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YhbY-like superfamily
SCOP classification
Superfamily statistics
Functional annotation
| General category | Other |
| Detailed category | Unknown function |
Document: Function annotation of SCOP domain superfamilies
Gene Ontology (high-coverage) (show details)
Highlighted in gray are those with either FDR_singleton>0.001 or FDR_all>0.001
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GO term |
FDR (all) |
IC level |
SDFO level |
Annotation (direct or inherited) |
| Biological Process (BP) |
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
3.644e-08 |
2.222 |
-- |
DIRECT |
| Biological Process (BP) |
RNA splicing |
1.807e-07 |
1.854 |
-- |
DIRECT |
| Biological Process (BP) |
nucleic acid metabolic process |
0.0002693 |
0.9066 |
-- |
DIRECT |
| Biological Process (BP) |
biological_process |
0.009218 |
0 |
-- |
INHERITED FROM: RNA metabolic process || RNA splicing || RNA splicing, via transesterification reactions || nucleic acid metabolic process || cellular aromatic compound metabolic process || Group II intron splicing || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
cellular process |
1 |
0.1415 |
-- |
INHERITED FROM: RNA metabolic process || RNA splicing || RNA splicing, via transesterification reactions || cellular aromatic compound metabolic process || Group II intron splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
primary metabolic process |
0.0645 |
0.2976 |
-- |
INHERITED FROM: RNA metabolic process || RNA splicing, via transesterification reactions || Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
macromolecule metabolic process |
0.2259 |
0.4634 |
-- |
INHERITED FROM: RNA metabolic process || RNA splicing, via transesterification reactions || Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
cellular metabolic process |
0.08974 |
0.2708 |
-- |
INHERITED FROM: RNA splicing || RNA metabolic process || RNA splicing, via transesterification reactions || cellular aromatic compound metabolic process || Group II intron splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
metabolic process |
0.3722 |
0.2411 |
-- |
INHERITED FROM: RNA splicing || RNA metabolic process || RNA splicing, via transesterification reactions || cellular aromatic compound metabolic process || Group II intron splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
organic substance metabolic process |
0.1062 |
0.2676 |
-- |
INHERITED FROM: RNA splicing || RNA metabolic process || RNA splicing, via transesterification reactions || Group II intron splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
nucleobase-containing compound metabolic process |
0.003354 |
0.7305 |
-- |
INHERITED FROM: Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile || RNA metabolic process || RNA splicing, via transesterification reactions |
| Biological Process (BP) |
cellular nitrogen compound metabolic process |
0.01078 |
0.585 |
-- |
INHERITED FROM: Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile || RNA metabolic process || RNA splicing, via transesterification reactions |
| Biological Process (BP) |
RNA processing |
0.0442 |
1.377 |
-- |
INHERITED FROM: Group II intron splicing || RNA splicing || RNA splicing, via transesterification reactions || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
cellular aromatic compound metabolic process |
0.0008752 |
0.6271 |
Least Informative |
DIRECT |
| Biological Process (BP) |
organic cyclic compound metabolic process |
0.001489 |
0.5817 |
Least Informative |
INHERITED FROM: RNA metabolic process || RNA splicing, via transesterification reactions || Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
nitrogen compound metabolic process |
0.003164 |
0.5171 |
Least Informative |
INHERITED FROM: RNA metabolic process || RNA splicing, via transesterification reactions || Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile |
| Biological Process (BP) |
heterocycle metabolic process |
0.007935 |
0.6308 |
Least Informative |
INHERITED FROM: Group II intron splicing || RNA splicing || nucleic acid metabolic process || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile || RNA metabolic process || RNA splicing, via transesterification reactions |
| Biological Process (BP) |
cellular macromolecule metabolic process |
0.1011 |
0.4976 |
Least Informative |
INHERITED FROM: Group II intron splicing || RNA splicing || RNA splicing, via transesterification reactions with bulged adenosine as nucleophile || RNA metabolic process || RNA splicing, via transesterification reactions |
| Biological Process (BP) |
RNA metabolic process |
1.291e-05 |
1.086 |
Moderately Informative |
DIRECT |
| Biological Process (BP) |
gene expression |
0.005635 |
0.8729 |
Moderately Informative |
INHERITED FROM: RNA splicing, via transesterification reactions with bulged adenosine as nucleophile || Group II intron splicing || RNA splicing || RNA splicing, via transesterification reactions |
| Biological Process (BP) |
RNA splicing, via transesterification reactions |
4.334e-08 |
2.097 |
Highly Informative |
DIRECT |
Document: GO annotation of SCOP domains
Arabidopsis Plant Ontology (AP) (show details)
Highlighted in gray are those with FDR_all>0.001
Document: AP annotation of SCOP domains
UniProtKB KeyWords (KW) (show details)
Highlighted in gray are those with FDR_all>0.001
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 [ 12429100], and bioinformatic data suggest a role for members in translation [11565746]. 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
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
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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.
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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.
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Browse and view proteins in genomes which have
different domain combinations including a YhbY-like domain.
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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.
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Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.
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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.
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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 ]
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