SUPERFAMILY 1.75 HMM library and genome assignments server

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FF domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Another 3-helical bundle [ 81602] (5)
Superfamily:   FF domain [ 81698]
Families:   FF domain [ 81699] (3)

Superfamily statistics
Genomes (422) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,504 3,305 6
Proteins 1,401 1,085 6

 Functional annotation
General category Other
Detailed category Unknown function

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) cellular aromatic compound metabolic process 5.063e-06 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.036e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.587e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.309e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.002085 Least Informative Inherited
Biological Process (BP) gene expression 1.946e-09 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 3.964e-10 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.03028 Moderately Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0005562 Informative Direct
Biological Process (BP) mRNA processing 0.000861 Highly Informative Direct
Biological Process (BP) RNA splicing, via transesterification reactions 0.4429 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4389 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.07237 Least Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 4.221e-06 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.002432 Moderately Informative Inherited
Cellular Component (CC) spliceosomal complex 4.551e-08 Highly Informative Direct
Cellular Component (CC) small nuclear ribonucleoprotein complex 2.835e-07 Highly Informative Direct

Document: GO annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least 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)shoot apex0Least InformativeDirect
Plant ANatomical entity (PAN)shoot internode0Least InformativeDirect
Plant ANatomical entity (PAN)root0Least InformativeDirect
Plant ANatomical entity (PAN)plant embryo0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)vascular leaf0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant ANatomical entity (PAN)petal0Least InformativeDirect
Plant ANatomical entity (PAN)stem0Least InformativeDirect
Plant ANatomical entity (PAN)pedicel0Least InformativeDirect
Plant ANatomical entity (PAN)androecium0Least InformativeDirect
Plant ANatomical entity (PAN)gynoecium0Least InformativeDirect
Plant ANatomical entity (PAN)leaf lamina0Least InformativeDirect
Plant ANatomical entity (PAN)collective leaf structure0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)phyllome apex0Least InformativeDirect
Plant ANatomical entity (PAN)microgametophyte0Least 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

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation4.055e-08Moderately InformativeDirect
Biological processmRNA splicing2.041e-14InformativeDirect
Cellular componentNucleus1.269e-15Least InformativeDirect
DomainRepeat0Least InformativeDirect
Post-translational modificationRepressor3.186e-08Moderately InformativeDirect
Post-translational modificationGTPase activation2.406e-14InformativeDirect
Post-translational modificationPhosphoprotein1.658e-10Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002713 SSF81698 Protein matches
Abstract The FF domain may be involved in protein-protein interaction [PubMed10390614]. It often occurs as multiple copies and often accompanies WW domains . PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [PubMed8622699].

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) · Worm Phenotype (WP) · 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 6 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 FF 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 6 hidden Markov models representing the FF 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 · Gene Ontology (high-coverage) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.