Origin IGS: taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta .........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 taagccttttttcatggttcgatttaacctccaaaaaaatatgacgtcatatttggaagaatatgacgtcatattcgctcaaatatgacgtcatatttcttagattgagacgtcatattcctcgaactgagacgtcatatagttttcattctgcccaaccaatagattcacgaggcaaatacattgccacttta Mask Tandem Repeat Region ================================================ taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnttttggaggttaaatcgaaccatgaaaaaaggctta Find is-nt database================================================ Query_seq: PI0162:PI0163|PI0162:PI0163:ADP-ribosylglycohydrolase (ADP-ribosyl-[dinitrogen reductase] hydrolase):conserved hypothetical protein:->->:157062..157255 194 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0162:PI0163|PI0162:PI0163:ADP-ribosylglycohydrolase (ADP-ribosyl-[dinitrogen reductase] hydrolase):conserved hypothetical protein:->->:157062..157255 194 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0162:PI0163|PI0162:PI0163:ADP-ribosylglycohydrolase (ADP-ribosyl-[dinitrogen reductase] hydrolase):conserved hypothetical protein:->->:157062..157255 194 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Predict ORF larger than 30AA ================================================ Protein_Len: 48 Strand: - Start: 1 End: 144 L T A I Y K G R S D I P Q A S H F S Y S T E T R P I H R R L R L F I V D Y K L S Y S T M N K W M .................................................. taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta 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================================================ PromScan Matrix: RpoN Strand: + Score: 82 Start: 5 End: 21 ....GTGGCAATGTATTTGCC............................................................................................................................................................................. taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 87 HP_score: -12.3 Tail_Score: -3.17392 Start: 96 End: 136 Full_Region: acgtcatatttggaa gaatatgacgtcatatt cgctca aatatgacgtcatatttc ttagattgagacgtc ...............................................................................................gaatatgacgtcatattcgctcaaatatgacgtcatatttc.......................................................... TransTerm Strand: + Conf: 100 HP_score: -20.2 Tail_Score: -5.43866 Start: 100 End: 155 Full_Region: TCTCAATCTAAGAAA TATGACGTCATATTTGAGCGAATATG ACGT CATATTCTTCCAAATATGACGTCATA TTTTTTTGGAGGTTA ...................................................................................................TATGACGTCATATTTGAGCGAATATGACGTCATATTCTTCCAAATATGACGTCATA....................................... TransTerm Strand: - Conf: 100 HP_score: -20.2 Tail_Score: -4.2528 Start: 100 End: 155 Full_Region: taacctccaaaaaaa tatgacgtcatatttggaagaatatg acgt catattcgctcaaatatgacgtcata tttcttagattgaga ...................................................................................................tatgacgtcatatttggaagaatatgacgtcatattcgctcaaatatgacgtcata....................................... TransTerm Strand: + Conf: 43 HP_score: -3.0 Tail_Score: -3.05596 Start: 110 End: 167 Full_Region: AGAAATATGACGTCA TATTTGAGCGAATATGACGTCATATT CTTCCA AATATGACGTCATATTTTTTTGGAGG TTAAATCGAACCATG .............................................................................................................TATTTGAGCGAATATGACGTCATATTCTTCCAAATATGACGTCATATTTTTTTGGAGG........................... Find igs database================================================ Query_seq: PI0162:PI0163|PI0162:PI0163:ADP-ribosylglycohydrolase (ADP-ribosyl-[dinitrogen reductase] hydrolase):conserved hypothetical protein:->->:157062..157255 194 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta Intra-Species Hit: Count: 1 Min: 1 Max: 194 Len: 194 Subject: pint_PI0162_PI0163|ADP-ribosylglycohydrolase (ADP-ribosyl-[dinitrogen reductase] hydrolase):conserved hypothetical protein|POSITIVE:POSITIVE|[157062,157255]|194 HSP 1 e-value: 1.0E-93 bit: 343.0 Len: 194 Query Start:1 Query End:194 Subject Strand: POSITIVE Subject Start: 1 Subject End: 194 taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatannnnnnnggaggttaaatcgaaccatgaaaaaaggctta taaagtggcaatgtatttgcctcgtgaatctattggttgggcagaatgaaaactatatgacgtctcagttcgaggaatatgacgtctcaatctaagaaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcatatttttttggaggttaaatcgaaccatgaaaaaaggctta HSP 2 e-value: 3.0E-11 bit: 69.9 Len: 59 Query Start:97 Query End:155 Subject Strand: NEGATIVE Subject Start: 100 Subject End: 158 ................................................................................................aaatatgacgtcatatttgagcgaatatgacgtcatattcttccaaatatgacgtcata....................................... ................................................................................................aaatatgacgtcatatttggaagaatatgacgtcatattcgctcaaatatgacgtcata....................................... Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAGUGGCAAUGUAUUUGCCUCGUGAAUCUAUUGGUUGGGCAGAAUGAAAACUAUAUGACGUCUCAGUUCGAGGAAUAUGACGUCUCAAUCUAAGAAAUAUGACGUCAUAUUUGAGCGAAUAUGACGUCAUAUUCUUCCAAAUAUGACGUCAUAUUUUUUUGGAGGUUAAAUCGAACCAUGAAAAAAGGCUUA ..(((((((((.....))))).......((...(((((.((.................((((((...((((...))))..))))))....(((((((((((((((((((((((((...(((((((....)))))))...)))))))))))))))).))))))))).......)).))))).))......)))). (-61.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGCCUUUUUUCAUGGUUCGAUUUAACCUCCAAAAAAAUAUGACGUCAUAUUUGGAAGAAUAUGACGUCAUAUUCGCUCAAAUAUGACGUCAUAUUUCUUAGAUUGAGACGUCAUAUUCCUCGAACUGAGACGUCAUAUAGUUUUCAUUCUGCCCAACCAAUAGAUUCACGAGGCAAAUACAUUGCCACUUUA ...(((((...((.(((((.(...............((((((((((((((((((((..(((((((....)))))))..))))))))))))))))))))..((((.(((((((((.(((((...))).)).)))))).........))).)))).).)))))...)).....))))).................. (-55.40) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 158 114 142 97 pint:PI0063|5end_transcriptional_regulator,_GntR_family_63181..63411_POSITIVE 508 135 97 228 190 pint:PI0108|5end_L-lactate_permease_104892..105122_POSITIVE 352 129 93 186 151 pint:PI1534|5end_ATPase/GTPase_1453679..1453909_POSITIVE 319 49 5 57 1 pint:PI1484|5end_conserved_hypothetical_protein_1404619..1404849_POSITIVE 315 45 7 65 14 pint:PI0927|5end_transglutaminase-related_protein_857283..857513_POSITIVE 303 150 105 133 86 pint:PI1636|5end_hypothetical_protein_1554246..1554476_POSITIVE 302 74 33 50 4 pint:PI1933|5end_hypothetical_protein_1879925..1880155_POSITIVE 292 135 97 182 144 pint:PI0001|5end_possible_Ton-B_receptor_400..630_POSITIVE 284 46 4 58 14 pint:PI0772|5end_conserved_hypothetical_protein_707157..707387_POSITIVE 277 48 4 211 161 pint:PI1299|5end_glycosyltransferase_1212191..1212421_POSITIVE 277 90 41 77 5 pint:PI0852|5end_conserved_hypothetical_protein_784552..784782_POSITIVE 274 68 21 148 91 pint:PI1690|5end_transcription_regulator;_possible_Fe2+/Zn2+_uptake_regulation_proteins_1604984..1605214_POSITIVE 272 49 6 231 184 pint:PI1377|5end_cAMP-binding_domain_protein_(cyclic_nucleotide-binding_domain)_1299289..1299519_POSITIVE 272 45 1 62 17 pint:PI0128|5end_dipeptidase,_pathogenicity_island-encoded_protein_D_120532..120762_POSITIVE 270 49 3 132 89 pint:PI1938|5end_hypothetical_protein_1891854..1892084_POSITIVE 268 42 6 173 122 pint:PI0058|5end_conserved_hypothetical_protein_56398..56628_POSITIVE 263 68 22 143 88 pint:PI1865|5end_chromate_transport_protein_1810935..1811165_POSITIVE 263 51 16 32 3 pint:PI0756|5end_50S_ribosomal_protein_L7/L12_687146..687376_POSITIVE 262 45 5 96 45 pint:PI0516|5end_ferredoxin,_4Fe-4S_475864..476094_POSITIVE 260 42 4 171 131 pint:PI2063|5end_conserved_hypothetical_protein_2023946..2024176_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 303 150 105 113 66 pint:PI1635|3end_hypothetical_protein_1554306..1554456_POSITIVE 298 156 125 36 5 pint:PI0162|3end_ADP-ribosylglycohydrolase_(ADP-ribosyl-[dinitrogen_reductase]_hydrolase)_157001..157151_POSITIVE 264 42 4 72 14 pint:PI1734|3end_possible_carboxyl-terminal_protease-related_protein_1653829..1653979_POSITIVE 264 44 4 143 115 pint:PI0835|3end_conserved_hypothetical_protein;_possible_protein-export_membrane_protein_771859..772009_POSITIVE 263 68 22 137 82 pint:PI1864|3end_chromate_transport_protein_1811009..1811159_POSITIVE 258 50 3 95 45 pint:PI0275|3end_hypothetical_protein_264489..264639_POSITIVE 246 50 3 95 29 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 243 128 81 99 53 pint:PI0279|3end_hypothetical_protein_266081..266231_POSITIVE 238 141 114 101 76 pint:PI2048|3end_possible_two-component_system_sensor_histidine_kinase_2002566..2002716_POSITIVE 238 139 117 24 2 pint:PI2006|3end_potassium_uptake_system_protein_1965846..1965996_POSITIVE 236 48 5 145 81 pint:PI0700|3end_UDP-glucose_4-epimerase_638413..638563_POSITIVE 235 99 53 111 62 pint:PI1459|3end_ribonucleotide_reductase,_alpha_subunit,_C-terminal_region_1382308..1382458_POSITIVE 234 75 34 151 120 pint:PI0976|3end_dihydrolipoamide_dehydrogenase_(dihydrolipoyl_dehydrogenanse)_903732..903882_POSITIVE 232 141 101 135 85 pint:PI0675|3end_hypothetical_protein_613957..614107_POSITIVE 230 50 7 65 19 pint:PI2155|3end_hypothetical_protein_2101052..2101202_POSITIVE 229 79 37 125 82 pint:PI2083|3end_hypothetical_protein_2040661..2040811_POSITIVE 229 44 5 37 3 pint:PI0728|3end_integrase_661508..661658_POSITIVE 229 75 35 42 9 pint:PI0305|3end_possible_aminotransferase_288967..289117_POSITIVE 226 49 4 101 53 pint:PI1867|3end_helicase_related_protein_1814668..1814818_POSITIVE 226 44 4 63 11 pint:PI1649|3end_hypothetical_protein_1563441..1563591_POSITIVE