Origin IGS: ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta .........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 taggtgttgtaaggtagatgcttcgcatagaagcaatatcacacgaagaagggcgtagcatctatctttaaagttcgagaacaaaaacataacaccacattcaaaaagaaagaaaatattaatgagcatcagattaaacaaagcaattcgagaactgaatataggactccaaacggcagtggagttcttggagaaacgacaggaactgggagaa Mask Tandem Repeat Region ================================================ ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Find is-nt database================================================ Query_seq: PI1954:PI1955|PI1954:PI1955:translation initiation factor IF-2:N utilization substance protein A:->->:1911708..1911921 214 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI1954:PI1955|PI1954:PI1955:translation initiation factor IF-2:N utilization substance protein A:->->:1911708..1911921 214 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI1954:PI1955|PI1954:PI1955:translation initiation factor IF-2:N utilization substance protein A:->->:1911708..1911921 214 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Predict ORF larger than 30AA ================================================ Protein_Len: 54 Strand: + Start: 53 End: 214 .................................................... M F S S R I A L F N L M L I N I F F L F E C G V M F L F S N F K D R C Y A L L R V I L L L C E A S T L Q H L Protein_Len: 50 Strand: - Start: 2 End: 151 . R G T G T T E G L V G S G N P T R Y E T R S N S Q K I Q H E N I N E K K K F T T N H K Q E R V K F M ............................................................... Protein_Len: 42 Strand: - Start: 1 End: 126 E G L E Q R K E L F E V A T Q L G I N L E R I A K N L R I S M L I K K R K S H P T M ........................................................................................ ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta 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================================================ ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI1954:PI1955|PI1954:PI1955:translation initiation factor IF-2:N utilization substance protein A:->->:1911708..1911921 214 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Intra-Species Hit: Count: 1 Min: 1 Max: 214 Len: 214 Subject: pint_PI1954_PI1955|translation initiation factor IF-2:N utilization substance protein A|POSITIVE:POSITIVE|[1911708,1911921]|214 HSP 1 e-value: 1.0E-118 bit: 424.0 Len: 214 Query Start:1 Query End:214 Subject Strand: POSITIVE Subject Start: 1 Subject End: 214 ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta ttctcccagttcctgtcgtttctccaagaactccactgccgtttggagtcctatattcagttctcgaattgctttgtttaatctgatgctcattaatattttctttctttttgaatgtggtgttatgtttttgttctcgaactttaaagatagatgctacgcccttcttcgtgtgatattgcttctatgcgaagcatctaccttacaacaccta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUCUCCCAGUUCCUGUCGUUUCUCCAAGAACUCCACUGCCGUUUGGAGUCCUAUAUUCAGUUCUCGAAUUGCUUUGUUUAAUCUGAUGCUCAUUAAUAUUUUCUUUCUUUUUGAAUGUGGUGUUAUGUUUUUGUUCUCGAACUUUAAAGAUAGAUGCUACGCCCUUCUUCGUGUGAUAUUGCUUCUAUGCGAAGCAUCUACCUUACAACACCUA ........((((..............((.((((((........)))))).))....((((....((((....))))......))))..........................))))..((((((..((((........))))....(((.(((((((.((((........))))....((((......)))).))))))).)))..)))))).. (-36.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAGGUGUUGUAAGGUAGAUGCUUCGCAUAGAAGCAAUAUCACACGAAGAAGGGCGUAGCAUCUAUCUUUAAAGUUCGAGAACAAAAACAUAACACCACAUUCAAAAAGAAAGAAAAUAUUAAUGAGCAUCAGAUUAAACAAAGCAAUUCGAGAACUGAAUAUAGGACUCCAAACGGCAGUGGAGUUCUUGGAGAAACGACAGGAACUGGGAGAA ..((((((((((((((((((((.(((...((.......))...(......).))).))))))))))))....(((....)))......))))))))..................................................(((.((..(((.....(((((((((........))))))))).(......)..)))...)).)))... (-46.60) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 196 158 46 9 pint:PI0129|5end_hypothetical_protein_121709..121939_POSITIVE 334 44 9 81 48 pint:PI1705|5end_3-oxoacyl-(acyl-carrier-protein)_synthase_III_1621781..1622011_POSITIVE 319 45 3 149 97 pint:PI1784|5end_possible_dTDP-glucose_4,6-dehydratase,_NAD-dependent_epimerase/dehydratase_family_1716201..1716431_POSITIVE 319 48 9 231 189 pint:PI0266|5end_DNA_primase_(bacterial_type)_257931..258161_POSITIVE 315 200 152 187 124 pint:PI1403|5end_conserved_hypothetical_protein_1323920..1324150_POSITIVE 313 41 3 198 158 pint:PI1635|5end_hypothetical_protein_1553948..1554178_POSITIVE 310 200 155 63 21 pint:PI1779|5end_16S_rRNA_processing_protein_1711335..1711565_POSITIVE 304 42 4 66 16 pint:PI0650|5end_conserved_hypothetical_protein_591617..591847_POSITIVE 303 46 5 93 50 pint:PI0263|5end_conjugative_transposon_protein,_TraM_255256..255486_POSITIVE 292 195 154 122 63 pint:PI0931|5end_hypothetical_protein_862652..862882_POSITIVE 290 45 18 214 188 pint:PI0548|5end_possible_acetylxylan_esterase_499532..499762_POSITIVE 289 189 155 85 40 pint:PI0836|5end_conserved_hypothetical_protein_772063..772293_POSITIVE 287 77 36 172 121 pint:PI1685|5end_GAF_domain-containing_protein_1601712..1601942_POSITIVE 287 77 36 54 3 pint:PI1686|5end_hypothetical_protein_1601594..1601824_POSITIVE 287 198 152 106 55 pint:PI0697|5end_5'-nucleotidase_family_protein_633560..633790_POSITIVE 287 48 1 73 3 pint:PI0035|5end_NAD-dependent_protein_deacetylase,_SIR2_family_37873..38103_POSITIVE 285 75 31 190 151 pint:PI0361|5end_hypothetical_protein_333062..333292_POSITIVE 278 198 156 72 36 pint:PI1724|5end_inosine-5'-monophosphate_dehydrogenase_1641075..1641305_POSITIVE 277 50 3 106 62 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 276 166 136 41 17 pint:PI1505|5end_2-amino-4-hydroxy-6-hydroxymethyldihydropteridine_pyrophosphokinase_1424922..1425152_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 371 196 158 83 46 pint:PI0128|3end_dipeptidase,_pathogenicity_island-encoded_protein_D_121826..121976_POSITIVE 310 200 155 47 5 pint:PI1778|3end_UDP-N-acetylglucosamine_1-carboxyvinyltransferase_1711399..1711549_POSITIVE 304 196 152 151 104 pint:PI1402|3end_3-deoxy-7-phosphoheptulonate_synthase_1323980..1324130_POSITIVE 290 45 18 68 42 pint:PI0547|3end_fructose-bisphosphate_aldolase_499466..499616_POSITIVE 287 198 152 66 15 pint:PI0696|3end_NADH_pyrophosphatase,_MutT_family_hydrolase_(NAD+_diphosphatase)_633600..633750_POSITIVE 286 50 5 118 73 pint:PI0183|3end_hypothetical_protein_174810..174960_POSITIVE 282 46 5 94 45 pint:PI0683|3end_hypothetical_protein_619797..619947_POSITIVE 280 71 36 144 102 pint:PI1684|3end_dimethyladenosine_transferase_1601773..1601923_POSITIVE 277 50 3 86 42 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 273 198 151 141 88 pint:PI1655|3end_hypothetical_protein_1570217..1570367_POSITIVE 269 206 161 85 33 pint:PI0067|3end_hypothetical_protein_66586..66736_POSITIVE 266 46 5 81 37 pint:PI1807|3end_hypothetical_protein_1742481..1742631_POSITIVE 265 79 31 71 18 pint:PI1706|3end_GTP-binding_protein_1623668..1623818_POSITIVE 265 199 153 124 71 pint:PI0742|3end_hypothetical_protein_672749..672899_POSITIVE 264 52 15 143 93 pint:PI1558|3end_conserved_hypothetical_protein_1476106..1476256_POSITIVE 263 46 8 146 104 pint:PI0258|3end_conjugative_transposon_protein,_TraG_252285..252435_POSITIVE 257 73 35 138 106 pint:PI1995|3end_hypothetical_protein_1950212..1950362_POSITIVE 257 48 1 151 113 pint:PI0380|3end_conserved_hypothetical_protein_350541..350691_POSITIVE 254 201 161 42 4 pint:PI1572|3end_hypothetical_protein_1498215..1498365_POSITIVE 252 195 155 139 98 pint:PI1716|3end_hypothetical_protein_1632006..1632156_POSITIVE