SUPERFAMILY 1.75 HMM library and genome assignments server


IHF-like DNA-binding proteins superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   IHF-like DNA-binding proteins [ 47728]
Superfamily:   IHF-like DNA-binding proteins [ 47729] (2)
Families:   Prokaryotic DNA-bending protein [ 47730] (4)
  DNA-binding domain (fragment?) of the TraM protein [ 63566]


Superfamily statistics
Genomes (2,498) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,506 42,534 12
Proteins 6,503 42,528 12


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process01.172e-06Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process04.555e-06Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process01.641e-05Least InformativeDirect
Biological Process (BP)heterocycle metabolic process01.019e-06Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process02.09e-06Least InformativeDirect
Molecular Function (MF)binding00.001529Least InformativeInherited
Molecular Function (MF)nucleic acid binding09.069e-09Moderately InformativeDirect
Molecular Function (MF)DNA binding04.595e-10InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 1.172e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 4.555e-06 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 1.641e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.019e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.09e-06 Least Informative Direct
Molecular Function (MF) binding 0.001529 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 9.069e-09 Moderately Informative Direct
Molecular Function (MF) DNA binding 4.595e-10 Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processTranslation regulation0InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA condensation0Highly InformativeDirect
Biological processConjugation7.235e-12Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010992 SSF47729 Protein matches
Abstract

Integration host factor (IHF) is a small heterodimeric protein that binds the minor groove of DNA in a sequence-specific manner and induces a large bend. This bending stabilises distinct DNA conformations that are required during several bacterial processes, such as recombination, transposition, replication and transcription [PubMed12842466]. The core structure of IHF consists of a partly opened 4-helical bundle that is capped with a beta-sheet.

Prokaryotic protein HU and the bacteriophage SPO1 transcription factor TF1 are closely related to IHF. These proteins are collectively referred to as type II DNA-binding proteins (DBPII), forming a group of basic, dimeric proteins found in all bacteria that are able to bind DNA to induce and stabilise DNA bending. HU plays a structural role in replication initiation, transcription regulation, site-specific recombination, and the compaction of the bacterial genome [PubMed12853489]. TF1 is essential for viral multiplication [PubMed10993726].

The DNA-binding domain of the TraM protein , an essential component of the DNA transfer machinery of the conjugative resistance plasmid R1, appears to have a similar structure to DBPII [PubMed11258958].


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

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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 9 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 IHF-like DNA-binding proteins 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 9 hidden Markov models representing the IHF-like DNA-binding proteins 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 ]