Origin IGS: ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag .........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 ctgtctataatcaaatttgctttttggcatacccgctgttcggaaaaaaagcaattatcccttttgatatacaataataatgtataagcctctccttgcacagtggatatgtttcttttgttatactacggacaaagatacgccattgttttaatatcggaaacaaagattccgataatttttgaattatacttattaatttgcaaatcgagctcgtggttaggctgtgactaacgcgacttttcaggcgtttttttgcacgaaaattatttgtagacttgtgaaaaaaggtctttatatcaacttgaaaataaagataatctatgtgtgattaaccgagtgaatcatcggtgccgataaaaaacaatgaacaggctgcggttaacatacatgagaaaagagtggcttgtag Mask Tandem Repeat Region ================================================ ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Find is-nt database================================================ Query_seq: TF1058:TF1059|TF1058:TF1059:N-acetylglucosamine kinase:possible xanthan lyase:->->:1126909..1127320 412 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1058:TF1059|TF1058:TF1059:N-acetylglucosamine kinase:possible xanthan lyase:->->:1126909..1127320 412 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1058:TF1059|TF1058:TF1059:N-acetylglucosamine kinase:possible xanthan lyase:->->:1126909..1127320 412 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 88 End: 399 ....................................................................................... M D Y L Y F Q V D I K T F F H K S T N N F R A K K R L K S R V S H S L T T S S I C K L I S I I Q K L S E S L F P I L K Q ............. Protein_Len: 36 Strand: + Start: 303 End: 410 .............................................................................................................................................................................................................................................................................................................. M S T V Q G E A Y T L L L Y I K R D N C F F S E Q R V C Q K A N L I I D .. Protein_Len: 33 Strand: - Start: 231 End: 329 ...................................................................................................................................................................................................................................... F N D S D K N G I N F C H R I K T R L I V F S V Y G S H L S L S M ................................................................................... Protein_Len: 43 Strand: - Start: 182 End: 310 ..................................................................................................................................................................................... D C G L W S S S K C I L L Y L E F I I P I K T E S I L V I A Y R Q G Y Y L L L F M D M ...................................................................................................... Protein_Len: 34 Strand: - Start: 85 End: 186 .................................................................................... V Y I I K I K L N I Y L G K K V L R C I I K T C F F A Q F T A N T M .................................................................................................................................................................................................................................. ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag 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================================================ ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 73 HP_score: -2.3 Tail_Score: -5.40072 Start: 163 End: 176 Full_Region: aggctgtgactaacg cgact tttc aggcg tttttttgcacgaaa ..................................................................................................................................................................cgacttttcaggcg............................................................................................................................................................................................................................................ TransTerm Strand: - Conf: 75 HP_score: -5.7 Tail_Score: -4.78752 Start: 235 End: 259 Full_Region: tacgccattgtttta atatcggaaac aaa gattccgataa tttttgaattatact ..........................................................................................................................................................................................................................................atatcggaaacaaagattccgataa......................................................................................................................................................... TransTerm Strand: - Conf: 76 HP_score: -9.2 Tail_Score: -3.46167 Start: 236 End: 258 Full_Region: acgccattgttttaa tatcggaaac aaa gattccgata atttttgaattatac ...........................................................................................................................................................................................................................................tatcggaaacaaagattccgata.......................................................................................................................................................... Find igs database================================================ Query_seq: TF1058:TF1059|TF1058:TF1059:N-acetylglucosamine kinase:possible xanthan lyase:->->:1126909..1127320 412 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Intra-Species Hit: Count: 1 Min: 1 Max: 412 Len: 412 Subject: tfor_TF1058_TF1059|N-acetylglucosamine kinase:possible xanthan lyase|POSITIVE:POSITIVE|[1126909,1127320]|412 HSP 1 e-value: 0.0 bit: 733.0 Len: 412 Query Start:1 Query End:412 Subject Strand: POSITIVE Subject Start: 1 Subject End: 412 ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcnnnnnnncgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgcnnnnnnnccgaacagcgggtatgccaaaaagcaaatttgattatagacag ctacaagccactcttttctcatgtatgttaaccgcagcctgttcattgttttttatcggcaccgatgattcactcggttaatcacacatagattatctttattttcaagttgatataaagaccttttttcacaagtctacaaataattttcgtgcaaaaaaacgcctgaaaagtcgcgttagtcacagcctaaccacgagctcgatttgcaaattaataagtataattcaaaaattatcggaatctttgtttccgatattaaaacaatggcgtatctttgtccgtagtataacaaaagaaacatatccactgtgcaaggagaggcttatacattattattgtatatcaaaagggataattgctttttttccgaacagcgggtatgccaaaaagcaaatttgattatagacag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUACAAGCCACUCUUUUCUCAUGUAUGUUAACCGCAGCCUGUUCAUUGUUUUUUAUCGGCACCGAUGAUUCACUCGGUUAAUCACACAUAGAUUAUCUUUAUUUUCAAGUUGAUAUAAAGACCUUUUUUCACAAGUCUACAAAUAAUUUUCGUGCAAAAAAACGCCUGAAAAGUCGCGUUAGUCACAGCCUAACCACGAGCUCGAUUUGCAAAUUAAUAAGUAUAAUUCAAAAAUUAUCGGAAUCUUUGUUUCCGAUAUUAAAACAAUGGCGUAUCUUUGUCCGUAGUAUAACAAAAGAAACAUAUCCACUGUGCAAGGAGAGGCUUAUACAUUAUUAUUGUAUAUCAAAAGGGAUAAUUGCUUUUUUUCCGAACAGCGGGUAUGCCAAAAAGCAAAUUUGAUUAUAGACAG ................(((.((((.(((((((((.((.........((....((((((....))))))..))))))))))).)).)))))))...(((((((..((.....)).))))))).............(((((.........((((((......(((((((....))..))))).((....)).....)))))).(((((((((................(((......((((((((.......)))))))).....((.((((((......)).)))).)).........))).(((((((.((((....(((((....((((((.......))))))...(((((.(....).))))))))))..)))).))))))).......))))).))))...))))).. (-84.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUGUCUAUAAUCAAAUUUGCUUUUUGGCAUACCCGCUGUUCGGAAAAAAAGCAAUUAUCCCUUUUGAUAUACAAUAAUAAUGUAUAAGCCUCUCCUUGCACAGUGGAUAUGUUUCUUUUGUUAUACUACGGACAAAGAUACGCCAUUGUUUUAAUAUCGGAAACAAAGAUUCCGAUAAUUUUUGAAUUAUACUUAUUAAUUUGCAAAUCGAGCUCGUGGUUAGGCUGUGACUAACGCGACUUUUCAGGCGUUUUUUUGCACGAAAAUUAUUUGUAGACUUGUGAAAAAAGGUCUUUAUAUCAACUUGAAAAUAAAGAUAAUCUAUGUGUGAUUAACCGAGUGAAUCAUCGGUGCCGAUAAAAAACAAUGAACAGGCUGCGGUUAACAUACAUGAGAAAAGAGUGGCUUGUAG .........((((((.(((((((((..(..((.....))...)..)))))))))........))))))..............((((((((.(((....((.(((.((((((..((((((.((((((((((((((((((.(((((.((((.....((((((((.......))))))))......((((((.......))))))))))...(((.(((((.((((.......))))))))))))....))))).))))))...........)))))))...))))).))))))....)))))).))))).............((((((((((.((((((((((...((((((....)))..........)))....))).)))))))))))))).)))...))).)))))))). (-96.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 360 78 34 196 141 tfor:TF2402|5end_outer_membrane_protein,_possibly_involved_in_nutrient_binding_2574582..2574812_POSITIVE 349 210 161 68 8 tfor:TF0379|5end_conserved_hypothetical_protein,_nif3_family_399458..399688_POSITIVE 335 210 164 214 154 tfor:TF3158|5end_inner_membrane_protein_3393729..3393959_POSITIVE 333 70 32 217 160 tfor:TF1952|5end_immunoreactive_84kD_antigen_PG93_2101443..2101673_POSITIVE 332 210 163 193 138 tfor:TF0765|5end_conserved_hypothetical_protein_811302..811532_POSITIVE 332 206 163 52 14 tfor:TF0462|5end_possible_cobalamin_biosynthesis_precorrin-3_methylase_477600..477830_POSITIVE 331 212 173 230 191 tfor:TF1228|5end_conserved_hypothetical_protein_1314103..1314333_POSITIVE 329 190 148 95 51 tfor:TF1250|5end_possible_cation_efflux_pump_1332324..1332554_POSITIVE 326 201 165 227 192 tfor:TF1175|5end_membrane-fusion_protein_1258140..1258370_POSITIVE 322 59 11 222 173 tfor:TF0961|5end_translation_initiation_inhibitor,_endoribonuclease_activity_1010445..1010675_POSITIVE 321 76 31 220 165 tfor:TF2390|5end_conserved_hypothetical_protein_2560509..2560739_POSITIVE 318 80 32 68 9 tfor:TF2974|5end_conserved_hypothetical_protein;_possible_hydrolase_3181418..3181648_POSITIVE 311 394 353 179 129 tfor:TF2368|5end_uridine_phosphorylase_2533666..2533896_POSITIVE 311 210 162 56 12 tfor:TF2257|5end_transfer_region-related_protein,_TraJ_2428541..2428771_POSITIVE 311 394 351 53 3 tfor:TF1981|5end_mannose-6-phosphate_isomerase_2130896..2131126_POSITIVE 310 206 164 43 9 tfor:TF1775|5end_oxidoreductase,_Gfo/Idh/MocA_family_1913135..1913365_POSITIVE 307 210 161 135 79 tfor:TF0215|5end_tRNA/rRNA_methyltransferase,_TrmH_family_241463..241693_POSITIVE 306 79 31 65 12 tfor:TF2125|5end_conserved_hypothetical_protein_2302119..2302349_POSITIVE 306 79 33 186 142 tfor:TF0205|5end_exsB_protein_231523..231753_POSITIVE 305 190 148 136 100 tfor:TF2205|5end_conserved_hypothetical_protein;_possible_transcriptional_regulator_2379055..2379285_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 333 70 32 141 84 tfor:TF1951|3end_xanthosine_triphosphate_pyrophosphatase,_Ham1-like_protein_2101447..2101597_POSITIVE 331 68 31 50 10 tfor:TF0011|3end_conserved_hypothetical_protein_5397..5547_POSITIVE 329 190 148 47 3 tfor:TF1249|3end_phosphoglycerate_kinase_(cytosolic_phosphoglycerate_kinase)_1332356..1332506_POSITIVE 311 394 353 143 93 tfor:TF2367|3end_delta-1-pyrroline-5-carboxylate_dehydrogenase_2533710..2533860_POSITIVE 311 210 162 49 5 tfor:TF2256|3end_transfer_region-related_protein,_TraI_2428614..2428764_POSITIVE 307 210 163 96 30 tfor:TF2850|3end_endoribonuclease_L-PSP_3038871..3039021_POSITIVE 307 205 164 80 21 tfor:TF0072|3end_hypothetical_protein_81070..81220_POSITIVE 306 79 31 57 4 tfor:TF2124|3end_conserved_hypothetical_protein;_possible_TonB_dependent_receptor_2302191..2302341_POSITIVE 305 190 148 123 87 tfor:TF2204|3end_conserved_hypothetical_protein_2379122..2379272_POSITIVE 305 201 165 40 5 tfor:TF0958|3end_conserved_hypothetical_protein_1004909..1005059_POSITIVE 297 45 8 67 31 tfor:TF1362|3end_hypothetical_protein_1444059..1444209_POSITIVE 296 76 38 140 98 tfor:TF2483|3end_hypothetical_protein_2660022..2660172_POSITIVE 293 199 151 61 14 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 292 210 161 95 29 tfor:TF3126|3end_glycosyltransferase,_group_2_family_3361685..3361835_POSITIVE 288 80 31 98 52 tfor:TF2343|3end_ribosome_recycling_factor_2507502..2507652_POSITIVE 288 201 166 65 26 tfor:TF1758|3end_conserved_hypothetical_protein_1895544..1895694_POSITIVE 286 204 163 151 109 tfor:TF0419|3end_conserved_hypothetical_protein_435794..435944_POSITIVE 283 75 32 76 25 tfor:TF1917|3end_hypothetical_protein_2070244..2070394_POSITIVE 282 199 154 115 65 tfor:TF2718|3end_hypothetical_protein_2892811..2892961_POSITIVE 282 59 11 76 13 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE