SUPERFAMILY 1.75 HMM library and genome assignments server

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GatB/YqeY motif superfamily

SCOP classification

Root:	SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:	All alpha proteins [ 46456] (284)
Fold:	GatB/YqeY motif [ 89094]
Superfamily:	GatB/YqeY motif [ 89095] (2)
Families:	GatB/YqeY domain [ 89096]
	GatB/GatE C-terminal domain-like [ 140757] (2)

Superfamily statistics

	Genomes (2,156)	Uniprot 2013_05	PDB chains (SCOP 1.75)
Domains	3,513	9,109	4
Proteins	3,476	9,048	4

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)
Cellular Component (CC)	cytoplasmic part	0.07221	Least Informative	Inherited
Cellular Component (CC)	intracellular membrane-bounded organelle	0.2671	Least Informative	Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)

	KW term	FDR (all)	SDKW level	Annotation (direct or inherited)
Cellular component	Mitochondrion	0	Moderately Informative	Direct
Domain	Transit peptide	0	Moderately Informative	Direct
Molecular function	Nucleotide-binding	0	Least Informative	Direct
Post-translational modification	Ligase	0	Moderately Informative	Direct

Document: KW annotation of SCOP domains

InterPro annotation

Cross references IPR003789 SSF89095 Protein matches

Abstract This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.

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) · 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 4 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 GatB/YqeY motif 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 4 hidden Markov models representing the GatB/YqeY motif 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) · UniProtKB KeyWords (KW) · Internal database links ]