SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


GLA-domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   GLA-domain [ 57629]
Superfamily:   GLA-domain [ 57630]
Families:   GLA-domain [ 57631] (6)


Superfamily statistics
Genomes (71) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 1,073 2,593 18
Proteins 1,072 2,574 18


Functional annotation
General category General
Detailed category General

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Coagulation factor Xa0Highly InformativeDirect
Enzyme Commission (EC)Coagulation factor IXa0.00000000005175Highly InformativeDirect
Enzyme Commission (EC)Protein C (activated)0.0000000008721Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)hematopoietic system disease0.00002096Moderately InformativeDirect
Disease Ontology (DO)syndrome0.0002617Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.000533Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.006293Moderately InformativeInherited
Disease Ontology (DO)artery disease0.4826Moderately InformativeInherited
Disease Ontology (DO)inherited blood coagulation disease0.00003779InformativeDirect
Disease Ontology (DO)atherosclerosis0.00004929InformativeDirect
Disease Ontology (DO)pancreas disease0.1591InformativeInherited
Disease Ontology (DO)myocardial infarction0.911InformativeInherited
Disease Ontology (DO)Behcet's disease0.00006451Highly InformativeDirect
Disease Ontology (DO)pancreatitis0.0002036Highly 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 cardiovascular system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.07478Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.2674Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the musculature0.7274Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal cardiovascular system physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.001794Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.1194Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.1644Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal muscle morphology0.2348Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the coagulation cascade0.0000000005104InformativeDirect
Phenotypic Abnormality (PA)Internal hemorrhage0.000000145InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebral vasculature0.00003435InformativeDirect
Phenotypic Abnormality (PA)Abnormal thrombosis0.001234InformativeInherited
Phenotypic Abnormality (PA)Functional respiratory abnormality0.05473InformativeInherited
Phenotypic Abnormality (PA)Intramuscular hematoma0.00000001594Highly InformativeDirect
Phenotypic Abnormality (PA)Joint hemorrhage0.00000006403Highly InformativeDirect
Phenotypic Abnormality (PA)Prolonged prothrombin time0.000002535Highly InformativeDirect
Phenotypic Abnormality (PA)Venous thrombosis0.00000266Highly InformativeDirect
Phenotypic Abnormality (PA)Prolonged bleeding following procedure0.0009558Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.001703Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.00005649Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal skeleton morphology0.8205Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood coagulation0.0000000004405InformativeDirect
Mammalian Phenotype (MP)hemorrhage0.0000003338InformativeDirect
Mammalian Phenotype (MP)abnormal adipose tissue amount0.05044InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.05647InformativeInherited
Mammalian Phenotype (MP)increased total body fat amount0.0008742Highly InformativeDirect

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)0Moderately InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR000294 SSF57630 Protein matches
Abstract

This domain contains post-translational modifications of many glutamate residues by vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla) [PubMed3106112, PubMed2183788]. The GLA domain is responsible for the high-affinity binding of calcium ions. It starts at the N-terminal extremity of the mature form of proteins and ends with a conserved aromatic residue; a conserved Gla-x(3)-Gla-x-Cys motif [PubMed3317405] is found in the middle of the domain which seems to be important for substrate recognition by the carboxylase.

The 3D structure of the Gla domain has been solved [PubMed7713897, PubMed8663165]. Calcium ions induce conformational changes in the Gla domain and are necessary for the Gla domain to fold properly. A common structural feature of functional Gla domains is the clustering of N-terminal hydrophobic residues into a hydrophobic patch that mediates interaction with the cell surface membrane [PubMed8663165].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 10 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 GLA-domain 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 10 hidden Markov models representing the GLA-domain 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 · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]