Origin IGS: caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa .........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 tttaatgcatcggccccgggggcagcctgtcagggcgatcgcgtttgaaaatttttagtctctttcctctatgatttgaatctctgacatatggattcgcacttgttttgaaaattgaatgtagcaatcatgagctttagatgtacgttagtggctgaaatgcgattgtcctgcctatgtcattgcagaagacatgaggggtagagatgcagacgtgagaaatagagcggactgtaagccccatgcacagcccggcagttg Mask Tandem Repeat Region ================================================ caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Find is-nt database================================================ Query_seq: PG0498:PG0499|PG0498:PG0499:S-ribosylhomocysteinase:hypothetical protein:->->:538588..538848 261 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0498:PG0499|PG0498:PG0499:S-ribosylhomocysteinase:hypothetical protein:->->:538588..538848 261 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0498:PG0499|PG0498:PG0499:S-ribosylhomocysteinase:hypothetical protein:->->:538588..538848 261 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 12 End: 122 ........... M C M G L T V R S I S H V C I S T P H V F C N D I G R T I A F Q P L T Y I ........................................................................................................................................... Protein_Len: 30 Strand: + Start: 101 End: 190 .................................................................................................... M S A T N V H L K L M I A T F N F Q N K C E S I C Q R F K S ....................................................................... Protein_Len: 42 Strand: + Start: 135 End: 257 ...................................................................................................................................... M L H S I F K T S A N P Y V R D S N H R G K R L K I F K R D R P D R L P P G P M H * .... Protein_Len: 35 Strand: - Start: 3 End: 107 .. S G P Q A H P K C D A R N R V D A D R G R M D E A I V Y A P C D C K M .......................................................................................................................................................... caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa 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================================================ caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PG0498:PG0499|PG0498:PG0499:S-ribosylhomocysteinase:hypothetical protein:->->:538588..538848 261 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Intra-Species Hit: Count: 6 Min: 1 Max: 261 Len: 261 Subject: NC_002950_PG0498_PG0499|S-ribosylhomocysteinase:hypothetical protein|POSITIVE:POSITIVE|[538588,538848]|261 HSP 1 e-value: 1.0E-146 bit: 517.0 Len: 261 Query Start:1 Query End:261 Subject Strand: POSITIVE Subject Start: 1 Subject End: 261 caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa caactgccgggctgtgcatggggcttacagtccgctctatttctcacgtctgcatctctacccctcatgtcttctgcaatgacataggcaggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa Subject: NC_002950_PG1059_PG1060|hypothetical protein:carboxyl-terminal protease|NEGATIVE:POSITIVE|[1126586,1126797]|212 HSP 1 e-value: 8.0E-65 bit: 248.0 Len: 173 Query Start:89 Query End:261 Subject Strand: NEGATIVE Subject Start: 1 Subject End: 172 ........................................................................................caggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa ........................................................................................cagggcaatcgcatttcagccactaacgtgcatctaaagctcatgattgctacacccgattatcaaa-caagtgcgaattcatatgtcagagattcaaatcatagaggaaagagactaaaaatttttaaacgcgatcgccctgacaggttgcccccggggccgacgcattaaa Subject: NC_002950_PG1397_PG1398|bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase:hypothetical protein|NEGATIVE:POSITIVE|[1480446,1480833]|388 HSP 1 e-value: 5.0E-60 bit: 232.0 Len: 129 Query Start:133 Query End:261 Subject Strand: POSITIVE Subject Start: 135 Subject End: 263 ....................................................................................................................................gattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa ....................................................................................................................................gattgctacattcaattatcaaaacaagtgcgaatccatatgccagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgacgcattaaa Subject: NC_002950_PG0104_PG0106|DNA topoisomerase III:glycosyl transferase, group 4 family protein|POSITIVE:POSITIVE|[127509,128857]|1349 HSP 1 e-value: 1.0E-54 bit: 214.0 Len: 132 Query Start:128 Query End:259 Subject Strand: NEGATIVE Subject Start: 975 Subject End: 1105 ...............................................................................................................................ctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcatta.. ...............................................................................................................................ctcatgattgctacattcaattatcaaa-caagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctacccccggggtcgacgcatta.. Subject: NC_002950_PG1362_PG1363|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[1443685,1443943]|259 HSP 1 e-value: 4.0E-48 bit: 192.0 Len: 145 Query Start:97 Query End:241 Subject Strand: POSITIVE Subject Start: 99 Subject End: 241 ................................................................................................tcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaaacaagtgcgaatccatatgtcagagattcaaatcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcc.................... ................................................................................................tcgcatttcagccactaacgtacatctaaagctcatga-tgctacgctcggttatc-aaacaagtacgaatccatatatcagagattcaattcatagaggaaagagactaaaaattttcaaacgcgatcgccctgacaggctgcc.................... Subject: NC_002950_PG1411_PG1414|potassium uptake protein TrkA, putative:hypothetical protein|NEGATIVE:POSITIVE|[1495257,1497148]|1892 HSP 1 e-value: 5.0E-23 bit: 109.0 Len: 67 Query Start:89 Query End:155 Subject Strand: POSITIVE Subject Start: 772 Subject End: 838 ........................................................................................caggacaatcgcatttcagccactaacgtacatctaaagctcatgattgctacattcaattttcaaa.......................................................................................................... ........................................................................................cagggcaatcgcatttcagccactaacgtacatctaaagctcatgattgctacatccaattatcaaa.......................................................................................................... HSP 2 e-value: 4.0E-14 bit: 79.8 Len: 56 Query Start:206 Query End:261 Subject Strand: NEGATIVE Subject Start: 1032 Subject End: 1086 .............................................................................................................................................................................................................aaaaattttcaaacgcgatcgccctgacaggctgcccccggggccgatgcattaaa .............................................................................................................................................................................................................aaaaattttcaaacgcgatcgtcctgacaggctg-ccccggggccgacgcattaaa Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAACUGCCGGGCUGUGCAUGGGGCUUACAGUCCGCUCUAUUUCUCACGUCUGCAUCUCUACCCCUCAUGUCUUCUGCAAUGACAUAGGCAGGACAAUCGCAUUUCAGCCACUAACGUACAUCUAAAGCUCAUGAUUGCUACAUUCAAUUUUCAAAACAAGUGCGAAUCCAUAUGUCAGAGAUUCAAAUCAUAGAGGAAAGAGACUAAAAAUUUUCAAACGCGAUCGCCCUGACAGGCUGCCCCCGGGGCCGAUGCAUUAAA .......((((((((((.....))..))))))))((((.((((((..((.((.((((((...(((.(((((.........))))))))..(((...((((((((.....((....))........(((........)))..................)))))))).))).......)))))).)).))....)))))))))).................((.(((((((((...((....)).))))).))))))...... (-65.20) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UUUAAUGCAUCGGCCCCGGGGGCAGCCUGUCAGGGCGAUCGCGUUUGAAAAUUUUUAGUCUCUUUCCUCUAUGAUUUGAAUCUCUGACAUAUGGAUUCGCACUUGUUUUGAAAAUUGAAUGUAGCAAUCAUGAGCUUUAGAUGUACGUUAGUGGCUGAAAUGCGAUUGUCCUGCCUAUGUCAUUGCAGAAGACAUGAGGGGUAGAGAUGCAGACGUGAGAAAUAGAGCGGACUGUAAGCCCCAUGCACAGCCCGGCAGUUG .....(((...(((....(((((.((((....))))..(((((((((..........((((((((((((.(((.(((....(..(((((((.(((((((((.(((((...............)))))...(.((((...(((....)))...)))).)..)))))..))))....)))))))..)....)))))))))))).)))))).)))))))))...((((......))))..))))).......)))..))).... (-74.76) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 816 140 91 225 176 NC_002950:PG0880|5end_bacterioferritin_comigratory_protein_942539..942769_POSITIVE 798 140 91 183 135 NC_002950:PG1060|5end_carboxyl-terminal_protease_1126658..1126888_POSITIVE 720 139 97 231 190 NC_002950:PG1362|5end_hypothetical_protein_1443594..1443824_NEGATIVE 643 260 218 185 143 NC_002950:PG1405|5end_hypothetical_protein_1490669..1490899_NEGATIVE 401 253 220 158 107 NC_002950:PG1672|5end_hypothetical_protein_1757637..1757867_POSITIVE 401 253 220 158 107 NC_002950:PG0100|5end_hypothetical_protein_119219..119449_NEGATIVE 391 258 220 136 98 NC_002950:PG2220|5end_hypothetical_protein_2334935..2335165_POSITIVE 390 256 215 150 91 NC_002950:PG1966|5end_hypothetical_protein_2056924..2057154_NEGATIVE 374 50 5 201 145 NC_002950:PG0365|5end_3'-5'_exonuclease_domain_protein_400178..400408_NEGATIVE 372 50 6 211 146 NC_002950:PG1476|5end_conjugative_transposon_protein_TraM_1553219..1553449_NEGATIVE 372 62 21 175 132 NC_002950:PG0329|5end_formiminotransferase-cyclodeaminase-related_protein_364429..364659_NEGATIVE 370 167 126 229 189 NC_002950:PG2221|5end_MiaB-like_tRNA_modifying_enzyme_2335426..2335656_POSITIVE 367 257 215 66 22 NC_002950:PG0448|5end_hypothetical_protein_488089..488319_POSITIVE 366 255 217 205 152 NC_002950:PG2112|5end_hypothetical_protein_2221471..2221701_POSITIVE 366 34 2 111 67 NC_002950:PG0017|5end_sensor_histidine_kinase_18307..18537_POSITIVE 365 259 215 78 32 NC_002950:PG1541|5end_2-amino-4-hydroxy-6-_hydroxymethyldihydropteridine_pyrophosphokinase_1620326..1620556_POSITIVE 364 256 212 109 43 NC_002950:PG0980|5end_hypothetical_protein_1040897..1041127_POSITIVE 361 254 211 231 180 NC_002950:PG1523|5end_naphthoate_synthase_1600988..1601218_NEGATIVE 359 254 217 227 188 NC_002950:PG2098|5end_hypothetical_protein_2206635..2206865_NEGATIVE 359 107 61 193 143 NC_002950:PG0121|5end_DNA-binding_protein_HU_144468..144698_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 445 59 11 61 10 NC_002950:PG1392|3end_rod_shape-determining_protein_RodA,_putative_1472959..1473109_NEGATIVE 428 250 219 132 92 NC_002950:PG1570|3end_rhodanese-like_domain_protein_1648582..1648732_NEGATIVE 379 35 4 101 57 NC_002950:PG1975|3end_hemagglutinin_protein_HagC_2064350..2064500_POSITIVE 374 50 5 124 68 NC_002950:PG0366|3end_hypothetical_protein_400255..400405_NEGATIVE 372 62 21 126 83 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 370 167 126 91 51 NC_002950:PG2220|3end_hypothetical_protein_2335368..2335518_POSITIVE 370 167 126 91 51 NC_002950:PG1251|3end_hypothetical_protein_1328212..1328362_POSITIVE 367 257 215 73 29 NC_002950:PG0447|3end_hypothetical_protein_488176..488326_POSITIVE 366 34 2 100 56 NC_002950:PG0016|3end_sigma-54_dependent_DNA-binding_response_regulator_18376..18526_POSITIVE 365 259 215 81 35 NC_002950:PG1540|3end_S-adenosylmethionine:tRNA_ribosyltransferase-isomerase_1620409..1620559_POSITIVE 365 45 4 67 9 NC_002950:PG1133|3end_hypothetical_protein_1214103..1214253_POSITIVE 364 48 5 65 8 NC_002950:PG1634|3end_hypothetical_protein_1714723..1714873_NEGATIVE 364 256 212 122 56 NC_002950:PG0979|3end_hypothetical_protein_1040990..1041140_POSITIVE 358 256 212 68 11 NC_002950:PG2094|3end_hypothetical_protein_2193321..2193471_NEGATIVE 350 260 211 94 44 NC_002950:PG1746|3end_ISPg2,_transposase_1831100..1831250_NEGATIVE 349 254 219 89 53 NC_002950:PG0606|3end_hypothetical_protein_662451..662601_NEGATIVE 348 255 223 146 112 NC_002950:PG0361|3end_hypothetical_protein_395481..395631_POSITIVE 347 50 5 70 19 NC_002950:PG1813|3end_ferredoxin,_4Fe-4S_1908147..1908297_NEGATIVE 347 44 5 149 106 NC_002950:PG0303|3end_ferredoxin_339603..339753_POSITIVE 343 254 218 150 116 NC_002950:PG0164|3end_hypothetical_protein_187081..187231_NEGATIVE