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 (2,448) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,432 35,173 20
Proteins 6,383 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)nitrogen compound metabolic process0.017180.4043Least InformativeInherited
Biological Process (BP)biosynthetic process0.00067290.06085Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.0019280.2401Least InformativeInherited
Biological Process (BP)single-organism cellular process0.4140.9442Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.000000048860.0000002173Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process0.000000000011450.0000000007642Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.0000011980.0000005299Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00000036210.000002035Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.0094320.03772Moderately 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 process0.0000000000000094410.0000000000005328InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000000000000014010.0000000000003642InformativeDirect
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) nitrogen compound metabolic process 0.4043 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.06085 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.2401 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.2827 Least Informative Inherited
Biological Process (BP) multicellular organismal 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 0.9442 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.0000002173 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0.0000000007642 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0000005299 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.000002035 Moderately Informative Direct
Biological Process (BP) organ development 0.3764 Moderately Informative Inherited
Biological Process (BP) immune system process 0.02957 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.01897 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5558 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.7356 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2827 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.03772 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 0.0000000000005328 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.00001611 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.0000003832 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0000008593 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000000000003642 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.002512 Informative Inherited
Biological Process (BP) growth 0.01134 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.001496 Informative Inherited
Biological Process (BP) regulation of anatomical structure size 0.004137 Informative Inherited
Biological Process (BP) regulation of organelle organization 0.0142 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.00305 Informative Inherited
Biological Process (BP) in utero embryonic development 0.00003639 Highly Informative Direct
Biological Process (BP) erythrocyte differentiation 0.000000003894 Highly Informative Direct
Biological Process (BP) regulation of actin cytoskeleton organization 0.00003258 Highly Informative Direct
Biological Process (BP) amino acid salvage 0 Highly Informative Direct
Biological Process (BP) regulation of protein complex assembly 0.00003073 Highly Informative Direct
Biological Process (BP) negative regulation of cytoskeleton organization 0.0000008548 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 0.00382 Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00000000173 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.3054 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7908 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0 Moderately Informative Direct
Cellular Component (CC) cell projection 0.002553 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2574 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.3414 Moderately Informative Inherited
Cellular Component (CC) cell cortex 0.00003784 Informative Direct
Cellular Component (CC) cell junction 0.0005596 Informative Direct
Cellular Component (CC) synapse 0.00000003337 Informative Direct
Cellular Component (CC) chromosome 0.5097 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 lyases4.839e-16Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.0008494Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric monoester hydrolases0.003375Moderately 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 processApoptosis0.0000009153Moderately InformativeDirect
Biological processCarbohydrate metabolism0.0423Moderately InformativeInherited
Biological processMethionine biosynthesis0Highly InformativeDirect
Cellular componentCytoplasm0.00000000008472Least InformativeDirect
Cellular componentCytoskeleton0.0008981Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalmodulin-binding0.0000000004038InformativeDirect
Molecular functionActin-binding0.000000001596InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase0.0000000597Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.0000000005307Least InformativeDirect
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)carbohydrate degradation0Moderately InformativeDirect
UniPathway (UP)L-methionine biosynthesis0InformativeDirect
UniPathway (UP)L-rhamnose metabolism0Highly InformativeDirect
UniPathway (UP)L-ascorbate degradation0Highly InformativeDirect
UniPathway (UP)L-methionine biosynthesis via salvage pathway0Highly InformativeDirect
UniPathway (UP)L-fucose metabolism0.000000000008931Highly InformativeDirect
UniPathway (UP)coenzyme F420 biosynthesis0.0000005033Highly InformativeDirect
UniPathway (UP)L-arabinose degradation via L-ribulose0.00001064Highly 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 ]