SUPERFAMILY 1.75 HMM library and genome assignments server


NHL repeat superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   6-bladed beta-propeller [ 50938] (11)
Superfamily:   NHL repeat [ 101898]
Families:   NHL repeat [ 101899] (2)


Superfamily statistics
Genomes (1,337) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 6,512 9,016 2
Proteins 6,311 8,730 2


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) 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) multicellular organismal process 7.423e-05 Least Informative Direct
Biological Process (BP) developmental process 7.44e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.1607 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.09931 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9422 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.04855 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1724 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4342 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4844 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.404 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.567 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.755 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01753 Least Informative Inherited
Biological Process (BP) nervous system development 9.965e-06 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0008143 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 2.117e-05 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0004032 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 7.415e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 0.8355 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.8662 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.002019 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1894 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.623 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3247 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4305 Moderately Informative Inherited
Biological Process (BP) regulation of programmed cell death 0.006978 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.01164 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1113 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.004792 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2138 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.001957 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.04476 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5736 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.4639 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.000568 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0002596 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0005091 Informative Direct
Biological Process (BP) biological adhesion 6.117e-07 Informative Direct
Biological Process (BP) cell projection organization 0.000105 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0003541 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 2.755e-05 Informative Direct
Biological Process (BP) generation of neurons 5.503e-07 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.576e-06 Informative Direct
Biological Process (BP) organelle assembly 0.0008306 Informative Direct
Biological Process (BP) cellular component movement 0.05217 Informative Inherited
Biological Process (BP) locomotion 0.02181 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.001191 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.00881 Informative Inherited
Biological Process (BP) cell cycle process 0.001769 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.00334 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.007069 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.004631 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.01878 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.1268 Informative Inherited
Biological Process (BP) protein catabolic process 0.002453 Informative Inherited
Biological Process (BP) proteolysis 0.03248 Informative Inherited
Biological Process (BP) regulation of translation 3.286e-06 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.0002478 Highly Informative Direct
Biological Process (BP) cell adhesion 8.739e-07 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 3.997e-05 Highly Informative Direct
Biological Process (BP) cell proliferation 3.154e-05 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 7.064e-06 Highly Informative Direct
Biological Process (BP) gene silencing 5.223e-06 Highly Informative Direct
Biological Process (BP) protein ubiquitination 2.098e-13 Highly Informative Direct
Biological Process (BP) neural tube development 5.503e-06 Highly Informative Direct
Biological Process (BP) cell cycle phase 4.871e-06 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0002706 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0001629 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001262 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 9.223e-06 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 4.362e-09 Highly Informative Direct
Biological Process (BP) neuron projection development 0.7626 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.005151 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.3494 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.5974 Highly Informative Inherited
Molecular Function (MF) binding 0.03769 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1152 Moderately Informative Inherited
Molecular Function (MF) RNA binding 0.0001396 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) protein dimerization activity 5.136e-06 Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 1.291e-10 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 2.483e-05 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.006304 Least Informative Inherited
Cellular Component (CC) membrane 0.01516 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.8536 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.9376 Least Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.0002132 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.001009 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1049 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.2105 Moderately Informative Inherited
Cellular Component (CC) plasma membrane part 0.01181 Moderately Informative Inherited
Cellular Component (CC) integral to membrane 0.0001013 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 1.153e-05 Informative Direct
Cellular Component (CC) contractile fiber part 0.000303 Informative Direct
Cellular Component (CC) synapse part 0.000753 Informative Direct
Cellular Component (CC) nucleoplasm part 0.01076 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 3.94e-12 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 0.0008448 Highly Informative Direct
Cellular Component (CC) nuclear body 9.268e-08 Highly Informative Direct
Cellular Component (CC) sarcomere 8.09e-05 Highly Informative Direct
Cellular Component (CC) synaptic membrane 3.848e-05 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases1.589e-07Least InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases7.054e-16InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc0Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormal eye physiology0InformativeDirect

Document: HP 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)abnormal neuron morphology0.4802Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neurite morphology0.06757Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least 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)organ system0Least InformativeDirect
Fly Anatomy (FA)cell0Least InformativeDirect
Fly Anatomy (FA)late embryo0Moderately InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least 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 plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)gamete0.001904InformativeInherited
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least 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
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases1.943e-07Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.001367Least InformativeInherited
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen2.566e-09InformativeDirect
Enzyme Commission (EC)Lyases acting on amides, amidines, etc0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation2.996e-11Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processCell adhesion3.141e-10InformativeDirect
Biological processRNA-mediated gene silencing9.825e-14Highly InformativeDirect
Cellular componentNucleus1.081e-06Least InformativeDirect
Cellular componentCell projection9.866e-12Moderately InformativeDirect
Cellular componentCell junction6.34e-05Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001347Moderately InformativeDirect
Cellular componentGolgi apparatus0.0006089Moderately InformativeDirect
Cellular componentSynapse5.783e-07InformativeDirect
Cellular componentSynaptosome1.647e-11Highly InformativeDirect
Cellular componentPostsynaptic cell membrane1.457e-08Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0.8646Least InformativeInherited
DomainZinc-finger3.061e-10Moderately InformativeDirect
DomainCoiled coil0.0003185Moderately InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionZinc2.316e-16Least InformativeDirect
Molecular functionMetal-binding3.667e-06Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor5.103e-07Moderately InformativeDirect
Post-translational modificationLigase1.929e-06Moderately InformativeDirect
Post-translational modificationGlycoprotein1.153e-05Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues6.64e-06Moderately InformativeDirect
Post-translational modificationUbl conjugation8.778e-06Moderately InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 2 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 NHL repeat 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 2 hidden Markov models representing the NHL repeat 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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]