TRNA Genes Check List 2009
Expectations in Verifying tRNAs
- tRNA Number: All 20 amino acids should have at least one corresponding tRNA gene
- Strand Alignment: There should be a forward and reverse DNA sequence for each tRNA that should be complementary to each other
- BLAST: The sequences of tRNAs should be rather conserved, because of their importance, and therefore similar to other tRNAs in at least Archaea and Eubacteria
- Transcription: There should NOT be an RBS consensus sequence in or upstream (4-10nt) of the tRNA gene
tRNA Number
There are 47 recorded sequences for H. mukohataei tRNAs. The amount of tRNA genes varies widely between species, so I cannot think of a way currently to predict how many we should be looking for.
There are 20 amino acids and there should be a tRNA forward and reverse sequence for each. The table below is a count of the forward and reverse sequences (47) and what gene they name. All of the amino acids have been named, but there is not a forward and reverse sequence for all of them.
BLAST Hits
1/3
2/3
Blasting the sequences under the nucleotide (nr/nt) database with megablast discontinuous in order to check for similar sequences in other organisms. I selected BLAST Hits that would suggest the given gene sequence is indeed a tRNA gene, or if there weren't any hits that satisfy that, just the hit that had the greatest homology.
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
3/3
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
