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 (2,700) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 16,891 32,219 21
Proteins 12,664 24,978 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)localization0.00014020Least InformativeDirect
Biological Process (BP)single-organism cellular process0.092440.00801Least InformativeInherited
Biological Process (BP)response to stimulus0.13970.04091Least InformativeInherited
Biological Process (BP)ion transport1.722e-070Moderately InformativeDirect
Biological Process (BP)homeostatic process9.311e-073.191e-08Moderately InformativeDirect
Biological Process (BP)metal ion transport6.494e-110.0004579InformativeDirect
Biological Process (BP)cation homeostasis1.328e-080InformativeDirect
Biological Process (BP)response to oxidative stress0.00013734.538e-06InformativeDirect
Biological Process (BP)transition metal ion transport2.737e-130Highly InformativeDirect
Biological Process (BP)transition metal ion homeostasis5.708e-111.096e-10Highly InformativeDirect
Molecular Function (MF)binding0.0020030.001928Least InformativeInherited
Molecular Function (MF)cation binding2.497e-100Moderately InformativeDirect
Molecular Function (MF)transition metal ion binding0.016532.514e-06InformativeInherited
Molecular Function (MF)copper ion binding00Highly 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 0.1941 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.497 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.3396 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.8079 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.3825 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4094 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.5349 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.698 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.04592 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.8945 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9662 Least Informative Inherited
Biological Process (BP) response to stimulus 0.04091 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.00801 Least Informative Inherited
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) homeostatic process 3.191e-08 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0003513 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 0.0004425 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0008671 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.8333 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.7514 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1958 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.373 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.05537 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.004759 Moderately Informative Inherited
Biological Process (BP) organ development 0.08585 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.05621 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.006173 Moderately Informative Inherited
Biological Process (BP) regulation of programmed cell death 0.006938 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.03259 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03882 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.04797 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.02368 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.03412 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.862 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.5475 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.5428 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.07224 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.3806 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.02249 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.3463 Moderately Informative Inherited
Biological Process (BP) tissue development 0.2284 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.7107 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.0481 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.2149 Moderately Informative Inherited
Biological Process (BP) metal ion transport 0.0004579 Informative Direct
Biological Process (BP) cation homeostasis 0 Informative Direct
Biological Process (BP) response to oxidative stress 4.538e-06 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.0008488 Informative Direct
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) response to inorganic substance 1.309e-10 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 7.065e-08 Informative Direct
Biological Process (BP) immune effector process 1.063e-05 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 1.596e-05 Informative Direct
Biological Process (BP) mitochondrion organization 3.538e-05 Informative Direct
Biological Process (BP) negative regulation of catalytic activity 0.0002436 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0004642 Informative Direct
Biological Process (BP) single-organism behavior 0.0007902 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0008095 Informative Direct
Biological Process (BP) cell death 0.02233 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.007415 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.05111 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.002241 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.001178 Informative Inherited
Biological Process (BP) cell activation 0.003354 Informative Inherited
Biological Process (BP) organ morphogenesis 0.01058 Informative Inherited
Biological Process (BP) negative regulation of cell death 0.004748 Informative Inherited
Biological Process (BP) generation of neurons 0.0836 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.008837 Informative Inherited
Biological Process (BP) central nervous system development 0.005701 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.002502 Informative Inherited
Biological Process (BP) cell projection organization 0.1221 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.02797 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.005103 Informative Inherited
Biological Process (BP) immune response 0.004768 Informative Inherited
Biological Process (BP) cardiovascular system development 0.004362 Informative Inherited
Biological Process (BP) transition metal ion transport 0 Highly Informative Direct
Biological Process (BP) transition metal ion homeostasis 1.096e-10 Highly Informative Direct
Biological Process (BP) superoxide metabolic process 6.967e-13 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 4.469e-10 Highly Informative Direct
Biological Process (BP) hair follicle development 2.378e-09 Highly Informative Direct
Biological Process (BP) response to toxic substance 1.236e-08 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 1.485e-08 Highly Informative Direct
Biological Process (BP) phenol-containing compound metabolic process 4.772e-08 Highly Informative Direct
Biological Process (BP) ion transmembrane transport 4.929e-08 Highly Informative Direct
Biological Process (BP) T cell differentiation 2.392e-07 Highly Informative Direct
Biological Process (BP) lung development 3.241e-07 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 3.964e-07 Highly Informative Direct
Biological Process (BP) connective tissue development 7.271e-07 Highly Informative Direct
Biological Process (BP) response to superoxide 1.619e-06 Highly Informative Direct
Biological Process (BP) negative regulation of neuron death 2.346e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 2.373e-06 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 3.57e-06 Highly Informative Direct
Biological Process (BP) locomotory behavior 9.37e-06 Highly Informative Direct
Biological Process (BP) cellular response to reactive oxygen species 1.053e-05 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 1.518e-05 Highly Informative Direct
Biological Process (BP) ATP metabolic process 3.87e-05 Highly Informative Direct
Biological Process (BP) skeletal system development 5.526e-05 Highly Informative Direct
Biological Process (BP) neuron projection development 0.00382 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.00479 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.02292 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.0002899 Least Informative Direct
Molecular Function (MF) binding 0.001928 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 2.514e-06 Informative Direct
Molecular Function (MF) nucleoside-triphosphatase activity 5.644e-12 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 5.184e-06 Informative Direct
Molecular Function (MF) active transmembrane transporter activity 7.028e-05 Informative Direct
Molecular Function (MF) inorganic cation transmembrane transporter activity 0.01176 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 1.406e-12 Highly Informative Direct
Cellular Component (CC) membrane 2.853e-07 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.07121 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.3287 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.001626 Least Informative Inherited
Cellular Component (CC) vesicle 0.001028 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 4.992e-08 Informative Direct
Cellular Component (CC) cell-cell junction 6.78e-05 Informative Direct
Cellular Component (CC) plastid 0.007199 Informative Inherited
Cellular Component (CC) trans-Golgi network 0 Highly Informative Direct
Cellular Component (CC) symplast 6.104e-07 Highly Informative Direct
Cellular Component (CC) cell body 9.708e-05 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)alkaline pH resistance3.813e-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)Oxidoreductases0.3903Least 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 processAntiport3.921e-05Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell membrane8.753e-08Moderately InformativeDirect
Cellular componentGolgi apparatus3.322e-06Moderately InformativeDirect
Cellular componentPeriplasm9.563e-07InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainRedox-active center1.376e-07InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding8.913e-06Least InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionFlavoprotein0.0007122Moderately InformativeDirect
Molecular functionCopper0InformativeDirect
Molecular functionFAD3.533e-07InformativeDirect
Molecular functionCadmium0Highly InformativeDirect
Molecular functionMercury0Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationPhosphoprotein2.567e-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 ]