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Class II aaRS and biotin synthetases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Class II aaRS and biotin synthetases [ 55680]
Superfamily:   Class II aaRS and biotin synthetases [ 55681] (4)
Families:   Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain [ 55682] (15)
  Biotin holoenzyme synthetase [ 55707] (2)
  LplA-like [ 143642] (5)
  PH0223-like [ 160611]


Superfamily statistics
Genomes (3,260) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 52,915 280,359 47
Proteins 52,727 279,888 47


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)macromolecule metabolic process0.00055540Least InformativeDirect
Biological Process (BP)biosynthetic process0.015630Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.24510Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0025560Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0084260Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.67810Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0073680Least InformativeInherited
Biological Process (BP)single-organism cellular process0.09570Least InformativeInherited
Biological Process (BP)primary metabolic process0.0086840.000000000000007296Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.010730Least InformativeInherited
Biological Process (BP)gene expression0.000011190Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.00038280Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.2851Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.054430Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0010730Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.8281Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.077521Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.0014840.4598Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.076241Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.11651Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.1531Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0087190.8842Moderately InformativeInherited
Biological Process (BP)peptide metabolic process0.0010850Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.034510Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process0.0000000046510InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.00023850.0000005809InformativeDirect
Biological Process (BP)peptidyl-amino acid modification0.00065270.0009101InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.0000059690.002169InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.0015820.8305InformativeInherited
Biological Process (BP)fatty acid metabolic process0.0019940.05597InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.00000000025460.0000009784Highly InformativeDirect
Biological Process (BP)protein maturation0.0000039530.02527Highly InformativeInherited
Molecular Function (MF)transferase activity0.037011Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.41320.008104Moderately InformativeInherited
Molecular Function (MF)ligase activity00InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.0000000046470.0002387InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.000057450.0000005023InformativeDirect
Cellular Component (CC)cytoplasmic part0.35780.00000000000002829Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.47230.1743Least InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000000000000007296 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.9915 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.03733 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.4048 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.7053 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9392 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.001904 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.4598 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.8842 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0000005809 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0009101 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000000008642 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0001353 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0004604 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.5677 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.07642 Informative Inherited
Biological Process (BP) response to extracellular stimulus 0.04934 Informative Inherited
Biological Process (BP) chromosome organization 1 Informative Inherited
Biological Process (BP) protein oligomerization 0.01532 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0656 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.08728 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.09428 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.4982 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.505 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.03837 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.002169 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.8305 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.05597 Informative Inherited
Biological Process (BP) circulatory system development 0.7331 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.0000009784 Highly Informative Direct
Biological Process (BP) biotin metabolic process 0.0000006663 Highly Informative Direct
Biological Process (BP) negative regulation of cytokine production 0.0006023 Highly Informative Direct
Biological Process (BP) angiogenesis 0.0008798 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.06221 Highly Informative Inherited
Biological Process (BP) histone modification 0.4983 Highly Informative Inherited
Biological Process (BP) mitochondrial gene expression 0.03515 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.5822 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.2252 Highly Informative Inherited
Biological Process (BP) negative regulation of translation 0.003668 Highly Informative Inherited
Biological Process (BP) regulation of cell size 0.04299 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.02129 Highly Informative Inherited
Biological Process (BP) protein maturation 0.02527 Highly Informative Inherited
Molecular Function (MF) binding 0.2335 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.01822 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.008104 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.0099 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.0345 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.7959 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.1136 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0002387 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.0000005023 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00000000005072 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0000004704 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.000004373 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.000006305 Informative Direct
Molecular Function (MF) RNA binding 0.00003962 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) DNA binding 1 Informative Inherited
Molecular Function (MF) ATP binding 0.000000001126 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.1202 Highly Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0.3723 Highly Informative Inherited
Molecular Function (MF) double-stranded DNA binding 0.2875 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.7623 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00000000000002829 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1743 Least Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) plastid 0.00006335 Informative Direct
Cellular Component (CC) spliceosomal complex 0.01122 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds1Moderately InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0InformativeDirect
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases1InformativeInherited
Enzyme Commission (EC)Aspartate--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amide) ligases (amide synthases)0Highly InformativeDirect
Enzyme Commission (EC)Proline--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Threonine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Alanine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Histidine--tRNA ligase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis1Moderately InformativeInherited
Biological processProtein biosynthesis0InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0.00004494Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationRNA-binding0.00000001617Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 38 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Class II aaRS and biotin synthetases domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 38 hidden Markov models representing the Class II aaRS and biotin synthetases superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]