TRNA Genes Check List 2009
From GcatWiki
Contents
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.
Strand Alignment
I attempted to see if the forward and reverse sequences of each tRNA would at least align with each other, which would make it very likely they are part of the same gene instead of parts of separate loci. I could not find an option to align the reverse complement in BLAST2, so I only used aPE (A Plasmid Editor). I had the forward and reverse sequences for Leu (Leucine):
and for Glu (Glutamic acid):
Finally, in order to see if the overall tRNA sequence is generally conserved, I assumed that all of the forward sequences and all of the reverse sequences should be similar to each other, differing mainly only around what would be the anticodon loop. So I aligned all of my forward (+) sequences:
And all my the reverse sequences:
aPE does not give much of any statistical data on how well the sequences align. But the assumption that tRNAs within the same genome would be similar may be incorrect, and I could sample a number of random tRNAs from E. coli or a well-studied Archaea in order to compare how well their various tRNA genes align to each other. I'm currently not sure where or how I would find those tRNA genes.
BLAST Hits
1/3
tRNA 644029747: 829..904 (+) (76bp): tRNA-Cys
Megablast results using the nr/nt database showed the following match: H.cutirubrum rRNA gene cluster, 23S rRNA, 5S rRNA and Cys-tRNA genes S = 119 bits (64) E-value = 2e-24 Query Coverage = 100% Identities = 72/76 (94%) Gaps = 0/76 (0%) Strand=Plus/Plus
Haloarcula marismortui 5S rRNA gene and tRNA-Cys gene, rrnA operon S = 86.1 bits (46) E-value = 2e-14 Query Coverage = 68% Identities = 51/53 (96%) Gaps = 2/53 (3%) Strand=Plus/Plus
Halobacterium halobium rRNA operon with genes for 16S rRNA, 23S rRNA, 5S rRNA and tRNA-Ala (UGC) S = 69.4 bits (37) E-value = 2e-09 Query Coverage = 52% Identities = 39/40 (97%) Gaps = 0/40 (0%) Strand=Plus/Plus
tRNA 644029772: 22327..22400(-) (74bp): tRNA-Phe
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Phe-tRNA S = 120 bits (132) E-value = 7e-25 Query Coverage = 100% Identities = 71/74 (95%) Gaps = 0/74 (0%) Strand=Plus/Plus
tRNA 644029840: 78836..78908(-) (73bp): tRNA-Arg
Halobacterium cutirubrum transfer RNA-Arg (GCG) S = 113 bits (61) E-value = 7e-23 Query Coverage = 100% Identities = 69/73 (94%) Gaps = 0/73 (0%) Strand=Plus/Plus
tRNA 644029846: 84056..84128(+) (73bp): tRNA-Asn
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Asn-tRNA S = 114 bits (126) E-value = 3e-23 Query Coverage = 100% Identities = 69/73 (94%) Gaps = 0/73 (0%) Strand=Plus/Plus
Halobacterium cutirubrum transfer RNA-Asn (GUU) S = 73.4 bits (80) E-value = 9e-11 Query Coverage = 100% Identities = 60/73 (82%) Gaps = 0/73 (0%) Strand=Plus/Plus
Methanothermus fervidus Asn-, Met-, Glu-, Leu-, and His-tRNA genes and ORF, 5' end S = 68.0 bits (74) E-value = 4e-09 Query Coverage = 100% Identities = 60/74 (81%) Gaps = 1/74 (1%) Strand=Plus/Plus
C.elegans Lys-tRNA gene and flanks, clone Cet 21 S = 64.4 bits (70) E-value = 5e-08 Query Coverage = 75% Identities = 47/55 (85%) Gaps = 0/55 (0%) Strand=Plus/Plus
Mycoplasma capricolum tRNA gene cluster encoding Asn-, Glu-, Val-, and Thr-tRNA S = 62.6 bits (68) E-value = 2e-07 Query Coverage = 78% Identities = 48/57 (84%) Gaps = 0/57 (0%) Strand=Plus/Plus
Mycoplasma mycoides Ans-tRNA, Glu-tRNA, Val-tRNA, Thr-tRNA gene cluster S = 62.6 bits (68) E-value = 2e-07 Query Coverage = 78% Identities = 48/57 (84%) Gaps = 0/57 (0%) Strand=Plus/Plus
Mycoplasma capricolum transfer RNA-Asn (GUU) S = 62.6 bits (68) E-value = 2e-07 Query Coverage = 78% Identities = 48/57 (84%) Gaps = 0/57 (0%) Strand=Plus/Plus
tRNA 644029847: 84398..84473(+) (76bp): tRNA-Met
Haloarcula marismortui LOCUS AY596297 S = 120 bits (132) E-value = 3.0e-38 Query Coverage = 100% Identities = 73/76 (96%) Gaps = 1/76 (1%) Strand = Plus/Minus
tRNA 644029864: 95971..96043(+) (73bp): tRNA-Lys
Halobacterium volcanii Lys-tRNA-2 S = 108 bits (58) E-value = 3e-21 Query Coverage = 100% Identities = 69/74 (93%) Gaps = 1/74 (1%) Strand=Plus/Plus
tRNA 644029894: 125395..125467(-) (73bp): tRNA-Asp
Halobacterium volcanii Asp-tRNA S = 113 bits (61) E-value = 7e-23 Query Coverage = 100% Identities = 70/74 (94%) Gaps = 2/74 (2%) Strand=Plus/Plus
tRNA 644029895: 125511..125583(-) (73bp): tRNA-Asp
Halobacterium volcanii Asp-tRNA S = 113 bits (61) E-value = 7e-23 Query Coverage = 100% Identities = 70/74 (94%) Gaps = 2/74 (2%) Strand=Plus/Plus
tRNA 644029917: 152036..152107(+) (72bp): tRNA-Ala
Halobacterium volcanii Ala-tRNA-2 S = 117 bits (63) E-value = 5e-24 Query Coverage = 100% Identities = 69/72 (95%) Gaps = 0/72 (0%) Strand=Plus/Plus
H. cutirubrum Ala-tRNA Score = 111 bits (60) E-value = 2e-22 Query Coverage = 100% Identities = 68/72 (94%) Gaps = 0/72 (0%) Strand=Plus/Plus
Halobacterium cutirubrum transfer RNA-Ala (CGC) Score = 106 bits (57) E-value = 1e-20 Query Coverage = 100% Identities = 67/72 (93%) Gaps = 0/72 (0%) Strand=Plus/Plus
tRNA 644029994: 205883..205955(-) (73bp): tRNA-Val
Blastn results using the nr/nt database showed the following match: Chain D, Crystal Structure Of Archaeosine Trna-Guanine Transglycosylase Complexed With Lambda-Form Trna(Val) S = 69.8 bits (76) E-value = 1e-09 Query Coverage = 98% Identities = 60/73 (82%) Gaps = 1/73 (1%) Strand=Plus/Plus
Chain C, Crystal Structure Of Archaeosine Trna-Guanine Transglycosylase Complexed With Lambda-Form Trna(Val) S = 69.8 bits (76) E-value = 1e-09 Query Coverage = 98% Identities = 60/73 (82%) Gaps = 1/73 (1%) Strand=Plus/Plus
tRNA 644030243: 450911..450984(+) (74bp): tRNA-Tyr
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Tyr-tRNA S = 93.3 bits (102) E-value = 1e-16 Query Coverage = 100% Identities = 65/74 (87%) Gaps = 0/74 (0%) Strand=Plus/Plus
Vibrio parahaemolyticus HTH gene for HTH-domain protein, complete cds, and tRNA-Met, complete sequence, strain: ASL37223 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus HTH gene for HTH-domain protein, complete cds, and tRNA-Met, complete sequence, strain: KX-V138 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus HTH gene for HTH-domain protein, complete cds, and tRNA-Met, complete sequence, strain: VP108 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus HTH gene for HTH-domain protein, complete cds, and tRNA-Met, complete sequence, strain: VP81 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
ibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: PS14966 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: VP229 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: VP262 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 100% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: AQ4814 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: U5474 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
ibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: VP230 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: U12365 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: W9273 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Vibrio parahaemolyticus gene for tRNA-Met, complete sequence, strain: AQ4037 S = 59.0 bits (64) E-value = 2e-06 Query Coverage = 90% Identities = 55/68 (80%) Gaps = 3/68 (4%) Strand=Plus/Minus
Caesalpinia hintonii isolate PLA2 tRNA-Leu (trnL) gene, partial sequence; trnL-trnF intergenic spacer, complete sequence; and tRNA-Phe (trnF) gene, partial sequence; plastid S = 50.0 bits (54) E-value = 0.001 Query Coverage = 72% Identities = 44/54 (81%) Gaps = 1/54 (1%) Strand=Plus/Plus
Caesalpinia hintonii isolate Inf5 tRNA-Leu (trnL) gene, partial sequence; trnL-trnF intergenic spacer, complete sequence; and tRNA-Phe (trnF) gene, partial sequence; plastid S = 50.0 bits (54) E-value = 0.001 Query Coverage = 72% Identities = 44/54 (81%) Gaps = 1/54 (1%) Strand=Plus/Plus
Caesalpinia oyamae isolate TEH4 tRNA-Leu (trnL) gene, partial sequence; trnL-trnF intergenic spacer, complete sequence; and tRNA-Phe (trnF) gene, partial sequence; plastid S = 50.0 bits (54) E-value = 0.001 Query Coverage = 72% Identities = 44/54 (81%) Gaps = 1/54 (1%) Strand=Plus/Plus
Caesalpinia oyamae isolate VTN9 tRNA-Leu (trnL) gene, partial sequence; trnL-trnF intergenic spacer, complete sequence; and tRNA-Phe (trnF) gene, partial sequence; plastid S = 50.0 bits (54) E-value = 0.001 Query Coverage = 72% Identities = 44/54 (81%) Gaps = 1/54 (1%) Strand=Plus/Plus
tRNA 644030369: 587278..587363(+) (86bp): tRNA-Ser
Blastn results using the nr/nt database showed the following match: H.volcanii Ser-tRNA-2 S = 107 bits (118) E-value = 6e-21 Query Coverage = 100% Identities = 76/86 (88%) Gaps = 1/86 (1%) Strand=Plus/Plus
H.volcanii Ser-tRNA-2 S = 104 bits (114) E-value = 7e-20 Query Coverage = 100% Identities = 75/86 (87%) Gaps = 1/86 (1%) Strand=Plus/Plus
Halobacterium cutirubrum transfer RNA-Ser (CGA) S = 80.6 bits (88) E-value = 8e-13 Query Coverage = 100% Identities = 70/86 (81%) Gaps = 1/86 (1%) Strand=Plus/Plus
Phaeognathus hubrichti voucher MVZFC13612 tRNA-Leu gene, complete sequence; NADH dehydrogenase subunit 1 (ND1) gene, complete cds; tRNA-Ile, tRNA-Gln, and tRNA-Met genes, complete sequence; NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, tRNA-Asn, tRNA-Cys, and tRNA-Tyr genes, complete sequence; and cytochrome c oxidase subunit I (COI) gene, partial cds; mitochondrial S = 37.4 bits (40) E-value = 8.7 Query Coverage = 23% Identities = 20/20 (100%) Gaps = 0/20 (0%) Strand=Plus/Plus
Mycoplasma capricolum tRNA gene cluster encoding Arg-, Pro-, Ala-, Met-, Ile-, Ser-, fMet-, Asp-, and Phe-tRNA S = 37.4 bits (40) E-value = 8.7 Query Coverage = 26% Identities = 22/23 (95%) Gaps = 0/23 (0%) Strand=Plus/Plus
Mycoplasma capricolum transfer RNA-Met (CAU) S = 37.4 bits (40) E-value = 8.7 Query Coverage = 26% Identities = 22/23 (95%) Gaps = 0/23 (0%) Strand=Plus/Plus
tRNA 644030693: 910533..910605(-) (73bp): tRNA-Gln
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Glu-tRNA-2 S = 55.4 bits (60) E-value = 2e-05 Query Coverage = 75% Identities = 47/57 (82%) Gaps = 2/57 (3%) Strand=Plus/Plus
Halobacterium cutirubrum transfer RNA-Gln (CUG) S = 51.8 bits (56) E-value = 3e-04 Query Coverage = 100% Identities = 55/73 (75%) Gaps = 0/73 (0%) Strand=Plus/Plus
Halobacterium volcanii Gln-tRNA S = 46.4 bits (50) E-value = 0.013 Query Coverage = 100% Identities = 54/73 (73%) Gaps = 0/73 (0%) Strand=Plus/Plus
Halobacterium volcanii Asp-tRNA S = 42.8 bits (46) E-value = 0.16 Query Coverage = 76% Identities = 43/56 (76%) Gaps = 0/56 (0%) Strand=Plus/Plus
Halobacterium volcanii Pro-tRNA-3 S = 41.0 bits (44) E-value = 0.54 Query Coverage = 47% Identities = 30/35 (85%) Gaps = 0/35 (0%) Strand=Plus/Plus
Giardia intestinalis tRNA-Gln (CTG) gene, strain ATCC 50803 S = 39.2 bits (42) E-value = 1.9 Query Coverage = 73% Identities = 41/54 (75%) Gaps = 0/54 (0%) Strand=Plus/Plus
Methanothermus fervidus Pro-, Thr-, Asp-, and Lys-tRNA gene S = 39.2 bits (42) E-value = 1.9 Query Coverage = 76% Identities = 43/56 (76%) Gaps = 1/56 (1%) Strand=Plus/Plus
tRNA 644030749: 969300..969374(+) (75bp): tRNA-Met
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii initiator Met-tRNA-i S = 109 bits (120) E-value = 1e-21 Query Coverage = 100% Identities = 69/75 (92%) Gaps = 0/75 (0%) Strand=Plus/Plus
Halococcus morrhuae initiator tRNA-Met(CAU) S = 109 bits (120) E-value = 1e-21 Query Coverage = 100% Identities = 69/75 (92%) Gaps = 0/75 (0%) Strand=Plus/Plus
Halobacterium cutirubrum transfer RNA-Met (CAU) S = 109 bits (120) E-value = 1e-21 Query Coverage = 100% Identities = 69/75 (92%) Gaps = 0/75 (0%) Strand=Plus/Plus
Thermoplasma acidophilum initiator tRNA-Met(CAU) S = 84.2 bits (92) E-value = 5e-14 Query Coverage = 100% Identities = 64/75 (85%) Gaps = 1/75 (1%) Strand=Plus/Plus
Pyrococcus furiosus pyrolysin (pls) gene, complete cds, and Met-tRNA gene, complete sequence S = 68.0 bits (74) E-value = 4e-09 Query Coverage = 100% Identities = 60/75 (80%) Gaps = 0/75 (0%) Strand=Plus/Minus
Staphylococcus aureus transfer RNA sequence with two rRNAs S = 68.0 bits (74) E-value = 4e-09 Query Coverage = 62% Identities = 43/47 (91%) Gaps = 0/47 (0%) Strand=Plus/Plus
S.hominis tRNA-Met & tRNA-Asp genes S = 64.4 bits (70) E-value = 5e-08 Query Coverage = 62% Identities = 43/47 (91%) Gaps = 1/47 (2%) Strand=Plus/Plus
tRNA 644030936: 1154730..1154803(-) (74bp): tRNA-Met
Blastn results using the nr/nt database showed the following match: Chlorella ellipsoida plastid trnR(ACG) gene for tRNA-ARG(ACG) S = 44.6 bits (48) E-value = 0.046 Query Coverage = 100% Identities = 54/74 (72%) Gaps = 0/74 (0%) Strand=Plus/Plus
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
