Origin IGS: atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat .........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 attctatatctattatgtattgcaaacataatgtttttatagcataatataaaatttcaagccaagtatttttctaataacttgttgtaaatactattttctctcaaaaagcatagtttacagaatatttttgcatatgtccacagatttctgccacgaaaacgcatattgtttcttaaaaataagcatctgaaaagaaacgtaaatagaatatcatcatccggctgactgcaaaaaaatccgatacatcgccttttttatcaaagtcttttcat Mask Tandem Repeat Region ================================================ atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Find is-nt database================================================ Query_seq: TF1539:TF1540|TF1539:TF1540:conserved hypothetical protein:possible ATPase:->->:1644402..1644676 275 atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF1539:TF1540|TF1539:TF1540:conserved hypothetical protein:possible ATPase:->->:1644402..1644676 275 atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF1539:TF1540|TF1539:TF1540:conserved hypothetical protein:possible ATPase:->->:1644402..1644676 275 atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Predict ORF larger than 30AA ================================================ Protein_Len: 60 Strand: + Start: 31 End: 216 .............................. M G F F C S Q P D D D I L F T F L F R C L F L R N N M R F R G R N L W T Y A K I F C K L C F L R E N S I Y N K L L E K Y ........................................................... Protein_Len: 41 Strand: - Start: 86 End: 208 ..................................................................................... I S I K L F C Y A N E H C F D T S M H L F I R Y V I S K S L F Y Y K C C T I L F M ................................................................... Protein_Len: 45 Strand: - Start: 51 End: 185 .................................................. G S S S I R N V N R K L H K N K L F L I R K R P L F R H V Y A F I N Q L S H K K L S F L M .......................................................................................... atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat 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: 83 Start: 228 End: 257 ...................................................................................................................................................................................................................................ATTGCAAACATAATGTTTTTATAGCATAAT.................. PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 132 End: 161 ...................................................................................................................................GTGGACATATGCAAAAATATTCTGTAAACT.................................................................................................................. Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TF1539:TF1540|TF1539:TF1540:conserved hypothetical protein:possible ATPase:->->:1644402..1644676 275 atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Intra-Species Hit: Count: 1 Min: 1 Max: 275 Len: 275 Subject: tfor_TF1539_TF1540|conserved hypothetical protein:possible ATPase|POSITIVE:POSITIVE|[1644402,1644676]|275 HSP 1 e-value: 1.0E-142 bit: 504.0 Len: 275 Query Start:1 Query End:275 Subject Strand: POSITIVE Subject Start: 1 Subject End: 275 atgaaaagactttgataaaaaaggcgatgtatcggannnnnnngcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat atgaaaagactttgataaaaaaggcgatgtatcggatttttttgcagtcagccggatgatgatattctatttacgtttcttttcagatgcttatttttaagaaacaatatgcgttttcgtggcagaaatctgtggacatatgcaaaaatattctgtaaactatgctttttgagagaaaatagtatttacaacaagttattagaaaaatacttggcttgaaattttatattatgctataaaaacattatgtttgcaatacataatagatatagaat Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUGAAAAGACUUUGAUAAAAAAGGCGAUGUAUCGGAUUUUUUUGCAGUCAGCCGGAUGAUGAUAUUCUAUUUACGUUUCUUUUCAGAUGCUUAUUUUUAAGAAACAAUAUGCGUUUUCGUGGCAGAAAUCUGUGGACAUAUGCAAAAAUAUUCUGUAAACUAUGCUUUUUGAGAGAAAAUAGUAUUUACAACAAGUUAUUAGAAAAAUACUUGGCUUGAAAUUUUAUAUUAUGCUAUAAAAACAUUAUGUUUGCAAUACAUAAUAGAUAUAGAAU .........((((......))))...((((((.((((.(((((((((((...(((((..((.............(((((((...((((....))))..))))))).....(((....)))..))...)))))..)))...)))))))).)))).((((((.(((.((((((..((...(((((((......(((((((.............))))))).......))))))).)).)))))))))...)))))).)))))).............. (-49.44) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUUCUAUAUCUAUUAUGUAUUGCAAACAUAAUGUUUUUAUAGCAUAAUAUAAAAUUUCAAGCCAAGUAUUUUUCUAAUAACUUGUUGUAAAUACUAUUUUCUCUCAAAAAGCAUAGUUUACAGAAUAUUUUUGCAUAUGUCCACAGAUUUCUGCCACGAAAACGCAUAUUGUUUCUUAAAAAUAAGCAUCUGAAAAGAAACGUAAAUAGAAUAUCAUCAUCCGGCUGACUGCAAAAAAAUCCGAUACAUCGCCUUUUUUAUCAAAGUCUUUUCAU ..........((((((((..((.((((.....)))).))..))))))))..........((((..(((...((((...((((((((.......................)))).))))...))))......)))...........((((((((..(((.....((.((((..........)))).)).(((....)))..)))...))))).))).......))))((((...((((((..(((....)))..)))))).....))))....... (-37.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 79 31 57 9 tfor:TF3119|5end_conserved_hypothetical_protein_3352723..3352953_POSITIVE 311 72 32 192 154 tfor:TF0764|5end_conserved_hypothetical_protein;_possible_exopolyphosphatase-related_protein_810251..810481_POSITIVE 307 60 23 76 32 tfor:TF2489|5end_hypothetical_protein_2664418..2664648_POSITIVE 292 67 23 208 161 tfor:TF2932|5end_capsule_biosynthesis_protein_3135514..3135744_POSITIVE 292 70 22 70 11 tfor:TF1505|5end_conserved_hypothetical_protein_1610773..1611003_POSITIVE 288 67 23 207 154 tfor:TF0657|5end_conserved_hypothetical_protein_702893..703123_POSITIVE 287 62 22 78 43 tfor:TF2675|5end_conserved_hypothetical_protein_2848864..2849094_POSITIVE 287 61 23 162 121 tfor:TF2088|5end_heptosyltransferase_protein_2257614..2257844_POSITIVE 283 90 42 199 152 tfor:TF0302|5end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_328641..328871_POSITIVE 283 90 42 60 12 tfor:TF0090|5end_conserved_hypothetical_protein_96285..96515_POSITIVE 279 70 22 214 167 tfor:TF2252|5end_transfer_region-related_protein,_TraF_2424621..2424851_POSITIVE 279 137 104 86 55 tfor:TF1935|5end_ATP-dependent_RNA_helicase,_DEAD/DEAH-related_helicase_2082002..2082232_POSITIVE 277 142 109 67 29 tfor:TF2674|5end_conserved_hypothetical_protein;_possible_phosphoesterase_2848176..2848406_POSITIVE 276 143 112 77 46 tfor:TF2477|5end_phosphatase_2654229..2654459_POSITIVE 275 57 22 222 180 tfor:TF2317|5end_3-oxoacyl-[acyl-carrier-protein]_synthase_II_2474418..2474648_POSITIVE 275 58 11 175 120 tfor:TF1061|5end_glycosyltransferase_1130264..1130494_POSITIVE 272 60 23 210 158 tfor:TF1667|5end_biotin_acetyl-CoA_carboxylase_ligase/biotin_operon_repressor_bifunctional_protein_1779809..1780039_POSITIVE 271 68 23 202 152 tfor:TF1687|5end_conserved_hypothetical_protein;_possible_periplasmic_protein_1801988..1802218_POSITIVE 270 67 22 177 129 tfor:TF2907|5end_CDP-diacylglycerol-serine-O-phosphatidyltransfera_se_3102861..3103091_POSITIVE 269 60 22 107 65 tfor:TF0990|5end_hypothetical_protein_1045395..1045625_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 313 79 31 78 30 tfor:TF3118|3end_conserved_hypothetical_protein_3352824..3352974_POSITIVE 311 72 32 146 108 tfor:TF0763|3end_chromate_transport_protein_810285..810435_POSITIVE 307 60 23 56 12 tfor:TF2488|3end_hypothetical_protein_2664478..2664628_POSITIVE 306 144 108 149 121 tfor:TF0541|3end_conserved_hypothetical_protein_571858..572008_POSITIVE 283 63 25 141 93 tfor:TF2533|3end_adenylosuccinate_synthetase_2717014..2717164_POSITIVE 278 79 33 59 3 tfor:TF0994|3end_maltose_O-acetyltransferase_1049782..1049932_POSITIVE 277 142 109 83 45 tfor:TF2673|3end_conserved_hypothetical_protein_2848272..2848422_POSITIVE 275 58 11 148 93 tfor:TF1059|3end_possible_xanthan_lyase_1130317..1130467_POSITIVE 272 148 110 48 10 tfor:TF0113|3end_4-deoxy-L-threo-5-hexosulose-uronate_ketol-isomerase_124068..124218_POSITIVE 263 64 22 133 94 tfor:TF0869|3end_conserved_hypothetical_protein;_possible_transcriptional_regulator_922014..922164_POSITIVE 261 81 41 83 40 tfor:TF2757|3end_hypothetical_protein_2942335..2942485_POSITIVE 258 57 20 80 46 tfor:TF1409|3end_outer_membrane_protein_TolC_1487079..1487229_POSITIVE 258 87 42 135 74 tfor:TF0177|3end_hypothetical_protein_187154..187304_POSITIVE 256 150 110 55 7 tfor:TF1252|3end_phosphofructokinase;_pyrophosphate-fructose_6-phosphate_1-phosphotransferase_(probable_beta_subunit)_1336084..1336234_POSITIVE 256 60 25 43 8 tfor:TF0308|3end_hypothetical_protein_334082..334232_POSITIVE 255 63 26 120 86 tfor:TF1968|3end_conserved_hypothetical_protein_2115959..2116109_POSITIVE 255 61 22 139 97 tfor:TF1838|3end_tRNA/rRNA_methyltransferase_1988745..1988895_POSITIVE 255 55 24 142 116 tfor:TF1270|3end_hypothetical_protein_1355595..1355745_POSITIVE 255 160 111 60 11 tfor:TF1022|3end_chromosomal_replication_initiator_ATPase,_DnaA_1079259..1079409_POSITIVE 252 68 23 63 13 tfor:TF1231|3end_NAD-dependent_DNA_ligase_1317411..1317561_POSITIVE