SUPERFAMILY 1.75 HMM library and genome assignments server


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 (241) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 295 686 11
Proteins 282 674 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 process00.000247Least InformativeDirect
Biological Process (BP)protein metabolic process00.0002983Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00.000565Least InformativeDirect
Biological Process (BP)single-organism metabolic process00.0007479Least InformativeDirect
Biological Process (BP)regulation of metabolic process00.5274Least InformativeInherited
Biological Process (BP)single-organism cellular process00.06612Least InformativeInherited
Biological Process (BP)developmental process00.01602Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process00.002336Least InformativeInherited
Biological Process (BP)multicellular organismal process00.02627Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis00.005323Least InformativeInherited
Biological Process (BP)response to stimulus00.009641Least InformativeInherited
Biological Process (BP)localization00.003411Least InformativeInherited
Biological Process (BP)regulation of multicellular organismal process04.361e-12Moderately InformativeDirect
Biological Process (BP)organic hydroxy compound metabolic process02.456e-08Moderately InformativeDirect
Biological Process (BP)macromolecule catabolic process01.306e-07Moderately InformativeDirect
Biological Process (BP)organic cyclic compound catabolic process01.725e-07Moderately InformativeDirect
Biological Process (BP)homeostatic process04.325e-07Moderately InformativeDirect
Biological Process (BP)organic substance transport01.324e-06Moderately InformativeDirect
Biological Process (BP)macromolecule localization01.529e-06Moderately InformativeDirect
Biological Process (BP)system process02.017e-06Moderately InformativeDirect
Biological Process (BP)cellular macromolecule biosynthetic process03.14e-06Moderately InformativeDirect
Biological Process (BP)cellular localization07.037e-06Moderately InformativeDirect
Biological Process (BP)nervous system development01.672e-05Moderately InformativeDirect
Biological Process (BP)anatomical structure morphogenesis09.001e-05Moderately InformativeDirect
Biological Process (BP)cell differentiation00.0001805Moderately InformativeDirect
Biological Process (BP)regulation of gene expression00.000204Moderately InformativeDirect
Biological Process (BP)cellular response to stress00.000954Moderately InformativeDirect
Biological Process (BP)single-organism developmental process00.001767Moderately InformativeInherited
Biological Process (BP)lipid localization01.541e-11InformativeDirect
Biological Process (BP)lipid catabolic process03.821e-11InformativeDirect
Biological Process (BP)blood circulation04.019e-11InformativeDirect
Biological Process (BP)steroid metabolic process06.155e-11InformativeDirect
Biological Process (BP)regulation of anatomical structure size03.844e-10InformativeDirect
Biological Process (BP)cellular chemical homeostasis02.24e-09InformativeDirect
Biological Process (BP)cation homeostasis02.357e-09InformativeDirect
Biological Process (BP)alcohol metabolic process02.585e-09InformativeDirect
Biological Process (BP)protein catabolic process04.542e-09InformativeDirect
Biological Process (BP)cardiovascular system development04.672e-08InformativeDirect
Biological Process (BP)cell projection organization02.477e-07InformativeDirect
Biological Process (BP)generation of neurons01.801e-06InformativeDirect
Biological Process (BP)response to oxidative stress01.957e-05InformativeDirect
Biological Process (BP)regulation of growth03.42e-05InformativeDirect
Biological Process (BP)response to wounding08.789e-05InformativeDirect
Biological Process (BP)steroid catabolic process00Highly InformativeDirect
Biological Process (BP)artery morphogenesis03.746e-15Highly InformativeDirect
Biological Process (BP)response to axon injury07.333e-15Highly InformativeDirect
Biological Process (BP)alcohol catabolic process03.114e-14Highly InformativeDirect
Biological Process (BP)vascular process in circulatory system03.281e-14Highly InformativeDirect
Biological Process (BP)lipoprotein metabolic process01.717e-13Highly InformativeDirect
Biological Process (BP)organic hydroxy compound transport02.755e-13Highly InformativeDirect
Biological Process (BP)maintenance of location01.582e-12Highly InformativeDirect
Biological Process (BP)sterol metabolic process01.91e-12Highly InformativeDirect
Biological Process (BP)cellular calcium ion homeostasis02.473e-11Highly InformativeDirect
Biological Process (BP)neuron projection development04.471e-08Highly InformativeDirect
Biological Process (BP)regulation of multicellular organism growth06.621e-06Highly InformativeDirect
Molecular Function (MF)binding00.04447Least InformativeInherited
Molecular Function (MF)transporter activity04.448e-07Moderately InformativeDirect
Molecular Function (MF)lipid transporter activity01.036e-14Highly InformativeDirect
Cellular Component (CC)extracellular region part02.973e-13Moderately 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 0.000247 Least Informative Direct
Biological Process (BP) protein metabolic process 0.0002983 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000565 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0007479 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.5274 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.06612 Least Informative Inherited
Biological Process (BP) developmental process 0.01602 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.002336 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.02627 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.005323 Least Informative Inherited
Biological Process (BP) response to stimulus 0.009641 Least Informative Inherited
Biological Process (BP) localization 0.003411 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 4.361e-12 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 2.456e-08 Moderately Informative Direct
Biological Process (BP) macromolecule catabolic process 1.306e-07 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 1.725e-07 Moderately Informative Direct
Biological Process (BP) homeostatic process 4.325e-07 Moderately Informative Direct
Biological Process (BP) organic substance transport 1.324e-06 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1.529e-06 Moderately Informative Direct
Biological Process (BP) system process 2.017e-06 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 3.14e-06 Moderately Informative Direct
Biological Process (BP) cellular localization 7.037e-06 Moderately Informative Direct
Biological Process (BP) nervous system development 1.672e-05 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 9.001e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0001805 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000204 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.000954 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 0.001767 Moderately Informative Inherited
Biological Process (BP) lipid localization 1.541e-11 Informative Direct
Biological Process (BP) lipid catabolic process 3.821e-11 Informative Direct
Biological Process (BP) blood circulation 4.019e-11 Informative Direct
Biological Process (BP) steroid metabolic process 6.155e-11 Informative Direct
Biological Process (BP) regulation of anatomical structure size 3.844e-10 Informative Direct
Biological Process (BP) cellular chemical homeostasis 2.24e-09 Informative Direct
Biological Process (BP) cation homeostasis 2.357e-09 Informative Direct
Biological Process (BP) alcohol metabolic process 2.585e-09 Informative Direct
Biological Process (BP) protein catabolic process 4.542e-09 Informative Direct
Biological Process (BP) cardiovascular system development 4.672e-08 Informative Direct
Biological Process (BP) cell projection organization 2.477e-07 Informative Direct
Biological Process (BP) generation of neurons 1.801e-06 Informative Direct
Biological Process (BP) response to oxidative stress 1.957e-05 Informative Direct
Biological Process (BP) regulation of growth 3.42e-05 Informative Direct
Biological Process (BP) response to wounding 8.789e-05 Informative Direct
Biological Process (BP) steroid catabolic process 0 Highly Informative Direct
Biological Process (BP) artery morphogenesis 3.746e-15 Highly Informative Direct
Biological Process (BP) response to axon injury 7.333e-15 Highly Informative Direct
Biological Process (BP) alcohol catabolic process 3.114e-14 Highly Informative Direct
Biological Process (BP) vascular process in circulatory system 3.281e-14 Highly Informative Direct
Biological Process (BP) lipoprotein metabolic process 1.717e-13 Highly Informative Direct
Biological Process (BP) organic hydroxy compound transport 2.755e-13 Highly Informative Direct
Biological Process (BP) maintenance of location 1.582e-12 Highly Informative Direct
Biological Process (BP) sterol metabolic process 1.91e-12 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 2.473e-11 Highly Informative Direct
Biological Process (BP) neuron projection development 4.471e-08 Highly Informative Direct
Biological Process (BP) regulation of multicellular organism growth 6.621e-06 Highly Informative Direct
Molecular Function (MF) binding 0.04447 Least Informative Inherited
Molecular Function (MF) transporter activity 4.448e-07 Moderately Informative Direct
Molecular Function (MF) lipid transporter activity 1.036e-14 Highly Informative Direct
Cellular Component (CC) extracellular region part 2.973e-13 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 processTransport6.556e-09Least InformativeDirect
Biological processLipid transport5.204e-14InformativeDirect
Cellular componentSecreted2.448e-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 ]