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 (1,863) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,292 0 9
Proteins 4,265 0 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 process0.0002810.6241Least InformativeInherited
Biological Process (BP)developmental process0.00011950.5092Least InformativeInherited
Biological Process (BP)response to stimulus0.61851Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)reproduction3.518e-111.158e-05Moderately InformativeDirect
Biological Process (BP)regulation of multicellular organismal process5.071e-050.006843Moderately InformativeInherited
Biological Process (BP)regulation of developmental process3.149e-050.004835Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.0011550.4199Moderately InformativeInherited
Biological Process (BP)response to abiotic stimulus0.0004810.02691Moderately InformativeInherited
Biological Process (BP)cell differentiation0.11050.9237Moderately InformativeInherited
Biological Process (BP)tissue development0.63670.6669Moderately InformativeInherited
Biological Process (BP)developmental process involved in reproduction3.591e-121.335e-09InformativeDirect
Biological Process (BP)response to light stimulus3.12e-060.0002106InformativeDirect
Biological Process (BP)reproductive system development3.98e-106.273e-08InformativeDirect
Biological Process (BP)cellular process involved in reproduction0.00072720.02095InformativeInherited
Biological Process (BP)epithelium development0.0015620.04018InformativeInherited
Biological Process (BP)sexual reproduction0.95481InformativeInherited
Biological Process (BP)single organism reproductive process0.00046320.009679InformativeInherited
Biological Process (BP)multicellular organismal reproductive process0.97541InformativeInherited
Biological Process (BP)epithelial cell development4.361e-065.914e-05Highly InformativeDirect
Biological Process (BP)spermatogenesis3.154e-050.0002981Highly InformativeDirect
Biological Process (BP)post-embryonic development1.358e-097.538e-07Highly InformativeDirect
Biological Process (BP)regulation of reproductive process1.861e-075.641e-06Highly InformativeDirect
Biological Process (BP)cellular process involved in reproduction in multicellular organism0.0099060.01166Highly InformativeInherited
Molecular Function (MF)binding0.78821Least InformativeInherited
Molecular Function (MF)anion binding3.408e-072.215e-05Moderately InformativeDirect
Molecular Function (MF)lipid binding1.555e-111.56e-09InformativeDirect

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 0.6241 Least Informative Inherited
Biological Process (BP) developmental process 0.5092 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 1.158e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.006843 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.004835 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.4199 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.02691 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9237 Moderately Informative Inherited
Biological Process (BP) tissue development 0.6669 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1.335e-09 Informative Direct
Biological Process (BP) response to light stimulus 0.0002106 Informative Direct
Biological Process (BP) reproductive system development 6.273e-08 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.02095 Informative Inherited
Biological Process (BP) epithelium development 0.04018 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) single organism reproductive process 0.009679 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 1 Informative Inherited
Biological Process (BP) epithelial cell development 5.914e-05 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0002981 Highly Informative Direct
Biological Process (BP) post-embryonic development 7.538e-07 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 5.641e-06 Highly Informative Direct
Biological Process (BP) cellular process involved in reproduction in multicellular organism 0.01166 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) anion binding 2.215e-05 Moderately Informative Direct
Molecular Function (MF) lipid binding 1.56e-09 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 processDifferentiation8.501e-07Moderately InformativeDirect
Cellular componentMitochondrion0.000485Moderately InformativeDirect
DomainTransit peptide3.897e-06Moderately InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Post-translational modificationDevelopmental protein3.78e-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 ]