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Apolipoprotein superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Four-helical up-and-down bundle [ 47161] (28)
Superfamily:   Apolipoprotein [ 47162]
Families:   Apolipoprotein [ 47163]

 Superfamily statistics
Genomes (208) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 262 686 11
Proteins 250 674 11

 Functional annotation
General category Metabolism
Detailed category Lipid 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)biosynthetic process00.0003369Least InformativeDirect
Biological Process (BP)protein metabolic process00.0005189Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00.0006607Least InformativeDirect
Biological Process (BP)single-organism metabolic process00.0007686Least InformativeDirect
Biological Process (BP)localization00.002278Least InformativeInherited
Biological Process (BP)single-organism cellular process00.09748Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis00.004093Least InformativeInherited
Biological Process (BP)developmental process00.01103Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process00.003681Least InformativeInherited
Biological Process (BP)multicellular organismal process00.01885Least InformativeInherited
Biological Process (BP)regulation of metabolic process00.4929Least InformativeInherited
Biological Process (BP)response to stimulus00.00574Least InformativeInherited
Biological Process (BP)regulation of multicellular organismal process06.375e-12Moderately InformativeDirect
Biological Process (BP)organic hydroxy compound metabolic process01.46e-08Moderately InformativeDirect
Biological Process (BP)homeostatic process01.287e-06Moderately InformativeDirect
Biological Process (BP)organic substance transport02.27e-06Moderately InformativeDirect
Biological Process (BP)macromolecule localization02.617e-06Moderately InformativeDirect
Biological Process (BP)system process03.421e-06Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process03.995e-06Moderately InformativeDirect
Biological Process (BP)cellular localization01.085e-05Moderately InformativeDirect
Biological Process (BP)organic substance catabolic process01.676e-05Moderately InformativeDirect
Biological Process (BP)nervous system development02.806e-05Moderately InformativeDirect
Biological Process (BP)anatomical structure morphogenesis00.0001573Moderately InformativeDirect
Biological Process (BP)cell differentiation00.0002626Moderately InformativeDirect
Biological Process (BP)regulation of gene expression00.0003359Moderately InformativeDirect
Biological Process (BP)cellular response to stress00.0008979Moderately InformativeDirect
Biological Process (BP)single-organism developmental process00.002698Moderately InformativeInherited
Biological Process (BP)lipid transport04.669e-12InformativeDirect
Biological Process (BP)lipid catabolic process07.537e-11InformativeDirect
Biological Process (BP)steroid metabolic process01.112e-10InformativeDirect
Biological Process (BP)metal ion homeostasis04.959e-10InformativeDirect
Biological Process (BP)regulation of anatomical structure size06.298e-10InformativeDirect
Biological Process (BP)alcohol metabolic process01.046e-09InformativeDirect
Biological Process (BP)cellular cation homeostasis01.435e-09InformativeDirect
Biological Process (BP)protein catabolic process06.086e-09InformativeDirect
Biological Process (BP)cardiovascular system development07.676e-08InformativeDirect
Biological Process (BP)cell projection organization03.991e-07InformativeDirect
Biological Process (BP)cellular component morphogenesis01.644e-06InformativeDirect
Biological Process (BP)generation of neurons02.81e-06InformativeDirect
Biological Process (BP)response to oxidative stress01.645e-05InformativeDirect
Biological Process (BP)regulation of growth04.594e-05InformativeDirect
Biological Process (BP)response to wounding09.95e-05InformativeDirect
Biological Process (BP)blood circulation17.877e-11InformativeInherited
Biological Process (BP)steroid catabolic process00Highly InformativeDirect
Biological Process (BP)response to axon injury01.716e-14Highly InformativeDirect
Biological Process (BP)alcohol catabolic process05.777e-14Highly InformativeDirect
Biological Process (BP)vascular process in circulatory system07.487e-14Highly InformativeDirect
Biological Process (BP)lipid homeostasis01.808e-13Highly InformativeDirect
Biological Process (BP)lipoprotein metabolic process03.303e-13Highly InformativeDirect
Biological Process (BP)organic hydroxy compound transport03.557e-13Highly InformativeDirect
Biological Process (BP)maintenance of location02.829e-12Highly InformativeDirect
Biological Process (BP)sterol metabolic process03.186e-12Highly InformativeDirect
Biological Process (BP)cellular calcium ion homeostasis04.107e-11Highly InformativeDirect
Biological Process (BP)axonogenesis01.315e-08Highly InformativeDirect
Biological Process (BP)regulation of multicellular organism growth09.79e-06Highly InformativeDirect
Molecular Function (MF)binding00.06233Least InformativeInherited
Molecular Function (MF)transporter activity06.962e-07Moderately InformativeDirect
Molecular Function (MF)lipid transporter activity02.113e-14Highly InformativeDirect
Cellular Component (CC)extracellular region03.85e-12Moderately InformativeDirect
Cellular Component (CC)extracellular space00InformativeDirect

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 0.0003369 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0005189 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0006607 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0007686 Least Informative Direct
Biological Process (BP) localization 0.002278 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.09748 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.004093 Least Informative Inherited
Biological Process (BP) developmental process 0.01103 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.003681 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01885 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.4929 Least Informative Inherited
Biological Process (BP) response to stimulus 0.00574 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 6.375e-12 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 1.46e-08 Moderately Informative Direct
Biological Process (BP) homeostatic process 1.287e-06 Moderately Informative Direct
Biological Process (BP) organic substance transport 2.27e-06 Moderately Informative Direct
Biological Process (BP) macromolecule localization 2.617e-06 Moderately Informative Direct
Biological Process (BP) system process 3.421e-06 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 3.995e-06 Moderately Informative Direct
Biological Process (BP) cellular localization 1.085e-05 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 1.676e-05 Moderately Informative Direct
Biological Process (BP) nervous system development 2.806e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0001573 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0002626 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0003359 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0008979 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.002698 Moderately Informative Inherited
Biological Process (BP) lipid transport 4.669e-12 Informative Direct
Biological Process (BP) lipid catabolic process 7.537e-11 Informative Direct
Biological Process (BP) steroid metabolic process 1.112e-10 Informative Direct
Biological Process (BP) metal ion homeostasis 4.959e-10 Informative Direct
Biological Process (BP) regulation of anatomical structure size 6.298e-10 Informative Direct
Biological Process (BP) alcohol metabolic process 1.046e-09 Informative Direct
Biological Process (BP) cellular cation homeostasis 1.435e-09 Informative Direct
Biological Process (BP) protein catabolic process 6.086e-09 Informative Direct
Biological Process (BP) cardiovascular system development 7.676e-08 Informative Direct
Biological Process (BP) cell projection organization 3.991e-07 Informative Direct
Biological Process (BP) cellular component morphogenesis 1.644e-06 Informative Direct
Biological Process (BP) generation of neurons 2.81e-06 Informative Direct
Biological Process (BP) response to oxidative stress 1.645e-05 Informative Direct
Biological Process (BP) regulation of growth 4.594e-05 Informative Direct
Biological Process (BP) response to wounding 9.95e-05 Informative Direct
Biological Process (BP) blood circulation 7.877e-11 Informative Direct
Biological Process (BP) steroid catabolic process 0 Highly Informative Direct
Biological Process (BP) response to axon injury 1.716e-14 Highly Informative Direct
Biological Process (BP) alcohol catabolic process 5.777e-14 Highly Informative Direct
Biological Process (BP) vascular process in circulatory system 7.487e-14 Highly Informative Direct
Biological Process (BP) lipid homeostasis 1.808e-13 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 3.303e-13 Highly Informative Direct
Biological Process (BP) organic hydroxy compound transport 3.557e-13 Highly Informative Direct
Biological Process (BP) maintenance of location 2.829e-12 Highly Informative Direct
Biological Process (BP) sterol metabolic process 3.186e-12 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 4.107e-11 Highly Informative Direct
Biological Process (BP) axonogenesis 1.315e-08 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 9.79e-06 Highly Informative Direct
Molecular Function (MF) binding 0.06233 Least Informative Inherited
Molecular Function (MF) transporter activity 6.962e-07 Moderately Informative Direct
Molecular Function (MF) lipid transporter activity 2.113e-14 Highly Informative Direct
Cellular Component (CC) extracellular region 3.85e-12 Moderately Informative Direct
Cellular Component (CC) extracellular space 0 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport6.543e-09Least InformativeDirect
Biological processLipid transport4.394e-14InformativeDirect
Cellular componentSecreted2.642e-07Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 1 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 Apolipoprotein 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 1 hidden Markov models representing the Apolipoprotein 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · 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.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.