Origin IGS: ttctgcgtagttgtagcgcttgaaaatctcacgggcaaagccctcaacatactgccacttggcagactcagcaggtaaaatatcctgcgttccttytggttttgtaatttcatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag .........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 ctattcttttgacagntattaatctcaaaaatgatatctaaatcctaatttttttctcactgwtttaatccctctatttatggtaaaataagactattaagtttaaagaggattccctatgaaattacaaaaccaraaggaacgcaggatattttacctgctgagtctgccaagtggcagtatgttgagggctttgcccgtgagattttcaagcgctacaactacgcagaa Mask Tandem Repeat Region ================================================ ttctgcgtagttgtagcgcttgaaaatctcacgggcaaagccctcaacatactgccacttggcagactcagcaggtaaaatatcctgcgttccttytggttttgtaatttcatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Find is-nt database================================================ Query_seq: SMT_1151:SMT_1152|SMT_1151:SMT_1152:histidyl-tRNA synthetase:hypothetical protein:<-<-:1096259..1096489 231 ttctgcgtagttgtagcgcttgaaaatctcacgggcaaagccctcaacatactgccacttggcagactcagcaggtaaaatatcctgcgttccttytggttttgtaatttcatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_1151:SMT_1152|SMT_1151:SMT_1152:histidyl-tRNA synthetase:hypothetical protein:<-<-:1096259..1096489 231 ttctgcgtagttgtagcgcttgaaaatctcacgggcaaagccctcaacatactgccacttggcagactcagcaggtaaaatatcctgcgttccttytggttttgtaatttcatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_1151:SMT_1152|SMT_1151:SMT_1152:histidyl-tRNA synthetase:hypothetical protein:<-<-:1096259..1096489 231 ttctgcgtagttgtagcgcttgaaaatctcacgggcaaagccctcaacatactgccacttggcagactcagcaggtaaaatatcctgcgttccttytggttttgtaatttcatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Intra-Species Hit: Count: 0 Inter-species Hit: Count: 10 Min: 1 Max: 111 Len: 111 Subject: UniRef90_Q97NC9 Cluster: Histidyl-tRNA synthetase; n=3; Streptococcus pneumoniae|Rep: Histidyl-tRNA synthetase - Streptococcus pneumoniae HSP 1 e-value: 2.0E-12 bit: 73.6 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ Subject: UniRef90_Q2ZXL9 Cluster: Histidyl-tRNA synthetase, class IIa; n=1; Streptococcus suis 89/1591|Rep: Histidyl-tRNA synthetase, class IIa - Streptococcus suis 89/1591 HSP 1 e-value: 5.0E-9 bit: 62.4 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 6 Subject End: 42 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D L L P Q D S A K W Q Y V E N F T R S I F K Q Y N Y A E ........................................................................................................................ Subject: UniRef90_A3CR40 Cluster: Histidyl-tRNA synthetase, putative; n=2; Streptococcus|Rep: Histidyl-tRNA synthetase, putative - Streptococcus sanguinis (strain SK36) HSP 1 e-value: 8.0E-9 bit: 61.6 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L P Q E S A K W Q Y V E D F A R K T F R K Y N Y G E ........................................................................................................................ Subject: UniRef90_Q5LXM9 Cluster: Histidyl-tRNA synthetase; n=3; Streptococcus thermophilus|Rep: Histidyl-tRNA synthetase - Streptococcus thermophilus (strain CNRZ 1066) HSP 1 e-value: 1.0E-8 bit: 61.2 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L P G D S A K W Q Y V E N V A R E T F K K Y N Y G E ........................................................................................................................ Subject: UniRef90_Q5X9E5 Cluster: Histidyl-tRNA synthetase; n=13; Streptococcus pyogenes|Rep: Histidyl-tRNA synthetase - Streptococcus pyogenes serotype M6 HSP 1 e-value: 3.0E-7 bit: 56.6 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L P G D A A K W Q Y V E S V A R D T F S Q Y N Y G E ........................................................................................................................ Subject: UniRef90_P67485 Cluster: Histidyl-tRNA synthetase; n=9; Streptococcus agalactiae|Rep: Histidyl-tRNA synthetase - Streptococcus agalactiae serotype III HSP 1 e-value: 3.0E-7 bit: 56.6 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L P G E S A K W Q Y V E N V I R N L F K Q Y H Y D E ........................................................................................................................ Subject: UniRef90_P30053 Cluster: Histidyl-tRNA synthetase; n=1; Streptococcus dysgalactiae subsp. equisimilis|Rep: Histidyl-tRNA synthetase - Streptococcus equisimilis HSP 1 e-value: 4.0E-7 bit: 55.8 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T Q D I L S V A A A K W Q Y V E G V A R E T F K Q Y H Y G E ........................................................................................................................ Subject: UniRef90_Q1WTV0 Cluster: Histidyl-tRNA synthetase; n=1; Lactobacillus salivarius subsp. salivarius UCC118|Rep: Histidyl-tRNA synthetase - Lactobacillus salivarius subsp. salivarius (strain UCC118) HSP 1 e-value: 6.0E-7 bit: 55.5 Len: 102 Query Start:1 Query End:102 Subject Strand: null Subject Start: 5 Subject End: 38 K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ................................................................................................................................. R P K G T A D I L P S E S A K W Q Y V E E K A R E L F K K Y R Y E E ................................................................................................................................. Subject: UniRef90_Q8CWW2 Cluster: Histidyl-tRNA synthetase; n=1; Streptococcus mutans|Rep: Histidyl-tRNA synthetase - Streptococcus mutans HSP 1 e-value: 6.0E-7 bit: 55.5 Len: 108 Query Start:1 Query End:108 Subject Strand: null Subject Start: 3 Subject End: 38 I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................... L Q K P K G T Q D I L P Q E T V K W Q Y V E N V A R K T F K K Y H Y G E ........................................................................................................................... Subject: UniRef90_Q9CE78 Cluster: Histidyl-tRNA synthetase; n=3; Lactococcus lactis|Rep: Histidyl-tRNA synthetase - Lactococcus lactis subsp. lactis (Streptococcus lactis) HSP 1 e-value: 5.0E-6 bit: 52.4 Len: 111 Query Start:1 Query End:111 Subject Strand: null Subject Start: 2 Subject End: 38 E I T K P X G T Q D I L P A E S A K W Q Y V E G F A R E I F K R Y N Y A E ........................................................................................................................ K L Q K P K G T A D L L P A E T A K W Q Y I E E I A R G V F N D Y N F K E ........................................................................................................................ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Predict ORF larger than 30AA ================================================ Protein_Len: 31 Strand: + Start: 20 End: 112 ................... M K I S R A K P S T Y C H L A D S A G K I S C V P X G F V I S ....................................................................................................................... Protein_Len: 37 Strand: - Start: 3 End: 113 .. Q T T T A S S F R V P L A R L M S G S P L S L L Y F I R R E K Q N Q L K M ...................................................................................................................... Protein_Len: 52 Strand: - Start: 1 End: 156 E A Y N Y R K F I E R A F G E V Y Q W K A S E A P L I D Q T G X P K T I E Y P I R K L S L L R I K G Y M ........................................................................... nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag 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================================================ nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_1151:SMT_1152|SMT_1151:SMT_1152:histidyl-tRNA synthetase:hypothetical protein:<-<-:1096259..1096489 231 nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Intra-Species Hit: Count: 1 Min: 112 Max: 231 Len: 120 Subject: smit_SMT_1151_SMT_1152|histidyl-tRNA synthetase:hypothetical protein|NEGATIVE:NEGATIVE|[1096259,1096489]|231 HSP 1 e-value: 1.0E-46 bit: 187.0 Len: 120 Query Start:112 Query End:231 Subject Strand: POSITIVE Subject Start: 112 Subject End: 231 ...............................................................................................................atagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagnnnnnnnttaggatttagatatcatttttgagattaatanctgtcaaaagaatag ...............................................................................................................atagggaatcctctttaaacttaatagtcttattttaccataaatagagggattaaawcagtgagaaaaaaattaggatttagatatcatttttgagattaatanctgtcaaaagaatag Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AUAGGGAAUCCUCUUUAAACUUAAUAGUCUUAUUUUACCAUAAAUAGAGGGAUUAAAWCAGUGAGAAAAAAAUUAGGAUUUAGAUAUCAUUUUUGAGAUUAAUANCUGUCAAAAGAAUAG .....(((((((..((...((((.(((((((((((......)))))...))))))......)))).....))..)))))))........(((((((.(........).)))))))..... (-13.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CUAUUCUUUUGACAGNUAUUAAUCUCAAAAAUGAUAUCUAAAUCCUAAUUUUUUUCUCACUGWUUUAAUCCCUCUAUUUAUGGUAAAAUAAGACUAUUAAGUUUAAAGAGGAUUCCCUAU ......((((((.(........).))))))........................................((((((((((((((........)))).)))))....)))))......... ( -9.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 404 29 1 231 203 smit:SMT_1151|5end_histidyl-tRNA_synthetase_1096168..1096398_NEGATIVE 274 45 1 50 10 smit:SMT_658|5end_hypothetical_protein_569645..569875_NEGATIVE 229 80 31 166 121 smit:SMT_1517|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1498313..1498543_POSITIVE 219 38 4 187 159 smit:SMT_803|5end_peptidoglycan_N-acetylglucosamine_deacetylase_713796..714026_NEGATIVE 217 99 62 191 152 smit:SMT_1424|5end_K02003_1409706..1409936_POSITIVE 208 49 4 48 2 smit:SMT_1119|5end_alcohol_dehydrogenase,_zinc-containing_1056292..1056522_NEGATIVE 204 68 25 177 128 smit:SMT_89|5end_chromosomal_replication_initiator_protein_19857..20087_POSITIVE 199 50 1 104 54 smit:SMT_821|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_732775..733005_POSITIVE 196 36 5 72 45 smit:SMT_218|5end_undecaprenyl_pyrophosphate_synthetase_150155..150385_POSITIVE 188 30 1 117 90 smit:SMT_144|5end_hypothetical_protein_predicted_by_Glimmer/Critica_95553..95783_POSITIVE 185 50 9 137 98 smit:SMT_232|5end_DNA_polymerase_III,_alpha_subunit,_Gram-positive_type_168246..168476_POSITIVE 182 49 4 194 139 smit:SMT_1162|5end_ATP-dependent_DNA_helicase_1108895..1109125_NEGATIVE 182 43 1 130 90 smit:SMT_697|5end_glucose-inhibited_division_protein_B_607489..607719_POSITIVE 182 52 26 150 126 smit:SMT_274|5end_ABC_transporter_substrate-binding_protein_-_oligopeptide_transport_215221..215451_POSITIVE 178 50 4 87 48 smit:SMT_2104|5end_UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-_diaminopimelate_ligase_1995547..1995777_POSITIVE 178 57 11 144 98 smit:SMT_1042|5end_hypothetical_cytosolic_protein_984972..985202_NEGATIVE 177 52 11 149 102 smit:SMT_790|5end_hypothetical_protein_701917..702147_NEGATIVE 176 50 9 140 100 smit:SMT_1148|5end_aspartyl-tRNA_synthetase_1093885..1094115_NEGATIVE 176 37 1 174 142 smit:SMT_1064|5end_phospho-2-dehydro-3-deoxyheptonate_aldolase_1003308..1003538_POSITIVE 175 42 9 134 98 smit:SMT_567|5end_conserved_hypothetical_protein_484845..485075_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 219 38 4 99 71 smit:SMT_804|3end_S-adenosylmethionine_synthetase_713884..714034_NEGATIVE 185 54 11 151 104 smit:SMT_1015|3end_galactose_operon_repressor_953019..953169_POSITIVE 176 37 1 93 61 smit:SMT_1063|3end_preprotein_translocase_SecA_subunit_1003307..1003457_POSITIVE 175 42 9 112 76 smit:SMT_566|3end_K07282_poly-gamma-glutamate_synthesis_protein_(capsule_biosynthesis_protein)_484903..485053_POSITIVE 172 29 4 54 31 smit:SMT_392|3end_acetyltransferase,_GNAT_family_324007..324157_POSITIVE 168 35 1 96 59 smit:SMT_1097|3end_alcohol_dehydrogenase_/_acetaldehyde_dehydrogenase_1038697..1038847_NEGATIVE 166 50 2 134 78 smit:SMT_1900|3end_K03710_GntR_family_transcriptional_regulator_1850620..1850770_POSITIVE 165 33 3 63 30 smit:SMT_1058|3end_primosomal_protein_DnaI_997462..997612_POSITIVE 164 22 1 38 16 smit:SMT_1446|3end_pneumococcal_vaccine_antigen_A_1428996..1429146_NEGATIVE 163 37 3 78 42 smit:SMT_809|3end_sensor_histidine_kinase_(homolog_to_BlpH_Spn)_718420..718570_NEGATIVE 163 85 44 117 75 smit:SMT_620|3end_hypothetical_protein_predicted_by_Glimmer/Critica_528971..529121_POSITIVE 157 65 24 78 31 smit:SMT_1302|3end_hypothetical_protein_1264649..1264799_POSITIVE 156 50 28 33 8 smit:SMT_231|3end_translation_elongation_factor_G_168222..168372_POSITIVE 155 89 46 82 37 smit:SMT_1122|3end_queuine_tRNA-ribosyltransferase_1058081..1058231_NEGATIVE 155 50 3 129 77 smit:SMT_353|3end_immunity_protein_BlpL_291364..291514_POSITIVE 154 52 12 52 10 smit:SMT_1220|3end_hypothetical_protein_predicted_by_Glimmer/Critica_1180509..1180659_NEGATIVE 153 62 33 40 11 smit:SMT_114|3end_alpha-mannosidase_65529..65679_POSITIVE 152 54 12 77 43 smit:SMT_602|3end_5'-methylthioadenosine_nucleosidase_/_S-adenosylhomocysteine_nucleosidase_517964..518114_POSITIVE 151 45 10 127 86 smit:SMT_938|3end_hypothetical_protein_890813..890963_NEGATIVE 151 80 31 66 22 smit:SMT_918|3end_hypothetical_protein_871290..871440_NEGATIVE