SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,736) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,261 0 21
Proteins 13,796 0 20


Functional annotation
General category Processes_IC
Detailed category Ion 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)localization0.00010820Least InformativeDirect
Biological Process (BP)single-organism cellular process0.085690.002911Least InformativeInherited
Biological Process (BP)response to stimulus0.25380.08678Least InformativeInherited
Biological Process (BP)homeostatic process5.867e-093.847e-10Moderately InformativeDirect
Biological Process (BP)ion transport3.479e-080Moderately InformativeDirect
Biological Process (BP)metal ion homeostasis2.35e-120InformativeDirect
Biological Process (BP)metal ion transport4.719e-120.000281InformativeDirect
Biological Process (BP)response to oxidative stress0.00029884.933e-06InformativeDirect
Biological Process (BP)cellular cation homeostasis0.77060.528InformativeInherited
Biological Process (BP)transition metal ion transport6.477e-150Highly InformativeDirect
Biological Process (BP)cellular transition metal ion homeostasis0.037332.485e-09Highly InformativeInherited
Molecular Function (MF)binding0.0028610.003065Least InformativeInherited
Molecular Function (MF)cation binding2.246e-090Moderately InformativeDirect
Molecular Function (MF)transition metal ion binding0.015831.34e-06InformativeInherited
Molecular Function (MF)copper ion binding1.32e-150Highly InformativeDirect

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) localization 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.2405 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.5753 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.4829 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9369 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.3148 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5954 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.4414 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4676 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.7609 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.06314 Least Informative Inherited
Biological Process (BP) response to stimulus 0.08678 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002911 Least Informative Inherited
Biological Process (BP) homeostatic process 3.847e-10 Moderately Informative Direct
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 9.669e-06 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.0001144 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0004648 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0005508 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.8923 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.001242 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.792 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.2287 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3743 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.07133 Moderately Informative Inherited
Biological Process (BP) organ development 0.124 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.0879 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.04603 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.05594 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.02342 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.03562 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9373 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5523 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.5511 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.09157 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.269 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.008257 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.02836 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.393 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2762 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.7832 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.05736 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.2097 Moderately Informative Inherited
Biological Process (BP) metal ion homeostasis 0 Informative Direct
Biological Process (BP) metal ion transport 0.000281 Informative Direct
Biological Process (BP) response to oxidative stress 4.933e-06 Informative Direct
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) response to inorganic substance 1.307e-10 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 9.385e-08 Informative Direct
Biological Process (BP) immune effector process 1.404e-05 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 2.069e-05 Informative Direct
Biological Process (BP) mitochondrion organization 4.285e-05 Informative Direct
Biological Process (BP) leukocyte activation 9.136e-05 Informative Direct
Biological Process (BP) tube development 0.0008456 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0009309 Informative Direct
Biological Process (BP) programmed cell death 0.8958 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.007374 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.06451 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.003176 Informative Inherited
Biological Process (BP) negative regulation of catalytic activity 0.03495 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.528 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.001113 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.001625 Informative Inherited
Biological Process (BP) organ morphogenesis 0.01558 Informative Inherited
Biological Process (BP) negative regulation of cell death 0.006158 Informative Inherited
Biological Process (BP) regulation of apoptotic process 1 Informative Inherited
Biological Process (BP) generation of neurons 0.107 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.01021 Informative Inherited
Biological Process (BP) central nervous system development 0.007137 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.002566 Informative Inherited
Biological Process (BP) cell projection organization 0.1528 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.02878 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.005453 Informative Inherited
Biological Process (BP) single-organism behavior 0.001147 Informative Inherited
Biological Process (BP) immune response 0.005084 Informative Inherited
Biological Process (BP) cardiovascular system development 0.005063 Informative Inherited
Biological Process (BP) transition metal ion transport 0 Highly Informative Direct
Biological Process (BP) cellular transition metal ion homeostasis 2.485e-09 Highly Informative Direct
Biological Process (BP) superoxide metabolic process 3.26e-12 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 5.25e-10 Highly Informative Direct
Biological Process (BP) hair follicle development 3.145e-09 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 1.122e-08 Highly Informative Direct
Biological Process (BP) response to toxic substance 1.207e-08 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.718e-08 Highly Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 5.769e-08 Highly Informative Direct
Biological Process (BP) T cell differentiation 2.809e-07 Highly Informative Direct
Biological Process (BP) respiratory tube development 5.283e-07 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 6.065e-07 Highly Informative Direct
Biological Process (BP) connective tissue development 1.039e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 3.093e-06 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 3.304e-06 Highly Informative Direct
Biological Process (BP) negative regulation of neuron death 3.593e-06 Highly Informative Direct
Biological Process (BP) response to superoxide 9.356e-06 Highly Informative Direct
Biological Process (BP) locomotory behavior 1.319e-05 Highly Informative Direct
Biological Process (BP) cellular response to reactive oxygen species 1.617e-05 Highly Informative Direct
Biological Process (BP) respiratory system development 1.713e-05 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 1.801e-05 Highly Informative Direct
Biological Process (BP) ATP metabolic process 5.949e-05 Highly Informative Direct
Biological Process (BP) skeletal system development 7.855e-05 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.005912 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.04082 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic process 0.003092 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0005226 Least Informative Direct
Molecular Function (MF) binding 0.003065 Least Informative Inherited
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) transition metal ion binding 1.34e-06 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 1.346e-11 Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 6.5e-11 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 2.064e-06 Informative Direct
Molecular Function (MF) active transmembrane transporter activity 0.000344 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.0079 Informative Inherited
Molecular Function (MF) copper ion binding 0 Highly Informative Direct
Molecular Function (MF) transition metal ion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) ATPase activity, coupled to transmembrane movement of ions 9.053e-12 Highly Informative Direct
Cellular Component (CC) membrane 2.728e-06 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.1847 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.4005 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.004481 Least Informative Inherited
Cellular Component (CC) vesicle 0.002377 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 7.003e-08 Informative Direct
Cellular Component (CC) cell-cell junction 9.055e-05 Informative Direct
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) symplast 7.264e-07 Highly Informative Direct
Cellular Component (CC) cell body 0.0001013 Highly Informative Direct

Document: GO annotation of SCOP domains

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 ATPase8.737e-15Highly 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)abnormal ion homeostasis0InformativeDirect
Mammalian Phenotype (MP)abnormal mineral homeostasis0InformativeDirect

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 resistance3.819e-06Highly InformativeDirect

Document: YP 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)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.3755Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0Highly InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; catalyzing transmembrane movement of substances0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Biological processAntiport3.849e-05Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane2.454e-07Moderately InformativeDirect
Cellular componentGolgi apparatus2.82e-06Moderately InformativeDirect
Cellular componentPeriplasm7.841e-07InformativeDirect
DomainTransmembrane3.093e-16Least InformativeDirect
DomainRedox-active center1.016e-07InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding1.335e-05Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionFlavoprotein0.0005947Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionFAD2.904e-07InformativeDirect
Molecular functionCadmium0Highly InformativeDirect
Molecular functionMercury0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein8.916e-09Least InformativeDirect

Document: KW 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 15 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 15 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]