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Class II aaRS and biotin synthetases superfamily

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


Superfamily statistics
Genomes (3,260) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 52,915 368,577 47
Proteins 52,727 368,031 47


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

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 disease0.08393Least InformativeInherited
Disease Ontology (DO)peripheral nervous system disease0.01061InformativeInherited
Disease Ontology (DO)neuromuscular disease0.00005841Highly 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 musculature0.005048Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.04223Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.5865Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5945Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.6545Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.00003223Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebrum0.006598Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.4496Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.9559Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.0004602InformativeDirect
Phenotypic Abnormality (PA)Abnormality of toe0.4094InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell development variant0.00001476Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00001703Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.00007232Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0001885Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0008417Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.003129Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.00314Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.007019Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.000000001546Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.0000004214Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.000008329Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.0000664Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0.00233Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.01746Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant0.06598Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5584Moderately InformativeInherited
Worm Phenotype (WP)oxygen response variant0InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000003194InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.00000002604InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000003321InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.0000005951InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.00002921InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.00006837InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.007136InformativeInherited
Worm Phenotype (WP)nuclear positioning variant0.007215InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.000000000001027Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.000005934Highly InformativeDirect
Worm Phenotype (WP)germ cell compartment anucleate0.0001143Highly 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 growth0.5217Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.01628Moderately InformativeInherited
Yeast Phenotype (YP)heat sensitivity0.00008831InformativeDirect
Yeast Phenotype (YP)respiratory metabolism0.0006091InformativeDirect
Yeast Phenotype (YP)respiratory growth0.0002609Highly InformativeDirect
Yeast Phenotype (YP)mitochondrial genome maintenance0.000276Highly 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)head0Moderately InformativeDirect
Zebrafish Anatomy (ZA)central nervous system0.3331Moderately InformativeInherited
Zebrafish Anatomy (ZA)trunk0InformativeDirect
Zebrafish Anatomy (ZA)blood vessel0.01229InformativeInherited
Zebrafish Anatomy (ZA)post-vent region0.08887InformativeInherited
Zebrafish Anatomy (ZA)cranial vasculature0.0001662Highly InformativeDirect
Zebrafish Anatomy (ZA)intersegmental vessel0.0003227Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tail0.000699InformativeDirect

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 stage0.00004858InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Aminoacyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Forming carbon-oxygen bonds0InformativeDirect
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

Jump to [ Top of page · SCOP classification · Functional annotation · 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) ]

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 49 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 49 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 · 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) · Internal database links ]