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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 musculature0.003733Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.06373Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.4371Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.5182Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.6899Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of acid-base homeostasis0.000006134Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.01488Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.04899Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.3675Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.9732Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral white matter0.0001972InformativeDirect
Phenotypic Abnormality (PA)Peripheral neuropathy0.1561InformativeInherited
Phenotypic Abnormality (PA)Abnormality of toe0.4464InformativeInherited
Phenotypic Abnormality (PA)Hypoplasia of the corpus callosum0.0006964Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal myelination0.001875Highly InformativeInherited
Phenotypic Abnormality (PA)Sensory impairment0.06286Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.00003309Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.00006297Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0002224Least InformativeDirect
Worm Phenotype (WP)cell development variant0.0005825Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.0008368Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.0009888Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.002728Least InformativeInherited
Worm Phenotype (WP)early embryonic lethal0.00000007861Moderately InformativeDirect
Worm Phenotype (WP)germ cell morphology variant0.000000467Moderately InformativeDirect
Worm Phenotype (WP)germ cell differentiation variant0.000007395Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport variant0.000009313Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.00004052Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0002971Moderately InformativeDirect
Worm Phenotype (WP)organism stress response variant0.003783Moderately InformativeInherited
Worm Phenotype (WP)reproductive system morphology variant0.01593Moderately InformativeInherited
Worm Phenotype (WP)cell cycle variant0.02531Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0.04534Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5526Moderately InformativeInherited
Worm Phenotype (WP)hypoxia response variant0InformativeDirect
Worm Phenotype (WP)pleiotropic defects severe early emb0.00000000003834InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn0.000000001385InformativeDirect
Worm Phenotype (WP)germ cell compartment expansion variant0.0000003377InformativeDirect
Worm Phenotype (WP)pachytene progression during oogenesis variant0.000000604InformativeDirect
Worm Phenotype (WP)oocyte physiology variant0.0000009535InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.000007957InformativeDirect
Worm Phenotype (WP)germ cell cytoplasmic morphology variant0.007043InformativeInherited
Worm Phenotype (WP)nuclear positioning variant0.007532InformativeInherited
Worm Phenotype (WP)hypoxia resistant0Highly InformativeDirect
Worm Phenotype (WP)cell differentiation variant0.00000000000005175Highly InformativeDirect
Worm Phenotype (WP)cytoplasmic processing body variant0.00000636Highly InformativeDirect
Worm Phenotype (WP)germ cell compartment anucleate0.0001109Highly 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 structure0.2548Least InformativeInherited
Zebrafish Anatomy (ZA)head0Moderately InformativeDirect
Zebrafish Anatomy (ZA)cardiovascular system0.03396Moderately InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.5951Moderately InformativeInherited
Zebrafish Anatomy (ZA)blood vasculature0.03062InformativeInherited
Zebrafish Anatomy (ZA)artery0.0009744Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)tail0.0007202InformativeDirect

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 ]