Origin IGS: agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct .........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 agcgaacttttttcttgttgatattcagtaaaactaacaatatagtgtgtatcatacatttttgtatgtacttgtgtattgtagtgcaaaggtataattttgcagtgatttcaacaatttaaaatacattttatggaaaagaaaatcgaaaaagttcgtcaattttacaccgctttggcacagggtgattttgaaacagtgggagct Mask Tandem Repeat Region ================================================ agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Find is-nt database================================================ Query_seq: PI0391:PI0392|PI0391:PI0392:conserved hypothetical protein:possible transcriptional regulator:->->:358277..358483 207 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0391:PI0392|PI0391:PI0392:conserved hypothetical protein:possible transcriptional regulator:->->:358277..358483 207 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0391:PI0392|PI0391:PI0392:conserved hypothetical protein:possible transcriptional regulator:->->:358277..358483 207 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Predict ORF larger than 30AA ================================================ Protein_Len: 45 Strand: + Start: 19 End: 153 .................. M T L C Q S G V K L T N F F D F L F H K M Y F K L L K S L Q N Y T F A L Q Y T S T Y K N V ...................................................... Protein_Len: 32 Strand: + Start: 110 End: 205 ............................................................................................................. M I P L H Y N T Q V H T K M Y D T H Y I V S F T E Y Q Q E K S S .. Protein_Len: 39 Strand: + Start: 90 End: 206 ......................................................................................... M V E I T A K L Y L C T T I H K Y I Q K C M I H T I L L V L L N I N K K K V R . Protein_Len: 35 Strand: - Start: 89 End: 193 ........................................................................................ I T S I V A F N Y R Q V V I C L Y M C F H I I C V I N N T K S F I L M .............. agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct 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: 162 End: 191 .................................................................................................................................................................GTTGATATTCAGTAAAACTAACAATATAGT................ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0391:PI0392|PI0391:PI0392:conserved hypothetical protein:possible transcriptional regulator:->->:358277..358483 207 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Intra-Species Hit: Count: 1 Min: 1 Max: 207 Len: 207 Subject: pint_PI0391_PI0392|conserved hypothetical protein:possible transcriptional regulator|POSITIVE:POSITIVE|[358277,358483]|207 HSP 1 e-value: 1.0E-114 bit: 410.0 Len: 207 Query Start:1 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 207 agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct agctcccactgtttcaaaatcaccctgtgccaaagcggtgtaaaattgacgaactttttcgattttcttttccataaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Inter-species Hit: Count: 3 Min: 76 Max: 207 Len: 132 Subject: NC_002950_PG1450_PG1451|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1534705,1534836]|132 HSP 1 e-value: 4.0E-69 bit: 262.0 Len: 132 Query Start:76 Query End:207 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 132 ...........................................................................aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct ...........................................................................aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Subject: NC_002950_PG0822_PG0823|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[880826,880957]|132 HSP 1 e-value: 4.0E-69 bit: 262.0 Len: 132 Query Start:76 Query End:207 Subject Strand: POSITIVE Subject Start: 1 Subject End: 132 ...........................................................................aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct ...........................................................................aaaatgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagttcgct Subject: tfor_TF0914_TF0915|conserved hypothetical protein; possible ketosteroid isomerase-related protein:possible transcriptional regulator|POSITIVE:POSITIVE|[955874,956006]|133 HSP 1 e-value: 3.0E-14 bit: 79.8 Len: 124 Query Start:80 Query End:203 Subject Strand: POSITIVE Subject Start: 6 Subject End: 129 ...............................................................................tgtattttaaattgttgaaatcactgcaaaattatacctttgcactacaatacacaagtacatacaaaaatgtatgatacacactatattgttagttttactgaatatcaacaagaaaaaagtt.... ...............................................................................tgtatttttaattgttagaaccactgcaaagttatacctttgcactacaatctgcaagtacctacaatattgtaggatacataccgtattattagatttattgattatcaagaataaaaaagtt.... Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAAAUGUAUUUUAAAUUGUUGAAAUCACUGCAAAAUUAUACCUUUGCACUACAAUACACAAGUACAUACAAAAAUGUAUGAUACACACUAUAUUGUUAGUUUUACUGAAUAUCAACAAGAAAAAAGUUCGCU ........((((...(((((((..(((..(((((........))))).((((((((.....(((((((((....)))))).)))......))))).)))......)))...))))))).))))......... (-21.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGCGAACUUUUUUCUUGUUGAUAUUCAGUAAAACUAACAAUAUAGUGUGUAUCAUACAUUUUUGUAUGUACUUGUGUAUUGUAGUGCAAAGGUAUAAUUUUGCAGUGAUUUCAACAAUUUAAAAUACAUUUU ..............(((((((...(((.....((((.(((((((....(((.((((((....)))))))))...)))))))))))((((((......))))))..)))..)))))))............... (-29.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 242 89 41 167 130 pint:PI0049|5end_outer_membrane_receptor_protein_(iron_transport)_48605..48835_POSITIVE 234 69 28 68 10 pint:PI0440|5end_transcription_antiterminator_410582..410812_POSITIVE 220 89 43 213 161 pint:PI0074|5end_Na+/phosphate_symporter_(sodium-dependent_inorganic_phosphate_(Pi)_transporter)_71853..72083_POSITIVE 206 55 15 73 28 pint:PI2017|5end_conserved_hypothetical_protein_1974862..1975092_POSITIVE 206 78 35 132 88 pint:PI1542|5end_mobilization_protein_1461728..1461958_POSITIVE 205 62 41 41 18 pint:PI1949|5end_aminotransferase,_class_V_1903218..1903448_POSITIVE 201 49 13 210 175 pint:PI0715|5end_hypothetical_protein_652311..652541_POSITIVE 199 49 17 153 116 pint:PI1769|5end_hypothetical_protein_1696507..1696737_POSITIVE 195 60 15 102 53 pint:PI1222|5end_hypothetical_protein_1142834..1143064_POSITIVE 192 49 14 35 1 pint:PI0716|5end_conserved_hypothetical_protein_652136..652366_POSITIVE 189 122 85 165 127 pint:PI0004|5end_hypothetical_protein_6199..6429_POSITIVE 186 86 43 108 60 pint:PI1992|5end_hypothetical_protein_1946427..1946657_POSITIVE 186 97 51 97 51 pint:PI1090|5end_tRNA_uracil_5-methyltransferase_1014366..1014596_POSITIVE 184 85 41 211 157 pint:PI0965|5end_hypothetical_protein_894154..894384_POSITIVE 181 58 19 138 91 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 181 58 19 73 26 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 181 70 21 177 118 pint:PI0664|5end_dihydroorotate_dehydrogenase,_electron_transfer_subunit_606891..607121_POSITIVE 179 64 41 181 160 pint:PI0218|5end_conserved_hypothetical_protein_210770..211000_POSITIVE 177 56 15 75 35 pint:PI1009|5end_cytochrome_c_nitrite_reductase,_large_subunit_929342..929572_POSITIVE 176 38 19 231 211 pint:PI1451|5end_outer_membrane_receptor_proteins,_tonB_dependent_(possibly_iron_transport_related)_1372931..1373161_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 225 85 42 98 59 pint:PI0576|3end_helicase,_UvrD/Rep_521724..521874_POSITIVE 220 89 43 65 13 pint:PI0073|3end_dihydropteroate_synthase_71785..71935_POSITIVE 206 55 15 64 19 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 206 78 35 95 51 pint:PI1540|3end_hypothetical_protein_1461771..1461921_POSITIVE 201 69 41 50 13 pint:PI0439|3end_conserved_hypothetical_protein;_possible_preprotein_translocase_subunit_SecE_410644..410794_POSITIVE 200 40 19 113 91 pint:PI1450|3end_hypothetical_protein_1372891..1373041_POSITIVE 196 73 39 149 114 pint:PI0982|3end_hypothetical_protein_909649..909799_POSITIVE 195 64 35 33 5 pint:PI0516|3end_ferredoxin,_4Fe-4S_476108..476258_POSITIVE 188 67 25 143 88 pint:PI0434|3end_possible_beta-lactamase_406890..407040_POSITIVE 181 58 19 73 26 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 180 109 61 51 8 pint:PI0943|3end_conserved_hypothetical_protein_875991..876141_POSITIVE 179 64 41 125 104 pint:PI0217|3end_conserved_hypothetical_protein;_possible_lipoprotein_210794..210944_POSITIVE 179 50 15 105 67 pint:PI0203|3end_conserved_hypothetical_protein_196064..196214_POSITIVE 175 97 52 140 94 pint:PI1539|3end_3-phosphoshikimate_1-carboxyvinyltransferase_1461134..1461284_POSITIVE 170 87 44 65 17 pint:PI1170|3end_possible_response_regulator_1091398..1091548_POSITIVE 168 77 39 115 78 pint:PI0094|3end_protoporphyrinogen_oxidase_90511..90661_POSITIVE 167 102 62 51 3 pint:PI0793|3end_ABC_transporter,_permease_protein_731078..731228_POSITIVE 166 44 18 143 117 pint:PI0584|3end_hypothetical_protein_527656..527806_POSITIVE 166 120 75 130 78 pint:PI0023|3end_internalin-related_protein_28070..28220_POSITIVE 164 113 73 99 52 pint:PI1449|3end_conserved_hypothetical_protein_1372514..1372664_POSITIVE