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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 (2,960) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 60,430 544,273 80
Proteins 59,514 539,777 80


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.23Least InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.1331Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.2273Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.002891InformativeInherited
Phenotypic Abnormality (PA)Urinary tract neoplasm0.0009122Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.08705Least InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.04735Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.06609Moderately InformativeInherited
Mammalian Phenotype (MP)liver/biliary system phenotype0.1297Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.1682Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2753Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neuron morphology0.2971Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3996Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.01118InformativeInherited
Mammalian Phenotype (MP)abnormal hearing physiology0.0298InformativeInherited
Mammalian Phenotype (MP)abnormal liver physiology0.09168InformativeInherited
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.4131InformativeInherited
Mammalian Phenotype (MP)impaired hearing0.001905Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear outer hair cell morphology0.006153Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.08654Highly InformativeInherited
Mammalian Phenotype (MP)neuron degeneration0.1213Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism segment morphology variant0.01042Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant0.00008385InformativeDirect
Worm Phenotype (WP)tail morphology variant0.001343InformativeInherited
Worm Phenotype (WP)male tail morphology variant0.000004581Highly InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect
Fly Phenotype (FP)lethal0Moderately InformativeDirect
Fly Phenotype (FP)sensory perception defective0.0008989InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

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FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0Least InformativeDirect
Fly Anatomy (FA)nervous system0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0Least InformativeDirect
Fly Anatomy (FA)organ system subdivision0Least InformativeDirect
Fly Anatomy (FA)somatic cell0Least InformativeDirect
Fly Anatomy (FA)larva0.1626Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)head0Moderately InformativeDirect
Fly Anatomy (FA)adult segment0Moderately InformativeDirect
Fly Anatomy (FA)central nervous system0Moderately InformativeDirect
Fly Anatomy (FA)neuron0Moderately InformativeDirect
Fly Anatomy (FA)ganglion0Moderately InformativeDirect
Fly Anatomy (FA)adult integumentary system0Moderately InformativeDirect
Fly Anatomy (FA)appendage0Moderately InformativeDirect
Fly Anatomy (FA)region of integument0Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.0003093Moderately InformativeDirect
Fly Anatomy (FA)adult nervous system0.01525Moderately InformativeInherited
Fly Anatomy (FA)sensory system0.03948Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.05417Moderately InformativeInherited
Fly Anatomy (FA)antennal segment0.00000279InformativeDirect
Fly Anatomy (FA)synaptic neuropil domain0.000004651InformativeDirect
Fly Anatomy (FA)chemosensory system0.000009928InformativeDirect
Fly Anatomy (FA)adult procephalic segment0.00005297InformativeDirect
Fly Anatomy (FA)adult external head0.000273InformativeDirect
Fly Anatomy (FA)larval abdomen0.001039InformativeInherited
Fly Anatomy (FA)eo-type sensillum0.002627InformativeInherited
Fly Anatomy (FA)brain0.01071InformativeInherited
Fly Anatomy (FA)adult central nervous system0.01072InformativeInherited
Fly Anatomy (FA)interneuron0.01525InformativeInherited
Fly Anatomy (FA)larval segment0.02795InformativeInherited
Fly Anatomy (FA)abdominal segment0.03191InformativeInherited
Fly Anatomy (FA)neuromere0.04318InformativeInherited
Fly Anatomy (FA)antennal lobe glomerulus VA1v0.000000006675Highly InformativeDirect
Fly Anatomy (FA)maxillary palp sense organ0.00000001072Highly InformativeDirect
Fly Anatomy (FA)eo neuron0.000001002Highly InformativeDirect
Fly Anatomy (FA)unilateral ACT relay interneuron0.000003349Highly InformativeDirect
Fly Anatomy (FA)antennal lobe projection neuron iPN0.000003349Highly InformativeDirect
Fly Anatomy (FA)neuroblast lineage clone0.000014Highly InformativeDirect
Fly Anatomy (FA)sensillum basiconicum0.0001075Highly InformativeDirect
Fly Anatomy (FA)olfactory sensory organ0.132Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

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ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.248Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.321Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.7681Least InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.2055Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.001279InformativeInherited
Zebrafish Anatomy (ZA)digestive system0.107InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.1593Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.4962Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.987Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)trunk1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.006065Moderately InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.02026Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.7355Moderately InformativeInherited
Xenopus ANatomical entity (XAN)neural plate0.00001033InformativeDirect
Xenopus ANatomical entity (XAN)spinal cord0.000261InformativeDirect
Xenopus ANatomical entity (XAN)cranial placode0.0005801InformativeDirect
Xenopus ANatomical entity (XAN)neural tube0.000989InformativeDirect
Xenopus ANatomical entity (XAN)mesenchyme0.004491InformativeInherited
Xenopus ANatomical entity (XAN)anatomical space0.08249InformativeInherited
Xenopus ANatomical entity (XAN)urinary system0.4252InformativeInherited
Xenopus ANatomical entity (XAN)presumptive midbrain-hindbrain boundary0.000002162Highly InformativeDirect
Xenopus ANatomical entity (XAN)chordal neural plate0.000007654Highly InformativeDirect
Xenopus ANatomical entity (XAN)proximal tubule0.0001922Highly InformativeDirect
Xenopus ANatomical entity (XAN)neuron0.0004291Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.0003972Moderately InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)pollen0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.6459Moderately InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationLyase0.000000000005232Moderately 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 45 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 45 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]