Difference between revisions of "TRNA Genes Check List 2009"
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+ | BLAST – blasting the sequences under the nucleotide (nr/nt) database with megablast discontinuous in order to check for similar sequences in other organisms | ||
+ | |||
+ | '''644030986 1198182..1198263(+) 82bp: tRNA-Ser''' | ||
+ | Natronomonas pharaonis DSM 2160 complete genome | ||
+ | S = 134 bits (148) | ||
+ | E-value = 4e-29 | ||
+ | Query coverage: 100% | ||
+ | Identities = 79/82 (96%) | ||
+ | Gaps = 0/82 (0%) | ||
+ | Strand=Plus/Minus | ||
+ | |||
+ | '''644030992 1202285..1202358(+) 74bp: tRNA-Thr''' | ||
+ | Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU) | ||
+ | S = 42.8 bits (46) | ||
+ | E-value = 0.16 | ||
+ | Query coverage: 68% | ||
+ | Identities = 34/41 (82%) | ||
+ | Gaps = 0/41 | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031031 1231822..1231906(-) 85bp: tRNA-Leu''' | ||
+ | H.volcanii Leu-tRNA-2 | ||
+ | S = 132 bits (146) | ||
+ | E-value = 1e-28 | ||
+ | Query Coverage: 100% | ||
+ | Identities = 80/85 (94%) | ||
+ | Gaps = 0/85 | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031036 1234256..1234340(-) 85bp: tRNA-Ser''' | ||
+ | Halobacterium marismortui ribosomal proteins (HmaS13, HmaS4, | ||
+ | HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA | ||
+ | S = 154 bits (170) | ||
+ | E-value = 4e-35 | ||
+ | Query Coverage: 100% | ||
+ | Identities = 85/85 | ||
+ | Gaps = 0/85 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031060 1255468..1255538(-) 71bp: tRNA-Gly''' | ||
+ | Methanococcoides burtonii DSM 6242, complete genome | ||
+ | Features flanking this part of subject sequence: | ||
+ | 120 bp at 5' side: Sep-tRNA:Cys-tRNA synthase | ||
+ | 16 bp at 3' side: 3-methyladenine DNA glycosylase-like protein | ||
+ | S = 69.8 bits (76) | ||
+ | E-value = 1e-09 | ||
+ | Query coverage: 100% | ||
+ | Identities = 58/71 (81%) | ||
+ | Gaps = 0/71 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031077 1270321..1270395(-)75bp: tRNA-Glu''' | ||
+ | Halobacterium volcanii Glu-tRNA-1 | ||
+ | S = 104 bits (114) | ||
+ | E-value = 6e-20 | ||
+ | Query coverage: 100% | ||
+ | Identities = 68/75 (90%) | ||
+ | Gaps = 0/75 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031243 1431550..1431623(+) 74bp: tRNA-Lys ''' | ||
+ | Methanococcus maripaludis tRNA-Lys gene, complete sequence | ||
+ | S = 80.6 bits (88) | ||
+ | E-value = 6e-13 | ||
+ | Query coverage: 100% | ||
+ | Identities = 62/74 (83%) | ||
+ | Gaps = 0/74 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031270 1452181..1452361(-) 181bp: tRNA-Trp''' | ||
+ | Halobacterium volcanii Trp-tRNA gene | ||
+ | S = 205 bits (226) | ||
+ | E-value = 8e-50 | ||
+ | Query coverage: 100% | ||
+ | Identities = 158/183 (86%) | ||
+ | Gaps = 6/183 (3%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031388 1563815..1563898(-) 84bp: tRNA-Leu''' | ||
+ | H.volcanii Leu-tRNA-1 | ||
+ | S = 84.2 bits (92) | ||
+ | E-value = 7e-14 | ||
+ | Query coverage: 100% | ||
+ | Identities = 70/85 (82%) | ||
+ | Gaps = 1/85 (1%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031409 1587360..1587443(+) 84bp: tRNA-Leu''' | ||
+ | H.volcanii Leu-tRNA-3 | ||
+ | S = 113 bits (124) | ||
+ | E-value = 1e-22 | ||
+ | Query coverage: 100% | ||
+ | Identities = 75/84 (89%) | ||
+ | Gaps = 0/84 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031498 1678478..1678549(-) 72bp: tRNA-Ala''' | ||
+ | Halobacterium volcanii Ala-tRNA-1 | ||
+ | S = 95.1 bits (104) | ||
+ | E-value = 3e-17 | ||
+ | Query coverage: 100% | ||
+ | Identities = 64/72 (88%) | ||
+ | Gaps = 0/72 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031556 1734070..1734154(+) 85bp: tRNA-Leu ''' | ||
+ | Halobacterium volcanii Leu-tRNA | ||
+ | S = 95.1 bits (104) | ||
+ | E-value = 4e-17 | ||
+ | Query coverage: 100% | ||
+ | Identities = 63/70 (90%) | ||
+ | Gaps = 0/70 (0%) | ||
+ | Strand=Plus/Minus | ||
+ | |||
+ | '''644031557 1734881..1734978(-) 98bp: tRNA-Trp''' | ||
+ | Had to use just blastn for this because with megablast, there were no sequences with significant similarity | ||
+ | Hit with some potential significance: | ||
+ | Thermococcus sibiricus MM 739, complete genome | ||
+ | Features flanking this part of subject sequence: | ||
+ | 44 bp at 5' side: Tyrosyl-tRNA synthetase | ||
+ | 104 bp at 3' side: Alanyl-tRNA synthetase-related protein | ||
+ | S = 39.2 bits (42) | ||
+ | E-value = 3.0 | ||
+ | Query coverage: 38% | ||
+ | Identities = 33/38 (86%) | ||
+ | Gaps = 2/38 (5%) | ||
+ | Strand=Plus/Minus | ||
+ | |||
+ | Hit with the best alignment: | ||
+ | Haloarcula marismortui ATCC 43049 chromosome I, complete sequence | ||
+ | Features flanking this part of subject sequence: | ||
+ | 263 bp at 5' side: unknown | ||
+ | 377 bp at 3' side: unknown | ||
+ | S = 84.2 bits (92) | ||
+ | E-value = 8e-14 | ||
+ | Query coverage: 100% | ||
+ | Identities = 82/102 (80%) | ||
+ | Gaps = 4/102 (3%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031574 1750267..1750341(+) 75bp: tRNA-Glu ''' | ||
+ | Halobacterium volcanii Glu-tRNA-2 | ||
+ | S = 109 bits (120) | ||
+ | E-value = 1e-21 | ||
+ | Query coverage = 100% | ||
+ | Identities = 69/75 (92%) | ||
+ | Gaps = 0/75 | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031638 1819028..1819102(-) 75bp: tRNA-Arg''' | ||
+ | Halobacterium volcanii Arg-tRNA-3 | ||
+ | S = 80.6 (88) | ||
+ | E-value = 7e-13 | ||
+ | Query coverage: 100% | ||
+ | Identities = 61/72 (84%) | ||
+ | Gaps = 0/72 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | '''644031690 1860756..1860829(-) 74bp: tRNA-Thr''' | ||
+ | Halobacterium volcanii Thr-tRNA-2 | ||
+ | S = 104 bits (114) | ||
+ | E-value = 6e-20 | ||
+ | Query coverage: 100% | ||
+ | Identities = 68/74 (91%) | ||
+ | Gaps = 1/74 (1%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | ---- | ||
+ | |||
'''tRNA 644031717: ''1888010..1888083 (-) (74bp)'': tRNA-Val''' | '''tRNA 644031717: ''1888010..1888083 (-) (74bp)'': tRNA-Val''' | ||
Megablast results in the nr/nt database showed a match with the following statistics: | Megablast results in the nr/nt database showed a match with the following statistics: |
Revision as of 03:07, 1 September 2009
BLAST – blasting the sequences under the nucleotide (nr/nt) database with megablast discontinuous in order to check for similar sequences in other organisms
644030986 1198182..1198263(+) 82bp: tRNA-Ser
Natronomonas pharaonis DSM 2160 complete genome S = 134 bits (148) E-value = 4e-29 Query coverage: 100% Identities = 79/82 (96%) Gaps = 0/82 (0%) Strand=Plus/Minus
644030992 1202285..1202358(+) 74bp: tRNA-Thr
Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU) S = 42.8 bits (46) E-value = 0.16 Query coverage: 68% Identities = 34/41 (82%) Gaps = 0/41 Strand=Plus/Plus
644031031 1231822..1231906(-) 85bp: tRNA-Leu
H.volcanii Leu-tRNA-2 S = 132 bits (146) E-value = 1e-28 Query Coverage: 100% Identities = 80/85 (94%) Gaps = 0/85 Strand=Plus/Plus
644031036 1234256..1234340(-) 85bp: tRNA-Ser
Halobacterium marismortui ribosomal proteins (HmaS13, HmaS4, HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA S = 154 bits (170) E-value = 4e-35 Query Coverage: 100% Identities = 85/85 Gaps = 0/85 (0%) Strand=Plus/Plus
644031060 1255468..1255538(-) 71bp: tRNA-Gly
Methanococcoides burtonii DSM 6242, complete genome Features flanking this part of subject sequence: 120 bp at 5' side: Sep-tRNA:Cys-tRNA synthase 16 bp at 3' side: 3-methyladenine DNA glycosylase-like protein S = 69.8 bits (76) E-value = 1e-09 Query coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus
644031077 1270321..1270395(-)75bp: tRNA-Glu
Halobacterium volcanii Glu-tRNA-1 S = 104 bits (114) E-value = 6e-20 Query coverage: 100% Identities = 68/75 (90%) Gaps = 0/75 (0%) Strand=Plus/Plus
644031243 1431550..1431623(+) 74bp: tRNA-Lys
Methanococcus maripaludis tRNA-Lys gene, complete sequence S = 80.6 bits (88) E-value = 6e-13 Query coverage: 100% Identities = 62/74 (83%) Gaps = 0/74 (0%) Strand=Plus/Plus
644031270 1452181..1452361(-) 181bp: tRNA-Trp
Halobacterium volcanii Trp-tRNA gene S = 205 bits (226) E-value = 8e-50 Query coverage: 100% Identities = 158/183 (86%) Gaps = 6/183 (3%) Strand=Plus/Plus
644031388 1563815..1563898(-) 84bp: tRNA-Leu
H.volcanii Leu-tRNA-1 S = 84.2 bits (92) E-value = 7e-14 Query coverage: 100% Identities = 70/85 (82%) Gaps = 1/85 (1%) Strand=Plus/Plus
644031409 1587360..1587443(+) 84bp: tRNA-Leu
H.volcanii Leu-tRNA-3 S = 113 bits (124) E-value = 1e-22 Query coverage: 100% Identities = 75/84 (89%) Gaps = 0/84 (0%) Strand=Plus/Plus
644031498 1678478..1678549(-) 72bp: tRNA-Ala
Halobacterium volcanii Ala-tRNA-1 S = 95.1 bits (104) E-value = 3e-17 Query coverage: 100% Identities = 64/72 (88%) Gaps = 0/72 (0%) Strand=Plus/Plus
644031556 1734070..1734154(+) 85bp: tRNA-Leu
Halobacterium volcanii Leu-tRNA S = 95.1 bits (104) E-value = 4e-17 Query coverage: 100% Identities = 63/70 (90%) Gaps = 0/70 (0%) Strand=Plus/Minus
644031557 1734881..1734978(-) 98bp: tRNA-Trp Had to use just blastn for this because with megablast, there were no sequences with significant similarity
Hit with some potential significance: Thermococcus sibiricus MM 739, complete genome Features flanking this part of subject sequence: 44 bp at 5' side: Tyrosyl-tRNA synthetase 104 bp at 3' side: Alanyl-tRNA synthetase-related protein S = 39.2 bits (42) E-value = 3.0 Query coverage: 38% Identities = 33/38 (86%) Gaps = 2/38 (5%) Strand=Plus/Minus Hit with the best alignment: Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Features flanking this part of subject sequence: 263 bp at 5' side: unknown 377 bp at 3' side: unknown S = 84.2 bits (92) E-value = 8e-14 Query coverage: 100% Identities = 82/102 (80%) Gaps = 4/102 (3%) Strand=Plus/Plus
644031574 1750267..1750341(+) 75bp: tRNA-Glu
Halobacterium volcanii Glu-tRNA-2 S = 109 bits (120) E-value = 1e-21 Query coverage = 100% Identities = 69/75 (92%) Gaps = 0/75 Strand=Plus/Plus
644031638 1819028..1819102(-) 75bp: tRNA-Arg
Halobacterium volcanii Arg-tRNA-3 S = 80.6 (88) E-value = 7e-13 Query coverage: 100% Identities = 61/72 (84%) Gaps = 0/72 (0%) Strand=Plus/Plus
644031690 1860756..1860829(-) 74bp: tRNA-Thr
Halobacterium volcanii Thr-tRNA-2 S = 104 bits (114) E-value = 6e-20 Query coverage: 100% Identities = 68/74 (91%) Gaps = 1/74 (1%) Strand=Plus/Plus
tRNA 644031717: 1888010..1888083 (-) (74bp): tRNA-Val
Megablast results in the nr/nt database showed a match with the following statistics: Halobacterium cutirubrum transfer RNA-Val (GAC) S = 99.0 bits (53) E-value = 2e-18 Query Coverage: 100% Identities = 69/76 (90%) Gaps = 3/76 (3%) Strand=Plus/Plus
tRNA 644031821: 1980512..1980582 (+) (71bp): tRNA-Gly
Blastn results in the nr/nt database showed the following matches: Halobacterium volcanii Gly-tRNA-1A S = 69.8 bits (76) E-value = 1e-09 Query Coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus Halobacterium cutirubrum transfer RNA-Gly (GCC) S = 69.8 bits (76) E-value = 1e-09 Query Coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus
tRNA 644031874: 2032528..2032601 (-) (74bp): tRNA-Val
Megablast results using the nr/nt database gave the following match: Halobacterium volcanii Val-tRNA-1 S = 115 bits (62) E-value = 2e-23 Query Coverage: 100% Identities = 71/75 (94%) Gaps = 1/75 (1%) Strand=Plus/Plus
tRNA 644031888: 2048515..2048657 (+) (143bp): tRNA-Met
Megablast results using the nr/nt database showed the following match: Haloferax volcanii (Halobacterium volcanii) elongator methionine-accepting transfer RNA-Met gene S = 78.7 bits (42) E-value = 7e-12 Query Coverage: 29% Identities = 42/42 (100%) Gaps = 0/42 (0%) Strand=Plus/Plus
tRNA 644031915: 2079098..2079168 (+) (71bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-2 S = 121 bits (65) E-value = 4e-25 Query Coverage: 100% Identities = 69/71 (97%) Gaps = 0/71 (0%) Strand=Plus/Plus
tRNA 644032052: 2201308..2201392 (-) (85bp) : tRNA-Leu
Blastn results in the nr/nt database showed the following matches: Chain D, The Crystal Structure Of Leucyl-Trna Synthetase And Trna(Leucine) Complex S = 89.7 bits (98) E-value = 2e-15 Query Coverage: 98% Identities = 70/84 (83%) Gaps = 0/84 (0%) Strand=Plus/Plus Chain C, The Crystal Structure Of Leucyl-Trna Synthetase And Trna(Leucine) Complex S = 89.7 bits (98) E-value = 2e-15 Query Coverage: 98% Identities = 70/84 (83%) Gaps = 0/84 (0%) Strand=Plus/Plus H.volcanii Leu-tRNA-5 S = 87.8 bits (96) E-value = 5e-15 Query Coverage: 100% Identities = 70/85 (82%) Gaps = 0/85 (0%) Strand=Plus/Plus
tRNA 644032072: 2221071..2221144 (+) (74bp): tRNA-Ile
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Ile-tRNA-1 S = 99.0 bits (53) E-value= 2e-18 Query Coverage: 100% Identities = 67/74 (90%) Gaps = 0/74 (0%) Strand=Plus/Plus
tRNA 644032209: 2353219..2353291 (+)(73bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-1 S = 97.1 bits (52) E-value = 7e-18 Query Coverage: 100% Identities = 68/75 (90%) Gaps = 4/75 (5%) Strand=Plus/Plus
tRNA 644032498: 2622662..2622733 (+)(72bp): tRNA-Thr
Megablast results using the nr/nt database showed the following matches: Halobacterium volcanii Thr-tRNA-1 S = 111 bits (60) E-value = 3e-22 Query Coverage = 100% Identities = 68/72 (94%) Gaps = 0/72 (0%) Strand = Plus/Plus Halobacterium cutirubrum transfer RNA-Thr (GGU) S = 106 bits (57) E-value = 1e-20 Query Coverage = 100% Identities = 67/72 (93%) Gaps = 0/72 (0%) Strand = Plus/Plus
tRNA 644032619: 2736702..2736774 (-)(73bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-3 S = 113 bits (61) E-value = 7e-23 Query Coverage = 100% Identities = 69/73 (94%) Gaps = 0/73 (0%) Strand = Plus/Plus
tRNA 644032625: 2743979..2744049 (-)(71bp): tRNA-His
Blastn results using the nr/nt database showed the following matches: Halobacterium volcanii His-tRNA S = 93.3 bits (102) E-value = 9e-17 Query Coverage = 100% Identities = 65/73 (89%) Gaps = 2/73 (2%) Strand = Plus/Plus Halobacterium cutirubrum transfer RNA-His (GUG) S = 77.0 bits (84) E-value = 7e-12 Query Coverage = 100% Identities = 61/73 (83%) Gaps = 2/73 (2%) Strand = Plus/Plus
tRNA 644032706: 2814103..2814206 (-)(104bp): tRNA-Arg
Blastn results show no promising matches
tRNA 644032751: 2856285..2856357 (+)(73bp): tRNA-Gln
Megablast results using the nr/nt database showed the following match: Halobacterium cutirubrum transfer RNA-Gln (CUG) S = 75.0 bits (40) E-value = 3e-11 Query Coverage = 71% Identities = 48/52 (92%) Gaps = 0/52 (0%) Strand = Plus/Plus
tRNA 644032818: 2918247..2918328 (-)(82bp): tRNA-Ser
Megablast results using the nr/nt database showed the following match: H.volcanii Ser-tRNA-3 S = 108 bits (58) E-value = 4e-21 Query Coverage = 100% Identities = 75/83 (90%) Gaps = 3/83 (3%) Strand = Plus/Plus
tRNA 644032961: 3065293..3065363 (+)(71bp): tRNA-Gly
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Gly-tRNA-3 S = 93.3 bits (102) E-value = 9e-17 Query Coverage = 100% Identities = 63/71 (88%) Gaps = 0/71 (0%) Strand = Plus/Plus
tRNA 644032998: 3109008..3109079 (+)(72bp): tRNA-Ala
Megablast results using the nr/nt database showed the following match: Halosimplex carlsbadense rrnC operon genes for 16S rRNA, tRNA-Ala, 23S rRNA, complete and partial sequence S = 111 bits (60) E-value = 3e-22 Query Coverage = 100% Identities = 68/72 (94%) Gaps = 0/72 (0%) Strand = Plus/Plus