SUPERFAMILY 1.75 HMM library and genome assignments server

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Probable bacterial effector-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Probable bacterial effector-binding domain [ 55135]
Superfamily:   Probable bacterial effector-binding domain [ 55136] (4)
Families:   Gyrase inhibitory protein GyrI (SbmC, YeeB) [ 75462]
  Multidrug-binding domain of transcription activator BmrR [ 55137]
  Rob transcription factor, C-terminal domain [ 55140]
  SOUL heme-binding protein [ 143481]

Superfamily statistics
Genomes (1,568) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,761 27,209 9
Proteins 4,649 26,878 9

Functional annotation
General category Other
Detailed category Unknown function

Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)binding0.079550.3761Least InformativeInherited
Molecular Function (MF)tetrapyrrole binding0.00000000000014340.000000000000002411InformativeDirect
Molecular Function (MF)heme binding0.000000000000086570Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) binding 0.3761 Least Informative Inherited
Molecular Function (MF) tetrapyrrole binding 0.000000000000002411 Informative Direct
Molecular Function (MF) heme binding 0 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0.0002605Moderately InformativeDirect
Biological processStress response0InformativeDirect
Cellular componentCytoplasm0.0000008541Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011256 SSF55136 Protein matches

The effector domain is found in bacterial regulatory proteins, such as transcription factors. The effector domain consists of a duplication of a beta/alpha/beta(2) motif, where the antiparallel beta sheets form a barrel structure. Several proteins contain this domain, such as the multidrug-binding domain of the transcription factor BmrR, which transcriptionally regulates multidrug transporters as well as acting as a multidrug-binding protein [PubMed12180910], the C-terminal domain of the Rob transcription factor, which belongs to the AraC/XylS protein family that regulate genes involved in resistace to antibiotics, organic solvents and heavy metals [PubMed10802742], and the gyrase inhibitory protein GyrI (SbmC, TeeB), which is induced by DNA damaging agents to suppress cell proliferation by inhibiting bacterial gyrase activity [PubMed11948793].

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) · 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 Probable bacterial effector-binding 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 4 hidden Markov models representing the Probable bacterial effector-binding 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-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]