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.


SMAD/FHA domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SMAD/FHA domain [ 49878]
Superfamily:   SMAD/FHA domain [ 49879] (4)
Families:   SMAD domain [ 49880] (4)
  FHA domain [ 49885] (11)
  Interferon regulatory factor 3 (IRF3), transactivation domain [ 101630]
  EssC N-terminal domain-like [ 141143]


Superfamily statistics
Genomes (1,762) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 17,190 79,873 38
Proteins 16,412 75,224 37


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)Oxidoreductases0.1289Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.000000000000007375Moderately InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0.00000000823Moderately InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation0.000000000001841InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)disease by infectious agent0.0003222Moderately InformativeDirect
Disease Ontology (DO)genetic disease0.03816Moderately InformativeInherited
Disease Ontology (DO)autosomal dominant disease0.0006953InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the head0.1012Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.104Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.3213Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal oral cavity morphology0.1985Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral nervous system morphology0.4088Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of upper lip0.112InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating protein level0.2211InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral myelination0.0009923Highly InformativeDirect
Phenotypic Abnormality (PA)Cleft upper lip0.06369Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.05196Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.1459Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.2904Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.4445Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.4813Least InformativeInherited
Mammalian Phenotype (MP)neoplasm0.001885Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.007937Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.02701Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.05211Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.07491Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.1214Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.1408Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.1509Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1543Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.2099Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.24Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.2515Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.2563Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.3001Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.5741Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.773Moderately InformativeInherited
Mammalian Phenotype (MP)increased gland tumor incidence0.000168InformativeDirect
Mammalian Phenotype (MP)increased carcinoma incidence0.0002101InformativeDirect
Mammalian Phenotype (MP)chromosomal instability0.0002904InformativeDirect
Mammalian Phenotype (MP)abnormal response to radiation0.002795InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.009747InformativeInherited
Mammalian Phenotype (MP)abnormal B cell differentiation0.01162InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.03847InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.06528InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.08243InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.1201InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive gland morphology0.2InformativeInherited
Mammalian Phenotype (MP)abnormal embryo development0.2254InformativeInherited
Mammalian Phenotype (MP)abnormal fertility/fecundity0.4068InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.691InformativeInherited
Mammalian Phenotype (MP)increased gonad tumor incidence0.000001964Highly InformativeDirect
Mammalian Phenotype (MP)abnormal embryonic epiblast morphology0.00002556Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cumulus expansion0.0000269Highly InformativeDirect
Mammalian Phenotype (MP)decreased interferon-alpha secretion0.0001578Highly InformativeDirect
Mammalian Phenotype (MP)abnormal digestive system development0.0004288Highly InformativeDirect
Mammalian Phenotype (MP)abnormal oocyte number0.0004297Highly InformativeDirect
Mammalian Phenotype (MP)absent primordial germ cells0.00072Highly InformativeDirect
Mammalian Phenotype (MP)abnormal gastrulation0.002322Highly InformativeInherited
Mammalian Phenotype (MP)premature aging0.004486Highly InformativeInherited
Mammalian Phenotype (MP)decreased dendritic cell number0.00552Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.3395Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism behavior variant0.0005532Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.003827Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.005246Least InformativeInherited
Worm Phenotype (WP)nervous system morphology variant0.00003936Moderately InformativeDirect
Worm Phenotype (WP)pericellular component development variant0.001939Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.05696Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.07333Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant0.2743Moderately InformativeInherited
Worm Phenotype (WP)movement variant0.6597Moderately InformativeInherited
Worm Phenotype (WP)velocity of movement variant0.0001679InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.0007671InformativeDirect
Worm Phenotype (WP)male morphology variant0.0017InformativeInherited
Worm Phenotype (WP)localized movement variant0.003541InformativeInherited
Worm Phenotype (WP)tail morphology variant0.00522InformativeInherited
Worm Phenotype (WP)body posture variant0.01077InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.01116InformativeInherited
Worm Phenotype (WP)sensillum morphology variant0.02613InformativeInherited
Worm Phenotype (WP)foraging behavior variant0.05082InformativeInherited
Worm Phenotype (WP)locomotor coordination variant0.05443InformativeInherited
Worm Phenotype (WP)body length variant0.5012InformativeInherited
Worm Phenotype (WP)locomotion reduced0.7868InformativeInherited
Worm Phenotype (WP)cuticle development variant0.0000008999Highly InformativeDirect
Worm Phenotype (WP)cuticle physiology variant0.000003013Highly InformativeDirect
Worm Phenotype (WP)male nervous system development variant0.0000181Highly InformativeDirect
Worm Phenotype (WP)social behavior variant0.00002125Highly InformativeDirect
Worm Phenotype (WP)short0.00002544Highly InformativeDirect
Worm Phenotype (WP)roaming variant0.00004069Highly InformativeDirect
Worm Phenotype (WP)coiling frequency0.00005481Highly InformativeDirect
Worm Phenotype (WP)forward locomotion decreased0.00006044Highly InformativeDirect
Worm Phenotype (WP)body posture amplitude variant0.0001024Highly InformativeDirect
Worm Phenotype (WP)male tail morphology variant0.0001047Highly InformativeDirect
Worm Phenotype (WP)backward point velocity variant0.0001052Highly InformativeDirect
Worm Phenotype (WP)nose movement variant0.0001895Highly InformativeDirect
Worm Phenotype (WP)amplitude of sinusoidal movement variant0.000223Highly InformativeDirect
Worm Phenotype (WP)frequency of body bend variant0.0002495Highly InformativeDirect
Worm Phenotype (WP)male nervous system morphology variant0.0002553Highly InformativeDirect
Worm Phenotype (WP)dauer development variant0.0004326Highly InformativeDirect
Worm Phenotype (WP)path curvature variant0.06293Highly InformativeInherited
Worm Phenotype (WP)body posture wavelength variant0.3855Highly InformativeInherited

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)decreased occurrence of cell division0.00005341Highly InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0Least InformativeDirect
Fly Anatomy (FA)multi-tissue structure0.08475Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)stem cell0.01211Moderately InformativeInherited
Fly Anatomy (FA)thoracic segment0.04691Moderately InformativeInherited
Fly Anatomy (FA)gonad0.07479Moderately InformativeInherited
Fly Anatomy (FA)imaginal disc0.01538InformativeInherited
Fly Anatomy (FA)larval thoracic segment0.01594InformativeInherited
Fly Anatomy (FA)ovariole0.02503InformativeInherited
Fly Anatomy (FA)germline cell0.0735InformativeInherited
Fly Anatomy (FA)female germline stem cell0.0005854Highly InformativeDirect
Fly Anatomy (FA)wing disc0.000882Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)cell0.04568Least InformativeInherited
Zebrafish Anatomy (ZA)multi-tissue structure0.09003Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.2099Least InformativeInherited
Zebrafish Anatomy (ZA)portion of tissue0.02005Moderately InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.06132Moderately InformativeInherited
Zebrafish Anatomy (ZA)hematopoietic system0.0000005837InformativeDirect
Zebrafish Anatomy (ZA)hematopoietic cell0.0001818InformativeDirect
Zebrafish Anatomy (ZA)immune system0.02576InformativeInherited
Zebrafish Anatomy (ZA)mononuclear phagocyte0.000000003122Highly InformativeDirect
Zebrafish Anatomy (ZA)professional antigen presenting cell0.000000005417Highly InformativeDirect
Zebrafish Anatomy (ZA)intermediate cell mass of mesoderm0.0000006815Highly InformativeDirect
Zebrafish Anatomy (ZA)floor plate0.00003118Highly InformativeDirect
Zebrafish Anatomy (ZA)embryonic structure0.2524Highly InformativeInherited

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0.1631Least InformativeInherited
Xenopus ANatomical entity (XAN)tissue0.3418Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.7662Least InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.1466Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cardiovascular system0.004802InformativeInherited

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0.1037Least InformativeInherited
Enzyme Commission (EC)Hydrolases0.1411Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases0.5919Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.000000000001007Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases0.0000000128Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0.4679Moderately InformativeInherited
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0InformativeDirect
Enzyme Commission (EC)Non-specific serine/threonine protein kinase5.004e-16InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporate0.00000002355InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters0Highly InformativeDirect
Enzyme Commission (EC)DNA-(apurinic or apyrimidinic site) lyase0.00005293Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008984 SSF49879 Protein matches
Abstract

FHA and SMAD (MH2) domains share a common structure consisting of a sandwich of eleven beta strands in two sheets with Greek key topology. Forkhead-associated (FHA) domains were originally identified as a sequence profile of about 75 amino acids, whereas the full-length domain is closer to about 150 amino acids. FHA domains are found in transcription factors, kinesin motors, and in a variety of other signalling molecules in organisms ranging from eubacteria to humans. FHA domains are protein-protein interaction domains that are specific for phosphoproteins. FHA-containing proteins function in maintaining cell-cycle checkpoints, DNA repair and transcriptional regulation. FHA domain proteins include the Chk2/Rad53/Cds1 family of proteins that contain one or more FHA domains, as well as a Ser/Thr kinase domain [PubMed11106755, PubMed12121644, PubMed12049740].

SMAD domain proteins are found in a range of species from nematodes to humans. These highly conserved proteins contain an N-terminal MH1 domain that contacts DNA, and is separated by a short linker region from the C-terminal MH2 domain, the later showing a striking similarity to FHA domains. SMAD proteins mediate signalling by the TGF-beta/activin/BMP-2/4 cytokines from receptor Ser/Thr protein kinases at the cell surface to the nucleus. SMAD proteins fall into three functional classes: the receptor-regulated SMADs (R-SMADs), including SMAD1, -2, -3, -5, and -8, each of which is involved in a ligand-specific signalling pathway [PubMed11779503]; the comediator SMADs (co-SMADs), including SMAD4, which interact with R-SMADs to participate in signalling [PubMed9214508]; and the inhibitory SMADs (I-SMADs), including SMAD6 and -7, which block the activation of R-SMADs and Co-SMADs, thereby negatively regulating signalling pathways [PubMed11483516].


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) · Disease Ontology (DO) · 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) ]

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 19 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 SMAD/FHA domain 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 19 hidden Markov models representing the SMAD/FHA domain 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) · Disease Ontology (DO) · 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) · Internal database links ]