SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


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 (465) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 7,145 20,244 7
Proteins 7,117 20,190 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

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)growth/size/body region phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.07324Least InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cell death0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0Moderately InformativeDirect
Mammalian Phenotype (MP)lethality during fetal growth through weaning0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal muscle physiology0.002162Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle morphology0.002193Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.01152Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.01719Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)premature death0InformativeDirect
Mammalian Phenotype (MP)increased apoptosis0InformativeDirect
Mammalian Phenotype (MP)impaired muscle contractility0.00006906InformativeDirect
Mammalian Phenotype (MP)abnormal neuron physiology0.000739InformativeDirect
Mammalian Phenotype (MP)abnormal cardiac muscle contractility0.01063InformativeInherited
Mammalian Phenotype (MP)perinatal lethality0.04829InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.06453InformativeInherited
Mammalian Phenotype (MP)enhanced paired-pulse facilitation0.00000004225Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cardiac muscle tissue morphology0.00008127Highly InformativeDirect
Mammalian Phenotype (MP)neonatal lethality0.002436Highly InformativeInherited

Document: MP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)cardiovascular system0Moderately InformativeDirect
Zebrafish Anatomy (ZA)anatomical cluster0Moderately InformativeDirect
Zebrafish Anatomy (ZA)pericardial region0InformativeDirect
Zebrafish Anatomy (ZA)heart0Highly InformativeDirect

Document: ZA 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)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)embryonic structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0InformativeDirect
Xenopus ANatomical entity (XAN)epithelium0.0000458InformativeDirect
Xenopus ANatomical entity (XAN)mesoderm0.01176InformativeInherited
Xenopus ANatomical entity (XAN)trunk musculature0.0000005242Highly InformativeDirect
Xenopus DEvelopment stage (XDE)post-embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0Moderately 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 plant0.05097Least InformativeInherited
Plant ANatomical entity (PAN)seed1Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue1Least InformativeInherited
Plant ANatomical entity (PAN)root system1Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis1Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure1Least InformativeInherited
Plant ANatomical entity (PAN)portion of ground tissue0.01661InformativeInherited
Plant ANatomical entity (PAN)root tip0.02096InformativeInherited
Plant ANatomical entity (PAN)embryo sac cell0Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.0001311Highly InformativeDirect
Plant ANatomical entity (PAN)plant ovule0.000567Highly InformativeDirect

Document: AP 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 · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 · Disease Ontology (DO) · Mouse Phenotype (MP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]