Origin IGS: tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg .........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 cccggccgacttcgtcgattcccgttctctgaggataaggggtttccatagccctgcatacatataggacagccaccttgttcgctttgcaaacgaggtggctgtcttcgtttttgttggttcgccataaggctttcggagcttgcgattgttatgcatatttttcggatgagtcgatagcctatttgccgagctttttctctagtatgcaaagttgtgattggcaccgtattagagacttttttggctcggtgttcgaaaaatggtaatttggcaccgccttagcgatggacactttctctaaggcttggtactgactacaaatcacaaaatatcaaata Mask Tandem Repeat Region ================================================ tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Find is-nt database================================================ Query_seq: PG1872:PG1874|PG1872:PG1874:urocanate hydratase:hypothetical protein:<-<-:1969002..1969342 341 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG1872:PG1874|PG1872:PG1874:urocanate hydratase:hypothetical protein:<-<-:1969002..1969342 341 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG1872:PG1874|PG1872:PG1874:urocanate hydratase:hypothetical protein:<-<-:1969002..1969342 341 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: + Start: 14 End: 157 ............. M I C S Q Y Q A L E K V S I A K A V P N Y H F S N T E P K K S L I R C Q S Q L C I L E K K L G K ........................................................................................................................................................................................ Protein_Len: 60 Strand: + Start: 115 End: 339 .................................................................................................................. M P I T T L H T R E K A R Q I G Y R L I R K I C I T I A S S E S L M A N Q Q K R R Q P P R L Q S E Q G G C P I C M Q G Y .. Protein_Len: 53 Strand: + Start: 183 End: 341 ...................................................................................................................................................................................... M H N N R K L R K P Y G E P T K T K T A T S F A K R T R W L S Y M Y A G L W K P L I L R E R E S T K S A G Protein_Len: 40 Strand: - Start: 165 End: 284 .................................................................................................................................................................... R S M R F I H M V I A L E S L R I A F W C F R L C G G R K C L S C P P Q G I H M ......................................................... Protein_Len: 60 Strand: - Start: 76 End: 294 ........................................................................... H W D C S Q M S S F F S P L Y A I S E D S F Y A Y C D C A G F A K H R V L L F S S L W R T Q L A F L T A T R Y T H L A M ............................................... Protein_Len: 33 Strand: - Start: 60 End: 158 ........................................................... P P A L N G N K S C R A L F T E L V T G I V V K C V L S F A R C M ....................................................................................................................................................................................... tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg 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================================================ PromScan Matrix: RpoN Strand: - Score: 82 Start: 55 End: 71 ......................................................TTGGCACCGCCTTAGCG.............................................................................................................................................................................................................................................................................. tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 100 HP_score: -15.2 Tail_Score: -5.1963 Start: 232 End: 278 Full_Region: tagccctgcatacat ataggacagccaccttgttcgc ttt gcaaacgaggtggctgtcttcg tttttgttggttcgc .......................................................................................................................................................................................................................................ataggacagccaccttgttcgctttgcaaacgaggtggctgtcttcg............................................................... TransTerm Strand: + Conf: 100 HP_score: -19.1 Tail_Score: -3.05022 Start: 235 End: 275 Full_Region: AACCAACAAAAACGA AGACAGCCACCTCGTTTGC AAA GCGAACAAGGTGGCTGTCC TATATGTATGCAGGG ..........................................................................................................................................................................................................................................AGACAGCCACCTCGTTTGCAAAGCGAACAAGGTGGCTGTCC.................................................................. TransTerm Strand: - Conf: 100 HP_score: -22.6 Tail_Score: -3.94974 Start: 236 End: 274 Full_Region: cctgcatacatatag gacagccaccttgttcgc ttt gcaaacgaggtggctgtc ttcgtttttgttggt ...........................................................................................................................................................................................................................................gacagccaccttgttcgctttgcaaacgaggtggctgtc................................................................... Find igs database================================================ Query_seq: PG1872:PG1874|PG1872:PG1874:urocanate hydratase:hypothetical protein:<-<-:1969002..1969342 341 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Intra-Species Hit: Count: 1 Min: 1 Max: 341 Len: 341 Subject: NC_002950_PG1872_PG1874|urocanate hydratase:hypothetical protein|NEGATIVE:NEGATIVE|[1969002,1969342]|341 HSP 1 e-value: 0.0 bit: 676.0 Len: 341 Query Start:1 Query End:341 Subject Strand: POSITIVE Subject Start: 1 Subject End: 341 tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg tatttgatattttgtgatttgtagtcagtaccaagccttagagaaagtgtccatcgctaaggcggtgccaaattaccatttttcgaacaccgagccaaaaaagtctctaatacggtgccaatcacaactttgcatactagagaaaaagctcggcaaataggctatcgactcatccgaaaaatatgcataacaatcgcaagctccgaaagccttatggcgaaccaacaaaaacgaagacagccacctcgtttgcaaagcgaacaaggtggctgtcctatatgtatgcagggctatggaaaccccttatcctcagagaacgggaatcgacgaagtcggccggg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUUUGAUAUUUUGUGAUUUGUAGUCAGUACCAAGCCUUAGAGAAAGUGUCCAUCGCUAAGGCGGUGCCAAAUUACCAUUUUUCGAACACCGAGCCAAAAAAGUCUCUAAUACGGUGCCAAUCACAACUUUGCAUACUAGAGAAAAAGCUCGGCAAAUAGGCUAUCGACUCAUCCGAAAAAUAUGCAUAACAAUCGCAAGCUCCGAAAGCCUUAUGGCGAACCAACAAAAACGAAGACAGCCACCUCGUUUGCAAAGCGAACAAGGUGGCUGUCCUAUAUGUAUGCAGGGCUAUGGAAACCCCUUAUCCUCAGAGAACGGGAAUCGACGAAGUCGGCCGGG ..(((((......((((((((......(((((..(((((((.((.........)).))))))))))))))))))))......)))))..(((.(((......(((........(((.(((.......((((((((((............(((.((...(((((.(((..((....))......(((.........))).....))).)))))..)).)))...............(((((((((((.((((((...)))))).)))))))))))......))))))))))...)))..))).....((((........))))...)))......)))))). (-102.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CCCGGCCGACUUCGUCGAUUCCCGUUCUCUGAGGAUAAGGGGUUUCCAUAGCCCUGCAUACAUAUAGGACAGCCACCUUGUUCGCUUUGCAAACGAGGUGGCUGUCUUCGUUUUUGUUGGUUCGCCAUAAGGCUUUCGGAGCUUGCGAUUGUUAUGCAUAUUUUUCGGAUGAGUCGAUAGCCUAUUUGCCGAGCUUUUUCUCUAGUAUGCAAAGUUGUGAUUGGCACCGUAUUAGAGACUUUUUUGGCUCGGUGUUCGAAAAAUGGUAAUUUGGCACCGCCUUAGCGAUGGACACUUUCUCUAAGGCUUGGUACUGACUACAAAUCACAAAAUAUCAAAUA .((.(((((....((((((((......((((((((...((((((.....))))))(((((((...(((((((((((((((((.((...)).))))))))))))))))).....((((.((((((((....))).....))))).)))).)).)))))....)))))))).)))))))).(((.((((((((((((...(((((((((((.......(((.....)))))))))))))).......)))))))).......)))))))...)))))...(((((((.((.(....)..)).)))))))..)).............................. (-113.22) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1017 70 21 161 112 NC_002950:PG1872|5end_urocanate_hydratase_1968911..1969141_NEGATIVE 429 340 291 173 104 NC_002950:PG0809|5end_hypothetical_protein_872014..872244_NEGATIVE 367 280 231 219 161 NC_002950:PG0804|5end_flavodoxin_861765..861995_NEGATIVE 366 340 307 224 175 NC_002950:PG0134|5end_magnesium_transporter_157135..157365_NEGATIVE 361 278 237 226 175 NC_002950:PG2081|5end_biotin_synthetase_2181661..2181891_NEGATIVE 354 340 300 67 26 NC_002950:PG1233|5end_hypothetical_protein_1309885..1310115_POSITIVE 345 275 240 201 172 NC_002950:PG1247|5end_3-dehydroquinate_synthase_1324444..1324674_POSITIVE 344 330 288 48 1 NC_002950:PG2155|5end_lipoprotein,_putative_2261862..2262092_NEGATIVE 341 70 25 90 45 NC_002950:PG0034|5end_thioredoxin_42549..42779_NEGATIVE 340 290 241 215 168 NC_002950:PG2154|5end_hypothetical_protein_2260945..2261175_NEGATIVE 339 291 252 228 177 NC_002950:PG0629|5end_inorganic_polyphosphate/ATP-NAD_kinase_683364..683594_NEGATIVE 338 287 241 220 164 NC_002950:PG1581|5end_hypothetical_protein_1658368..1658598_POSITIVE 334 70 23 90 39 NC_002950:PG1840|5end_hypothetical_protein_1937102..1937332_POSITIVE 333 295 252 216 161 NC_002950:PG1693|5end_HesA/MoeB/ThiF_family_protein_1777919..1778149_NEGATIVE 326 68 23 82 36 NC_002950:PG0723|5end_hypothetical_protein_774949..775179_POSITIVE 324 290 241 209 152 NC_002950:PG0634|5end_ThiJ/PfpI_family_protein_686143..686373_POSITIVE 323 68 21 56 4 NC_002950:PG1466|5end_hypothetical_protein_1542623..1542853_POSITIVE 323 340 304 127 88 NC_002950:PG0164|5end_hypothetical_protein_187395..187625_NEGATIVE 319 340 295 59 13 NC_002950:PG2146|5end_hypothetical_protein_2253815..2254045_POSITIVE 317 274 232 62 22 NC_002950:PG0630|5end_pyridoxal_phosphate_biosynthetic_protein_683392..683622_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 338 303 127 87 NC_002950:PG0045|3end_heat_shock_protein_90_56193..56343_POSITIVE 327 277 232 71 23 NC_002950:PG0340|3end_hypothetical_protein_376436..376586_POSITIVE 323 68 21 59 7 NC_002950:PG1465|3end_hypothetical_protein_1542706..1542856_POSITIVE 319 340 295 102 56 NC_002950:PG2145|3end_polysaccharide_deacetylase_2253938..2254088_POSITIVE 314 294 252 147 101 NC_002950:PG2159|3end_protoporphyrinogen_oxidase_2265874..2266024_POSITIVE 314 340 299 57 3 NC_002950:PG1010|3end_ABC_transporter,_ATP-binding_protein_1068509..1068659_NEGATIVE 313 70 26 60 1 NC_002950:PG1152|3end_hypothetical_protein_1234674..1234824_NEGATIVE 310 340 302 48 1 NC_002950:PG2044|3end_hypothetical_protein_2144165..2144315_POSITIVE 310 338 299 56 17 NC_002950:PG0312|3end_hypothetical_protein_346509..346659_NEGATIVE 309 330 281 90 33 NC_002950:PG0525|3end_CTP_synthetase_570698..570848_POSITIVE 308 220 171 130 73 NC_002950:PG2214|3end_hypothetical_protein_2325301..2325451_NEGATIVE 308 310 265 82 20 NC_002950:PG0686|3end_hypothetical_protein_741131..741281_NEGATIVE 306 79 31 123 70 NC_002950:PG1858|3end_flavodoxin_1956538..1956688_NEGATIVE 306 178 136 56 17 NC_002950:PG1835|3end_lipoprotein,_putative_1928520..1928670_POSITIVE 305 310 264 97 60 NC_002950:PG0767|3end_4-alpha-glucanotransferase_818557..818707_NEGATIVE 304 340 312 114 76 NC_002950:PG1213|3end_ribonuclease_H_1293163..1293313_POSITIVE 304 85 41 151 103 NC_002950:PG0676|3end_oxidoreductase,_short_chain_dehydrogenase/reductase_family_726514..726664_NEGATIVE 303 339 294 54 8 NC_002950:PG2033|3end_glutamate_synthase,_small_subunit_2133415..2133565_NEGATIVE 302 339 296 60 20 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 301 179 131 103 42 NC_002950:PG2046|3end_hypothetical_protein_2145793..2145943_POSITIVE