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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 (3,258) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 52,735 280,359 47
Proteins 52,548 279,888 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 process0.00050040Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process0.68530Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.0070310Least InformativeInherited
Biological Process (BP)biosynthetic process0.016340Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.0088460Least InformativeInherited
Biological Process (BP)single-organism cellular process0.098260Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0029910Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.25060Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.010990Least InformativeInherited
Biological Process (BP)primary metabolic process0.008750.0000000000001327Least InformativeInherited
Biological Process (BP)amide biosynthetic process0.00040770Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.077111Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.0570Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.81141Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0095910.7892Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.11761Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.1531Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.0015970.3594Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.28981Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.079031Moderately InformativeInherited
Biological Process (BP)peptide metabolic process0.0011680Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0011420Moderately InformativeInherited
Biological Process (BP)gene expression0.12890Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.035430Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process0.0000000049950InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.00025580.0000001746InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.000007060.002143InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.001660.769InformativeInherited
Biological Process (BP)fatty acid metabolic process0.0020940.0565InformativeInherited
Molecular Function (MF)transferase activity0.063731Least InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups0.000000000045310.0001638InformativeDirect
Molecular Function (MF)ligase activity0.0000000000000040630InformativeDirect

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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000000001327 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) peptide metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.02936 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3389 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9702 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.005698 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic 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) sulfur compound metabolic process 0.3594 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.7892 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.000000287 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0004005 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.0000001746 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) response to extracellular stimulus 0.03244 Informative Inherited
Biological Process (BP) protein oligomerization 0.01534 Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 0.001223 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.7579 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.7382 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.8306 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.5709 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.002143 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.769 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.0565 Informative Inherited
Biological Process (BP) tissue development 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) circulatory system development 1 Informative Inherited
Biological Process (BP) biotin metabolic process 0.0000004508 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.04546 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular amide metabolic process 0.002224 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.01259 Highly Informative Inherited
Biological Process (BP) angiogenesis 0.02373 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.9285 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.6162 Highly Informative Inherited
Molecular Function (MF) binding 0.1707 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.323 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.01482 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.01377 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.02677 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.9662 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.9782 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.00002727 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0001638 Informative Direct
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.000003947 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.000005674 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.0000004382 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) kinase activity 0.8826 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.7063 Informative Inherited
Molecular Function (MF) ATP binding 0.000000001019 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00000001561 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.2565 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.00000000000005146 Least Informative Direct
Cellular Component (CC) macromolecular complex 0.8223 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1023 Least Informative Inherited
Cellular Component (CC) plastid 0.00006939 Informative Direct

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

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)nervous system disease0.08367Least InformativeInherited
Disease Ontology (DO)peripheral nervous system disease0.01045InformativeInherited
Disease Ontology (DO)neuromuscular disease0.00005702Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the musculature0.003505Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.6092Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.7833Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.00001706Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of muscle physiology0.0005337Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal genital system morphology0.7811Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.02565InformativeInherited
Phenotypic Abnormality (PA)Premature ovarian failure0.0002397Highly InformativeDirect

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.00000421Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00001581Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.00005931Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0003804Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.001704Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.003148Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.007049Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00000006319Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000004213Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.0002201Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.02003Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.03278Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.2355Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2376Moderately InformativeInherited
Worm Phenotype (WP)oxygen response variant0.00000000000008875InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000003623InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00000002747InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000003042InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.0000003343InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0000005219InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.00002713InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.00003064InformativeDirect
Worm Phenotype (WP)nuclear positioning variant0.005135InformativeInherited
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.0715InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.0000000000005455Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.000006631Highly InformativeDirect
Worm Phenotype (WP)germ cell compartment anucleate0.0001117Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.0009296Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.5205Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.01622Moderately InformativeInherited
Yeast Phenotype (YP)heat sensitivity0.00008662InformativeDirect
Yeast Phenotype (YP)respiratory metabolism0.0006106InformativeDirect
Yeast Phenotype (YP)respiratory growth0.0002621Highly InformativeDirect
Yeast Phenotype (YP)mitochondrial genome maintenance0.0002726Highly InformativeDirect

Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)cardiovascular system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)sensory system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)head0Moderately InformativeDirect
Zebrafish Anatomy (ZA)trunk0Moderately InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch0InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0.01867Least InformativeInherited
Xenopus ANatomical entity (XAN)lung0.0009931InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)0 seed germination stage0.00004863InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.00000000000002763Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Other carbon--nitrogen ligases1InformativeInherited
Enzyme Commission (EC)Phenylalanine--tRNA ligase0Highly InformativeDirect
Enzyme Commission (EC)Acid--ammonia (or amine) ligases (amide synthases)0Highly InformativeDirect
Enzyme Commission (EC)Acid--thiol ligases1Highly InformativeInherited

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 functionMagnesium0.00005488Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationRNA-binding0.00000001952Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationtRNA-binding0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0.0688Moderately InformativeInherited
UniPathway (UP)L-histidine biosynthesis0InformativeDirect
UniPathway (UP)tRNA modification0InformativeDirect
UniPathway (UP)protein maturation0InformativeDirect
UniPathway (UP)L-asparagine biosynthesis0Highly InformativeDirect
UniPathway (UP)protein lipoylation0Highly InformativeDirect
UniPathway (UP)aminoacyl-tRNA biosynthesis0Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Disease Ontology (DO) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]