Difference between revisions of "TRNA Genes Check List 2009"

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

@@ Line 2: / Line 2: @@
 '''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$=nuclalign&blast_rank=1 Natronomonas pharaonis DSM 2160 complete genome]
       S = 134 bits (148)
       E-value = 4e-29
@@ Line 11: / Line 11: @@
 '''644030992	1202285..1202358(+) 74bp: tRNA-Thr'''
-   Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU)
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=51965749&dopt=GenBank&RID=9SZ7VBHN01S&log$=nuclalign&blast_rank=12 Guillardia theta nucleomorph chromosome 1 tRNA-Arg (UCU)]
       S = 42.8 bits (46)
       E-value = 0.16
@@ Line 20: / Line 20: @@
 '''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$=nuclalign&blast_rank=10 H.volcanii Leu-tRNA-2]
       S = 132 bits (146)
       E-value = 1e-28
@@ Line 29: / Line 29: @@
 '''644031036	1234256..1234340(-) 85bp: tRNA-Ser'''
-   Halobacterium marismortui ribosomal proteins (HmaS13, HmaS4,
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148769&dopt=GenBank&RID=9T01778Z014&log$=nuclalign&blast_rank=2 Halobacterium marismortui ribosomal proteins] (HmaS13, HmaS4,
    HmaS11, HL29, HmaRp-alpha) genes, complete cds, Ser-tRNA, Leu-tRNA
       S = 154 bits (170)
@@ Line 39: / Line 39: @@
 '''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$=nuclalign&blast_rank=7 Methanococcoides burtonii DSM 6242, complete genome]
     Features flanking this part of subject sequence:
 bp at 5' side: Sep-tRNA:Cys-tRNA synthase
@@ Line 51: / Line 51: @@
 '''644031077	1270321..1270395(-)75bp: tRNA-Glu'''
-   Halobacterium volcanii Glu-tRNA-1
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174710&dopt=GenBank&RID=9T0K8FBA016&log$=nuclalign&blast_rank=10 Halobacterium volcanii Glu-tRNA-1]
       S = 104 bits (114)
       E-value = 6e-20
@@ Line 60: / Line 60: @@
 '''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$=nuclalign&blast_rank=21 Methanococcus maripaludis tRNA-Lys gene, complete sequence]
       S = 80.6 bits (88)
       E-value = 6e-13
@@ Line 69: / Line 69: @@
 '''644031270	1452181..1452361(-) 181bp: tRNA-Trp'''
-   Halobacterium volcanii Trp-tRNA gene
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=148822&dopt=GenBank&RID=9T0XT9RV012&log$=nuclalign&blast_rank=3 Halobacterium volcanii Trp-tRNA gene]
       S = 205 bits (226)
       E-value = 8e-50
@@ Line 78: / Line 78: @@
 '''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$=nuclalign&blast_rank=6 H.volcanii Leu-tRNA-1]
       S = 84.2 bits (92)
       E-value = 7e-14
@@ Line 87: / Line 87: @@
 '''644031409	1587360..1587443(+) 84bp: tRNA-Leu'''
-  H.volcanii Leu-tRNA-3
+ [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174725&dopt=GenBank&RID=9T1D0U5N01N&log$=nuclalign&blast_rank=4  H.volcanii Leu-tRNA-3]
       S = 113 bits (124)
       E-value = 1e-22
@@ Line 96: / Line 96: @@
 '''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$=nuclalign&blast_rank=7 Halobacterium volcanii Ala-tRNA-1]
       S = 95.1 bits (104)
       E-value = 3e-17
@@ Line 105: / Line 105: @@
 '''644031556	1734070..1734154(+) 85bp: tRNA-Leu	'''
-   Halobacterium volcanii Leu-tRNA
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174722&dopt=GenBank&RID=9T1U53DN01N&log$=nuclalign&blast_rank=3 Halobacterium volcanii Leu-tRNA]
       S = 95.1 bits (104)
       E-value = 4e-17
@@ Line 113: / Line 113: @@
       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
    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$=nuclalign&blast_rank=24 Thermococcus sibiricus MM 739, complete genome]
       Features flanking this part of subject sequence:
 bp at 5' side: Tyrosyl-tRNA synthetase
@@ Line 128: / Line 128: @@
    Hit with the best alignment:
-   Haloarcula marismortui ATCC 43049 chromosome I, complete sequence
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=55229667&dopt=GenBank&RID=9T22N2GW014&log$=nuclalign&blast_rank=1 Haloarcula marismortui ATCC 43049 chromosome I, complete sequence]
       Features flanking this part of subject sequence:
 bp at 5' side: unknown
@@ Line 140: / Line 140: @@
 '''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$=nuclalign&blast_rank=5 Halobacterium volcanii Glu-tRNA-2]
       S = 109 bits (120)
       E-value = 1e-21
@@ Line 149: / Line 149: @@
 '''644031638	1819028..1819102(-) 75bp: tRNA-Arg'''
-   Halobacterium volcanii Arg-tRNA-3
+   [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=Nucleotide&list_uids=174737&dopt=GenBank&RID=9T2NJSHV016&log$=nuclalign&blast_rank=8 Halobacterium volcanii Arg-tRNA-3]
       S = 80.6 (88)
       E-value = 7e-13
@@ Line 158: / Line 158: @@
 '''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)
        E-value = 6e-20
@@ Line 165: / Line 165: @@
        Gaps = 1/74 (1%)
        Strand=Plus/Plus
+<br><br>
 ----
+<br>
 '''tRNA 644031717: ''1888010..1888083 (-) (74bp)'': tRNA-Val'''

Difference between revisions of "TRNA Genes Check List 2009"

Revision as of 03:35, 1 September 2009

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