Difference between revisions of "TRNA Genes Check List 2009"

Latest revision as of 16:40, 3 September 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.

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

Difference between revisions of "TRNA Genes Check List 2009"

Latest revision as of 16:40, 3 September 2009

Contents

Expectations in Verifying tRNAs

tRNA Number

Strand Alignment

BLAST Hits

1/3

2/3

3/3

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@@ Line 1: / Line 1: @@
-'''tRNA 644031717: tRNA-Val'''
+== 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 [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=TaxonDetail&page=rnas&taxon_oid=643886133&locus_type=tRNA 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.
+[[Image:tRNA-AminoAcid-Count.png|center|250px]]
+== 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 [http://www.biology.utah.edu/jorgensen/wayned/ape/ aPE (A Plasmid Editor)]. I had the forward and reverse sequences for Leu (Leucine):
+[[Image:Leu-align-FandR.png|center|650px]]
+and for Glu (Glutamic acid):
+[[Image:Glu-align-FandR.png|center|650px]]
+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:
+[[Image:tRNA-for-align.png|center|650px]]
+And all my the reverse sequences:
+[[Image:tRNA-rev-align.png|center|650px]]
+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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=7&list_uids=148796 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=8&list_uids=6468293 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SZDXSV9016&log%24=nucltop&blast_rank=9&list_uids=43554 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y3V0C1W01S&log%24=nucltop&blast_rank=10&list_uids=174712 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'''
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T0CJ19301S&log%24=nucltop&blast_rank=4&list_uids=43442 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=3&list_uids=174730 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=9&list_uids=43443 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=14&list_uids=149813 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=63&list_uids=156315 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=76&list_uids=216786 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=77&list_uids=150212 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y4AE5RM01S&log%24=nucltop&blast_rank=78&list_uids=44253 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'''
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T0Y7F1W014&log%24=nucltop&blast_rank=2&list_uids=174721 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'''
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T15FMVM016&log%24=nucltop&blast_rank=8&list_uids=174709 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'''
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1G3XW0016&log%24=nucltop&blast_rank=8&list_uids=174709 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'''
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=6&list_uids=174706 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=11&list_uids=174704 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9T1T00SS012&log%24=nucltop&blast_rank=13&list_uids=43458 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5EENYJ016&log%24=nucltop&blast_rank=28&list_uids=31615444 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5EENYJ016&log%24=nuclalign&blast_rank=29&list_uids=31615443 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nucltop&blast_rank=10&list_uids=174750 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nucltop&blast_rank=15&list_uids=226069481 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
+ [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=16&list_uids=226069479 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=17&list_uids=226069477 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=18&list_uids=226069475 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=19&list_uids=226069470 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=20&list_uids=226069469 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=21&list_uids=226069468 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=22&list_uids=226069467 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=23&list_uids=226069466 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=24&list_uids=226069465 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=25&list_uids=226069464 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=26&list_uids=226069463 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=27&list_uids=226069462 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=62&list_uids=78098152 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=63&list_uids=78098148 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
+ [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=64&list_uids=78098136 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y5W5TEF014&log%24=nuclalign&blast_rank=65&list_uids=78098125 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nucltop&blast_rank=5&list_uids=174741 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nuclalign&blast_rank=6&list_uids=174740 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nucltop&blast_rank=11&list_uids=43456 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nucltop&blast_rank=50&list_uids=114150453 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nuclalign&blast_rank=60&list_uids=216788 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y7KXM7T014&log%24=nuclalign&blast_rank=61&list_uids=44252 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=45&list_uids=174711 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=50&list_uids=43444 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=58&list_uids=174734 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=63&list_uids=174709 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=73&list_uids=174733 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=81&list_uids=110835876 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9Y89GR95014&log%24=nucltop&blast_rank=86&list_uids=149812 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=7&list_uids=174729 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=8&list_uids=43628 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=9&list_uids=43447 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=24&list_uids=48117 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=70&list_uids=1556462 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=71&list_uids=310605 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UJ8UYTD014&log%24=nucltop&blast_rank=86&list_uids=47143 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9UGVEB5H016&log%24=nucltop&blast_rank=26&list_uids=11363 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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=76556520&dopt=GenBank&RID=9SZGY6RY01S&log$=nuclalign&blast_rank=1 Natronomonas pharaonis DSM 2160 complete genome]
+     S = 134 bits (148)
+     E-value = 4e-29
+     Query coverage: 100%
+     Identities = 79/82 (96%)
+     Gaps = 0/82 (0%)
+     Strand=Plus/Minus
+'''644030992	1202285..1202358(+) 74bp: tRNA-Thr'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=51965749&dopt=GenBank&RID=9SZ7VBHN01S&log$=nuclalign&blast_rank=12 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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174724&dopt=GenBank&RID=9SZMPJHD014&log$=nuclalign&blast_rank=10 H.volcanii Leu-tRNA-2]
+     S = 132 bits (146)
+     E-value = 1e-28
+     Query Coverage: 100%
+     Identities = 80/85 (94%)
+     Gaps = 0/85
+     Strand=Plus/Plus
+'''644031036	1234256..1234340(-) 85bp: tRNA-Ser'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148769&dopt=GenBank&RID=9T01778Z014&log$=nuclalign&blast_rank=2 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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=91711097&dopt=GenBank&RID=9T090VYW01S&log$=nuclalign&blast_rank=7 Methanococcoides burtonii DSM 6242, complete genome]
+   Features flanking this part of subject sequence:
+bp at 5' side: Sep-tRNA:Cys-tRNA synthase
+bp at 3' side: 3-methyladenine DNA glycosylase-like protein
+     S = 69.8 bits (76)
+     E-value = 1e-09
+     Query coverage: 100%
+     Identities = 58/71 (81%)
+     Gaps = 0/71 (0%)
+     Strand=Plus/Plus
+'''644031077	1270321..1270395(-)75bp: tRNA-Glu'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174710&dopt=GenBank&RID=9T0K8FBA016&log$=nuclalign&blast_rank=10 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	'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=4324641&dopt=GenBank&RID=9T0SMT9N01S&log$=nuclalign&blast_rank=21 Methanococcus maripaludis tRNA-Lys gene, complete sequence]
+     S = 80.6 bits (88)
+     E-value = 6e-13
+     Query coverage: 100%
+     Identities = 62/74 (83%)
+     Gaps = 0/74 (0%)
+     Strand=Plus/Plus
+'''644031270	1452181..1452361(-) 181bp: tRNA-Trp'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148822&dopt=GenBank&RID=9T0XT9RV012&log$=nuclalign&blast_rank=3 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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174723&dopt=GenBank&RID=9T124K5001N&log$=nuclalign&blast_rank=6 H.volcanii Leu-tRNA-1]
+     S = 84.2 bits (92)
+     E-value = 7e-14
+     Query coverage: 100%
+     Identities = 70/85 (82%)
+     Gaps = 1/85 (1%)
+     Strand=Plus/Plus
+'''644031409	1587360..1587443(+) 84bp: tRNA-Leu'''
+ [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174725&dopt=GenBank&RID=9T1D0U5N01N&log$=nuclalign&blast_rank=4  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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174705&dopt=GenBank&RID=9T1KN1AJ012&log$=nuclalign&blast_rank=7 Halobacterium volcanii Ala-tRNA-1]
+     S = 95.1 bits (104)
+     E-value = 3e-17
+     Query coverage: 100%
+     Identities = 64/72 (88%)
+     Gaps = 0/72 (0%)
+     Strand=Plus/Plus
+'''644031556	1734070..1734154(+) 85bp: tRNA-Leu	'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174722&dopt=GenBank&RID=9T1U53DN01N&log$=nuclalign&blast_rank=3 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'''<br>
+Had to use just blastn for this because with megablast, there were no sequences with significant similarity
+  Hit with some potential significance:
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=242264390&dopt=GenBank&RID=9T22N2GW014&log$=nuclalign&blast_rank=24 Thermococcus sibiricus MM 739, complete genome]
+     Features flanking this part of subject sequence:
+bp at 5' side: Tyrosyl-tRNA synthetase
+bp at 3' side: Alanyl-tRNA synthetase-related protein
+     S = 39.2 bits (42)
+     E-value = 3.0
+     Query coverage: 38%
+     Identities = 33/38 (86%)
+     Gaps = 2/38 (5%)
+     Strand=Plus/Minus
+  Hit with the best alignment:
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=55229667&dopt=GenBank&RID=9T22N2GW014&log$=nuclalign&blast_rank=1 Haloarcula marismortui ATCC 43049 chromosome I, complete sequence]
+     Features flanking this part of subject sequence:
+bp at 5' side: unknown
+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	'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174711&dopt=GenBank&RID=9T2H30MU01N&log$=nuclalign&blast_rank=5 Halobacterium volcanii Glu-tRNA-2]
+     S = 109 bits (120)
+     E-value = 1e-21
+     Query coverage = 100%
+     Identities = 69/75 (92%)
+     Gaps = 0/75
+     Strand=Plus/Plus
+'''644031638	1819028..1819102(-) 75bp: tRNA-Arg'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174737&dopt=GenBank&RID=9T2NJSHV016&log$=nuclalign&blast_rank=8 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'''
+  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174744&dopt=GenBank&RID=9T2TXKVX016&log$=nuclalign&blast_rank=8 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:
       [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9RYTV7DV01N&log%24=nucltop&blast_rank=4&list_uids=43459     Halobacterium cutirubrum transfer RNA-Val (GAC)]
-       E-value: 2e-18
+      S = 99.0 bits (53)
+       E-value = 2e-18
        Query Coverage: 100%
-       Max Identity: 90%
+       Identities = 69/76 (90%)
+      Gaps = 3/76 (3%)
+      Strand=Plus/Plus
-'''tRNA 644031821: tRNA-Gly'''
+'''tRNA 644031821: ''1980512..1980582 (+) (71bp)'': tRNA-Gly'''
    Blastn results in the nr/nt database showed the following matches:
      [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9RZFNDE6014&log%24=nucltop&blast_rank=6&list_uids=174713 Halobacterium volcanii Gly-tRNA-1A]
       S = 69.8 bits (76)
-      E-value: 1e-09
+      E-value = 1e-09
       Query Coverage: 100%
       Identities = 58/71 (81%)
       Gaps = 0/71 (0%)
       Strand=Plus/Plus
-    [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9RZFNDE6014&log%24=nucltop&blast_rank=7&list_uids=43445 Halobacterium cutirubrum transfer RNA-Gly (GCC)]
+ [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9RZFNDE6014&log%24=nucltop&blast_rank=7&list_uids=43445 Halobacterium cutirubrum transfer RNA-Gly (GCC)]
       S = 69.8 bits (76)
-      E-value: 1e-09
+      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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S07YKWK01S&log%24=nucltop&blast_rank=4&list_uids=174745 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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S0G9A5001S&log%24=nucltop&blast_rank=3&list_uids=149021 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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S0Z0XUB016&log%24=nucltop&blast_rank=2&list_uids=174732 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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S1S4GV701N&log%24=nucltop&blast_rank=14&list_uids=75765432 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
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S1S4GV701N&log%24=nucltop&blast_rank=15&list_uids=75765431 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
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S1S4GV701N&log%24=nucltop&blast_rank=19&list_uids=174727 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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S2VTD1701N&log%24=nucltop&blast_rank=4&list_uids=174718 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:
+   [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9S2P89T0014&log%24=nucltop&blast_rank=8&list_uids=174731 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SEPUHG5012&log%24=nuclalign&blast_rank=9&list_uids=174743 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
+ [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SEPUHG5012&log%24=nuclalign&blast_rank=10&list_uids=43457 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SFYU7AW01N&log%24=nuclalign&blast_rank=3&list_uids=174733 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SG6VG5R01S&log%24=nuclalign&blast_rank=3&list_uids=174717 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
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SG6VG5R01S&log%24=nuclalign&blast_rank=6&list_uids=43446 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SGW1XPY01S&log%24=nuclalign&blast_rank=5&list_uids=43444 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SH5EFXR016&log%24=nuclalign&blast_rank=4&list_uids=174742 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SHBM29C01S&log%24=nuclalign&blast_rank=6&list_uids=174716 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:
+  [http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=nucleotide&dopt=GenBank&RID=9SNVPZ8A01N&log%24=nuclalign&blast_rank=2&list_uids=29837133 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