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 (1,381) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,723 13,740 2
Proteins 7,488 13,378 2


Functional annotation
General category Metabolism
Detailed category Other enzymes

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) developmental process 0.0000006391 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001079 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.1893 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.00242 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7572 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.6537 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.09565 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.05076 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.3617 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.4852 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.5167 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.5809 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1779 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9102 Least Informative Inherited
Biological Process (BP) nervous system development 0.00002579 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00009196 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0004008 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.2314 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.399 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.6374 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.06885 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.3989 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.7777 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.06359 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.03628 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.00214 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1492 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.005953 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.001069 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2111 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9217 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.003398 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.01984 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3803 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.5856 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.4807 Moderately Informative Inherited
Biological Process (BP) protein modification by small protein conjugation or removal 0.0000000000009219 Informative Direct
Biological Process (BP) generation of neurons 0.0000002814 Informative Direct
Biological Process (BP) biological adhesion 0.000001026 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.000005615 Informative Direct
Biological Process (BP) cell projection organization 0.0000229 Informative Direct
Biological Process (BP) cell proliferation 0.00002793 Informative Direct
Biological Process (BP) regulation of cellular component biogenesis 0.00006499 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00007796 Informative Direct
Biological Process (BP) posttranscriptional regulation of gene expression 0.0003349 Informative Direct
Biological Process (BP) ncRNA metabolic process 0.000402 Informative Direct
Biological Process (BP) cellular component morphogenesis 0.0004151 Informative Direct
Biological Process (BP) regulation of nervous system development 0.0005222 Informative Direct
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.0007247 Informative Direct
Biological Process (BP) cellular component movement 0.0007573 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.002543 Informative Inherited
Biological Process (BP) cell cycle process 0.01685 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.02818 Informative Inherited
Biological Process (BP) protein catabolic process 0.005819 Informative Inherited
Biological Process (BP) proteolysis 0.06616 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.01366 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.01026 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.005515 Informative Inherited
Biological Process (BP) locomotion 0.01271 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.01258 Informative Inherited
Biological Process (BP) epithelium development 0.00824 Informative Inherited
Biological Process (BP) tube development 0.02354 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.0238 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.173 Informative Inherited
Biological Process (BP) regulation of cell development 0.005048 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.2155 Informative Inherited
Biological Process (BP) protein ubiquitination 0.000000000000001913 Highly Informative Direct
Biological Process (BP) regulation of neural precursor cell proliferation 0.00000001569 Highly Informative Direct
Biological Process (BP) stem cell proliferation 0.0000001446 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0000002938 Highly Informative Direct
Biological Process (BP) regulation of translation 0.00000212 Highly Informative Direct
Biological Process (BP) gene silencing 0.000004701 Highly Informative Direct
Biological Process (BP) neural tube development 0.000007328 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.00001677 Highly Informative Direct
Biological Process (BP) mitotic cell cycle phase transition 0.00002193 Highly Informative Direct
Biological Process (BP) positive regulation of cellular component biogenesis 0.00002854 Highly Informative Direct
Biological Process (BP) cellular component assembly involved in morphogenesis 0.00003739 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.00004554 Highly Informative Direct
Biological Process (BP) regulation of neuron apoptotic process 0.0001477 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.0001751 Highly Informative Direct
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.0003673 Highly Informative Direct
Biological Process (BP) positive regulation of neurogenesis 0.0005797 Highly Informative Direct
Biological Process (BP) neuron projection development 0.6534 Highly Informative Inherited
Biological Process (BP) chemotaxis 0.001652 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.4926 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.01309 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.000005909 Least Informative Direct
Molecular Function (MF) binding 0.02462 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.1188 Moderately Informative Inherited
Molecular Function (MF) protein dimerization activity 0.000007326 Informative Direct
Molecular Function (MF) RNA binding 0.000191 Informative Direct
Molecular Function (MF) ubiquitin-protein transferase activity 0 Highly Informative Direct
Molecular Function (MF) protein homodimerization activity 0.0000000002479 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.00002313 Highly Informative Direct
Cellular Component (CC) membrane 0.01125 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.04346 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3722 Least Informative Inherited
Cellular Component (CC) plasma membrane part 0.0002709 Moderately Informative Direct
Cellular Component (CC) ribonucleoprotein complex 0.0008866 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.2786 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1406 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.003988 Moderately Informative Inherited
Cellular Component (CC) contractile fiber part 0.0003754 Informative Direct
Cellular Component (CC) nucleoplasm part 0.0003889 Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.0004009 Informative Direct
Cellular Component (CC) synapse 0.01449 Informative Inherited
Cellular Component (CC) integral component of membrane 0.001618 Informative Inherited
Cellular Component (CC) cytoplasmic ribonucleoprotein granule 0.00000003978 Highly Informative Direct
Cellular Component (CC) nuclear body 0.000000119 Highly Informative Direct
Cellular Component (CC) postsynaptic membrane 0.0000007319 Highly Informative Direct
Cellular Component (CC) sarcomere 0.0001273 Highly Informative Direct
Cellular Component (CC) integral component of plasma membrane 0.0001865 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)Lyases0.0000001589Least 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

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 morphology0.4788Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neurite morphology0.06904Highly 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)Lyases0.0000001948Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases0.001316Least InformativeInherited
Enzyme Commission (EC)Carbon-nitrogen lyases0.000000000000008504InformativeDirect
Enzyme Commission (EC)Acting on paired donors, with incorporation or reduction of molecular oxygen0.000000002447InformativeDirect
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 processDifferentiation0.00000000003477Moderately InformativeDirect
Biological processUbl conjugation pathway0InformativeDirect
Biological processCell adhesion0.0000000003285InformativeDirect
Biological processRNA-mediated gene silencing0.0000000000001083Highly InformativeDirect
Cellular componentNucleus0.00000118Least InformativeDirect
Cellular componentCell projection0.00000000001297Moderately InformativeDirect
Cellular componentCell junction0.00006751Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.0001561Moderately InformativeDirect
Cellular componentGolgi apparatus0.0006245Moderately InformativeDirect
Cellular componentSynapse0.0000006629InformativeDirect
Cellular componentSynaptosome0.00000000001881Highly InformativeDirect
Cellular componentPostsynaptic cell membrane0.00000001521Highly InformativeDirect
DomainRepeat0Least InformativeDirect
DomainTransmembrane0.854Least InformativeInherited
DomainZinc-finger0.0000000003024Moderately InformativeDirect
DomainCoiled coil0.0003399Moderately InformativeDirect
DomainEGF-like domain0InformativeDirect
Molecular functionZinc2.32e-16Least InformativeDirect
Molecular functionMetal-binding0.000006355Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationRepressor0.0000006034Moderately InformativeDirect
Post-translational modificationLigase0.000001831Moderately InformativeDirect
Post-translational modificationGlycoprotein0.00001159Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.000006318Moderately InformativeDirect
Post-translational modificationUbl conjugation0.00001065Moderately 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-coverage) · Enzyme Commission (EC) · 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-coverage) · Enzyme Commission (EC) · 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 ]