Origin IGS: taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag .........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 ctactcatattaagttaaagagttgaagctttgaataactcttctttaactgtttagttatggaagaaagatctatattttgtaaaaatatttttatcagaatacgataaattcactttgacattccaaaagcggttgttttgcgatgcaaaacctacgcttttaccgtgtaaaacagccgcttttggaacgcgaaacaataggttttacaatgtcttgatagacaacaagttaagcaatagttacgcttgtgaaaaagatttacaactatcgagcctttttccacctataattta Mask Tandem Repeat Region ================================================ taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Find is-nt database================================================ Query_seq: PI1117:PI1118|PI1117:PI1118:glycosyl transferase, family 2:glycosyl transferases, group 1:->->:1042340..1042635 296 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1117:PI1118|PI1117:PI1118:glycosyl transferase, family 2:glycosyl transferases, group 1:->->:1042340..1042635 296 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1117:PI1118|PI1117:PI1118:glycosyl transferase, family 2:glycosyl transferases, group 1:->->:1042340..1042635 296 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 11 End: 139 .......... M E K G S I V V N L F H K R N Y C L T C C L S R H C K T Y C F A F Q K R L F Y T V K A ............................................................................................................................................................. Protein_Len: 48 Strand: + Start: 97 End: 240 ................................................................................................ M F R V P K A A V L H G K S V G F A S Q N N R F W N V K V N L S Y S D K N I F T K Y R S F F H N ........................................................ Protein_Len: 35 Strand: + Start: 185 End: 289 ........................................................................................................................................................................................ M Y R I L I K I F L Q N I D L S S I T K Q L K K S Y S K L Q L F N L I ....... Protein_Len: 60 Strand: - Start: 3 End: 209 .. Q L D K E C A Y S N S L K N D I L V N Y F R N N R T G F A A T K C P L L T P K A D C F L R K Q F T L T F K D Y E S L F M ....................................................................................... taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag 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: 84 End: 113 ...................................................................................TTTGGAACGCGAAACAATAGGTTTTACAAT....................................................................................................................................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 77 HP_score: -7.6 Tail_Score: -4.07568 Start: 115 End: 165 Full_Region: tttgacattccaaaa gcggttgttttgcgatgcaaaacc tac gcttttaccgtgtaaaacagccgc ttttggaacgcgaaa ..................................................................................................................gcggttgttttgcgatgcaaaacctacgcttttaccgtgtaaaacagccgc................................................................................................................................... TransTerm Strand: - Conf: 70 HP_score: -4.4 Tail_Score: -4.84359 Start: 207 End: 221 Full_Region: tggaagaaagatcta tatttt gta aaaata tttttatcagaatac ..............................................................................................................................................................................................................tattttgtaaaaata........................................................................... Find igs database================================================ Query_seq: PI1117:PI1118|PI1117:PI1118:glycosyl transferase, family 2:glycosyl transferases, group 1:->->:1042340..1042635 296 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Intra-Species Hit: Count: 10 Min: 1 Max: 296 Len: 296 Subject: pint_PI1117_PI1118|glycosyl transferase, family 2:glycosyl transferases, group 1|POSITIVE:POSITIVE|[1042340,1042635]|296 HSP 1 e-value: 1.0E-167 bit: 587.0 Len: 296 Query Start:1 Query End:296 Subject Strand: POSITIVE Subject Start: 1 Subject End: 296 taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag taaattataggtggaaaaaggctcgatagttgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattctgataaaaatatttttacaaaatatagatctttcttccataactaaacagttaaagaagagttattcaaagcttcaactctttaacttaatatgagtag Subject: pint_PI1271_PI1272|transcriptional regulator, AraC/XylS family:possible transcriptional regulator|POSITIVE:POSITIVE|[1191345,1191841]|497 HSP 1 e-value: 4.0E-27 bit: 123.0 Len: 138 Query Start:31 Query End:168 Subject Strand: NEGATIVE Subject Start: 307 Subject End: 444 ..............................tgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttt................................................................................................................................ ..............................tgtaaatatttttcacaaacataactattgcataacttgttcgttatcagtgtattgcaaaacctacgcttttgcgttccaaaagcggctgttttgtacggtaaaagcgtaggttttgcatcgcaaaagaaccgcttt................................................................................................................................ Subject: pint_PI0023_PI0024|internalin-related protein:hypothetical protein|POSITIVE:POSITIVE|[28131,28517]|387 HSP 1 e-value: 4.0E-27 bit: 123.0 Len: 110 Query Start:84 Query End:193 Subject Strand: NEGATIVE Subject Start: 241 Subject End: 350 ...................................................................................attgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgt....................................................................................................... ...................................................................................attgtaaaacctattgttttgcattccaaaagcggctgttttgcacggtaaaagcgtaggttttgcgttgcaaaacagccgctttcgcaatgccaaatcgaaattatcgt....................................................................................................... Subject: pint_PI1174_PI1175|hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1097103,1097511]|409 HSP 1 e-value: 6.0E-26 bit: 119.0 Len: 151 Query Start:31 Query End:181 Subject Strand: NEGATIVE Subject Start: 139 Subject End: 289 ..............................tgtaaatctttttcacaagcgtaactattgcttaacttg-ttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaag................................................................................................................... ..............................tgtaaatatttttcacaggcataactattgtgtaacttacttgt-tatcaacgcattgcaaaacctattgttttgcattccaaaagcggctgttttgcacggtaaaagcgtaggttttgcgttgcaaaagagccgctttcgcaacgtcaaag................................................................................................................... Subject: pint_PI2088_PI2089|conserved hypothetical protein; possible PAP2 superfamily protein:conserved hypothetical protein|POSITIVE:POSITIVE|[2045876,2046339]|464 HSP 1 e-value: 1.0E-23 bit: 111.0 Len: 116 Query Start:83 Query End:198 Subject Strand: NEGATIVE Subject Start: 176 Subject End: 291 ..................................................................................cattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaagtgaatttatcgtattct.................................................................................................. ..................................................................................cattataaaacctattgttttgcattccaaaagcggctgttttgcacggtaaaagcgtaggttttgcgttgcaaaacagcagctttcgcaacgtcaaatcgaaattatcgttttct.................................................................................................. Subject: pint_PI0932_PI0933|conserved hypothetical protein; possible hemin receptor:hypothetical protein|POSITIVE:POSITIVE|[865425,865839]|415 HSP 1 e-value: 2.0E-19 bit: 97.6 Len: 105 Query Start:76 Query End:180 Subject Strand: POSITIVE Subject Start: 166 Subject End: 270 ...........................................................................atcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaa.................................................................................................................... ...........................................................................atcaaggcattgtaaaacctattgtttcgcgttccaaaagcgtaggttttgcacggtaaaagcggctcttttgcattgcaaaacctacgcttttgcaatgtcaaa.................................................................................................................... Subject: pint_PI0962_PI0963|phosphoglycerate mutase:hypothetical protein|POSITIVE:POSITIVE|[892763,893337]|575 HSP 1 e-value: 1.0E-17 bit: 91.7 Len: 150 Query Start:31 Query End:180 Subject Strand: NEGATIVE Subject Start: 183 Subject End: 332 ..............................tgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaa.................................................................................................................... ..............................tgtaaatatttttcacaagcgtaaccattgcataactatctcactatcaagactttgcaaaacctattgttttgcattccaaaagcgtaggttttgcacggtaaaagcggctcttttgcaacgcaaaacctacgctttcgcaatgtcaaa.................................................................................................................... Subject: pint_PI0945_PI0946|sodium:solute symporter family protein:glutathione peroxidase|POSITIVE:POSITIVE|[877685,878112]|428 HSP 1 e-value: 8.0E-16 bit: 85.7 Len: 107 Query Start:75 Query End:181 Subject Strand: NEGATIVE Subject Start: 117 Subject End: 223 ..........................................................................tatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatgtcaaag................................................................................................................... ..........................................................................tatcaacacattacaaaacctattgttttgcattccaaaagcgtaggttttacacggtaaaagcggctcttttgcatcgcaaaacagccgctttcgcaatgccaaag................................................................................................................... Subject: pint_PI1915_PI1916|conserved hypothetical protein:conserved hypothetical protein|POSITIVE:POSITIVE|[1859967,1860350]|384 HSP 1 e-value: 5.0E-14 bit: 79.8 Len: 64 Query Start:112 Query End:175 Subject Strand: POSITIVE Subject Start: 165 Subject End: 228 ...............................................................................................................aaagcggctgttttacacggtaaaagcgtaggttttgcatcgcaaaacaaccgcttttggaatg......................................................................................................................... ...............................................................................................................aaagcggctgttttgcacggtaaaagcgtatgttttacgttgcaaaacagccgcttttggaatg......................................................................................................................... HSP 2 e-value: 5.0E-11 bit: 69.9 Len: 51 Query Start:75 Query End:125 Subject Strand: NEGATIVE Subject Start: 208 Subject End: 258 ..........................................................................tatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgtttt........................................................................................................................................................................... ..........................................................................tatcaatacattataaaacctattgttttgcattccaaaagcggctgtttt........................................................................................................................................................................... Subject: pint_PI0854_PI0855|MiaB-like tRNA modifying enzyme:hypothetical protein|POSITIVE:POSITIVE|[788060,789233]|1174 HSP 1 e-value: 7.0E-10 bit: 65.9 Len: 109 Query Start:31 Query End:139 Subject Strand: NEGATIVE Subject Start: 821 Subject End: 929 ..............................tgtaaatctttttcacaagcgtaactattgcttaacttgttgtctatcaagacattgtaaaacctattgtttcgcgttccaaaagcggctgttttacacggtaaaagcg............................................................................................................................................................. ..............................tgtaaatatttttcacagatgcaactatcgcataactttctgtttatcaacatattataaaacctattgttttgcattccaaaagcgtaggttttgcacggtaaaagcg............................................................................................................................................................. HSP 2 e-value: 7.0E-7 bit: 56.0 Len: 36 Query Start:134 Query End:169 Subject Strand: POSITIVE Subject Start: 792 Subject End: 827 .....................................................................................................................................aaagcgtaggttttgcatcgcaaaacaaccgctttt............................................................................................................................... .....................................................................................................................................aaagcgtaggttttgcaacgcaaaacagccgctttt............................................................................................................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAUUAUAGGUGGAAAAAGGCUCGAUAGUUGUAAAUCUUUUUCACAAGCGUAACUAUUGCUUAACUUGUUGUCUAUCAAGACAUUGUAAAACCUAUUGUUUCGCGUUCCAAAAGCGGCUGUUUUACACGGUAAAAGCGUAGGUUUUGCAUCGCAAAACAACCGCUUUUGGAAUGUCAAAGUGAAUUUAUCGUAUUCUGAUAAAAAUAUUUUUACAAAAUAUAGAUCUUUCUUCCAUAACUAAACAGUUAAAGAAGAGUUAUUCAAAGCUUCAACUCUUUAACUUAAUAUGAGUAG ....(((((.((((((.((((.((.....(((((((.....(((((.((((.......))))..((....(((((....)))))..))...............(((((((((((((((.((((((...((((.(((((....)))))..)))).)))))).)))))))))))))))....)))))(((((((.....)))))))......)))))))......)).)))).))))))........(((((((((.(((((......)))))....)))))))))...))))).... (-74.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACUCAUAUUAAGUUAAAGAGUUGAAGCUUUGAAUAACUCUUCUUUAACUGUUUAGUUAUGGAAGAAAGAUCUAUAUUUUGUAAAAAUAUUUUUAUCAGAAUACGAUAAAUUCACUUUGACAUUCCAAAAGCGGUUGUUUUGCGAUGCAAAACCUACGCUUUUACCGUGUAAAACAGCCGCUUUUGGAACGCGAAACAAUAGGUUUUACAAUGUCUUGAUAGACAACAAGUUAAGCAAUAGUUACGCUUGUGAAAAAGAUUUACAACUAUCGAGCCUUUUUCCACCUAUAAUUUA ..........(((((((.((.((.(((((((.((.....((((((.(((((....))))).)))))).((((((.((((((((((((....))))).))))))).......(((((.......((((((((((((((((((((((....((((.......))))....)))))))))))))))))))))).(((.(((.....((((.((..(((((....)))))....)).))))....))).)))..)))))..)))))).......))))))....))).)))).))))))) (-75.80) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 837 160 111 68 19 pint:PI1204|5end_hypothetical_protein_1124430..1124660_POSITIVE 822 150 104 189 143 pint:PI0991|5end_conserved_hypothetical_protein_915309..915539_POSITIVE 805 149 104 61 16 pint:PI2022|5end_hypothetical_protein_1978631..1978861_POSITIVE 802 150 104 195 149 pint:PI2046|5end_hypothetical_protein_1999030..1999260_POSITIVE 802 150 104 209 163 pint:PI0887|5end_hypothetical_protein_817536..817766_POSITIVE 802 150 104 102 56 pint:PI0867|5end_hypothetical_protein_803859..804089_POSITIVE 785 149 104 194 149 pint:PI0024|5end_hypothetical_protein_28378..28608_POSITIVE 783 140 91 225 176 pint:PI2024|5end_hypothetical_protein_1978804..1979034_POSITIVE 783 150 104 102 56 pint:PI0119|5end_hypothetical_protein_111506..111736_POSITIVE 782 160 111 53 4 pint:PI0089|5end_hypothetical_protein_88162..88392_POSITIVE 776 149 104 221 176 pint:PI1333|5end_conserved_hypothetical_protein_1250777..1251007_POSITIVE 761 160 111 50 1 pint:PI0638|5end_hypothetical_protein_582218..582448_POSITIVE 739 158 111 51 4 pint:PI0568|5end_hypothetical_protein_512950..513180_POSITIVE 713 149 104 208 163 pint:PI0827|5end_hypothetical_protein_763991..764221_POSITIVE 710 149 104 208 163 pint:PI0575|5end_hypothetical_protein_519561..519791_POSITIVE 707 140 91 52 3 pint:PI0322|5end_hypothetical_protein_303508..303738_POSITIVE 681 158 111 162 115 pint:PI1804|5end_hypothetical_protein_1738109..1738339_POSITIVE 681 158 111 49 2 pint:PI1786|5end_hypothetical_protein_1718124..1718354_POSITIVE 672 158 112 110 64 pint:PI0978|5end_hypothetical_protein_904867..905097_POSITIVE 643 180 132 49 1 pint:PI0866|5end_hypothetical_protein_803776..804006_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 822 150 104 144 98 pint:PI0568|3end_hypothetical_protein_513131..513281_POSITIVE 822 150 104 68 22 pint:PI0567|3end_hypothetical_protein_513055..513205_POSITIVE 802 150 104 95 49 pint:PI0819|3end_hypothetical_protein_759919..760069_POSITIVE 802 150 104 144 98 pint:PI0815|3end_hypothetical_protein_754677..754827_POSITIVE 785 149 104 143 98 pint:PI0095|3end_hypothetical_protein_91850..92000_POSITIVE 782 150 104 144 98 pint:PI0081|3end_hypothetical_protein_80700..80850_POSITIVE 779 140 91 146 97 pint:PI1041|3end_hypothetical_protein_960675..960825_POSITIVE 763 140 91 146 97 pint:PI1797|3end_hypothetical_protein_1731559..1731709_POSITIVE 763 140 91 146 97 pint:PI0885|3end_hypothetical_protein_817563..817713_POSITIVE 763 140 91 146 97 pint:PI0866|3end_hypothetical_protein_803993..804143_POSITIVE 763 140 91 146 97 pint:PI0820|3end_hypothetical_protein_759980..760130_POSITIVE 763 140 91 146 97 pint:PI0089|3end_hypothetical_protein_88355..88505_POSITIVE 761 160 111 149 100 pint:PI0637|3end_hypothetical_protein_582397..582547_POSITIVE 746 150 104 144 98 pint:PI0638|3end_hypothetical_protein_582402..582552_POSITIVE 744 140 91 146 97 pint:PI0118|3end_hypothetical_protein_111640..111790_POSITIVE 690 157 111 151 105 pint:PI1252|3end_hypothetical_protein_1175440..1175590_POSITIVE 687 140 91 146 97 pint:PI1005|3end_hypothetical_protein_926481..926631_POSITIVE 672 150 104 144 98 pint:PI1155|3end_hypothetical_protein_1080352..1080502_POSITIVE 611 139 91 106 58 pint:PI0905|3end_hypothetical_protein_834697..834847_POSITIVE 611 139 91 84 36 pint:PI0560|3end_hypothetical_protein_508910..509060_POSITIVE