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 (1,371) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,546 0 2
Proteins 7,319 0 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 1.392e-05 Least Informative Direct
Biological Process (BP) developmental process 2.702e-07 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.07132 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.03547 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9089 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.05759 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.1742 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.4348 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.4852 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4054 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5672 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7445 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.01434 Least Informative Inherited
Biological Process (BP) cellular protein modification process 0.000284 Moderately Informative Direct
Biological Process (BP) nervous system development 1.91e-05 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.0009644 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.482e-06 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0004612 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 8.26e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 0.8977 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.9102 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2046 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7388 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3253 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4298 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.582 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1104 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2222 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.00583 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.005642 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.04495 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5478 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.2294 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0005178 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.0002969 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0005154 Informative Direct
Biological Process (BP) cell cycle process 0.000578 Informative Direct
Biological Process (BP) biological adhesion 8.769e-07 Informative Direct
Biological Process (BP) cell projection organization 4.537e-05 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0006968 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.0003829 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 3.341e-05 Informative Direct
Biological Process (BP) generation of neurons 1.615e-07 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.596e-06 Informative Direct
Biological Process (BP) protein modification by small protein conjugation or removal 5.009e-13 Informative Direct
Biological Process (BP) organelle assembly 0.0008556 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.002085 Informative Inherited
Biological Process (BP) cellular component movement 0.001253 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01311 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.003402 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.004091 Informative Inherited
Biological Process (BP) locomotion 0.01064 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.008233 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.02674 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.1585 Informative Inherited
Biological Process (BP) protein catabolic process 0.00531 Informative Inherited
Biological Process (BP) proteolysis 0.06272 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.07509 Informative Inherited
Biological Process (BP) regulation of translation 3.154e-06 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.0002627 Highly Informative Direct
Biological Process (BP) cell adhesion 1.98e-06 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 3.665e-05 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 1.649e-05 Highly Informative Direct
Biological Process (BP) protein ubiquitination 0 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0002515 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0001402 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.0001049 Highly Informative Direct
Biological Process (BP) interphase 4.175e-09 Highly Informative Direct
Biological Process (BP) axon development 8.065e-05 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 9.183e-06 Highly Informative Direct
Biological Process (BP) stem cell proliferation 1.798e-07 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 1.35e-08 Highly Informative Direct
Biological Process (BP) chemotaxis 0.001958 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.01315 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 0.03149 Highly Informative Inherited
Molecular Function (MF) binding 0.052 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.06482 Moderately Informative Inherited
Molecular Function (MF) RNA binding 2.971e-05 Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct
Molecular Function (MF) protein dimerization activity 5.541e-06 Informative Direct
Molecular Function (MF) small conjugating protein ligase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 1.522e-10 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 2.378e-05 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.02338 Least Informative Inherited
Cellular Component (CC) membrane 0.01792 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.7735 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) ribonucleoprotein complex 0.0007562 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.0008631 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.2165 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.364 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 0.01887 Moderately Informative Inherited
Cellular Component (CC) integral to membrane 0.000438 Informative Direct
Cellular Component (CC) intrinsic to plasma membrane 3.344e-06 Informative Direct
Cellular Component (CC) contractile fiber part 0.0002682 Informative Direct
Cellular Component (CC) synapse part 0.0007563 Informative Direct
Cellular Component (CC) nucleoplasm part 0.003241 Informative Inherited
Cellular Component (CC) cytoplasmic mRNA processing body 4.015e-12 Highly Informative Direct
Cellular Component (CC) integral to plasma membrane 1.374e-06 Highly Informative Direct
Cellular Component (CC) nuclear body 9.962e-08 Highly Informative Direct
Cellular Component (CC) sarcomere 9.235e-05 Highly Informative Direct
Cellular Component (CC) postsynaptic membrane 6.306e-07 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 morphology0.4694Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neurite morphology0.07021Highly 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.0004324Least InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen7.194e-10InformativeDirect
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 processDifferentiation2.856e-11Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processCell adhesion2.95e-10InformativeDirect
Biological processRNA-mediated gene silencing9.991e-14Highly InformativeDirect
Cellular componentNucleus8.6e-07Least InformativeDirect
Cellular componentCell projection1.041e-11Moderately InformativeDirect
Cellular componentCell junction6.233e-05Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001349Moderately InformativeDirect
Cellular componentGolgi apparatus0.0005682Moderately InformativeDirect
Cellular componentSynapse6.137e-07InformativeDirect
Cellular componentSynaptosome1.766e-11Highly InformativeDirect
Cellular componentPostsynaptic cell membrane1.431e-08Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0.9252Least InformativeInherited
DomainZinc-finger2.158e-10Moderately InformativeDirect
DomainCoiled coil0.0002817Moderately InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding3.408e-06Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor4.855e-07Moderately InformativeDirect
Post-translational modificationLigase1.493e-06Moderately InformativeDirect
Post-translational modificationGlycoprotein6.536e-06Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues5.439e-06Moderately InformativeDirect
Post-translational modificationUbl conjugation7.235e-06Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP 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) · 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 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) · UniProtKB UniPathway (UP) · Internal database links ]