Origin IGS: tcactttcttgtctgttatactcaatgaaaatcaaaaagcaaactakgmagcgagccgcaggttgctcaaagcactgctttgaagttgtagatagaactacatatatacggcaaggcgaagctgacgtggtttgaagagattttcgaagagtattattctataaatgttactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga .........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.........1.........2.........3.........4.........5.........6.........7.........8.........9 tccagacctcccttgattttgttacattgtacccttttttttctttcttggcaatgtctagggtgtttctctcgttcacatctaggggcaaatgtggtatacttaggagtaacatttatagaataatactcttcgaaaatctcttcaaaccacgtcagcttcgccttgccgtatatatgtagttctatctacaacttcaaagcagtgctttgagcaacctgcggctcgctkcmtagtttgctttttgattttcattgagtataacagacaagaaagtga Mask Tandem Repeat Region ================================================ tcactttcttgtctgttatactcaatgaaaatcaaaaagcaaactakgmagcgagccgcaggttgctcaaagcactgctttgaagttgtagatagaactacatatatacggcaaggcgaagctgacgtggtttgaagagattttcgaagagtattattctataaatgttactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Find is-nt database================================================ Query_seq: SMT_775:SMT_776|SMT_775:SMT_776:alpha-acetolactate decarboxylase:hypothetical protein:<-->:686063..686341 279 tcactttcttgtctgttatactcaatgaaaatcaaaaagcaaactakgmagcgagccgcaggttgctcaaagcactgctttgaagttgtagatagaactacatatatacggcaaggcgaagctgacgtggtttgaagagattttcgaagagtattattctataaatgttactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: SMT_775:SMT_776|SMT_775:SMT_776:alpha-acetolactate decarboxylase:hypothetical protein:<-->:686063..686341 279 tcactttcttgtctgttatactcaatgaaaatcaaaaagcaaactakgmagcgagccgcaggttgctcaaagcactgctttgaagttgtagatagaactacatatatacggcaaggcgaagctgacgtggtttgaagagattttcgaagagtattattctataaatgttactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: SMT_775:SMT_776|SMT_775:SMT_776:alpha-acetolactate decarboxylase:hypothetical protein:<-->:686063..686341 279 tcactttcttgtctgttatactcaatgaaaatcaaaaagcaaactakgmagcgagccgcaggttgctcaaagcactgctttgaagttgtagatagaactacatatatacggcaaggcgaagctgacgtggtttgaagagattttcgaagagtattattctataaatgttactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Intra-Species Hit: Count: 0 Inter-species Hit: Count: 7 Min: 16 Max: 160 Len: 145 Subject: UniRef90_Q04I61 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 1.0E-10 bit: 49.7 Len: 84 Query Start:16 Query End:99 Subject Strand: null Subject Start: 23 Subject End: 50 ............... L Y S M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ............... L Y S M K I K V Q T R K L A A G C S K H C F E V V D E T .................................................................................................................................................................................... HSP 2 e-value: 1.0E-10 bit: 38.1 Len: 54 Query Start:101 Query End:154 Subject Strand: null Subject Start: 56 Subject End: 73 .................................................................................................... H I Y G K A K L T W F E E I F E E Y ............................................................................................................................. .................................................................................................... H T Y G K A T L T W F E E I F E K Y ............................................................................................................................. Subject: UniRef90_Q04IR5 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 6.0E-10 bit: 45.1 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G C S K H C F E V V D E T .................................................................................................................................................................................... HSP 2 e-value: 6.0E-10 bit: 40.4 Len: 54 Query Start:101 Query End:154 Subject Strand: null Subject Start: 31 Subject End: 48 .................................................................................................... H I Y G K A K L T W F E E I F E E Y ............................................................................................................................. .................................................................................................... H T Y G K V K L T W F E E I F E E Y ............................................................................................................................. Subject: UniRef90_Q04LB4 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 1.0E-9 bit: 47.0 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G C S K H C F E V V D R T .................................................................................................................................................................................... HSP 2 e-value: 1.0E-9 bit: 37.7 Len: 54 Query Start:101 Query End:154 Subject Strand: null Subject Start: 46 Subject End: 63 .................................................................................................... H I Y G K A K L T W F E E I F E E Y ............................................................................................................................. .................................................................................................... H T Y G R A T M T W F E E I F E E Y ............................................................................................................................. Subject: UniRef90_Q04M07 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 8.0E-9 bit: 42.0 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G C S K Q C F E V V D E T .................................................................................................................................................................................... HSP 2 e-value: 8.0E-9 bit: 39.7 Len: 54 Query Start:101 Query End:154 Subject Strand: null Subject Start: 31 Subject End: 48 .................................................................................................... H I Y G K A K L T W F E E I F E E Y ............................................................................................................................. .................................................................................................... H T Y G K A K L M W F E E I F E E Y ............................................................................................................................. Subject: UniRef90_Q04L28 Cluster: Hypothetical protein; n=2; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 2.0E-7 bit: 44.3 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G C S K H C F E V A D K T .................................................................................................................................................................................... HSP 2 e-value: 2.0E-7 bit: 32.7 Len: 60 Query Start:101 Query End:160 Subject Strand: null Subject Start: 46 Subject End: 65 .................................................................................................... H I Y G K A K L T W F E E I F E E Y Y S ....................................................................................................................... .................................................................................................... H T Y G K A T L T R I E E I F E E Y K S ....................................................................................................................... Subject: UniRef90_Q04I51 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 1.0E-6 bit: 45.8 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G C S K H C F E V M D R T .................................................................................................................................................................................... HSP 2 e-value: 1.0E-6 bit: 28.5 Len: 39 Query Start:101 Query End:139 Subject Strand: null Subject Start: 46 Subject End: 58 .................................................................................................... H I Y G K A K L T W F E E ............................................................................................................................................ .................................................................................................... H T Y G E V K L T W F E E ............................................................................................................................................ Subject: UniRef90_Q04KB8 Cluster: Hypothetical protein; n=1; Streptococcus pneumoniae D39|Rep: Hypothetical protein - Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) HSP 1 e-value: 1.0E-6 bit: 37.4 Len: 54 Query Start:101 Query End:154 Subject Strand: null Subject Start: 31 Subject End: 48 .................................................................................................... H I Y G K A K L T W F E E I F E E Y ............................................................................................................................. .................................................................................................... H T Y S K A T L T W F E E I F E E Y ............................................................................................................................. HSP 2 e-value: 1.0E-6 bit: 37.0 Len: 75 Query Start:25 Query End:99 Subject Strand: null Subject Start: 1 Subject End: 25 ........................ M K I K K Q T X X R A A G C S K H C F E V V D R T .................................................................................................................................................................................... ........................ M K I K E Q T R K L A A G Y S K H S F E V V D E T .................................................................................................................................................................................... tcactttcttgtctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Predict ORF larger than 30AA ================================================ Protein_Len: 40 Strand: + Start: 13 End: 132 ............ M L Y S M K I K K Q T X X R A A G C S K H C F E V V D R T T Y I R Q G E A D V V ................................................................................................................................................... Protein_Len: 60 Strand: + Start: 92 End: 277 ........................................................................................... M E L H I Y G K A K L T W F E E I F E E Y Y S I N V T P K Y T T F A P R C E R E K H P R H C Q E R K K R V Q C N K I K G .. Protein_Len: 38 Strand: + Start: 165 End: 278 .................................................................................................................................................................... M L L L S I P H L P L D V N E R N T L D I A K K E K K G Y N V T K S R E V W . Protein_Len: 37 Strand: - Start: 157 End: 267 ............................................................................................................................................................ E I F T V G L Y V V N A G L H S R S F C G L C Q W S L F F L T C H L L I M ............ Protein_Len: 51 Strand: - Start: 101 End: 253 .................................................................................................... M Y V A L R L Q R P K F L N E F L I I R Y I N S R L I G C K G R S T F S L F V R S M A L F S F F P Y M .......................... Protein_Len: 35 Strand: - Start: 3 End: 107 .. S E Q R N Y E I F I L F C V X X R A A P Q E F C Q K S T T S L V V Y M ............................................................................................................................................................................ tcactttcttgtctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga 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: 86 Start: 223 End: 252 ..............................................................................................................................................................................................................................ATTGCCAAGAAAGAAAAAAAAGGGTACAAT........................... PromScan Matrix: RpoD-17 Strand: - Score: 84 Start: 175 End: 204 ..............................................................................................................................................................................GTTCACATCTAGGGGCAAATGTGGTATACT........................................................................... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tcactttcttgtctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: SMT_775:SMT_776|SMT_775:SMT_776:alpha-acetolactate decarboxylase:hypothetical protein:<-->:686063..686341 279 tcactttcttgtctgnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnactcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Intra-Species Hit: Count: 1 Min: 170 Max: 279 Len: 110 Subject: smit_SMT_775_SMT_776|alpha-acetolactate decarboxylase:hypothetical protein|NEGATIVE:POSITIVE|[686063,686341]|279 HSP 1 e-value: 2.0E-41 bit: 170.0 Len: 110 Query Start:170 Query End:279 Subject Strand: POSITIVE Subject Start: 170 Subject End: 279 .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagnnnnnnnngggtacaatgtaacaaaatcaagggaggtctgga .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Inter-species Hit: Count: 3 Min: 170 Max: 279 Len: 110 Subject: NC_008533_SPD_1224_SPD_1225|alpha-acetolactate decarboxylase:hypothetical protein|NEGATIVE:POSITIVE|[1256714,1256854]|141 HSP 1 e-value: 2.0E-34 bit: 147.0 Len: 110 Query Start:170 Query End:279 Subject Strand: POSITIVE Subject Start: 32 Subject End: 141 .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagnnnnnnnngggtacaatgtaacaaaatcaagggaggtctgga .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacgctctagacattgccaagaaggaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Subject: NC_003098_spr1249_spr1250|Alpha-acetolactate decarboxylase:hypothetical protein|NEGATIVE:POSITIVE|[1249183,1249323]|141 HSP 1 e-value: 2.0E-34 bit: 147.0 Len: 110 Query Start:170 Query End:279 Subject Strand: POSITIVE Subject Start: 32 Subject End: 141 .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagnnnnnnnngggtacaatgtaacaaaatcaagggaggtctgga .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacgctctagacattgccaagaaggaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Subject: NC_003028_SP_1392_SP_1393|alpha-acetolactate decarboxylase:hypothetical protein|NEGATIVE:POSITIVE|[1316615,1316755]|141 HSP 1 e-value: 2.0E-34 bit: 147.0 Len: 110 Query Start:170 Query End:279 Subject Strand: POSITIVE Subject Start: 32 Subject End: 141 .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacaccctagacattgccaagaaagnnnnnnnngggtacaatgtaacaaaatcaagggaggtctgga .........................................................................................................................................................................actcctaagtataccacatttgcccctagatgtgaacgagagaaacgctctagacattgccaagaaggaaaaaaaagggtacaatgtaacaaaatcaagggaggtctgga Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACUCCUAAGUAUACCACAUUUGCCCCUAGAUGUGAACGAGAGAAACACCCUAGACAUUGCCAAGAAAGAAAAAAAAGGGUACAAUGUAACAAAAUCAAGGGAGGUCUGGA .(((((........((((((((....))))))))............(((((........................)))))..................)))))....... (-18.46) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UCCAGACCUCCCUUGAUUUUGUUACAUUGUACCCUUUUUUUUCUUUCUUGGCAAUGUCUAGGGUGUUUCUCUCGUUCACAUCUAGGGGCAAAUGUGGUAUACUUAGGAGU .......((((..(((...((..(((((...(((...............(((...)))..((((((...........)))))).)))...)))))..))...))))))). (-19.00) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 271 50 3 89 19 smit:SMT_1849|5end_hypothetical_protein_1813074..1813304_POSITIVE 264 62 22 143 102 smit:SMT_2061|5end_K02011_iron(III)_transport_system_permease_protein_1970087..1970317_POSITIVE 259 59 19 50 7 smit:SMT_1353|5end_GTP-binding_protein_1331589..1331819_NEGATIVE 258 60 12 67 1 smit:SMT_175|5end_50S_ribosomal_protein_L22_117724..117954_POSITIVE 257 60 15 223 186 smit:SMT_755|5end_shikimate_5-dehydrogenase_659917..660147_NEGATIVE 251 48 1 190 146 smit:SMT_358|5end_hypothetical_protein_293947..294177_POSITIVE 247 65 21 60 5 smit:SMT_1602|5end_hypothetical_protein_1592385..1592615_POSITIVE 246 65 22 196 151 smit:SMT_1984|5end_phosphinothricin_N-acetyltransferase_1914028..1914258_NEGATIVE 246 65 22 196 151 smit:SMT_1869|5end_phosphinothricin_N-acetyltransferase_1829215..1829445_NEGATIVE 242 60 15 135 89 smit:SMT_941|5end_hypothetical_protein_893558..893788_NEGATIVE 240 86 45 60 18 smit:SMT_2047|5end_choline_binding_protein_F_1957818..1958048_NEGATIVE 240 53 13 59 19 smit:SMT_117|5end_K02025_multiple_sugar_transport_system_permease_protein_68487..68717_POSITIVE 239 46 16 48 9 smit:SMT_822|5end_putative_mucus_binding_protein_740574..740804_NEGATIVE 235 43 1 230 189 smit:SMT_1835|5end_hypothetical_protein_predicted_by_Glimmer/Critica_1803894..1804124_POSITIVE 230 59 11 141 90 smit:SMT_2045|5end_K+_transport_system,_NAD-binding_component_1956139..1956369_POSITIVE 229 65 23 172 123 smit:SMT_1552|5end_RNA_binding_protein_1535119..1535349_POSITIVE 229 69 22 116 63 smit:SMT_826|5end_hypothetical_protein_750022..750252_NEGATIVE 227 80 37 71 29 smit:SMT_2162|5end_hypothetical_protein_2036931..2037161_POSITIVE 226 40 1 216 162 smit:SMT_794|5end_hypothetical_protein_703487..703717_NEGATIVE 223 69 21 151 106 smit:SMT_481|5end_K03308_neurotransmitter:Na+_symporter,_NSS_family_418240..418470_NEGATIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 264 62 22 59 18 smit:SMT_2060|3end_hypothetical_protein_1970083..1970233_POSITIVE 251 48 1 63 19 smit:SMT_357|3end_tRNA_(guanine-N7-)-methyltransferase_293900..294050_POSITIVE 251 60 28 55 12 smit:SMT_174|3end_30S_ribosomal_protein_S19_117792..117942_POSITIVE 243 51 14 149 108 smit:SMT_608|3end_laminin-binding_surface_protein_521187..521337_POSITIVE 234 50 9 116 74 smit:SMT_306|3end_3-oxoacyl-_249117..249267_POSITIVE 231 57 11 66 18 smit:SMT_777|3end_hypothetical_protein_686618..686768_NEGATIVE 225 54 16 130 87 smit:SMT_1966|3end_DNA_polymerase_III_alpha_subunit_1898328..1898478_POSITIVE 217 53 13 148 110 smit:SMT_1857|3end_hypothetical_protein_1821145..1821295_POSITIVE 215 58 19 64 18 smit:SMT_967|3end_K01992_ABC-2_type_transport_system_permease_protein_912215..912365_NEGATIVE 215 64 22 74 24 smit:SMT_959|3end_1-acyl-sn-glycerol-3-phosphate_acyltransferase_906112..906262_POSITIVE 215 37 3 39 9 smit:SMT_667|3end_hypothetical_protein_578128..578278_POSITIVE 214 70 21 69 26 smit:SMT_1632|3end_hypothetical_protein_1618371..1618521_NEGATIVE 213 50 8 61 21 smit:SMT_458|3end_hypothetical_protein_predicted_by_Glimmer/Critica_396729..396879_NEGATIVE 212 43 1 124 87 smit:SMT_276|3end_exopolysaccharide_biosynthesis_protein_219632..219782_POSITIVE 209 68 43 30 2 smit:SMT_1790|3end_hypothetical_protein_1765915..1766065_POSITIVE 208 61 21 84 34 smit:SMT_1620|3end_hypothetical_protein_1606695..1606845_NEGATIVE 207 47 16 130 98 smit:SMT_2024|3end_hypothetical_protein_1940690..1940840_POSITIVE 207 107 76 35 5 smit:SMT_1837|3end_adenylosuccinate_synthetase_1804698..1804848_NEGATIVE 207 107 76 35 5 smit:SMT_1675|3end_adenylosuccinate_synthetase_1660701..1660851_NEGATIVE 207 62 41 87 60 smit:SMT_269|3end_phospho-N-acetylmuramoyl-pentapeptide-transferas_e_208785..208935_POSITIVE