SUPERFAMILY 1.75 HMM library and genome assignments server


PABC (PABP) domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PABP domain-like [ 63569] (2)
Superfamily:   PABC (PABP) domain [ 63570]
Families:   PABC (PABP) domain [ 63571] (2)


Superfamily statistics
Genomes (477) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,486 1,532 5
Proteins 1,448 1,489 5


Functional annotation
General category Information
Detailed category Transcription

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) regulation of metabolic process 0.0002072 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.05468 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.006369 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.003718 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.004525 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.007551 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.007499 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.0004169 Moderately Informative Direct
Biological Process (BP) gene expression 6.188e-05 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 5.982e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0007406 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.3234 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.2385 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1348 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.6021 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.3854 Moderately Informative Inherited
Biological Process (BP) posttranscriptional regulation of gene expression 1.019e-05 Informative Direct
Biological Process (BP) regulation of cellular catabolic process 4.509e-09 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 5.288e-05 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.3773 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.4722 Informative Inherited
Biological Process (BP) RNA processing 0.006074 Informative Inherited
Biological Process (BP) positive regulation of catabolic process 1.49e-06 Highly Informative Direct
Biological Process (BP) gene silencing 3e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular catabolic process 4.751e-10 Highly Informative Direct
Biological Process (BP) mRNA processing 0.01578 Highly Informative Inherited
Molecular Function (MF) binding 4.769e-06 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) RNA binding 0 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.0002887 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 2.465e-09 Moderately 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)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)gamete0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)lung0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1.303e-10Least InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processmRNA transport0Highly InformativeDirect
Biological processNonsense-mediated mRNA decay1.226e-14Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm2.901e-09Least InformativeDirect
DomainRepeat0Least InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.0001537Least InformativeDirect
Post-translational modificationAcetylation0.0007177Least InformativeDirect
Post-translational modificationMethylation5.454e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002004 SSF63570 Protein matches
Abstract

The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains [PubMed11287654]. PABP recognises the 3' mRNA poly(A) tail and plays an essential role in eukaryotic translation initiation and mRNA stabilisation/degradation. PABC domains of PABP are peptide-binding domains that mediate PABP homo-oligomerisation and protein-protein interactions. In mammals, the PABC domain of PABP functions to recruit several different translation factors to the mRNA poly(A) tail [PubMed11940585].


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-coverage) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · 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 5 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 PABC (PABP) domain 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 5 hidden Markov models representing the PABC (PABP) domain 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-coverage) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]