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lambda repressor-like DNA-binding domains superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   lambda repressor-like DNA-binding domains [ 47412]
Superfamily:   lambda repressor-like DNA-binding domains [ 47413] (13)
Families:   POU-specific domain [ 47414] (3)
  Phage repressors [ 47419] (7)
  SinR domain-like [ 47432] (8)
  Cyanase N-terminal domain [ 47435]
  GalR/LacI-like bacterial regulator [ 47438] (4)
  YdiL-like [ 109813] (2)
  CUT domain [ 116891] (4)
  Probable transcriptional regulator VC1968, N-terminal domain [ 116898]
  Bacteriophage CII protein [ 140520]
  NE0471 C-terminal domain-like [ 140523]
  PrgX N-terminal domain-like [ 140526]
  EDF1-like [ 140529]
  NE1354 [ 140532] (2)


Superfamily statistics
Genomes (2,958) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 60,398 420,069 80
Proteins 59,487 416,535 80


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)biological regulation0.97950.00000000000161Least InformativeInherited
Biological Process (BP)regulation of gene expression0.000034470Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000016320Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00010320Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.00086440Moderately InformativeDirect
Molecular Function (MF)binding10.000009205Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0000047090Moderately InformativeDirect
Molecular Function (MF)DNA binding0.0000000025510InformativeDirect
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding0.00000010190InformativeDirect
Molecular Function (MF)transcription regulatory region DNA binding0.00000000047910Highly InformativeDirect
Cellular Component (CC)protein-DNA complex0.00074160InformativeDirect

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) biological regulation 0.00000000000161 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.07723 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.00003832 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00000001509 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4316 Moderately Informative Inherited
Biological Process (BP) single organism signaling 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3421 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.03231 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.5545 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.07549 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.4027 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.05249 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1929 Moderately Informative Inherited
Biological Process (BP) gene expression 0.8689 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.6169 Moderately Informative Inherited
Biological Process (BP) transcription, DNA-templated 0.00001306 Informative Direct
Biological Process (BP) positive regulation of gene expression 0.000007699 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0001808 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.4569 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.1676 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 0.1286 Informative Inherited
Biological Process (BP) locomotion 0.3665 Informative Inherited
Biological Process (BP) cell development 0.3023 Informative Inherited
Biological Process (BP) cell death 0.08515 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.5617 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.1685 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.8216 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.1601 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.2842 Informative Inherited
Biological Process (BP) embryo development 0.9528 Informative Inherited
Biological Process (BP) epithelium development 0.8733 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.952 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.009109 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) reproductive system development 1 Informative Inherited
Biological Process (BP) positive regulation of immune system process 1 Informative Inherited
Biological Process (BP) generation of neurons 0.8312 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.7562 Informative Inherited
Biological Process (BP) cellular response to lipid 0.002094 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.8732 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1562 Informative Inherited
Biological Process (BP) system process 0.01287 Informative Inherited
Biological Process (BP) behavior 0.1513 Informative Inherited
Biological Process (BP) kidney development 0.0001182 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0.0006323 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.00001767 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.000000435 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 0.0000743 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00003414 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.00007958 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0.0004995 Highly Informative Direct
Biological Process (BP) neuron development 0.007747 Highly Informative Inherited
Biological Process (BP) plasma membrane bounded cell projection organization 0.002529 Highly Informative Inherited
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.003409 Highly Informative Inherited
Biological Process (BP) apoptotic process 0.1065 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.03707 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) gastrulation 0.004115 Highly Informative Inherited
Biological Process (BP) positive regulation of cellular component biogenesis 0.1487 Highly Informative Inherited
Biological Process (BP) sex differentiation 0.05162 Highly Informative Inherited
Biological Process (BP) regulation of hemopoiesis 0.01024 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.003733 Highly Informative Inherited
Biological Process (BP) nervous system process 0.002326 Highly Informative Inherited
Molecular Function (MF) binding 0.000009205 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0.000000000006605 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.0007567 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.00002722 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.00000000002451 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.005678 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.000075 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01164 Moderately Informative Inherited
Cellular Component (CC) protein-DNA complex 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processDifferentiation0.0000006646Moderately InformativeDirect
Biological processCarbohydrate metabolism1Moderately InformativeInherited
Biological processPurine biosynthesis0InformativeDirect
Biological processCell shape0.0000000000001769InformativeDirect
Biological processNeurogenesis0.0000001269InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane0.977Moderately InformativeInherited
Cellular componentCell inner membrane0.00004415InformativeDirect
Developmental stageEarly protein0.0000000001554Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainSignal-anchor0InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.0002746Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010982 SSF47413 Protein matches
Abstract

Bacteriophage lambda C1 repressor controls the expression of viral genes as part of the lysogeny/lytic growth switch. C1 is essential for maintaining lysogeny, where the phage replicates non-disruptively along with the host. If the host cell is threatened, then lytic growth is induced. The Lambda C1 repressor consists of two domains connected by a linker: an N-terminal DNA-binding domain that also mediates interactions with RNA polymerase, and a C-terminal dimerisation domain [PubMed10892750]. The DNA-binding domain consists of four helices in a closed folded leaf motif. Several different phage repressors from different helix-turn-helix families contain DNA-binding domains that adopt a similar topology. These include the Lambda Cro repressor, Bacteriophage 434 C1 and Cro repressors, P22 C2 repressor, and Bacteriophage Mu Ner protein.

The DNA-binding domain of Bacillus subtilis spore inhibition repressor SinR is identical to that of phage repressors [PubMed9799632]. SinR represses sporulation, which only occurs in response to adverse conditions. This provides a possible evolutionary link between the two adaptive responses of bacterial sporulation and prophage induction.

Other DNA-binding domains also display similar structural folds to that of Lambda C1. These include bacterial regulators such as the purine repressor (PurR), the lactose repressor (Lacr) and the fructose repressor (FruR), each of which has an N-terminal DNA-binding domain that exhibits a fold similar to that of lambda C1, except that they lack the first helix [PubMed7973627, PubMed10700279, PubMed9237914]. POU-specific domains found in transcription factors such as in Oct-1, Pit-1 and Hepatocyte nuclear factor 1a (LFB1/HNF1) display four-helical fold DNA-binding domains similar to that of Lambda C1 [PubMed11583619, PubMed9009203, PubMed12453420]. The N-terminal domain of cyanase has an alpha-helix bundle motif similar to Lambda C1, but it probably does not bind DNA. Cyanase is an enzyme found in bacteria and plants that catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide in response to extracellular cyanate [PubMed10801492].


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) · Enzyme Commission (EC) · 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 43 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 lambda repressor-like DNA-binding domains 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 43 hidden Markov models representing the lambda repressor-like DNA-binding domains 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]