SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from supfam.org. Please contact us if you experience any problems.

  Home > SCOP hierarchy > HMA, heavy metal-associated domain superfamily


HMA, heavy metal-associated domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   HMA, heavy metal-associated domain [ 55008]
Families:   HMA, heavy metal-associated domain [ 55009] (8)

Superfamily statistics
Genomes (2,753) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 19,032 107,674 21
Proteins 14,393 84,646 20

 Functional annotation
General category Processes_IC
Detailed category Ion 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)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.3102Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembran0InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0InformativeDirect
Enzyme Commission (EC)Copper-exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Mercury(II) reductase0Highly InformativeDirect
Enzyme Commission (EC)Cu(+) exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Cadmium-exporting ATPase0Highly InformativeDirect
Enzyme Commission (EC)Zinc-exporting ATPase0.000000000000008737Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO 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)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.07335Least InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.004685Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.00586Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.009397Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.01149Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal ion homeostasis0InformativeDirect
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.00002076InformativeDirect
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0007641InformativeDirect
Mammalian Phenotype (MP)abnormal mineral level0.9491Highly InformativeInherited

Document: MP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)alkaline pH resistance0.00000371Highly InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.2483Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases0.4141Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0.0000000003308Moderately InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0Highly InformativeDirect
Enzyme Commission (EC)Linked to the hydrolysis of a nucleoside triphosphate0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR006121 SSF55008 Protein matches
Abstract

Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures.

These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases [PubMed8091505].

A conserved domain has been found in a number of these heavy metal transport or detoxification proteins [PubMed8091505]. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding.

Structure solution of the fourth HMA domain of the Menke¿s copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold [PubMed9437429]. This fold is common to other domains and is classified as "ferredoxin-like".


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) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · 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 33 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 HMA, heavy metal-associated 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 33 hidden Markov models representing the HMA, heavy metal-associated 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) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

Please send feedback, comments or questions to superfamily@cs.bris.ac.uk or use the feedback form.

© Copyright 2013 The SUPERFAMILY authors and Julian Gough.