PANDIT+

KeywordFamilyClanGene   

Entry: tRNA-synt_2 (PF00152)

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search can be done either by clan ID
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Pfam summary

Description

tRNA synthetases class II (D, K and N)

 
Literature
 
Clan

CL0040 (tRNA_synt_II)

The clan contains the following members: PF03099(BPL_LipA_LipB); PF01409(tRNA-synt_2d); PF03590(AsnA); PF04424(DUF544); PF00152(tRNA-synt_2); PF00587(tRNA-synt_2b); PF01411(tRNA-synt_2c); PF02091(tRNA-synt_2e);
 
InterPro entry IPR004364
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 109 aligned sequences:

  O74858_SCHPO/182-530   O81892_ARATH/198-611   O94242_SCHPO/138-579   Q6AHD6_LEIXX/101-419   Q6AQS4_DESPS/140-579   Q6BRH4_DEBHA/177-668   Q6BZ12_DEBHA/190-549   Q6C700_YARLI/128-469   Q6C814_YARLI/195-554   Q6CLY6_KLULA/143-620   Q6CX40_KLULA/145-470   Q6F1A0_MESFL/115-551   Q6F944_ACIAD/4-329   Q6KI16_MYCMO/110-541   Q6ME91_PARUW/129-567   Q6MI59_BDEBA/162-604   Q6MPY6_BDEBA/81-404   Q6NEX1_CORDI/708-1045   Q725Q7_DESVH/142-576   Q73HX6_WOLPM/133-574   Q73MC2_TREDE/124-564   Q74D56_GEOSL/128-566   Q74IX4_LACJO/123-562   Q74MV5_NANEQ/94-400   Q7NBK8_MYCGA/32-363   Q7NBS8_MYCGA/119-554   Q7P704_FUSNV/123-564   Q7Q3E7_ANOGA/123-568   Q7SFD2_NEUCR/259-590   Q7UH30_RHOBA/67-394   Q7UK37_RHOBA/210-545   Q8BGV0_MOUSE/135-473   Q8D388_WIGBR/116-550   Q8EX85_LEPIN/1-330   Q8PAB4_XANCP/1-324   Q8SQK8_ENCCU/175-498   Q8ZUX9_PYRAE/23-343   Q8ZWD4_PYRAE/145-481   Q8ZYM8_PYRAE/116-424   Q97DB5_CLOAB/160-475   Q980V3_SULSO/113-425   Q98QM9_MYCPU/122-552   Q9F112_9RHIZ/4-352   Q9HB23_HUMAN/250-603   Q9HKI9_THEAC/20-325   Q9LCY8_THETH/104-418   Q9VJH2_DROME/521-960   SYD1_STRMU/118-557   SYD_AERPE/118-438   SYD_AQUAE/128-577   SYD_BACSU/123-562   More...

The full alignment for this family in the Pfam database contains 5631 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Pirellula sp. (3);   Leptospira interrogans (3);   Thermoplasma acidophilum (3);   Pyrobaculum aerophilum (3);   Vibrio cholerae (2);   Kluyveromyces lactis (2);   Debaryomyces hansenii (2);   Thermus thermophilus (2);   Mycoplasma gallisepticum (2);   Homo sapiens (2);   Schizosaccharomyces pombe (2);   Buchnera aphidicola (Acyrthosiphon pisum) (2);   Mycoplasma genitalium (2);   Bdellovibrio bacteriovorus (2);   Ureaplasma parvum (2);   Yarrowia lipolytica (2);   Chlamydia trachomatis (2);   Buchnera aphidicola (Baizongia pistaciae) (2);   Sulfolobus solfataricus (2);   Corynebacterium diphtheriae (1);   Borrelia burgdorferi (1);   Xanthomonas campestris pv. campestris (1);   Methanothermobacter thermautotrophicus str. Delta H (1);   Candidatus Protochlamydia amoebophila UWE25 (1);   Bacteroides thetaiotaomicron (1);   Treponema pallidum (1);   Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis (1);   Halobacterium salinarum (1);   Acinetobacter sp. ADP1 (1);   Aquifex aeolicus (1);   Thermotoga maritima (1);   Enterococcus faecalis (1);   Streptococcus mutans (1);   Streptococcus pneumoniae R6 (1);   Anopheles gambiae (1);   Clostridium tetani (1);   Pyrococcus horikoshii (1);   Staphylococcus aureus subsp. aureus MSSA476 (1);   Chlorobaculum tepidum (1);   Sinorhizobium meliloti (1);   Leifsonia xyli subsp. xyli (1);   Prochlorococcus marinus subsp. pastoris str. CCMP1986 (1);   Lactobacillus johnsonii (1);   Campylobacter jejuni (1);   Deinococcus radiodurans (1);   Mycoplasma pulmonis (1);   Neisseria meningitidis serogroup A (1);   Treponema denticola (1);   Methanosarcina mazei (1);   Clostridium acetobutylicum (1);   Mycoplasma penetrans (1);   More...

The full alignment covers 1036 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-52984.69-52470.599068-52470.599068-51046.526758-51046.526973

Tree Length  

191.10191.1009191.1009191.1009191.1009

κ  

1.101.2025161.2025161.0355971.035598

ω-ratio  

ω=0.13405p0=0.707326 ~ ω0=0.159228
p1=0.292674 ~ ω1=1
p0=0.707326 ~ ω0=0.159228
p1=0.148629 ~ ω1=1
p2=0.144045 ~ ω2=1
ω~Β(0.822835,4.330703)p0=0.999999 ~ ω~Β(0.82283,4.330694)
p1=1e-06 ~ ω=3.113037

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=1
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-80438.92212-80347.3189

Mean ω-ratio  

ω = 0.20255ω = 0.21473

Coeff. of variation  
of ω-ratio  

CVω = 0.59917CVω = 0.67303
 

Annotations

InteractionsThis family has 3 known interactions:
PF00152; PF01336; PF02938;

StructuresThis family has 42 structures:
Notation: PDB_ID (PDB chain, PDB residues)
  • 1x55  (A, 114-430)
  • 1x56  (A, 114-430)
  • 1x54  (A, 114-430)
  • 1efw  (B, 123-553)
  • 1g51  (B, 1123-1553)
  • 1l0w  (B, 1123-1553)
  • 1efw  (A, 123-553)
  • 1l0w  (A, 123-553)
  • 1g51  (A, 123-553)
  • 3bju  (A, 222-575)
  • 3bju  (C, 222-575)
  • 3bju  (B, 222-575)
  • 3bju  (D, 222-575)
  • 1eqr  (C, 117-559)
  • 1eqr  (A, 117-559)
  • 1eqr  (B, 117-559)
  • 1il2  (A, 117-559)
  • 1c0a  (A, 117-559)
  • 1il2  (B, 1117-1559)
  • 1nnh  (A, 2-182)
  • 1e1t  (A, 161-502)
  • 1lyl  (C, 161-502)
  • 1lyl  (A, 161-502)
  • 1lyl  (B, 161-502)
  • 1e1o  (A, 161-502)
  • 1e22  (A, 161-502)
  • 1e24  (A, 161-502)
  • 1asy  (B, 227-553)
  • 1eov  (A, 227-553)
  • 1asz  (A, 227-553)
More...

Gene Ontologies
Cellular component
 cytoplasm[GO:0005737]
Biological Process
 tRNA aminoacylation for protein translation[GO:0006418]
 translation[GO:0006412]
Molecular Function
 ATP binding[GO:0005524]
 nucleotide binding[GO:0000166]
 aminoacyl-tRNA ligase activity[GO:0004812]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Energy Metabolism
Nitrogen metabolism [KEGG]
Amino Acid Metabolism
Alanine and aspartate metabolism [KEGG]
Lysine biosynthesis [KEGG]
Histidine metabolism [KEGG]
Phenylalanine, tyrosine and tryptophan biosynthesis [KEGG]
Metabolism of Other Amino Acids
Cyanoamino acid metabolism [KEGG]
Metabolism of Cofactors and Vitamins
Folate biosynthesis [KEGG]
Genetic Information Processing
Translation
Aminoacyl-tRNA biosynthesis [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens
Drosophila melanogaster
Mus musculus

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment
 
Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
 
601421 (1) 108410 (1) 610956 (1) 603084 (1)