Origin IGS: aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactgtttacgtgccaaaaatcagccactctacagtccgcaaaacgtggttcgagaaaattttcgttttggttcgggaagcaaaaaattctcgcgccacaacgaaaaaattctcgcgcctgtttttcaggattctcagaccgcaatccgagcatttcccgttcgtattttcgagaaagcagatcagctgacactcgcctaccggcccgaacatgcagggaggacaagcctcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt .........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 aagcagtgtcgattagaatgtgagtgagttcggataccgaagatagtcgtttttcctgttttcttttgcaattttcacaatcatccatgtagatcgttttttaccgaggcttgtcctccctgcatgttcgggccggtaggcgagtgtcagctgatctgctttctcgaaaatacgaacgggaaatgctcggattgcggtctgagaatcctgaaaaacaggcgcgagaattttttcgttgtggcgcgagaattttttgcttcccgaaccaaaacgaaaattttctcgaaccacgttttgcggactgtagagtggctgatttttggcacgtaaacagttttaatcgtgtctacaggatattgttaggaaactcttatatttgtctgatagatatatcgggaaagtcgaagaagagtcgctatccccgaattaggtttttgcaatcttttaataacggaacagtt Mask Tandem Repeat Region ================================================ aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactgtttacgtgccaaaaatcagccactctacagtccgcaaaacgtggttcgagaaaattttcgttttggttcgggaagcaaaaaattctcgcgccacaacgaaaaaattctcgcgcctgtttttcaggattctcagaccgcaatccgagcatttcccgttcgtattttcgagaaagcagatcagctgacactcgcctaccggcccgaacatgcagggaggacaagcctcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Find is-nt database================================================ Query_seq: PG1949:PG1950|PG1949:PG1950:malate dehydrogenase:hypothetical protein:<-->:2039279..2039739 461 aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactgtttacgtgccaaaaatcagccactctacagtccgcaaaacgtggttcgagaaaattttcgttttggttcgggaagcaaaaaattctcgcgccacaacgaaaaaattctcgcgcctgtttttcaggattctcagaccgcaatccgagcatttcccgttcgtattttcgagaaagcagatcagctgacactcgcctaccggcccgaacatgcagggaggacaagcctcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1949:PG1950|PG1949:PG1950:malate dehydrogenase:hypothetical protein:<-->:2039279..2039739 461 aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactgtttacgtgccaaaaatcagccactctacagtccgcaaaacgtggttcgagaaaattttcgttttggttcgggaagcaaaaaattctcgcgccacaacgaaaaaattctcgcgcctgtttttcaggattctcagaccgcaatccgagcatttcccgttcgtattttcgagaaagcagatcagctgacactcgcctaccggcccgaacatgcagggaggacaagcctcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1949:PG1950|PG1949:PG1950:malate dehydrogenase:hypothetical protein:<-->:2039279..2039739 461 aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactgtttacgtgccaaaaatcagccactctacagtccgcaaaacgtggttcgagaaaattttcgttttggttcgggaagcaaaaaattctcgcgccacaacgaaaaaattctcgcgcctgtttttcaggattctcagaccgcaatccgagcatttcccgttcgtattttcgagaaagcagatcagctgacactcgcctaccggcccgaacatgcagggaggacaagcctcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 3 Min: 130 Max: 354 Len: 225 Subject: UniRef90_Q7MUH1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-11 bit: 70.9 Len: 165 Query Start:132 Query End:296 Subject Strand: null Subject Start: 9 Subject End: 63 ................................................................................................................................... L R A K N Q P L Y S P Q N V V R E N F R F G S G S K K F S R H N E K I L A P V F Q D S Q T A I R A F P V R I F ..................................................................................................................................................................... ................................................................................................................................... L G S K I F P F A T P Q N A V R K L F Y F G V G S K K F S R H N E K I L A P L F Q G I R A T I G A F P V R V F ..................................................................................................................................................................... Subject: UniRef90_Q7MTB1 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 1.0E-6 bit: 54.3 Len: 189 Query Start:166 Query End:354 Subject Strand: null Subject Start: 4 Subject End: 66 ..................................................................................................................................................................... K T W F E K I F V L V R E A K N S R A T T K K F S R L F F R I L R P Q S E H F P F V F S R K Q I S * H S P T G P N M Q G G Q A ........................................................................................................... ..................................................................................................................................................................... K T W R E N F F V L V R E V K N L R A T A K K I S R H F F R K Y E P Q P G V F W F V F H L S R S H P F P F L K P L L S G D Q A ........................................................................................................... Subject: UniRef90_Q7MWR8 Cluster: Hypothetical protein; n=1; Porphyromonas gingivalis|Rep: Hypothetical protein - Porphyromonas gingivalis (Bacteroides gingivalis) HSP 1 e-value: 3.0E-6 bit: 53.1 Len: 153 Query Start:130 Query End:282 Subject Strand: null Subject Start: 9 Subject End: 59 ................................................................................................................................. V Y V P K I S H S T V R K T W F E K I F V L V R E A K N S R A T T K K F S R L F F R I L R P Q S E H F ................................................................................................................................................................................... ................................................................................................................................. V S V P K S A P L S F V K T W R E K I F A L A R K F F V S R T K T E K I S R V F S R I Y E P Q S E H F ................................................................................................................................................................................... aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 121 End: 312 ........................................................................................................................ M K T V Y V P K I S H S T V R K T W F E K I F V L V R E A K N S R A T T K K F S R L F F R I L R P Q S E H F P F V F S R ..................................................................................................................................................... Protein_Len: 60 Strand: + Start: 128 End: 358 ............................................................................................................................... M F T C Q K S A T L Q S A K R G S R K F S F W F G K Q K I L A P Q R K N S R A C F S G F S D R N P S I S R S Y F R E S R ....................................................................................................... Protein_Len: 60 Strand: + Start: 171 End: 446 .......................................................................................................................................................................... M V R E N F R F G S G S K K F S R H N E K I L A P V F Q D S Q T A I R A F P V R I F E K A D Q L T L A Y R P E H A G R T ............... Protein_Len: 31 Strand: + Start: 368 End: 460 ............................................................................................................................................................................................................................................................................................................................................................................... M Y M D D C E N C K R K Q E K R L S S V S E L T H I L I D T A . Protein_Len: 60 Strand: - Start: 135 End: 428 ...................................................................................................................................... K L I R L G C D S C K G N T N E L F C I L Q C E G V P G F M C P P C A E T F F S R C P H N H F N C F F V P F V V I K P M ................................. Protein_Len: 60 Strand: - Start: 1 End: 369 N Q N P F C F I R A G C R F F E R A Q K E P N E S R L G L M E R E Y K R S L L D A S V R R G A R V H L S S L G R Y F V M ............................................................................................ aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 49 HP_score: -5.1 Tail_Score: -2.58427 Start: 184 End: 233 Full_Region: ACGTGGTTCGAGAAA ATTTTCGTTTTGGTTCGGGAA GCAAAAAA TTCTCGCGCCACAACGAAAAA ATTCTCGCGCCTGTT .......................................................................................................................................................................................ATTTTCGTTTTGGTTCGGGAAGCAAAAAATTCTCGCGCCACAACGAAAAA.................................................................................................................................................................................................................................... TransTerm Strand: - Conf: 63 HP_score: -4.2 Tail_Score: -4.36914 Start: 185 End: 232 Full_Region: acaggcgcgagaatt ttttcgttgtggcgcgagaa ttttttgc ttcccgaaccaaaacgaaaa ttttctcgaaccacg ........................................................................................................................................................................................ttttcgttgtggcgcgagaattttttgcttcccgaaccaaaacgaaaa..................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: PG1949:PG1950|PG1949:PG1950:malate dehydrogenase:hypothetical protein:<-->:2039279..2039739 461 aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Intra-Species Hit: Count: 1 Min: 1 Max: 461 Len: 461 Subject: NC_002950_PG1949_PG1950|malate dehydrogenase:hypothetical protein|NEGATIVE:POSITIVE|[2039279,2039739]|461 HSP 1 e-value: 6.0E-67 bit: 256.0 Len: 129 Query Start:1 Query End:129 Subject Strand: POSITIVE Subject Start: 1 Subject End: 129 aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaact............................................................................................................................................................................................................................................................................................................................................ aactgttccgttattaaaagattgcaaaaacctaattcggggatagcgactcttcttcgactttcccgatatatctatcagacaaatataagagtttcctaacaatatcctgtagacacgattaaaact............................................................................................................................................................................................................................................................................................................................................ HSP 2 e-value: 8.0E-54 bit: 212.0 Len: 107 Query Start:355 Query End:461 Subject Strand: POSITIVE Subject Start: 355 Subject End: 461 ..................................................................................................................................................................................................................................................................................................................................................................tcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt ..................................................................................................................................................................................................................................................................................................................................................................tcggtaaaaaacgatctacatggatgattgtgaaaattgcaaaagaaaacaggaaaaacgactatcttcggtatccgaactcactcacattctaatcgacactgctt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AACUGUUCCGUUAUUAAAAGAUUGCAAAAACCUAAUUCGGGGAUAGCGACUCUUCUUCGACUUUCCCGAUAUAUCUAUCAGACAAAUAUAAGAGUUUCCUAACAAUAUCCUGUAGACACGAUUAAAACUGUUUACGUGCCAAAAAUCAGCCACUCUACAGUCCGCAAAACGUGGUUCGAGAAAAUUUUCGUUUUGGUUCGGGAAGCAAAAAAUUCUCGCGCCACAACGAAAAAAUUCUCGCGCCUGUUUUUCAGGAUUCUCAGACCGCAAUCCGAGCAUUUCCCGUUCGUAUUUUCGAGAAAGCAGAUCAGCUGACACUCGCCUACCGGCCCGAACAUGCAGGGAGGACAAGCCUCGGUAAAAAACGAUCUACAUGGAUGAUUGUGAAAAUUGCAAAAGAAAACAGGAAAAACGACUAUCUUCGGUAUCCGAACUCACUCACAUUCUAAUCGACACUGCUU .........(((((((...((((((...........(((((((...(((.......)))...)))))))......................(((..((((.........(((((((((((..((((....))))))))...............))))))).....((((((.(((.((((((..((((((((.((((.((((((........)))))).)))).))))))))..)))))).)))))))))..))))..))).....)))))).(((..(((((.(((((.......(((..(((......)))....)))(((....))).))))).(((((.((((.....))))........((((((.........)))))).....)))))..........)))))..........(((((...)))))....)))......)))).)))....... (-115.76) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCAGUGUCGAUUAGAAUGUGAGUGAGUUCGGAUACCGAAGAUAGUCGUUUUUCCUGUUUUCUUUUGCAAUUUUCACAAUCAUCCAUGUAGAUCGUUUUUUACCGAGGCUUGUCCUCCCUGCAUGUUCGGGCCGGUAGGCGAGUGUCAGCUGAUCUGCUUUCUCGAAAAUACGAACGGGAAAUGCUCGGAUUGCGGUCUGAGAAUCCUGAAAAACAGGCGCGAGAAUUUUUUCGUUGUGGCGCGAGAAUUUUUUGCUUCCCGAACCAAAACGAAAAUUUUCUCGAACCACGUUUUGCGGACUGUAGAGUGGCUGAUUUUUGGCACGUAAACAGUUUUAAUCGUGUCUACAGGAUAUUGUUAGGAAACUCUUAUAUUUGUCUGAUAGAUAUAUCGGGAAAGUCGAAGAAGAGUCGCUAUCCCCGAAUUAGGUUUUUGCAAUCUUUUAAUAACGGAACAGUU .....((..(((((((((((..((..(((((((.....((((((((.........))))))))....((..((((.(((((.((((.(((((((((.....((((..((((((..(.........)..))))))))))(.((((.(((((((..(((((..((.((.....(((..(((((....(((((((....)))))))..))))).......((..((((((..((((((((.(((..((.(((........))).))..))).))))))))..))))))..)).)))....))))..)))))..))))))).)))).).................)).)))))))))))))))).)))).((((((..((((..((((((....))))))..)))).....)))))).)).....))))))).....))..))...)))))))..))..)).... (-136.50) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 931 80 31 171 122 NC_002950:PG1949|5end_malate_dehydrogenase_2039188..2039418_NEGATIVE 651 256 213 120 78 NC_002950:PG1617|5end_hypothetical_protein_1697755..1697985_NEGATIVE 595 230 185 168 123 NC_002950:PG2063|5end_hypothetical_protein_2160596..2160826_NEGATIVE 580 239 191 164 116 NC_002950:PG0132|5end_hypothetical_protein_152879..153109_POSITIVE 472 258 213 147 102 NC_002950:PG0007|5end_hypothetical_protein_6913..7143_NEGATIVE 460 256 213 87 44 NC_002950:PG2064|5end_hypothetical_protein_2160550..2160780_POSITIVE 452 260 213 136 80 NC_002950:PG1980|5end_hypothetical_protein_2067930..2068160_NEGATIVE 451 360 311 123 59 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 422 228 185 56 13 NC_002950:PG0080|5end_hypothetical_protein_93832..94062_NEGATIVE 418 256 213 88 46 NC_002950:PG0313|5end_hypothetical_protein_347366..347596_POSITIVE 415 255 213 122 80 NC_002950:PG0174|5end_pyridine_nucleotide-disulphide_oxidoreductase_family_protein_197628..197858_NEGATIVE 403 276 236 41 1 NC_002950:PG1655|5end_hypothetical_protein_1737095..1737325_POSITIVE 401 360 313 53 5 NC_002950:PG1305|5end_glycine_dehydrogenase_1386538..1386768_NEGATIVE 395 256 213 101 58 NC_002950:PG1799|5end_hypothetical_protein_1894499..1894729_POSITIVE 382 349 304 61 2 NC_002950:PG1340|5end_L-lactate_permease_1421848..1422078_NEGATIVE 374 290 241 192 130 NC_002950:PG1524|5end_2-succinyl-6-hydroxy-2,_4-cyclohexadiene-1-carboxylic_acid_synthase/2-oxoglutarate_decarboxylase_1602746..1602976_NEGATIVE 374 358 311 186 124 NC_002950:PG0635|5end_ribosomal_protein_L11_methyltransferase_687773..688003_NEGATIVE 374 358 311 84 40 NC_002950:PG0422|5end_hypothetical_protein_462302..462532_NEGATIVE 372 80 39 180 134 NC_002950:PG0790|5end_GTP-binding_protein_Obg_842583..842813_NEGATIVE 370 203 161 163 121 NC_002950:PG0081|5end_hypothetical_protein_93805..94035_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 764 244 201 49 6 NC_002950:PG0542|3end_hypothetical_protein_595377..595527_NEGATIVE 536 210 161 50 1 NC_002950:PG0732|3end_hypothetical_protein_783018..783168_POSITIVE 425 368 322 110 48 NC_002950:PG1095|3end_RNA_methyltransferase,_TrmA_family_1161702..1161852_POSITIVE 425 299 251 65 17 NC_002950:PG1024|3end_hypothetical_protein_1086876..1087026_POSITIVE 405 355 313 133 77 NC_002950:PG1027|3end_hypothetical_protein_1089197..1089347_NEGATIVE 403 289 242 134 89 NC_002950:PG0198|3end_hypothetical_protein_237501..237651_POSITIVE 386 257 213 54 8 NC_002950:PG0155|3end_riboflavin_biosynthesis_protein_RibD_177861..178011_NEGATIVE 384 360 314 48 1 NC_002950:PG1306|3end_metallo-beta-lactamase_family_protein_1386543..1386693_NEGATIVE 382 230 185 143 98 NC_002950:PG1718|3end_hypothetical_protein_1806532..1806682_NEGATIVE 381 355 312 86 36 NC_002950:PG1723|3end_ribosomal_protein_S20_1813403..1813553_POSITIVE 377 306 265 50 9 NC_002950:PG2227|3end_hypothetical_protein_2342744..2342894_POSITIVE 374 304 261 86 40 NC_002950:PG0062|3end_TPR_domain_protein_75810..75960_POSITIVE 371 346 301 88 36 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 371 329 281 108 45 NC_002950:PG1324|3end_Holliday_junction_resolvase_1402862..1403012_NEGATIVE 361 360 320 46 11 NC_002950:PG1582|3end_batA_protein_1660384..1660534_POSITIVE 358 359 312 132 69 NC_002950:PG1641|3end_phosphotyrosine_protein_phosphatase_1721260..1721410_NEGATIVE 358 349 303 139 82 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 356 348 302 71 25 NC_002950:PG1574|3end_hypothetical_protein_1652461..1652611_NEGATIVE 353 356 312 79 33 NC_002950:PG1391|3end_hypothetical_protein_1472961..1473111_POSITIVE 352 360 311 109 53 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE