SUPERFAMILY 1.75 HMM library and genome assignments server


AraD/HMP-PK domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   AraD/HMP-PK domain-like [ 53638]
Superfamily:   AraD/HMP-PK domain-like [ 53639] (2)
Families:   AraD-like aldolase/epimerase [ 53640] (4)
  Phosphomethylpyrimidine kinase C-terminal domain-like [ 159768] (2)


Superfamily statistics
Genomes (2,447) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,428 35,173 20
Proteins 6,379 35,043 20


Functional annotation
General category Metabolism
Detailed category Other enzymes

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)biosynthetic process0.00078190.06028Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.024450.2105Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.016190.3834Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process6.859e-082.514e-07Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process3.704e-121.155e-10Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process8.783e-082.089e-06Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process3.897e-071.949e-06Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.0096680.0381Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process00InformativeDirect
Biological Process (BP)aspartate family amino acid metabolic process00InformativeDirect
Biological Process (BP)cellular metabolic compound salvage00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process4.845e-151.237e-13InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process2.007e-144.997e-13InformativeDirect
Biological Process (BP)amino acid salvage00Highly InformativeDirect
Biological Process (BP)L-methionine biosynthetic process00Highly 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) biosynthetic process 0.06028 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2105 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.3834 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2628 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 2.514e-07 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 1.155e-10 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 2.089e-06 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.949e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.4931 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2433 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.01946 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.8677 Moderately Informative Inherited
Biological Process (BP) immune system process 0.032 Moderately Informative Inherited
Biological Process (BP) organ development 0.3868 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7191 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0381 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0 Informative Direct
Biological Process (BP) cellular metabolic compound salvage 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 1.237e-13 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 1.606e-05 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0009833 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 4.997e-13 Informative Direct
Biological Process (BP) regulation of organelle organization 0.01 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.002092 Informative Inherited
Biological Process (BP) growth 0.01214 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.003099 Informative Inherited
Biological Process (BP) erythrocyte differentiation 3.994e-09 Highly Informative Direct
Biological Process (BP) regulation of actin cytoskeleton organization 3.282e-05 Highly Informative Direct
Biological Process (BP) amino acid salvage 0 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 2.729e-05 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 6.892e-07 Highly Informative Direct
Biological Process (BP) L-methionine biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) structural molecule activity 0 Moderately Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.003787 Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.627e-08 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0.6767 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.5784 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.3308 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2642 Moderately Informative Inherited
Cellular Component (CC) cell cortex 3.577e-05 Informative Direct
Cellular Component (CC) cell junction 0.0005697 Informative Direct
Cellular Component (CC) chromosome 0.4614 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.0009987Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0.997Least InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.003305Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0InformativeDirect

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases4.824e-16Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0008575Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.003397Moderately InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0Highly InformativeDirect
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processApoptosis9.093e-07Moderately InformativeDirect
Biological processCarbohydrate metabolism0.04228Moderately InformativeInherited
Biological processMethionine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm8.498e-11Least InformativeDirect
Cellular componentCytoskeleton0.0008836Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalmodulin-binding4.179e-10InformativeDirect
Molecular functionActin-binding1.588e-09InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase6.051e-08Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0Moderately InformativeDirect
UniPathway (UP)L-arabinose degradation0InformativeDirect
UniPathway (UP)L-arabinose degradation via L-ribulose0Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001303 SSF53639 Protein matches
Abstract

This entry represents the alpha/beta/alpha domain found in class II aldolases and adducin, usually at the N-terminus. These proteins form part of a family that includes: rhamnulose-1-phosphate aldolase , L-fuculose phosphate aldolase [PubMed8515438, PubMed8676381] that is involved in the third step in fucose metabolism, L-ribulose- 5-phosphate 4-epimerase involved in the third step of L-arabinose catabolism, a probable sugar isomerase SgbE, hypothetical proteins and the metazoan adducins which have not been ascribed any enzymatic function but which play a role in cell membrane cytoskeleton organisation.

Adducins are members of the Ig superfamily and encode cell surface sialoglycoproteins expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Adducin is a cell-membrane skeletal protein that was first purified from human erythrocytes and subsequently isolated from bovine brain membranes. Isoforms of this protein have been detected in lung, kidney, testes and liver. Erythrocyte adducin is a 200-kDa heterodimer protein, composed of alpha and beta subunits, present at about 30,000 copies per cell. It binds with high affinity to Ca(2+)/calmodulin and is a substrate for protein kinases A and C. Both alpha-adducin and beta-adducin show alternative splicing. Thus, there may be several different heterodimeric or homodimeric forms of adducin, each with a different functional specificity. It is thought to play a role in assembly of the spectrin-actin lattice that underlies the plasma membrane [PubMed102560]. Missense mutations in both the alpha- and beta-adducin genes that alter amino acids that are normally phosphorylated have been associated with the regulation of blood pressure in the Milan hypertensive strain (MHS) of rats. Gamma adducin was isolated from human foetal brain [PubMed8893809]. It shows a high degree of similarity to the alpha and beta adducins.


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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 6 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 AraD/HMP-PK domain-like 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 6 hidden Markov models representing the AraD/HMP-PK domain-like 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]