Difference between revisions of "TRNA Genes Check List 2009"
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'''644030986 1198182..1198263(+) 82bp: tRNA-Ser''' | '''644030986 1198182..1198263(+) 82bp: tRNA-Ser''' | ||
− | Natronomonas pharaonis DSM 2160 complete genome | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=76556520&dopt=GenBank&RID=9SZGY6RY01S&log$=nuclalign&blast_rank=1 Natronomonas pharaonis DSM 2160 complete genome] |
S = 134 bits (148) | S = 134 bits (148) | ||
E-value = 4e-29 | E-value = 4e-29 | ||
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'''644030992 1202285..1202358(+) 74bp: tRNA-Thr''' | '''644030992 1202285..1202358(+) 74bp: tRNA-Thr''' | ||
− | Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU) | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=51965749&dopt=GenBank&RID=9SZ7VBHN01S&log$=nuclalign&blast_rank=12 Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU)] |
S = 42.8 bits (46) | S = 42.8 bits (46) | ||
E-value = 0.16 | E-value = 0.16 | ||
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'''644031031 1231822..1231906(-) 85bp: tRNA-Leu''' | '''644031031 1231822..1231906(-) 85bp: tRNA-Leu''' | ||
− | H.volcanii Leu-tRNA-2 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174724&dopt=GenBank&RID=9SZMPJHD014&log$=nuclalign&blast_rank=10 H.volcanii Leu-tRNA-2] |
S = 132 bits (146) | S = 132 bits (146) | ||
E-value = 1e-28 | E-value = 1e-28 | ||
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'''644031036 1234256..1234340(-) 85bp: tRNA-Ser''' | '''644031036 1234256..1234340(-) 85bp: tRNA-Ser''' | ||
− | Halobacterium marismortui ribosomal proteins (HmaS13, HmaS4, | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148769&dopt=GenBank&RID=9T01778Z014&log$=nuclalign&blast_rank=2 Halobacterium marismortui ribosomal proteins] (HmaS13, HmaS4, |
HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA | HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA | ||
S = 154 bits (170) | S = 154 bits (170) | ||
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'''644031060 1255468..1255538(-) 71bp: tRNA-Gly''' | '''644031060 1255468..1255538(-) 71bp: tRNA-Gly''' | ||
− | Methanococcoides burtonii DSM 6242, complete genome | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=91711097&dopt=GenBank&RID=9T090VYW01S&log$=nuclalign&blast_rank=7 Methanococcoides burtonii DSM 6242, complete genome] |
Features flanking this part of subject sequence: | Features flanking this part of subject sequence: | ||
120 bp at 5' side: Sep-tRNA:Cys-tRNA synthase | 120 bp at 5' side: Sep-tRNA:Cys-tRNA synthase | ||
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'''644031077 1270321..1270395(-)75bp: tRNA-Glu''' | '''644031077 1270321..1270395(-)75bp: tRNA-Glu''' | ||
− | Halobacterium volcanii Glu-tRNA-1 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174710&dopt=GenBank&RID=9T0K8FBA016&log$=nuclalign&blast_rank=10 Halobacterium volcanii Glu-tRNA-1] |
S = 104 bits (114) | S = 104 bits (114) | ||
E-value = 6e-20 | E-value = 6e-20 | ||
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'''644031243 1431550..1431623(+) 74bp: tRNA-Lys ''' | '''644031243 1431550..1431623(+) 74bp: tRNA-Lys ''' | ||
− | Methanococcus maripaludis tRNA-Lys gene, complete sequence | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=4324641&dopt=GenBank&RID=9T0SMT9N01S&log$=nuclalign&blast_rank=21 Methanococcus maripaludis tRNA-Lys gene, complete sequence] |
S = 80.6 bits (88) | S = 80.6 bits (88) | ||
E-value = 6e-13 | E-value = 6e-13 | ||
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'''644031270 1452181..1452361(-) 181bp: tRNA-Trp''' | '''644031270 1452181..1452361(-) 181bp: tRNA-Trp''' | ||
− | Halobacterium volcanii Trp-tRNA gene | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148822&dopt=GenBank&RID=9T0XT9RV012&log$=nuclalign&blast_rank=3 Halobacterium volcanii Trp-tRNA gene] |
S = 205 bits (226) | S = 205 bits (226) | ||
E-value = 8e-50 | E-value = 8e-50 | ||
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'''644031388 1563815..1563898(-) 84bp: tRNA-Leu''' | '''644031388 1563815..1563898(-) 84bp: tRNA-Leu''' | ||
− | H.volcanii Leu-tRNA-1 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174723&dopt=GenBank&RID=9T124K5001N&log$=nuclalign&blast_rank=6 H.volcanii Leu-tRNA-1] |
S = 84.2 bits (92) | S = 84.2 bits (92) | ||
E-value = 7e-14 | E-value = 7e-14 | ||
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'''644031409 1587360..1587443(+) 84bp: tRNA-Leu''' | '''644031409 1587360..1587443(+) 84bp: tRNA-Leu''' | ||
− | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174725&dopt=GenBank&RID=9T1D0U5N01N&log$=nuclalign&blast_rank=4 H.volcanii Leu-tRNA-3] | |
S = 113 bits (124) | S = 113 bits (124) | ||
E-value = 1e-22 | E-value = 1e-22 | ||
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'''644031498 1678478..1678549(-) 72bp: tRNA-Ala''' | '''644031498 1678478..1678549(-) 72bp: tRNA-Ala''' | ||
− | Halobacterium volcanii Ala-tRNA-1 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174705&dopt=GenBank&RID=9T1KN1AJ012&log$=nuclalign&blast_rank=7 Halobacterium volcanii Ala-tRNA-1] |
S = 95.1 bits (104) | S = 95.1 bits (104) | ||
E-value = 3e-17 | E-value = 3e-17 | ||
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'''644031556 1734070..1734154(+) 85bp: tRNA-Leu ''' | '''644031556 1734070..1734154(+) 85bp: tRNA-Leu ''' | ||
− | Halobacterium volcanii Leu-tRNA | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174722&dopt=GenBank&RID=9T1U53DN01N&log$=nuclalign&blast_rank=3 Halobacterium volcanii Leu-tRNA] |
S = 95.1 bits (104) | S = 95.1 bits (104) | ||
E-value = 4e-17 | E-value = 4e-17 | ||
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Strand=Plus/Minus | Strand=Plus/Minus | ||
− | '''644031557 1734881..1734978(-) 98bp: tRNA-Trp''' | + | '''644031557 1734881..1734978(-) 98bp: tRNA-Trp'''<br> |
Had to use just blastn for this because with megablast, there were no sequences with significant similarity | Had to use just blastn for this because with megablast, there were no sequences with significant similarity | ||
Hit with some potential significance: | Hit with some potential significance: | ||
− | Thermococcus sibiricus MM 739, complete genome | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=242264390&dopt=GenBank&RID=9T22N2GW014&log$=nuclalign&blast_rank=24 Thermococcus sibiricus MM 739, complete genome] |
Features flanking this part of subject sequence: | Features flanking this part of subject sequence: | ||
44 bp at 5' side: Tyrosyl-tRNA synthetase | 44 bp at 5' side: Tyrosyl-tRNA synthetase | ||
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Hit with the best alignment: | Hit with the best alignment: | ||
− | Haloarcula marismortui ATCC 43049 chromosome I, complete sequence | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=55229667&dopt=GenBank&RID=9T22N2GW014&log$=nuclalign&blast_rank=1 Haloarcula marismortui ATCC 43049 chromosome I, complete sequence] |
Features flanking this part of subject sequence: | Features flanking this part of subject sequence: | ||
263 bp at 5' side: unknown | 263 bp at 5' side: unknown | ||
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'''644031574 1750267..1750341(+) 75bp: tRNA-Glu ''' | '''644031574 1750267..1750341(+) 75bp: tRNA-Glu ''' | ||
− | Halobacterium volcanii Glu-tRNA-2 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174711&dopt=GenBank&RID=9T2H30MU01N&log$=nuclalign&blast_rank=5 Halobacterium volcanii Glu-tRNA-2] |
S = 109 bits (120) | S = 109 bits (120) | ||
E-value = 1e-21 | E-value = 1e-21 | ||
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'''644031638 1819028..1819102(-) 75bp: tRNA-Arg''' | '''644031638 1819028..1819102(-) 75bp: tRNA-Arg''' | ||
− | Halobacterium volcanii Arg-tRNA-3 | + | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174737&dopt=GenBank&RID=9T2NJSHV016&log$=nuclalign&blast_rank=8 Halobacterium volcanii Arg-tRNA-3] |
S = 80.6 (88) | S = 80.6 (88) | ||
E-value = 7e-13 | E-value = 7e-13 | ||
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'''644031690 1860756..1860829(-) 74bp: tRNA-Thr''' | '''644031690 1860756..1860829(-) 74bp: tRNA-Thr''' | ||
− | Halobacterium volcanii Thr-tRNA-2 | + | [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) | S = 104 bits (114) | ||
E-value = 6e-20 | E-value = 6e-20 | ||
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Gaps = 1/74 (1%) | Gaps = 1/74 (1%) | ||
Strand=Plus/Plus | Strand=Plus/Plus | ||
− | + | <br><br> | |
---- | ---- | ||
+ | <br> | ||
'''tRNA 644031717: ''1888010..1888083 (-) (74bp)'': tRNA-Val''' | '''tRNA 644031717: ''1888010..1888083 (-) (74bp)'': tRNA-Val''' |
Revision as of 03:35, 1 September 2009
BLAST – blasting the sequences under the nucleotide (nr/nt) database with megablast discontinuous in order to check for similar sequences in other organisms
644030986 1198182..1198263(+) 82bp: tRNA-Ser
Natronomonas pharaonis DSM 2160 complete genome S = 134 bits (148) E-value = 4e-29 Query coverage: 100% Identities = 79/82 (96%) Gaps = 0/82 (0%) Strand=Plus/Minus
644030992 1202285..1202358(+) 74bp: tRNA-Thr
Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU) S = 42.8 bits (46) E-value = 0.16 Query coverage: 68% Identities = 34/41 (82%) Gaps = 0/41 Strand=Plus/Plus
644031031 1231822..1231906(-) 85bp: tRNA-Leu
H.volcanii Leu-tRNA-2 S = 132 bits (146) E-value = 1e-28 Query Coverage: 100% Identities = 80/85 (94%) Gaps = 0/85 Strand=Plus/Plus
644031036 1234256..1234340(-) 85bp: tRNA-Ser
Halobacterium marismortui ribosomal proteins (HmaS13, HmaS4, HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA S = 154 bits (170) E-value = 4e-35 Query Coverage: 100% Identities = 85/85 Gaps = 0/85 (0%) Strand=Plus/Plus
644031060 1255468..1255538(-) 71bp: tRNA-Gly
Methanococcoides burtonii DSM 6242, complete genome Features flanking this part of subject sequence: 120 bp at 5' side: Sep-tRNA:Cys-tRNA synthase 16 bp at 3' side: 3-methyladenine DNA glycosylase-like protein S = 69.8 bits (76) E-value = 1e-09 Query coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus
644031077 1270321..1270395(-)75bp: tRNA-Glu
Halobacterium volcanii Glu-tRNA-1 S = 104 bits (114) E-value = 6e-20 Query coverage: 100% Identities = 68/75 (90%) Gaps = 0/75 (0%) Strand=Plus/Plus
644031243 1431550..1431623(+) 74bp: tRNA-Lys
Methanococcus maripaludis tRNA-Lys gene, complete sequence S = 80.6 bits (88) E-value = 6e-13 Query coverage: 100% Identities = 62/74 (83%) Gaps = 0/74 (0%) Strand=Plus/Plus
644031270 1452181..1452361(-) 181bp: tRNA-Trp
Halobacterium volcanii Trp-tRNA gene S = 205 bits (226) E-value = 8e-50 Query coverage: 100% Identities = 158/183 (86%) Gaps = 6/183 (3%) Strand=Plus/Plus
644031388 1563815..1563898(-) 84bp: tRNA-Leu
H.volcanii Leu-tRNA-1 S = 84.2 bits (92) E-value = 7e-14 Query coverage: 100% Identities = 70/85 (82%) Gaps = 1/85 (1%) Strand=Plus/Plus
644031409 1587360..1587443(+) 84bp: tRNA-Leu
H.volcanii Leu-tRNA-3 S = 113 bits (124) E-value = 1e-22 Query coverage: 100% Identities = 75/84 (89%) Gaps = 0/84 (0%) Strand=Plus/Plus
644031498 1678478..1678549(-) 72bp: tRNA-Ala
Halobacterium volcanii Ala-tRNA-1 S = 95.1 bits (104) E-value = 3e-17 Query coverage: 100% Identities = 64/72 (88%) Gaps = 0/72 (0%) Strand=Plus/Plus
644031556 1734070..1734154(+) 85bp: tRNA-Leu
Halobacterium volcanii Leu-tRNA S = 95.1 bits (104) E-value = 4e-17 Query coverage: 100% Identities = 63/70 (90%) Gaps = 0/70 (0%) Strand=Plus/Minus
644031557 1734881..1734978(-) 98bp: tRNA-Trp
Had to use just blastn for this because with megablast, there were no sequences with significant similarity
Hit with some potential significance: Thermococcus sibiricus MM 739, complete genome Features flanking this part of subject sequence: 44 bp at 5' side: Tyrosyl-tRNA synthetase 104 bp at 3' side: Alanyl-tRNA synthetase-related protein S = 39.2 bits (42) E-value = 3.0 Query coverage: 38% Identities = 33/38 (86%) Gaps = 2/38 (5%) Strand=Plus/Minus Hit with the best alignment: Haloarcula marismortui ATCC 43049 chromosome I, complete sequence Features flanking this part of subject sequence: 263 bp at 5' side: unknown 377 bp at 3' side: unknown S = 84.2 bits (92) E-value = 8e-14 Query coverage: 100% Identities = 82/102 (80%) Gaps = 4/102 (3%) Strand=Plus/Plus
644031574 1750267..1750341(+) 75bp: tRNA-Glu
Halobacterium volcanii Glu-tRNA-2 S = 109 bits (120) E-value = 1e-21 Query coverage = 100% Identities = 69/75 (92%) Gaps = 0/75 Strand=Plus/Plus
644031638 1819028..1819102(-) 75bp: tRNA-Arg
Halobacterium volcanii Arg-tRNA-3 S = 80.6 (88) E-value = 7e-13 Query coverage: 100% Identities = 61/72 (84%) Gaps = 0/72 (0%) Strand=Plus/Plus
644031690 1860756..1860829(-) 74bp: tRNA-Thr
Halobacterium volcanii Thr-tRNA-2 S = 104 bits (114) E-value = 6e-20 Query coverage: 100% Identities = 68/74 (91%) Gaps = 1/74 (1%) Strand=Plus/Plus
tRNA 644031717: 1888010..1888083 (-) (74bp): tRNA-Val
Megablast results in the nr/nt database showed a match with the following statistics: Halobacterium cutirubrum transfer RNA-Val (GAC) S = 99.0 bits (53) E-value = 2e-18 Query Coverage: 100% Identities = 69/76 (90%) Gaps = 3/76 (3%) Strand=Plus/Plus
tRNA 644031821: 1980512..1980582 (+) (71bp): tRNA-Gly
Blastn results in the nr/nt database showed the following matches: Halobacterium volcanii Gly-tRNA-1A S = 69.8 bits (76) E-value = 1e-09 Query Coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus Halobacterium cutirubrum transfer RNA-Gly (GCC) S = 69.8 bits (76) E-value = 1e-09 Query Coverage: 100% Identities = 58/71 (81%) Gaps = 0/71 (0%) Strand=Plus/Plus
tRNA 644031874: 2032528..2032601 (-) (74bp): tRNA-Val
Megablast results using the nr/nt database gave the following match: Halobacterium volcanii Val-tRNA-1 S = 115 bits (62) E-value = 2e-23 Query Coverage: 100% Identities = 71/75 (94%) Gaps = 1/75 (1%) Strand=Plus/Plus
tRNA 644031888: 2048515..2048657 (+) (143bp): tRNA-Met
Megablast results using the nr/nt database showed the following match: Haloferax volcanii (Halobacterium volcanii) elongator methionine-accepting transfer RNA-Met gene S = 78.7 bits (42) E-value = 7e-12 Query Coverage: 29% Identities = 42/42 (100%) Gaps = 0/42 (0%) Strand=Plus/Plus
tRNA 644031915: 2079098..2079168 (+) (71bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-2 S = 121 bits (65) E-value = 4e-25 Query Coverage: 100% Identities = 69/71 (97%) Gaps = 0/71 (0%) Strand=Plus/Plus
tRNA 644032052: 2201308..2201392 (-) (85bp) : tRNA-Leu
Blastn results in the nr/nt database showed the following matches: Chain D, The Crystal Structure Of Leucyl-Trna Synthetase And Trna(Leucine) Complex S = 89.7 bits (98) E-value = 2e-15 Query Coverage: 98% Identities = 70/84 (83%) Gaps = 0/84 (0%) Strand=Plus/Plus Chain C, The Crystal Structure Of Leucyl-Trna Synthetase And Trna(Leucine) Complex S = 89.7 bits (98) E-value = 2e-15 Query Coverage: 98% Identities = 70/84 (83%) Gaps = 0/84 (0%) Strand=Plus/Plus H.volcanii Leu-tRNA-5 S = 87.8 bits (96) E-value = 5e-15 Query Coverage: 100% Identities = 70/85 (82%) Gaps = 0/85 (0%) Strand=Plus/Plus
tRNA 644032072: 2221071..2221144 (+) (74bp): tRNA-Ile
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Ile-tRNA-1 S = 99.0 bits (53) E-value= 2e-18 Query Coverage: 100% Identities = 67/74 (90%) Gaps = 0/74 (0%) Strand=Plus/Plus
tRNA 644032209: 2353219..2353291 (+)(73bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-1 S = 97.1 bits (52) E-value = 7e-18 Query Coverage: 100% Identities = 68/75 (90%) Gaps = 4/75 (5%) Strand=Plus/Plus
tRNA 644032498: 2622662..2622733 (+)(72bp): tRNA-Thr
Megablast results using the nr/nt database showed the following matches: Halobacterium volcanii Thr-tRNA-1 S = 111 bits (60) E-value = 3e-22 Query Coverage = 100% Identities = 68/72 (94%) Gaps = 0/72 (0%) Strand = Plus/Plus Halobacterium cutirubrum transfer RNA-Thr (GGU) S = 106 bits (57) E-value = 1e-20 Query Coverage = 100% Identities = 67/72 (93%) Gaps = 0/72 (0%) Strand = Plus/Plus
tRNA 644032619: 2736702..2736774 (-)(73bp): tRNA-Pro
Megablast results using the nr/nt database showed the following match: Halobacterium volcanii Pro-tRNA-3 S = 113 bits (61) E-value = 7e-23 Query Coverage = 100% Identities = 69/73 (94%) Gaps = 0/73 (0%) Strand = Plus/Plus
tRNA 644032625: 2743979..2744049 (-)(71bp): tRNA-His
Blastn results using the nr/nt database showed the following matches: Halobacterium volcanii His-tRNA S = 93.3 bits (102) E-value = 9e-17 Query Coverage = 100% Identities = 65/73 (89%) Gaps = 2/73 (2%) Strand = Plus/Plus Halobacterium cutirubrum transfer RNA-His (GUG) S = 77.0 bits (84) E-value = 7e-12 Query Coverage = 100% Identities = 61/73 (83%) Gaps = 2/73 (2%) Strand = Plus/Plus
tRNA 644032706: 2814103..2814206 (-)(104bp): tRNA-Arg
Blastn results show no promising matches
tRNA 644032751: 2856285..2856357 (+)(73bp): tRNA-Gln
Megablast results using the nr/nt database showed the following match: Halobacterium cutirubrum transfer RNA-Gln (CUG) S = 75.0 bits (40) E-value = 3e-11 Query Coverage = 71% Identities = 48/52 (92%) Gaps = 0/52 (0%) Strand = Plus/Plus
tRNA 644032818: 2918247..2918328 (-)(82bp): tRNA-Ser
Megablast results using the nr/nt database showed the following match: H.volcanii Ser-tRNA-3 S = 108 bits (58) E-value = 4e-21 Query Coverage = 100% Identities = 75/83 (90%) Gaps = 3/83 (3%) Strand = Plus/Plus
tRNA 644032961: 3065293..3065363 (+)(71bp): tRNA-Gly
Blastn results using the nr/nt database showed the following match: Halobacterium volcanii Gly-tRNA-3 S = 93.3 bits (102) E-value = 9e-17 Query Coverage = 100% Identities = 63/71 (88%) Gaps = 0/71 (0%) Strand = Plus/Plus
tRNA 644032998: 3109008..3109079 (+)(72bp): tRNA-Ala
Megablast results using the nr/nt database showed the following match: Halosimplex carlsbadense rrnC operon genes for 16S rRNA, tRNA-Ala, 23S rRNA, complete and partial sequence S = 111 bits (60) E-value = 3e-22 Query Coverage = 100% Identities = 68/72 (94%) Gaps = 0/72 (0%) Strand = Plus/Plus