 90 NC_002950:PG0897|5end_alpha-amylase_family_protein_962472..962702_NEGATIVE 288 104 61 51 1 NC_002950:PG1900|5end_ribosome-associated_GTPase_2000746..2000976_NEGATIVE 287 199 154 78 25 NC_002950:PG1612|5end_methylmalonyl-CoA_decarboxylase,_alpha_subunit_1693065..1693295_NEGATIVE 287 285 243 223 183 NC_002950:PG1475|5end_conjugative_transposon_protein_TraN_1551835..1552065_NEGATIVE 286 106 67 103 60 NC_002950:PG1398|5end_hypothetical_protein_1480694..1480924_POSITIVE 282 130 81 45 2 NC_002950:PG2094|5end_hypothetical_protein_2197868..2198098_NEGATIVE 282 297 254 146 109 NC_002950:PG0059|5end_hypothetical_protein_71526..71756_POSITIVE 279 287 245 227 184 NC_002950:PG0215|5end_hypothetical_protein_251460..251690_POSITIVE 278 290 246 104 67 NC_002950:PG0463|5end_folylpolyglutamate_synthase_507606..507836_NEGATIVE 276 99 58 192 143 NC_002950:PG1998|5end_polyprenyl_synthetase_2088029..2088259_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 338 193 152 151 109 NC_002950:PG0393|3end_ribosomal_protein_L7/L12_425017..425167_POSITIVE 325 198 151 82 15 NC_002950:PG0134|3end_magnesium_transporter_155783..155933_NEGATIVE 296 104 62 93 46 NC_002950:PG1310|3end_exsB_protein_1389826..1389976_POSITIVE 296 204 161 105 49 NC_002950:PG1302|3end_hypothetical_protein_1379939..1380089_NEGATIVE 295 204 164 142 102 NC_002950:PG1230|3end_hypothetical_protein_1305960..1306110_NEGATIVE 294 290 242 128 76 NC_002950:PG0481|3end_2-amino-3-ketobutyrate_coenzyme_A_ligase_521432..521582_NEGATIVE 291 80 31 113 66 NC_002950:PG0786|3end_hypothetical_protein_837570..837720_NEGATIVE 289 287 242 64 3 NC_002950:PG0898|3end_hypothetical_protein_962559..962709_NEGATIVE 288 298 253 113 66 NC_002950:PG0768|3end_hypothetical_protein_821275..821425_NEGATIVE 285 289 246 117 70 NC_002950:PG0445|3end_peptidase_T_486549..486699_POSITIVE 282 297 254 132 95 NC_002950:PG0058|3end_nicotinic_acid_mononucleotide_adenyltransferase_71592..71742_POSITIVE 280 130 81 76 13 NC_002950:PG1137|3end_porS_protein_1218290..1218440_NEGATIVE 278 290 246 107 70 NC_002950:PG0464|3end_adenylosuccinate_synthetase_507603..507753_NEGATIVE 275 290 244 69 31 NC_002950:PG1694|3end_hypothetical_protein_1777916..1778066_NEGATIVE 275 310 268 130 86 NC_002950:PG1328|3end_CoA_ligase_family_protein_1406623..1406773_NEGATIVE 274 196 161 114 80 NC_002950:PG1778|3end_hypothetical_protein_1867922..1868072_POSITIVE 273 158 121 65 27 NC_002950:PG1364|3end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_1444388..1444538_NEGATIVE 271 79 31 128 68 NC_002950:PG0753|3end_protease_800288..800438_POSITIVE 270 189 158 70 38 NC_002950:PG0840|3end_hypothetical_protein_902483..902633_POSITIVE 265 199 156 140 99 NC_002950:PG1353|3end_orotate_phosphoribosyltransferase_1433201..1433351_NEGATIVE