SUPERFAMILY 1.75 HMM library and genome assignments server


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 (3,210) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 52,133 117,636 47
Proteins 51,961 117,538 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)cellular macromolecule metabolic process0.00068320Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.022440Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.66640Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.40730Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.15470Least InformativeInherited
Biological Process (BP)protein metabolic process0.0038830Least InformativeInherited
Biological Process (BP)biosynthetic process0.012140Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.019490Least InformativeInherited
Biological Process (BP)RNA metabolic process0.52270Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.10581Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.00020780.1326Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.051941Moderately InformativeInherited
Biological Process (BP)cellular lipid metabolic process0.039741Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.00049090.3639Moderately InformativeInherited
Biological Process (BP)lipid biosynthetic process0.014091Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.059231Moderately InformativeInherited
Biological Process (BP)single-organism biosynthetic process0.025681Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.08041Moderately InformativeInherited
Biological Process (BP)ncRNA metabolic process0.00074660InformativeDirect
Biological Process (BP)coenzyme biosynthetic process1.979e-060.005125InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.00091620.8706InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.016980.04196InformativeInherited
Biological Process (BP)fatty acid metabolic process0.0037620.1366InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.56530.3033Moderately InformativeInherited
Molecular Function (MF)nucleotidyltransferase activity5.704e-050.001932InformativeInherited
Molecular Function (MF)DNA polymerase activity3.285e-084.48e-07Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.064420.08657Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.074620Least 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) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic 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) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
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) organ development 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.3982 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01592 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) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.4668 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.05307 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.1326 Moderately Informative Inherited
Biological Process (BP) lipid biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.3639 Moderately Informative Inherited
Biological Process (BP) translation 0 Informative Direct
Biological Process (BP) mitochondrion organization 1.086e-14 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 1.249e-07 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 8.984e-10 Informative Direct
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) reproductive structure development 0.009512 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 1 Informative Inherited
Biological Process (BP) hexose metabolic process 0.08448 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.8765 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.0637 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.005125 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.8706 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.04196 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.1366 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.68 Informative Inherited
Biological Process (BP) cellular amide metabolic process 1 Informative Inherited
Biological Process (BP) regulation of translation 1.431e-14 Highly Informative Direct
Biological Process (BP) ER-nucleus signaling pathway 1.223e-05 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0003681 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 0.0002545 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.01278 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.005325 Highly Informative Inherited
Biological Process (BP) monosaccharide biosynthetic process 0.001817 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.002732 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.9519 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.03516 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.3033 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 3.777e-05 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 1.946e-05 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.5881 Informative Inherited
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 1 Informative Inherited
Molecular Function (MF) kinase activity 1 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 1 Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.001932 Informative Inherited
Molecular Function (MF) RNA binding 0.00222 Informative Inherited
Molecular Function (MF) ATP binding 1.381e-07 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 4.48e-07 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.0003777 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.2745 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.08657 Least Informative Inherited
Cellular Component (CC) plastid 2.042e-08 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 disease0.1091Least InformativeInherited
Disease Ontology (DO)neuromuscular disease0.0005102InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.6073Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0008151Moderately InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.0001569Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.002224Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal8.31e-08Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0001255Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.0002205Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0003423Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.0009283Moderately InformativeDirect
Worm Phenotype (WP)cell organization biogenesis variant0.1877Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.4728Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb4.98e-11InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant4.291e-07InformativeDirect
Worm Phenotype (WP)rachis morphology variant4.989e-07InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant5.472e-07InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective9.107e-06InformativeDirect
Worm Phenotype (WP)transgene expression increased9.949e-06InformativeDirect
Worm Phenotype (WP)germline nuclear positioning variant0.0001403InformativeDirect
Worm Phenotype (WP)germ cell compartment anucleate0.0001414Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)nutrient utilization0.009057Moderately InformativeInherited
Yeast Phenotype (YP)heat sensitivity0.0001549InformativeDirect
Yeast Phenotype (YP)utilization of carbon source0.002548InformativeInherited
Yeast Phenotype (YP)respiratory growth5.08e-05Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)cell size defective0.001597InformativeInherited
Fly Phenotype (FP)decreased cell size0.0006122Highly InformativeDirect

Document: FP 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)viscus0Least InformativeDirect

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 stage4.856e-05InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
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 amide) ligases (amide synthases)0Highly InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases1Highly InformativeInherited
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 functionMetal-binding1.407e-08Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0.9317Moderately InformativeInherited
Molecular functiontRNA-binding0InformativeDirect
Molecular functionBiotin0.0006418Highly InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationAcyltransferase0InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)L-asparagine 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]