SUPERFAMILY 1.75 HMM library and genome assignments server


YhbY-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   IF3-like [ 55199] (8)
Superfamily:   YhbY-like [ 75471]
Families:   YhbY-like [ 75472] (3)


Superfamily statistics
Genomes (1,471) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,626 13,644 3
Proteins 2,570 13,028 3


Functional annotation
General category Other
Detailed category Unknown function

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) cellular aromatic compound metabolic process 0.0004731 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0008323 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.001754 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.002132 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.02077 Least Informative Inherited
Biological Process (BP) RNA metabolic process 6.41e-06 Moderately Informative Direct
Biological Process (BP) gene expression 0.0004595 Moderately Informative Direct
Biological Process (BP) RNA processing 0.003126 Informative Inherited
Biological Process (BP) RNA splicing 1.662e-09 Highly Informative Direct

Document: GO annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processmRNA splicing0InformativeDirect
Cellular componentPlastid1.23e-12Moderately InformativeDirect
Cellular componentChloroplast7.311e-13InformativeDirect
DomainRepeat1.622e-07Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionRNA-binding0Moderately InformativeDirect
Post-translational modificationRibonucleoprotein7.226e-11Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001890 SSF75471 Protein matches
Abstract

E. coli YhbY belongs to a conserved family of proteins represented in eubacteria, archaea, and plants. Three maize proteins harbouring UPF0044-like domains are required for chloroplast group II intron splicing [PubMed12429100], and bioinformatic data suggest a role for members in translation [PubMed11565746]. The crystal structure of YhbY has been determined. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. Modelling studies indicate that the same surface is highly basic in all members of this family, suggesting a conserved RNA binding surface.


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) · 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 3 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 YhbY-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 3 hidden Markov models representing the YhbY-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-coverage) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]