SUPERFAMILY 1.75 HMM library and genome assignments server


SRF-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   SRF-like [ 55454]
Superfamily:   SRF-like [ 55455]
Families:   SRF-like [ 55456] (4)


Superfamily statistics
Genomes (402) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 5,582 7,436 7
Proteins 5,577 7,434 7


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) developmental process 5.966e-15 Least Informative Direct
Biological Process (BP) multicellular organismal process 2.414e-11 Least Informative Direct
Biological Process (BP) regulation of metabolic process 5.676e-05 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.3162 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.03518 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.9467 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1297 Least Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) reproduction 1.716e-14 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.202e-13 Moderately Informative Direct
Biological Process (BP) regulation of cellular metabolic process 1.169e-12 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 1.297e-11 Moderately Informative Direct
Biological Process (BP) organ development 1.132e-09 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 5.378e-09 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 7.661e-08 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1.009e-07 Moderately Informative Direct
Biological Process (BP) tissue development 7.4e-06 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1.489e-05 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.0001912 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0002221 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.664 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.9196 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.09829 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.371 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.3128 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.05933 Moderately Informative Inherited
Biological Process (BP) system process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 0.3002 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.8482 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.7992 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.011 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03475 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.03649 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.04551 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.0963 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.9813 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.09358 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.07921 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1698 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.02932 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2912 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.05693 Moderately Informative Inherited
Biological Process (BP) regulation of reproductive process 5.086e-14 Informative Direct
Biological Process (BP) reproductive system development 8.164e-14 Informative Direct
Biological Process (BP) developmental process involved in reproduction 1.516e-13 Informative Direct
Biological Process (BP) positive regulation of gene expression 1.61e-12 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 2.345e-12 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1.442e-11 Informative Direct
Biological Process (BP) muscle structure development 2.871e-11 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 1.871e-09 Informative Direct
Biological Process (BP) muscle tissue development 6.726e-08 Informative Direct
Biological Process (BP) response to light stimulus 6.938e-08 Informative Direct
Biological Process (BP) anatomical structure formation involved in morphogenesis 3.466e-06 Informative Direct
Biological Process (BP) response to external stimulus 5.582e-06 Informative Direct
Biological Process (BP) cellular process involved in reproduction 1.853e-05 Informative Direct
Biological Process (BP) transcription, DNA-dependent 2.959e-05 Informative Direct
Biological Process (BP) response to inorganic substance 4.579e-05 Informative Direct
Biological Process (BP) intracellular signal transduction 7.473e-05 Informative Direct
Biological Process (BP) actin filament-based process 7.679e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 8.703e-05 Informative Direct
Biological Process (BP) response to lipid 0.0004048 Informative Direct
Biological Process (BP) cardiovascular system development 0.0006657 Informative Direct
Biological Process (BP) organ morphogenesis 0.0007578 Informative Direct
Biological Process (BP) tube development 0.0009127 Informative Direct
Biological Process (BP) epithelium development 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.1166 Informative Inherited
Biological Process (BP) regulation of response to stress 0.01025 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.6771 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.02301 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.001621 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.1336 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.00728 Informative Inherited
Biological Process (BP) response to other organism 0.8717 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.4697 Informative Inherited
Biological Process (BP) regulation of system process 0.01564 Informative Inherited
Biological Process (BP) regulation of growth 0.245 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.05484 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.5582 Informative Inherited
Biological Process (BP) synaptic transmission 0.1085 Informative Inherited
Biological Process (BP) cell projection organization 0.2827 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1554 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.005771 Informative Inherited
Biological Process (BP) mitochondrion organization 0.003384 Informative Inherited
Biological Process (BP) cell activation 0.02527 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.001068 Informative Inherited
Biological Process (BP) generation of neurons 0.01795 Informative Inherited
Biological Process (BP) regulation of cell development 1 Informative Inherited
Biological Process (BP) regulation of nervous system development 1 Informative Inherited
Biological Process (BP) negative regulation of cell death 0.2233 Informative Inherited
Biological Process (BP) response to organic nitrogen 0.5003 Informative Inherited
Biological Process (BP) cellular response to nitrogen compound 0.1429 Informative Inherited
Biological Process (BP) cell proliferation 0.2102 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.006079 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 0.2755 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 0.2613 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.07252 Informative Inherited
Biological Process (BP) growth 0.002298 Informative Inherited
Biological Process (BP) multi-organism reproductive process 0.6799 Informative Inherited
Biological Process (BP) cellular membrane organization 0.02811 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.3236 Informative Inherited
Biological Process (BP) regulation of immune response 0.008712 Informative Inherited
Biological Process (BP) immune response 0.1897 Informative Inherited
Biological Process (BP) post-embryonic organ development 0 Highly Informative Direct
Biological Process (BP) response to calcium ion 0 Highly Informative Direct
Biological Process (BP) external encapsulating structure organization 0 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 2.076e-15 Highly Informative Direct
Biological Process (BP) response to cold 1.158e-14 Highly Informative Direct
Biological Process (BP) response to UV 2.081e-14 Highly Informative Direct
Biological Process (BP) post-embryonic development 4.382e-14 Highly Informative Direct
Biological Process (BP) MAPK cascade 3.695e-10 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 8.327e-08 Highly Informative Direct
Biological Process (BP) ossification 8.584e-08 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 2.569e-07 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 3.397e-07 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 1.324e-06 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 1.884e-06 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 2.166e-06 Highly Informative Direct
Biological Process (BP) negative regulation of reproductive process 3.246e-06 Highly Informative Direct
Biological Process (BP) actomyosin structure organization 3.652e-06 Highly Informative Direct
Biological Process (BP) cellular membrane fusion 3.872e-06 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 3.982e-06 Highly Informative Direct
Biological Process (BP) regulation of binding 4.903e-06 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 1.037e-05 Highly Informative Direct
Biological Process (BP) epithelial tube morphogenesis 1.45e-05 Highly Informative Direct
Biological Process (BP) negative regulation of neuron death 1.778e-05 Highly Informative Direct
Biological Process (BP) connective tissue development 4.481e-05 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 7.646e-05 Highly Informative Direct
Biological Process (BP) regulation of behavior 0.0001425 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0001565 Highly Informative Direct
Biological Process (BP) cell growth 0.0002464 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0.0002639 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte proliferation 0.0005134 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0005305 Highly Informative Direct
Biological Process (BP) immune response-regulating signaling pathway 0.0005583 Highly Informative Direct
Biological Process (BP) pattern specification process 0.0005944 Highly Informative Direct
Biological Process (BP) response to toxic substance 0.0006682 Highly Informative Direct
Biological Process (BP) activation of immune response 0.0007707 Highly Informative Direct
Biological Process (BP) muscle organ development 0.0008905 Highly Informative Direct
Biological Process (BP) skeletal system development 0.0009101 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.0009572 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0.00659 Highly Informative Inherited
Biological Process (BP) kidney development 0.1181 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.005115 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.2447 Highly Informative Inherited
Biological Process (BP) regulation of neurological system process 0.5207 Highly Informative Inherited
Biological Process (BP) organelle localization 0.007189 Highly Informative Inherited
Biological Process (BP) positive regulation of cell activation 0.08659 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte activation 0.004626 Highly Informative Inherited
Biological Process (BP) regulation of neuron differentiation 0.007079 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.1012 Highly Informative Inherited
Biological Process (BP) regulation of myeloid cell differentiation 0.02136 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic process 0.04385 Highly Informative Inherited
Biological Process (BP) cell fate commitment 0.08343 Highly Informative Inherited
Biological Process (BP) B cell activation 0.006261 Highly Informative Inherited
Biological Process (BP) response to drug 0.004845 Highly Informative Inherited
Biological Process (BP) stem cell development 0.1595 Highly Informative Inherited
Biological Process (BP) developmental growth 0.02108 Highly Informative Inherited
Biological Process (BP) multi-multicellular organism process 0.006331 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.002292 Highly Informative Inherited
Molecular Function (MF) binding 1.033e-05 Least Informative Direct
Molecular Function (MF) heterocyclic compound binding 8.834e-05 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0.0001429 Moderately Informative Direct
Molecular Function (MF) protein binding 0.07151 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 1.474e-08 Informative Direct
Molecular Function (MF) enzyme binding 0.007332 Informative Inherited
Molecular Function (MF) RNA binding 1 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 5.625e-07 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.108 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.1019 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.7327 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.2632 Informative Inherited
Cellular Component (CC) chromosome 0.1244 Informative Inherited
Cellular Component (CC) nuclear body 0.0009933 Highly Informative Direct
Cellular Component (CC) chromatin 0.004279 Highly Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.006825 Highly Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details) Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)abnormal heart morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0Moderately InformativeDirect
Mammalian Phenotype (MP)preweaning lethality0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal heart ventricle morphology0InformativeDirect

Document: MP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0InformativeDirect
Xenopus ANatomical entity (XAN)heart0InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0InformativeDirect
Xenopus ANatomical entity (XAN)neural plate0InformativeDirect
Xenopus ANatomical entity (XAN)trunk somite0Highly InformativeDirect
Xenopus ANatomical entity (XAN)trunk musculature0Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0Least 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)plant cell0.7512Least InformativeInherited
Plant ANatomical entity (PAN)shoot apex1Least InformativeInherited
Plant ANatomical entity (PAN)root1Least InformativeInherited
Plant ANatomical entity (PAN)seed1Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.02174InformativeInherited
Plant ANatomical entity (PAN)root tip0.0268InformativeInherited
Plant ANatomical entity (PAN)integument9.132e-05Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.0001879Highly InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Biological processApoptosis8.003e-11Moderately InformativeDirect
Biological processNeurogenesis1.205e-14InformativeDirect
Cellular componentNucleus0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.0001715Least InformativeDirect
Post-translational modificationIsopeptide bond2.013e-12Moderately InformativeDirect
Post-translational modificationUbl conjugation1.539e-08Moderately InformativeDirect
Post-translational modificationAcetylation2.023e-05Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002100 SSF55455 Protein matches
Abstract Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [PubMed7637780], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins.

Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see


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-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 SRF-like 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 SRF-like 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-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]