SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,950) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 60,325 409,262 80
Proteins 59,426 407,008 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)regulation of cellular process0.81065.234e-07Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.12280Least InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.001480Moderately InformativeInherited
Biological Process (BP)regulation of cellular biosynthetic process0.012360Moderately InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.014850Moderately InformativeInherited
Biological Process (BP)regulation of gene expression0.0045540Moderately InformativeInherited
Molecular Function (MF)binding13.162e-06Least InformativeInherited
Molecular Function (MF)nucleic acid binding0.0002530Moderately InformativeDirect
Molecular Function (MF)DNA binding1.828e-060InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity0.0001070InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity9.484e-050Highly InformativeDirect

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) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) regulation of cellular process 5.234e-07 Least Informative Direct
Biological Process (BP) developmental process 1.974e-08 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.532e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.8471 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.8948 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1.148e-09 Moderately Informative Direct
Biological Process (BP) cell differentiation 0 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.421e-08 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 7.318e-06 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 7.864e-06 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 7.895e-06 Moderately Informative Direct
Biological Process (BP) nervous system development 9.317e-05 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0001517 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.264 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.6034 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.5207 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.002902 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 1 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.007074 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4512 Moderately Informative Inherited
Biological Process (BP) organ development 0.005335 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.008372 Moderately Informative Inherited
Biological Process (BP) gene expression 0.02516 Moderately Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 8.122e-10 Informative Direct
Biological Process (BP) positive regulation of gene expression 3.741e-15 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 2.537e-08 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 3.34e-08 Informative Direct
Biological Process (BP) transcription, DNA-dependent 2.146e-11 Informative Direct
Biological Process (BP) embryonic morphogenesis 2.288e-05 Informative Direct
Biological Process (BP) regulation of nervous system development 3.542e-05 Informative Direct
Biological Process (BP) sensory organ development 0.0003668 Informative Direct
Biological Process (BP) leukocyte activation 0.0009612 Informative Direct
Biological Process (BP) cell projection organization 0.0009716 Informative Direct
Biological Process (BP) negative regulation of cell death 0.6097 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.07152 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.9617 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) tube development 0.05552 Informative Inherited
Biological Process (BP) epithelium development 0.4786 Informative Inherited
Biological Process (BP) organ morphogenesis 0.9116 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.2958 Informative Inherited
Biological Process (BP) synaptic transmission 1 Informative Inherited
Biological Process (BP) regulation of cell development 0.1929 Informative Inherited
Biological Process (BP) generation of neurons 0.08298 Informative Inherited
Biological Process (BP) positive regulation of cellular component organization 0.6598 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.231 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1295 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.5785 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.6279 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.283 Informative Inherited
Biological Process (BP) organelle assembly 0.2037 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 1 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.332 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.4573 Informative Inherited
Biological Process (BP) secretion by cell 0.006508 Informative Inherited
Biological Process (BP) gland development 0.5952 Informative Inherited
Biological Process (BP) central nervous system development 0.008586 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.03909 Informative Inherited
Biological Process (BP) single-organism behavior 0.3202 Informative Inherited
Biological Process (BP) chromosome organization 0.5266 Informative Inherited
Biological Process (BP) nitrogen compound transport 0.2252 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 1 Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 4.243e-06 Highly Informative Direct
Biological Process (BP) endocrine system development 7.318e-15 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 1.913e-07 Highly Informative Direct
Biological Process (BP) regulation of membrane potential 2.319e-06 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 2.472e-06 Highly Informative Direct
Biological Process (BP) cell fate commitment 5.782e-06 Highly Informative Direct
Biological Process (BP) renal system development 1.009e-05 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 2.595e-05 Highly Informative Direct
Biological Process (BP) hormone transport 2.877e-05 Highly Informative Direct
Biological Process (BP) positive regulation of neurogenesis 3.43e-05 Highly Informative Direct
Biological Process (BP) diencephalon development 8.402e-05 Highly Informative Direct
Biological Process (BP) respiratory system development 0.0002061 Highly Informative Direct
Biological Process (BP) amide transport 0.0002907 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.0003493 Highly Informative Direct
Biological Process (BP) learning or memory 0.0004734 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.0009651 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic process 0.007002 Highly Informative Inherited
Biological Process (BP) neuromuscular process 0.06609 Highly Informative Inherited
Biological Process (BP) ear development 0.01289 Highly Informative Inherited
Biological Process (BP) epidermal cell differentiation 0.05908 Highly Informative Inherited
Biological Process (BP) cell projection assembly 0.025 Highly Informative Inherited
Biological Process (BP) cilium organization 0.04262 Highly Informative Inherited
Biological Process (BP) cellular component assembly involved in morphogenesis 0.4945 Highly Informative Inherited
Biological Process (BP) regulation of multicellular organism growth 0.00923 Highly Informative Inherited
Biological Process (BP) positive regulation of growth 0.5449 Highly Informative Inherited
Biological Process (BP) B cell activation 0.004048 Highly Informative Inherited
Biological Process (BP) signal release 0.07316 Highly Informative Inherited
Biological Process (BP) sensory perception 0.05273 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.5331 Highly Informative Inherited
Biological Process (BP) regulation of cell adhesion 0.7224 Highly Informative Inherited
Molecular Function (MF) binding 3.162e-06 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) chromatin binding 6.444e-09 Informative Direct
Molecular Function (MF) protein dimerization activity 4.362e-05 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 7.702e-10 Highly Informative Direct
Molecular Function (MF) transcription factor binding 1.286e-06 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.2422 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.01427 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.001843 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 6.461e-12 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0009007 Moderately Informative Direct
Cellular Component (CC) nucleoplasm part 8.909e-08 Informative Direct
Cellular Component (CC) chromosome 0.006031 Informative Inherited

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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.3595Least InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.07362Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2941Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.5961Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.125InformativeInherited
Mammalian Phenotype (MP)abnormal cerebrum morphology0.3976InformativeInherited
Mammalian Phenotype (MP)abnormal temporal bone morphology0.0004092Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral cortex morphology0.2392Highly 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 variant0.004634Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant1.966e-05InformativeDirect
Worm Phenotype (WP)male tail morphology variant7.122e-07Highly 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)sensory perception defective0.0007181InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.07863Least InformativeInherited
Fly Anatomy (FA)anatomical group0.09013Least InformativeInherited
Fly Anatomy (FA)adult0.09404Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.1212Least InformativeInherited
Fly Anatomy (FA)larva0.1639Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)neuron0Moderately InformativeDirect
Fly Anatomy (FA)multi-cell-component structure0.0004413Moderately InformativeDirect
Fly Anatomy (FA)adult sense organ0.007618Moderately InformativeInherited
Fly Anatomy (FA)tagmatic subdivision of integument0.01023Moderately InformativeInherited
Fly Anatomy (FA)adult integumentary system0.01083Moderately InformativeInherited
Fly Anatomy (FA)sensillum0.01652Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.0201Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.02241Moderately InformativeInherited
Fly Anatomy (FA)external sensory organ0.02705Moderately InformativeInherited
Fly Anatomy (FA)peripheral nervous system0.05943Moderately InformativeInherited
Fly Anatomy (FA)appendage0.06724Moderately InformativeInherited
Fly Anatomy (FA)adult head0.1373Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.2056Moderately InformativeInherited
Fly Anatomy (FA)antennal segment2.367e-06InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion5.484e-06InformativeDirect
Fly Anatomy (FA)adult external head7.343e-06InformativeDirect
Fly Anatomy (FA)chemosensory system8.507e-06InformativeDirect
Fly Anatomy (FA)synaptic neuropil1.686e-05InformativeDirect
Fly Anatomy (FA)neuromere1.729e-05InformativeDirect
Fly Anatomy (FA)adult brain1.864e-05InformativeDirect
Fly Anatomy (FA)adult procephalic segment6.183e-05InformativeDirect
Fly Anatomy (FA)interneuron0.01224InformativeInherited
Fly Anatomy (FA)sensory organ cell0.02021InformativeInherited
Fly Anatomy (FA)appendage segment0.02205InformativeInherited
Fly Anatomy (FA)antennal lobe glomerulus VA1v5.711e-09Highly InformativeDirect
Fly Anatomy (FA)maxillary palpus1.932e-06Highly InformativeDirect
Fly Anatomy (FA)eo neuron2.178e-06Highly InformativeDirect
Fly Anatomy (FA)unilateral ACT relay interneuron2.368e-06Highly InformativeDirect
Fly Anatomy (FA)antennal lobe projection neuron iPN2.368e-06Highly InformativeDirect
Fly Anatomy (FA)sensillum basiconicum0.0001041Highly InformativeDirect
Fly Anatomy (FA)chemosensory neuron0.0006853Highly InformativeDirect
Fly Anatomy (FA)olfactory sensory organ0.1101Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)nervous system0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)cavitated compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)central nervous system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)brain0InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.2762Least InformativeInherited
Xenopus ANatomical entity (XAN)central nervous system0.5004Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.6653Least InformativeInherited
Xenopus ANatomical entity (XAN)head1Least InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.3388Moderately InformativeInherited
Xenopus ANatomical entity (XAN)chordal neural plate3.487e-05InformativeDirect
Xenopus ANatomical entity (XAN)midbrain-hindbrain boundary0.0005313Highly 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 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 phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0.6865Moderately 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)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processCarbohydrate metabolism1Moderately InformativeInherited
Biological processPurine biosynthesis0InformativeDirect
Biological processCell shape1.279e-13InformativeDirect
Biological processNeurogenesis5.175e-05InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentCell membrane0.9763Moderately InformativeInherited
Cellular componentCell inner membrane1.825e-05InformativeDirect
Developmental stageEarly protein7.694e-11Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainSignal-anchor0InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately 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) · 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 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) · 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 ]