GtRNAdb

tRNAscan-SE Analysis of Silicibacter TM1040

>> Main Overview
>> tRNAs by Isotype
>> tRNAs by Locus
>> Secondary Structures
>> tRNA Alignments
>> FASTA Seqs
>> Run Options/Stats
>> Analysis Notes
>> Genome DB
>> Genome Seq
Structurally Aligned tRNAs (by Isotype & Anticodon)

Structural alignments are generated by aligning tRNA sequences against domain-specific tRNA covariance models with the use of COVE.


[Ala] [Arg] [Asn] [Asp] [Cys] [Gln] [Glu] [Gly] [His] [Ile] [Leu] [Lys] [Met] [Phe] [Pro] [Ser] [Thr] [Trp] [Tyr] [Val]
[Suppressor] [Selenocysteine]


Ala tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGCATGGCATGCAGGAG...........GtCAGCGGTTCGATCCCGCTAGGCTCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna12-AlaGGC Sc: 87.77 >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGATTTGCATTCAGGAG...........GtCAGGAGTTCGATCCTCCTAGGCTCCACCA Silicibacter_sp_TM1040_plasmid_unnamed.trna3-AlaTGC Sc: 89.52 GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGATTTGCATTCAGGAG...........GtCAGGAGTTCGATCCTCCTAGGCTCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna5-AlaTGC Sc: 89.52 GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGATTTGCATTCAGGAG...........GtCAGGAGTTCGATCCTCCTAGGCTCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna2-AlaTGC Sc: 89.52 GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGATTTGCATTCAGGAG...........GtCAGGAGTTCGATCCTCCTAGGCTCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna15-AlaTGC Sc: 89.52 GGGGCCTTAGCTCAGCTGGGAGAGCGCCTGATTTGCATTCAGGAG...........GtCAGGAGTTCGATCCTCCTAGGCTCCACCA Silicibacter_sp_TM1040.trna2-AlaTGC Sc: 89.52

Arg tRNAs

>>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGACCGATAGCTCAGCTGGAt.AGAGTACTTGACTACGAATCAAGGG...........GtCGGGGGTTCGAATCCTCCTCGGTCCGCCA Silicibacter_sp_TM1040_mega_plasmid.trna13-ArgACG Sc: 86.67 GGACCGATAGCTCAGCTGGAt.AGAGTACTTGACTACGAATCAAGGG...........GtCGGGGGTTCGAATCCTCCTCGGTCCGCCA Silicibacter_sp_TM1040.trna4-ArgACG Sc: 86.67 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCACCTGTAGCTCAGCTGGAt.AGAGCGCTGCCCTCCGAAGGCAGAG...........GcCAGAGGTTCGAATCCTCTCAGGTGCGCCA Silicibacter_sp_TM1040.trna35-ArgCCG Sc: 89.29 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGCCCCGTGGCTCAACTGGAt.AGAGCAGCCCCCTCCTAAGGGGCAG...........GtTGCAGGTTCGAATCCTGCCGGGGTCGCCA Silicibacter_sp_TM1040_mega_plasmid.trna17-ArgCCT Sc: 86.89 >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGTTAGCTCAGCTGGAttAGAGCAGGGAACTTCTAATTCTCAG...........GtCGGGGGTTCGAGTCCTCCACGGCTCGCCA Silicibacter_sp_TM1040.trna27-ArgTCT Sc: 79.91

Asn tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... TCCGGCGTAGCTCAGCGGTA.GAGCAGTTGACTGTTAATCAATTG...........GtCGTAGGTTCGATCCCTACCGCCGGAGCCA Silicibacter_sp_TM1040.trna37-AsnGTT Sc: 87.59 TCCGGCGTAGCTCAGCGGTA.GAGCAGTTGACTGTTAATCAATTG...........GtCGTAGGTTCGATCCCTACCGCCGGAGCCA Silicibacter_sp_TM1040.trna15-AsnGTT Sc: 87.59

Asp tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGTTGTAGCTCAGTTGGTtAGAGTACCGGCCTGTCACGCCGGGG...........GtCGCGGGTTCGAGCCCCGTCAACCGCGCCA Silicibacter_sp_TM1040.trna9-AspGTC Sc: 94.74 GCGGTTGTAGCTCAGTTGGTtAGAGTACCGGCCTGTCACGCCGGGG...........GtCGCGGGTTCGAGCCCCGTCAACCGCGCCA Silicibacter_sp_TM1040.trna8-AspGTC Sc: 94.74 GCGGTTGTAGCTCAGTTGGTtAGAGTACCGGCCTGTCACGCCGGGG...........GtCGCGGGTTCGAGCCCCGTCAACCGCGCCA Silicibacter_sp_TM1040.trna10-AspGTC Sc: 94.74

Cys tRNAs

>>>>>>>..>>>..........<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GGCGAGTTGGCGGAGTGGTG.ACGCAGCGGATTGCAAATCCGTGT...........ACACCGGTTCGATTCCGGTACTCGCCTCCA Silicibacter_sp_TM1040.trna31-CysGCA Sc: 76.36

Gln tRNAs

>>>>>>>..>>>..........<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... TGGGGTGTAGCCAAGCGGTA.AGGCAGCGGTTTTTGGTACCGTGT...........AcCGTAGGTTCGAATCCTACCACCCCAGCCA Silicibacter_sp_TM1040.trna5-GlnTTG Sc: 70.93

Glu tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<...............>>>>>.......<<<<<<<<<<<<.... GCTCCGTTCGTCTATCGGTtA.GGACGCCAGGTTTTCAACCTGGAA...........AGAGGGGTTCGATTCCCCTACGGAGTACCA Silicibacter_sp_TM1040.trna20-GluTTC Sc: 58.22 GCTCCGTTCGTCTATCGGTtA.GGACGCCAGGTTTTCAACCTGGAA...........AGAGGGGTTCGATTCCCCTACGGAGTACCA Silicibacter_sp_TM1040.trna19-GluTTC Sc: 58.22

Gly tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCGGGCGTAGCTCAGGGGTA.GAGCATAACCTTGCCAAGGTTAGG...........GtCGGGCGTTCGAATCGCCTCGCCCGCTCCA Silicibacter_sp_TM1040.trna18-GlyGCC Sc: 82.56 GCGGGCGTAGCTCAGGGGTA.GAGCATAACCTTGCCAAGGTTAGG...........GtCGGGCGTTCGAATCGCCTCGCCCGCTCCA Silicibacter_sp_TM1040.trna17-GlyGCC Sc: 82.56 GCGGGCGTAGCTCAGGGGTA.GAGCATAACCTTGCCAAGGTTAGG...........GtCGGGCGTTCGAATCGCCTCGCCCGCTCCA Silicibacter_sp_TM1040.trna16-GlyGCC Sc: 82.56 >>>>>>>..>>>>........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GCGGGTGTAGCTCAATGGTA.GAGCAGCAGCTTCCCAAGCTGACG...........A.CGAGGGTTCGATTCCCTTCACCCGCTCCA Silicibacter_sp_TM1040.trna13-GlyCCC Sc: 82.31 >>>>>>>..>>>>........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GCGGGTATGGTGAAATGGTA.TCATAAGAGCCTTCCAAGCTTAAG...........G.TGCGGGTTCGATTCCCGCTACCCGCTCCA Silicibacter_sp_TM1040.trna30-GlyTCC Sc: 66.99

His tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCGCCTTAGCTCAGTTGGTtAGAGCGCTTGATTGTGGATCAAGAG...........GtCCCTGGTTCGAGACCAGGAGGTGGTACCA Silicibacter_sp_TM1040.trna28-HisGTG Sc: 83.06

Ile tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTCGGTAGCTCAGGTGGTtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAGGTTCAAGTCCTCCTCGACCCACCA Silicibacter_sp_TM1040_plasmid_unnamed.trna2-IleGAT Sc: 94.31 GGGTCGGTAGCTCAGGTGGTtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAGGTTCAAGTCCTCCTCGACCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna4-IleGAT Sc: 94.31 GGGTCGGTAGCTCAGGTGGTtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAGGTTCAAGTCCTCCTCGACCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna14-IleGAT Sc: 94.31 GGGTCGGTAGCTCAGGTGGTtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAGGTTCAAGTCCTCCTCGACCCACCA Silicibacter_sp_TM1040_mega_plasmid.trna1-IleGAT Sc: 94.31 GGGTCGGTAGCTCAGGTGGTtAGAGCGCACGCCTGATAAGCGTGAG...........GtCGGAGGTTCAAGTCCTCCTCGACCCACCA Silicibacter_sp_TM1040.trna1-IleGAT Sc: 94.31

Leu tRNAs

>>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>...............<<<..>>>>>.......<<<<<.<<<<<<<.... GCGGTCGTGGCGGAATTGGTaG.ACGCGCAGCGTTGAGGTCGCTGTGGGG...TAACt.......CCCGTGGAAGTTCGAGTCTTCT.CGACCGCACCA Silicibacter_sp_TM1040_mega_plasmid.trna18-LeuGAG Sc: 70.14 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>.............<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCCAGATGGCGGAATTGGTaG.ACGCGCTAGCTTCAGGTGCTAGT.GTCC..GTAT.......GGACGTGGAGGTTCGAGTCCTCT.TCTGGGCACCA Silicibacter_sp_TM1040.trna25-LeuCAG Sc: 78.83 GCCCAGATGGCGGAATTGGTaG.ACGCGCTAGCTTCAGGTGCTAGT.GTCC..GTAT.......GGACGTGGAGGTTCGAGTCCTCT.TCTGGGCACCA Silicibacter_sp_TM1040.trna24-LeuCAG Sc: 78.83 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>...............<<<..>>>>>.......<<<<<.<<<<<<<.... GCGGGTGTGGCGGAATTGGTaG.ACGCACCAGATTTAGGTTCTGGC.GCC...GCAA........GGCGTGGGGGTTCAAGTCCCTT.CACCCGCACCA Silicibacter_sp_TM1040.trna34-LeuTAG Sc: 80.62 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>.>.........<.<<<<..>>>>>.......<<<<<.<<<<<<<.... GCCCAAGTGGCGGAAT.GGTaG.ACGCAGGGGATTCAAAATCCCCC.GCTGGT.........GACAGCGTGCCGGTTCGAGTCCGGC.CTTGGGTACCA Silicibacter_sp_TM1040.trna12-LeuCAA Sc: 71.99 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>...............<<<..>>>>>.......<<<<<.<<<<<<<.... GCGGGCGTGGTGGAAT.GGTaG.ACACAGGGGACTTAAAATCCCCA.GGC...TTTA........GCCGTGCGGGTTCGAGTCCCGC.CGCCCGTACCA Silicibacter_sp_TM1040.trna32-LeuTAA Sc: 76.32

Lys tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCCGTTAGCTCAGTTGGTAGAGCAACTGACTTTTAATCAGTGG...........GtCGCAGGTTCGAATCCTGCACGGCTCACCA Silicibacter_sp_TM1040.trna26-LysTTT Sc: 100.36

Met tRNAs

>>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGCGGAGTAGCTCAGTT.GGTtA.GAGCAGCGGAATCATAATCCGCGT...........GtCGGGGGTTCAAGTCCCTCCTCCGCTACCA Silicibacter_sp_TM1040.trna39-MetCAT Sc: 91.49 GGGAGATTAGCTCAGC..GGTtA.GAGCAGAGCGCTCATAACGCTTTG...........GtCCAGAGTTCGAATCTCTGATCTCCCACCA Silicibacter_sp_TM1040.trna14-MetCAT Sc: 86.92 .>>>>>>..>>>>...........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<..... CGCGGGATGGAGCAGCCaGGT.A.GCTCGTCAGGCTCATAACCTGAAG...........GtCGTAGGTTCAAATCCTACTCCCGCAACCA Silicibacter_sp_TM1040_plasmid_unnamed.trna4-MetCAT Sc: 80.92 CGCGGGATGGAGCAGCCaGGT.A.GCTCGTCAGGCTCATAACCTGAAG...........GtCGTAGGTTCAAATCCTACTCCCGCAACCA Silicibacter_sp_TM1040_mega_plasmid.trna6-MetCAT Sc: 80.92 CGCGGGATGGAGCAGCCaGGT.A.GCTCGTCAGGCTCATAACCTGAAG...........GtCGTAGGTTCAAATCCTACTCCCGCAACCA Silicibacter_sp_TM1040_mega_plasmid.trna3-MetCAT Sc: 80.92 CGCGGGATGGAGCAGCCaGGT.A.GCTCGTCAGGCTCATAACCTGAAG...........GtCGTAGGTTCAAATCCTACTCCCGCAACCA Silicibacter_sp_TM1040_mega_plasmid.trna16-MetCAT Sc: 80.92 CGCGGGATGGAGCAGCCaGGT.A.GCTCGTCAGGCTCATAACCTGAAG...........GtCGTAGGTTCAAATCCTACTCCCGCAACCA Silicibacter_sp_TM1040.trna3-MetCAT Sc: 80.92

Phe tRNAs

>>>>>>>..>>>>........<<<<.>.>>>.......<<<.<................>>>>>.......<<<<<<<<<<<<.... GCCCGGGTAGCTCAGGGGTA.GAGCAGTGGATTGAAAATCCTCGT...........GtCGGTGGTTCGATTCCGCCCCCGGGCACCA Silicibacter_sp_TM1040_mega_plasmid.trna11-PheGAA Sc: 80.69

Pro tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGCTATGGCGCAGCCtGGTAGCGCGTCCGTCTGGGGGACGGAAG...........GtCGCAGGTTCGAGTCCTGCTAGCCCGACCA Silicibacter_sp_TM1040.trna38-ProGGG Sc: 83.39 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGAGCGTAGCTCAGCCtGGTAGAGCACTGTCTTCGGGAGGCAGGG...........GcCGGAGGTTCGAATCCTCTCGCTCCGACCA Silicibacter_sp_TM1040_mega_plasmid.trna7-ProCGG Sc: 78.27 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... CGGGGCGTGGCGCAGTCtGGTAGCGCACCTGTTTTGGGTACAGGGG...........GtCGTGAGTTCGAATCTCGCCGCCCCGACCA Silicibacter_sp_TM1040.trna11-ProTGG Sc: 85.12

SeC tRNAs

Ser tRNAs

>>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGGCCGAGTGGTcgA.AGGCGCACGCCTGGAAAGTGTGTAGGCGG.GAAA..CCGTCTCCAGGGTTCGAATCCCTG..TCTCTCCGCCA Silicibacter_sp_TM1040.trna33-SerGGA Sc: 69.16 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGAGGTGCCGGAGTGGTcgA.ACGGGGCGGTCTCGAAAACCGTTGTGCCT.TCAC..GGGCACCCAGGGTTCGAATCCCTG..TCTCTCCGCCA Silicibacter_sp_TM1040.trna36-SerCGA Sc: 64.26 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>>.....<<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGGGAGGTGGCAGAGTGGTcgA.ATGCGGCGGTCTTGAAAACCGTT.GAACGTGAGA.GCGTTC.CCAGGGTTCGAATCCCTG..TCTCCCCGCCA Silicibacter_sp_TM1040_mega_plasmid.trna9-SerTGA Sc: 64.45 >>>>>>>..>>>............<<<.>>>>>.......<<<<<..>>>>>.......<<<<<..>>>>>.......<<<<<..<<<<<<<.... GGAGACGTGGCCGAGTGGTcgA.AGGCGCTCCCCTGCTAAGGGAGTAGGCGG.GAAA..CCGTCTCGAGGGTTCGAATCCCTT..CGTCTCCGCCA Silicibacter_sp_TM1040.trna22-SerGCT Sc: 78.28

Sup tRNAs

Thr tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCTGCTGTAGCTCAGA.GGTA.GAGCACTCCCTTGGTAAGGGAGAG...........GtCGAGAGTTCAATTCTCTCCAGCAGCACCA Silicibacter_sp_TM1040_mega_plasmid.trna10-ThrGGT Sc: 88.81 >>>>>>>..>>>>.........<<<<..>>>>.......<<<<.................>>>>>.......<<<<<<<<<<<<.... GCCTCAATAGCTCAGCTGGTA.GAGCAGGTCCTTCGTAAGGACAAG...........GtCGGGGGTTCGAGTCCCTCTTGAGGCACCA Silicibacter_sp_TM1040.trna23-ThrCGT Sc: 90.45 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GCCCCTATAGCTCAGCTGGTA.GAGCAACTGATTTGTAATCAGTAG...........GtCCGCGGTTCGAGTCCGTGTGGGGGCACCA Silicibacter_sp_TM1040_plasmid_unnamed.trna1-ThrTGT Sc: 95.59 GCCCCTATAGCTCAGCTGGTA.GAGCAACTGATTTGTAATCAGTAG...........GtCCGCGGTTCGAGTCCGTGTGGGGGCACCA Silicibacter_sp_TM1040_mega_plasmid.trna8-ThrTGT Sc: 95.59

Trp tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... AGGGGTATAGCTCAGTTGGTAGAGCGACGGTCTCCAAAACCGTAG...........GtCGCGGGTTCGAACCCTGCTGCCCCTGCCA Silicibacter_sp_TM1040.trna21-TrpCCA Sc: 88.85

Tyr tRNAs

>>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.>>>........<<<...>>>>>.......<<<<<.<<<<<<<.... GGGCGACAGGCCGCAAGGTG.TGGCAGGGGACTGTAACTCCCTCGCGGAGA....CGCAcGCCTGGTTCGATTCCAGG.GTCGCCCACCA Silicibacter_sp_TM1040.trna29-TyrGTA Sc: 32.27

Val tRNAs

>>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGCGGTTAGCTCAGC.GGTA.GAGCACTTCGTTGACATCGAAGGG...........GtCACAAGTTCGATCCTTGTACCGCCCACCA Silicibacter_sp_TM1040.trna40-ValGAC Sc: 87.93 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTGATTAGCTCAGT.GGTA.GAGCGCTTCGTTCACATCGAAGAT...........GtCAGGAGTTCAAATCTCTTATCACCCACCA Silicibacter_sp_TM1040.trna6-ValCAC Sc: 85.22 >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<................>>>>>.......<<<<<<<<<<<<.... GGGTCGTTAGCTCAGTTGGTA.GAGCGCTTCGTTTACACCGAAGAT...........GtCGGGAGTTCGAGCCTCTCACGACCCACCA Silicibacter_sp_TM1040.trna7-ValTAC Sc: 89.32

The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.