SUPERFAMILY 1.75 HMM library and genome assignments server


PEBP-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   PEBP-like [ 49776]
Superfamily:   PEBP-like [ 49777] (2)
Families:   Phosphatidylethanolamine binding protein [ 49778] (3)
  Prokaryotic PEBP-like proteins [ 63701] (2)


Superfamily statistics
Genomes (1,826) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,897 7,531 9
Proteins 3,878 7,515 9


Functional annotation
General category General
Detailed category Small molecule binding

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)multicellular organismal process0.00015360.5488Least InformativeInherited
Biological Process (BP)developmental process6.725e-050.4436Least InformativeInherited
Biological Process (BP)response to stimulus0.561Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)reproduction1.745e-118.035e-06Moderately InformativeDirect
Biological Process (BP)regulation of multicellular organismal process1.641e-050.006441Moderately InformativeInherited
Biological Process (BP)regulation of developmental process1.296e-050.004486Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.0011350.4123Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.00043520.02726Moderately InformativeInherited
Biological Process (BP)cell differentiation0.09990.9001Moderately InformativeInherited
Biological Process (BP)tissue development0.62820.658Moderately InformativeInherited
Biological Process (BP)response to light stimulus2.684e-060.0002121InformativeDirect
Biological Process (BP)reproductive structure development1.768e-087.785e-08InformativeDirect
Biological Process (BP)cellular process involved in reproduction0.00072310.02105InformativeInherited
Biological Process (BP)epithelium development0.0014280.03791InformativeInherited
Biological Process (BP)sexual reproduction0.95771InformativeInherited
Biological Process (BP)single organism reproductive process0.000430.009172InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.97821InformativeInherited
Biological Process (BP)epithelial cell development3.163e-065.346e-05Highly InformativeDirect
Biological Process (BP)spermatogenesis2.781e-050.0002927Highly InformativeDirect
Biological Process (BP)post-embryonic development1.67e-096.001e-07Highly InformativeDirect
Biological Process (BP)regulation of reproductive process9.127e-085.807e-06Highly InformativeDirect
Biological Process (BP)cellular process involved in reproduction in multicellular organism0.008940.01081Highly InformativeInherited
Molecular Function (MF)binding0.83881Least InformativeInherited
Molecular Function (MF)anion binding2.581e-060.0001075Moderately InformativeDirect
Molecular Function (MF)lipid binding3.757e-102.412e-08InformativeDirect

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) multicellular organismal process 0.5488 Least Informative Inherited
Biological Process (BP) developmental process 0.4436 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) reproduction 8.035e-06 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.006441 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.004486 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.4123 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.02726 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9001 Moderately Informative Inherited
Biological Process (BP) tissue development 0.658 Moderately Informative Inherited
Biological Process (BP) response to light stimulus 0.0002121 Informative Direct
Biological Process (BP) reproductive structure development 7.785e-08 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.02105 Informative Inherited
Biological Process (BP) epithelium development 0.03791 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) single organism reproductive process 0.009172 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 1 Informative Inherited
Biological Process (BP) epithelial cell development 5.346e-05 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0002927 Highly Informative Direct
Biological Process (BP) post-embryonic development 6.001e-07 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 5.807e-06 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.01081 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 0.0001075 Moderately Informative Direct
Molecular Function (MF) lipid binding 2.412e-08 Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation8.094e-07Moderately InformativeDirect
Cellular componentMitochondrion0.0004865Moderately InformativeDirect
DomainTransit peptide3.719e-06Moderately InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationDevelopmental protein3.786e-05Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008914 SSF49777 Protein matches
Abstract

The PEBP family is a highly conserved group of proteins that have been identified in numerous tissues in a wide variety of organisms, including bacteria, yeast, nematodes, plants, drosophila and mammals. The various functions described for members of this family include lipid binding, neuronal development [PubMed12492898], serine protease inhibition [PubMed11034991], the control of the morphological switch between shoot growth and flower structures [PubMed10764580], and the regulation of several signalling pathways such as the MAP kinase pathway [PubMed12551925], and the NF-kappaB pathway [PubMed11585904]. The control of the latter two pathways involves the PEBP protein RKIP, which interacts with MEK and Raf-1 to inhibit the MAP kinase pathway, and with TAK1, NIK, IKKalpha and IKKbeta to inhibit the NF-kappaB pathway. Other PEBP-like proteins that show strong structural homology to PEBP include Escherichia coli YBHB and YBCL, the rat neuropeptide HCNP, and Antirrhinum centroradialis CEN.

Structures have been determined for several members of the PEBP-like family, all of which show extensive fold conservation. The structure consists of a large central beta-sheet flanked by a smaller beta-sheet on one side, and an alpha helix on the other. Sequence alignments show two conserved central regions, CR1 and CR2, that form a consensus signature for the PEBP family. These two regions form part of the ligand-binding site, which can accommodate various anionic groups. The N- and C-terminal regions are the least conserved, and may be involved in interactions with different protein partners. The N-terminal residues 2-12 form the natural cleavage peptide HCNP involved in neuronal development. The C-terminal region is deleted in plant and bacterial PEBP homologues, and may help control accessibility to the active site.


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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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 7 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 PEBP-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 7 hidden Markov models representing the PEBP-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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]