SUPERFAMILY 1.75 HMM library and genome assignments server


Ferritin-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Ferritin-like [ 47239] (6)
Superfamily:   Ferritin-like [ 47240] (9)
Families:   Ferritin [ 47241] (9)
  Ribonucleotide reductase-like [ 47253] (8)
  Manganese catalase (T-catalase) [ 100951]
  YciF-like [ 140445] (2)
  half-ferritin [ 140450]
  PMT1231-like [ 158402]
  MiaE-like [ 158405]
  AMB4284-like [ 158408]
  Rv2844-like [ 158411]


Superfamily statistics
Genomes (2,458) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 17,348 52,859 108
Proteins 17,199 52,622 108


Functional annotation
General category Processes_IC
Detailed category Ion metabolism and transport

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)biosynthetic process0.010091.488e-06Least InformativeInherited
Biological Process (BP)regulation of cellular process0.2051Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.060861.004e-06Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0087550.0001828Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.42680.05527Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.025712.59e-05Least InformativeInherited
Biological Process (BP)heterocycle metabolic process0.093560.007395Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.47471Least InformativeInherited
Biological Process (BP)response to stimulus6.816e-060.0092Least InformativeInherited
Biological Process (BP)localization0.9421Least InformativeInherited
Biological Process (BP)single-organism cellular process0.05950.9992Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.92751Least InformativeInherited
Biological Process (BP)multicellular organismal process0.16061Least InformativeInherited
Biological Process (BP)developmental process0.038191Least InformativeInherited
Biological Process (BP)organophosphate metabolic process0.00095188.017e-12Moderately InformativeDirect
Biological Process (BP)homeostatic process2.614e-142.881e-08Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.00014677.225e-06Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.00028683.077e-10Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.41390.5521Moderately InformativeInherited
Biological Process (BP)cellular localization0.17650.6631Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.011439.579e-06Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.011297.738e-05Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.013221.414e-05Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.057140.0005509Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0042741.386e-10Moderately InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.0064292.085e-07Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.00014250.1999Moderately InformativeInherited
Biological Process (BP)organelle organization0.34190.4993Moderately InformativeInherited
Biological Process (BP)immune system process4.482e-050.002426Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0047350.1382Moderately InformativeInherited
Biological Process (BP)system process0.25720.7239Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.061211Moderately InformativeInherited
Biological Process (BP)organ development0.08321Moderately InformativeInherited
Biological Process (BP)DNA metabolic process1.079e-050.0002537InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process3.437e-097.064e-11InformativeDirect
Biological Process (BP)immune response3.419e-051.908e-05InformativeDirect
Biological Process (BP)response to oxidative stress4.492e-056.882e-09InformativeDirect
Biological Process (BP)mitochondrion organization1.038e-051.027e-05InformativeDirect
Biological Process (BP)nucleotide biosynthetic process4.474e-051.673e-06InformativeDirect
Biological Process (BP)regulation of cell proliferation1.018e-060.000477InformativeDirect
Biological Process (BP)cellular ketone metabolic process8.819e-075.998e-09InformativeDirect
Biological Process (BP)coenzyme biosynthetic process0.0021947.827e-05InformativeInherited
Biological Process (BP)response to inorganic substance0.013580.001105InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.59051InformativeInherited
Biological Process (BP)cellular cation homeostasis0.054760.004778InformativeInherited
Biological Process (BP)metal ion homeostasis0.021960.107InformativeInherited
Biological Process (BP)kidney development2.084e-060.0002775Highly InformativeDirect
Biological Process (BP)DNA replication6.375e-122.046e-09Highly InformativeDirect
Biological Process (BP)cellular iron ion homeostasis3.897e-061.762e-09Highly InformativeDirect
Biological Process (BP)negative regulation of cell proliferation2.3e-071.341e-06Highly InformativeDirect
Biological Process (BP)deoxyribonucleoside triphosphate metabolic process7.767e-093.791e-13Highly InformativeDirect
Biological Process (BP)deoxyribonucleotide metabolic process1.82e-130Highly InformativeDirect
Biological Process (BP)quinone cofactor metabolic process7.564e-112.524e-10Highly InformativeDirect
Biological Process (BP)maintenance of location4.681e-097.058e-07Highly InformativeDirect
Biological Process (BP)quinone biosynthetic process3.287e-130Highly InformativeDirect
Molecular Function (MF)binding0.02660.7964Least InformativeInherited
Molecular Function (MF)oxidoreductase activity5.125e-080Moderately InformativeDirect
Molecular Function (MF)cation binding6.715e-160Moderately InformativeDirect
Molecular Function (MF)transition metal ion binding2.005e-079.256e-08InformativeDirect
Molecular Function (MF)iron ion binding00Highly InformativeDirect
Cellular Component (CC)protein complex1.074e-050.007677Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.39430.09756Least InformativeInherited

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) cellular aromatic compound metabolic process 0.0001828 Least Informative Direct
Biological Process (BP) biosynthetic process 1.488e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1.004e-06 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.59e-05 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.007395 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.05527 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.0092 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9992 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 2.085e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 9.579e-06 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 7.738e-05 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 8.017e-12 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0004425 Moderately Informative Direct
Biological Process (BP) homeostatic process 2.881e-08 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 1.414e-05 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 7.225e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 3.077e-10 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 1.386e-10 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0005509 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.5521 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.6631 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1999 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.4993 Moderately Informative Inherited
Biological Process (BP) immune system process 0.002426 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.1382 Moderately Informative Inherited
Biological Process (BP) system process 0.7239 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0.0002537 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 7.064e-11 Informative Direct
Biological Process (BP) immune response 1.908e-05 Informative Direct
Biological Process (BP) response to oxidative stress 6.882e-09 Informative Direct
Biological Process (BP) mitochondrion organization 1.027e-05 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 7.827e-05 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 1.673e-06 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.000477 Informative Direct
Biological Process (BP) cellular ketone metabolic process 5.998e-09 Informative Direct
Biological Process (BP) response to inorganic substance 0.001105 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 1 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.004778 Informative Inherited
Biological Process (BP) metal ion homeostasis 0.107 Informative Inherited
Biological Process (BP) kidney development 0.0002775 Highly Informative Direct
Biological Process (BP) DNA replication 2.046e-09 Highly Informative Direct
Biological Process (BP) cellular iron ion homeostasis 1.762e-09 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 1.341e-06 Highly Informative Direct
Biological Process (BP) deoxyribonucleoside triphosphate metabolic process 3.791e-13 Highly Informative Direct
Biological Process (BP) deoxyribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) quinone cofactor metabolic process 2.524e-10 Highly Informative Direct
Biological Process (BP) maintenance of location 7.058e-07 Highly Informative Direct
Biological Process (BP) quinone biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) binding 0.7964 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0 Moderately Informative Direct
Molecular Function (MF) transition metal ion binding 9.256e-08 Informative Direct
Molecular Function (MF) iron ion binding 0 Highly Informative Direct
Cellular Component (CC) protein complex 0.007677 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.09756 Least Informative Inherited
Cellular Component (CC) plastid 0.01141 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or red0Moderately InformativeDirect
Enzyme Commission (EC)Oxidizing metal ions0InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation3.244e-09InformativeDirect
Enzyme Commission (EC)Peroxidases0.0003203InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)disease of metabolism0.02272Moderately InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.02435Least InformativeInherited
Worm Phenotype (WP)pattern of transgene expression variant0.0009528Moderately InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.002185InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)developmental rate defective3.559e-05Highly InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical entity in vitro0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)sepal0Least InformativeDirect
Plant structure DEvelopment stage (PDE)seed development stage0.0001624InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)Acting on a peroxide as acceptor1InformativeInherited
Enzyme Commission (EC)Oxidizing metal ions0Highly InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect
Enzyme Commission (EC)With NADH or NADPH as one donor, and incorporation of one atom of oxygen9.223e-08Highly InformativeDirect
Enzyme Commission (EC)Peroxidases0.0003629Highly InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0.001862Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details) Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processLipid metabolism3.919e-10Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processFatty acid metabolism0InformativeDirect
Biological processPhotosynthesis0InformativeDirect
Biological processLipid biosynthesis1.603e-14InformativeDirect
Biological processAromatic hydrocarbons catabolism0.0002556InformativeDirect
Biological processChlorophyll biosynthesis0Highly InformativeDirect
Biological processDNA condensation0Highly InformativeDirect
Biological processUbiquinone biosynthesis0Highly InformativeDirect
Cellular componentMembrane0.0001453Least InformativeDirect
Cellular componentPlastid0Moderately InformativeDirect
Cellular componentCell membrane9.028e-15Moderately InformativeDirect
Developmental stageEarly protein2.952e-13Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionIron0Moderately InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationMonooxygenase0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0.0515Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)fatty acid metabolism4.459e-16Moderately InformativeDirect
UniPathway (UP)aromatic compound degradation0.0003407Moderately InformativeDirect
UniPathway (UP)pigment biosynthesis0InformativeDirect
UniPathway (UP)heterocycle biosynthesis0InformativeDirect
UniPathway (UP)quinone cofactor biosynthesis0InformativeDirect
UniPathway (UP)ubiquinone biosynthesis0Highly InformativeDirect
UniPathway (UP)DNA replication0Highly InformativeDirect
UniPathway (UP)chlorophyll biosynthesis (light-independent)0Highly InformativeDirect
UniPathway (UP)bacteriochlorophyll biosynthesis (light-independent)0.0008048Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR009078 SSF47240 Protein matches
Abstract

Ferritin is one of the major non-haem iron storage proteins in animals, plants, and microorganisms. Ferritin is a multisubunit protein with a hollow interior, which contains a mineral core of hydrated ferric oxide, thereby ensuring its solubility in an aqueous environment [PubMed9668036]. Each subunit consists of a closed, four-helical bundle with a left-handed twist and one crossover connection.

This family contains ferritin and other ferritin-like proteins such as bacterioferritin (cytochrome b1) that binds haem between two subunits, non-haem ferritin, dodecameric ferritin homologue (DPS) that binds to and protects DNA, and the N-terminal domain of rubrerythrin that is found in many air-sensitive bacteria and archaea [PubMed12175244]. In addition, ribonucleotide reductase-like proteins show a similar structure to the ferritin-like fold; these di-iron carboxylate proteins constitute a diverse class of non-haem iron enzymes performing a multitude of redox reactions [PubMed11315567]. This family includes the alpha and beta subunits of methane monooxygenase hydrolase, delta 9-stearoyl-acyl carrier protein desaturase and manganese catalase (T-catalase).


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) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 62 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 Ferritin-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 62 hidden Markov models representing the Ferritin-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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]