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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 (3,253) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 52,607 268,710 47
Proteins 52,421 268,507 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 process0.0026450Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.44990Least InformativeInherited
Biological Process (BP)primary metabolic process0.010430.0000000000001693Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0011260Least InformativeInherited
Biological Process (BP)biosynthetic process0.03270Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.032340Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.017140Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process0.60190Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.81930Least InformativeInherited
Biological Process (BP)single-organism cellular process0.12410.000000000000231Least InformativeInherited
Biological Process (BP)peptide metabolic process0.00025570Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.0010640Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.11790Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.6381Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.0069280.6974Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.070361Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.0011350.3041Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.078361Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.13621Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0060150Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.08430Moderately InformativeInherited
Biological Process (BP)gene expression0.22110Moderately InformativeInherited
Biological Process (BP)tRNA metabolic process0.00000011130InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.000005730.001605InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.00096490.6952InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.0015210.000003253InformativeInherited
Biological Process (BP)fatty acid metabolic process0.0062540.1221InformativeInherited
Molecular Function (MF)transferase activity0.062781Least InformativeInherited
Molecular Function (MF)ligase activity0.0000000000000040070InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.000000000030560.0004174InformativeDirect
Cellular Component (CC)cytoplasmic part0.14170Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.40990.0619Least 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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0000000000001693 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) biosynthetic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000000000231 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic 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 0.7408 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) amide biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid 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) gene expression 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) nucleobase-containing compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.3575 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.9451 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.008055 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.6974 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) sulfur compound metabolic process 0.3041 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2709 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.9337 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tRNA metabolic process 0 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 0.000003253 Informative Direct
Biological Process (BP) mitochondrion organization 0.000000000000003692 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.0000009537 Informative Direct
Biological Process (BP) regulation of cellular amide metabolic process 0.0001445 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0004927 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) protein oligomerization 0.01002 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.747 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.4087 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.4568 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.7277 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.001605 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.6952 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.1221 Informative Inherited
Biological Process (BP) circulatory system development 0.9824 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) biotin metabolic process 0.000004092 Highly Informative Direct
Biological Process (BP) negative regulation of translation 0.0006583 Highly Informative Direct
Biological Process (BP) response to nutrient levels 0.02087 Highly Informative Inherited
Biological Process (BP) cellular response to external stimulus 0.07648 Highly Informative Inherited
Biological Process (BP) angiogenesis 0.02059 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.6474 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.9513 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.1684 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.8851 Moderately Informative Inherited
Molecular Function (MF) protein binding 0.001725 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.05639 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.065 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.08534 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.8543 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.0004174 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00001069 Informative Direct
Molecular Function (MF) ribonucleoside binding 0.0000249 Informative Direct
Molecular Function (MF) purine nucleoside binding 0.00002577 Informative Direct
Molecular Function (MF) RNA binding 0.00003524 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00006477 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00008635 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.7827 Informative Inherited
Molecular Function (MF) kinase activity 0.9354 Informative Inherited
Molecular Function (MF) ATP binding 0.00000006664 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.00009106 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.3337 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 0.0619 Least Informative Inherited
Cellular Component (CC) plastid 0.00002228 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 disease0.08655Least InformativeInherited
Disease Ontology (DO)peripheral nervous system disease0.01011InformativeInherited
Disease Ontology (DO)neuromuscular disease0.00005566Highly 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 metabolism/homeostasis0.697Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.718Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0001012Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal genital system morphology0.7357Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.0209InformativeInherited
Phenotypic Abnormality (PA)Premature ovarian failure0.0001937Highly 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 variant0.000002459Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00001042Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.00003391Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0003697Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.001562Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.004993Least InformativeInherited
Worm Phenotype (WP)organ system morphology variant0.008636Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00000006957Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000004322Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.0002077Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0004854Moderately InformativeDirect
Worm Phenotype (WP)level of transgene expression variant0.0008569Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.02121Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.1893Moderately InformativeInherited
Worm Phenotype (WP)gametogenesis variant0.2441Moderately InformativeInherited
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000003546InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00000002828InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000003283InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.0000003443InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0000005447InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.00002776InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.00003918InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.06999InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.1194InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.0000000000004302Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.000006912Highly InformativeDirect
Worm Phenotype (WP)germ cell compartment anucleate0.0001149Highly InformativeDirect
Worm Phenotype (WP)pachytene region organization variant0.000928Highly 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 growth0.5042Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.01628Moderately InformativeInherited
Yeast Phenotype (YP)heat sensitivity0.00008767InformativeDirect
Yeast Phenotype (YP)respiratory metabolism0.000616InformativeDirect
Yeast Phenotype (YP)respiratory growth0.0002647Highly InformativeDirect
Yeast Phenotype (YP)mitochondrial genome maintenance0.0002746Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP 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)eye0InformativeDirect
Zebrafish Anatomy (ZA)pharyngeal arch0Highly InformativeDirect

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)tail0.0009764InformativeDirect

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)Acyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compounds0InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases1InformativeInherited
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 functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0.7675Moderately InformativeInherited
Molecular functiontRNA-binding0InformativeDirect
Molecular functionBiotin0.0006031Highly 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)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0.06625Moderately 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) · Fly Phenotype (FP) · 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) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]