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 (3,252) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 52,596 268,710 47
Proteins 52,407 268,507 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)single-organism metabolic process0.0026910Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.01410Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.75820Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.51040Least InformativeInherited
Biological Process (BP)protein metabolic process0.007810Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.001550Least InformativeInherited
Biological Process (BP)biosynthetic process0.0064160Least InformativeInherited
Biological Process (BP)single-organism cellular process0.17980.00000001642Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.012730Least InformativeInherited
Biological Process (BP)RNA metabolic process0.52510Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.09591Moderately InformativeInherited
Biological Process (BP)sulfur compound metabolic process0.000071410.1943Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.0035811Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.00018361Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.00032541Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.00017320.2971Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process0.049231Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.025341Moderately InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.00000035720.0008402InformativeDirect
Biological Process (BP)ncRNA metabolic process0.00094870InformativeDirect
Biological Process (BP)monocarboxylic acid biosynthetic process0.0052520.02709InformativeInherited
Biological Process (BP)sulfur compound biosynthetic process0.00026190.9165InformativeInherited
Biological Process (BP)fatty acid metabolic process0.00079950.09132InformativeInherited
Molecular Function (MF)transferase activity0.0032571Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.60490.4143Moderately InformativeInherited
Molecular Function (MF)ligase activity0.00000000021590InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.00008070.003159InformativeInherited
Molecular Function (MF)DNA polymerase activity0.000000037440.0000006534Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.060320.01752Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.066910Least 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) single-organism cellular process 0.00000001642 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) 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) reproductive process 0.9721 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.5524 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.8182 Moderately Informative Inherited
Biological Process (BP) signal transduction 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) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.5831 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.4709 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.2971 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.1943 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1212 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) mitochondrion organization 0.0000000000004343 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.0008402 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00000007818 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.000000003706 Informative Direct
Biological Process (BP) ncRNA metabolic process 0 Informative Direct
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) reproductive structure development 0.04694 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.9946 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.1694 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.02709 Informative Inherited
Biological Process (BP) sulfur compound biosynthetic process 0.9165 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.7755 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.09132 Informative Inherited
Biological Process (BP) regulation of translation 0.00000000000005513 Highly Informative Direct
Biological Process (BP) ER-nucleus signaling pathway 0.00001611 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.0006428 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 0.0003373 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 0.01226 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.0287 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 0.04361 Least Informative Inherited
Molecular Function (MF) anion binding 0.023 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.4143 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.02032 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.01828 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 1 Moderately Informative Inherited
Molecular Function (MF) ligase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.000008311 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000004058 Informative Direct
Molecular Function (MF) protein dimerization activity 0 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.003159 Informative Inherited
Molecular Function (MF) nucleotide binding 0.07854 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) RNA binding 0.001386 Informative Inherited
Molecular Function (MF) ATP binding 0.00000001616 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0.0000006534 Highly Informative Direct
Molecular Function (MF) carboxylic ester hydrolase activity 0.0005881 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.3485 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.01752 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) plastid 0.00001243 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 disease0.08905Least InformativeInherited
Disease Ontology (DO)neuropathy0.00831InformativeInherited
Disease Ontology (DO)neuromuscular disease0.00008822Highly 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/homeostasis0.6003Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.0008277Moderately 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 lethal0.0000000831Moderately 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 emb0.0000000000498InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000004291InformativeDirect
Worm Phenotype (WP)rachis morphology variant0.0000004989InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0000005472InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.000009107InformativeDirect
Worm Phenotype (WP)transgene expression increased0.000009949InformativeDirect
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)metabolism and growth0.4017Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.009685Moderately InformativeInherited
Yeast Phenotype (YP)heat sensitivity0.00007888InformativeDirect
Yeast Phenotype (YP)utilization of carbon source0.002778InformativeInherited
Yeast Phenotype (YP)respiratory growth0.00005888Highly InformativeDirect
Yeast Phenotype (YP)mitochondrial genome maintenance0.0008537Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)decreased cell size0.0005283Highly 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 stage0.00004856InformativeDirect

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

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)blood and blood forming organs0.002537Least InformativeInherited
Drugbank ATC_code (DB)iron preparations0.0001555InformativeDirect

Document: DB 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-binding0.000003972Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionRNA-binding0.8455Moderately InformativeInherited
Molecular functiontRNA-binding0InformativeDirect
Molecular functionBiotin0.0006007Highly 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 biosynthesis0.07748Moderately 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]