SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


HD-domain/PDEase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   HD-domain/PDEase-like [ 109603]
Superfamily:   HD-domain/PDEase-like [ 109604] (5)
Families:   HD domain [ 101340] (13)
  PDEase [ 48548] (6)
  modified HD domain [ 116973]
  MioX-like [ 140769]
  Ppx associated domain [ 140773]


Superfamily statistics
Genomes (3,165) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 34,274 195,322 45
Proteins 33,602 191,738 45


Functional annotation
General category Metabolism
Detailed category Other enzymes

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)single-organism metabolic process0.96410Least InformativeInherited
Biological Process (BP)primary metabolic process10.0007246Least InformativeInherited
Biological Process (BP)single-organism cellular process10.001071Least InformativeInherited
Biological Process (BP)single-organism catabolic process0.0045810Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.060030Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.00096660.7252Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.02280Moderately InformativeInherited
Biological Process (BP)alcohol metabolic process0.00000028691InformativeInherited
Biological Process (BP)carbohydrate catabolic process0.0000072570.8177InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.0000042550.1371InformativeInherited
Biological Process (BP)alcohol catabolic process0.00000000007330.00000004394Highly InformativeDirect
Biological Process (BP)polyol metabolic process0.00000000029280.0004085Highly InformativeDirect
Biological Process (BP)cellular carbohydrate catabolic process0.0000000000028480.003957Highly InformativeInherited
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)oxidoreductase activity0.015961Moderately InformativeInherited
Molecular Function (MF)metal ion binding0.005230.01317Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.000000000000068440.0000000000292Highly InformativeDirect
Molecular Function (MF)iron ion binding0.00023920.01031Highly 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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000001559 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0007246 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1479 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001071 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism catabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000000001035 Moderately Informative Direct
Biological Process (BP) cell communication 0.0000003416 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.00001024 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.00002555 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0006646 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.0008304 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.001678 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2692 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.9908 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.005967 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1223 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.09241 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) defense response 0.8598 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9886 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5109 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.3474 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.01513 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01572 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.7252 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 0.3391 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 0.003595 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.5966 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9467 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7853 Moderately Informative Inherited
Biological Process (BP) immune system process 0.149 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) system process 0 Informative Direct
Biological Process (BP) negative regulation of transport 0.00000000000535 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.000000004744 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000009661 Informative Direct
Biological Process (BP) response to nitrogen compound 0.00001896 Informative Direct
Biological Process (BP) regulation of protein localization 0.00007994 Informative Direct
Biological Process (BP) regulation of peptide transport 0.0002457 Informative Direct
Biological Process (BP) mitochondrion organization 0.0004376 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0005991 Informative Direct
Biological Process (BP) regulation of defense response 0.0006055 Informative Direct
Biological Process (BP) regulation of transmembrane transport 0.2516 Informative Inherited
Biological Process (BP) regulation of ion transport 0.8535 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2462 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.05678 Informative Inherited
Biological Process (BP) localization of cell 0.08736 Informative Inherited
Biological Process (BP) protein localization to organelle 0.00533 Informative Inherited
Biological Process (BP) locomotion 0.3585 Informative Inherited
Biological Process (BP) cellular response to lipid 0.01327 Informative Inherited
Biological Process (BP) response to bacterium 0.233 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.003054 Informative Inherited
Biological Process (BP) regulation of cell differentiation 1 Informative Inherited
Biological Process (BP) immune effector process 0.3642 Informative Inherited
Biological Process (BP) defense response to other organism 0.9094 Informative Inherited
Biological Process (BP) movement of cell or subcellular component 1 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.01719 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.01138 Informative Inherited
Biological Process (BP) carbohydrate catabolic process 0.8177 Informative Inherited
Biological Process (BP) regulation of system process 0.001739 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.6709 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.02564 Informative Inherited
Biological Process (BP) response to radiation 0.2663 Informative Inherited
Biological Process (BP) response to extracellular stimulus 0.7635 Informative Inherited
Biological Process (BP) behavior 0.05692 Informative Inherited
Biological Process (BP) multi-organism reproductive process 1 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.9302 Informative Inherited
Biological Process (BP) intracellular transport 0.572 Informative Inherited
Biological Process (BP) protein transport 0.1103 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.1371 Informative Inherited
Biological Process (BP) cell development 0.1027 Informative Inherited
Biological Process (BP) epithelium development 0.08268 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.1715 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3955 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.4529 Informative Inherited
Biological Process (BP) alcohol catabolic process 0.00000004394 Highly Informative Direct
Biological Process (BP) polyol metabolic process 0.0004085 Highly Informative Direct
Biological Process (BP) nucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) second-messenger-mediated signaling 0 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0 Highly Informative Direct
Biological Process (BP) response to drug 0 Highly Informative Direct
Biological Process (BP) purine-containing compound catabolic process 0 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.000000000000003734 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.000000000000003734 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.000000000000003734 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.000000000002601 Highly Informative Direct
Biological Process (BP) establishment of protein localization to mitochondrion 0.00000000007783 Highly Informative Direct
Biological Process (BP) deoxyribonucleoside triphosphate metabolic process 0.0000000001509 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000000002591 Highly Informative Direct
Biological Process (BP) myeloid cell homeostasis 0.00000000295 Highly Informative Direct
Biological Process (BP) cell chemotaxis 0.000000004245 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.00000001324 Highly Informative Direct
Biological Process (BP) leukocyte migration 0.00000001474 Highly Informative Direct
Biological Process (BP) cellular response to biotic stimulus 0.00000002101 Highly Informative Direct
Biological Process (BP) mitochondrial transport 0.0000002964 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.0000005229 Highly Informative Direct
Biological Process (BP) regulation of protein import 0.00000065 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.0000007628 Highly Informative Direct
Biological Process (BP) negative regulation of phosphate metabolic process 0.0000008346 Highly Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.000001803 Highly Informative Direct
Biological Process (BP) protein targeting 0.000002066 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0.00000284 Highly Informative Direct
Biological Process (BP) deoxyribose phosphate metabolic process 0.000006593 Highly Informative Direct
Biological Process (BP) response to molecule of bacterial origin 0.00001181 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.00002924 Highly Informative Direct
Biological Process (BP) cellular response to abiotic stimulus 0.0001142 Highly Informative Direct
Biological Process (BP) response to mechanical stimulus 0.0004232 Highly Informative Direct
Biological Process (BP) regulation of calcium ion transport 0.004171 Highly Informative Inherited
Biological Process (BP) regulation of cation transmembrane transport 0.5628 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.03928 Highly Informative Inherited
Biological Process (BP) response to virus 0.05585 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.3447 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.3353 Highly Informative Inherited
Biological Process (BP) cellular carbohydrate catabolic process 0.003957 Highly Informative Inherited
Biological Process (BP) cellular response to extracellular stimulus 0.1011 Highly Informative Inherited
Biological Process (BP) nucleoside triphosphate catabolic process 0.008935 Highly Informative Inherited
Biological Process (BP) single-organism behavior 0.003187 Highly Informative Inherited
Biological Process (BP) nervous system process 1 Highly Informative Inherited
Biological Process (BP) muscle system process 0.01228 Highly Informative Inherited
Biological Process (BP) deoxyribonucleotide metabolic process 0.006685 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.05991 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000002925 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.7349 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.01317 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0.801 Moderately Informative Inherited
Molecular Function (MF) purine nucleotide binding 0.0000000006939 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00000007013 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.007178 Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.03792 Informative Inherited
Molecular Function (MF) signal transducer activity 1 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on single donors with incorporation of molecular oxygen 0.0000000000292 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0 Highly Informative Direct
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) tubulin binding 0.000001758 Highly Informative Direct
Molecular Function (MF) iron ion binding 0.01031 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.4849 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) endomembrane system 0.5817 Moderately Informative Inherited
Cellular Component (CC) cytoskeleton 0.5872 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.03477 Moderately Informative Inherited
Cellular Component (CC) plasma membrane 0.7083 Moderately Informative Inherited
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) cilium 0.009619 Informative Inherited
Cellular Component (CC) neuron projection 0.9756 Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.02344 Informative Inherited
Cellular Component (CC) plasma membrane region 0.001179 Informative Inherited
Cellular Component (CC) microtubule cytoskeleton 0.02758 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.0000000366 Highly Informative Direct
Cellular Component (CC) exocytic vesicle 0.00000008051 Highly Informative Direct
Cellular Component (CC) presynapse 0.000000878 Highly Informative Direct
Cellular Component (CC) microtubule organizing center 0.00008055 Highly Informative Direct
Cellular Component (CC) dendrite 0.2189 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0.7809Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)In phosphorous-containing anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Ligases forming aminoacyl-tRNA and related compoun0Moderately InformativeDirect
Enzyme Commission (EC)Diphosphotransferases0InformativeDirect
Enzyme Commission (EC)Acting on single donors with incorporation of mole0.0000002853InformativeDirect
Enzyme Commission (EC)[Protein-PII] uridylyltransferase0Highly InformativeDirect
Enzyme Commission (EC)GTP diphosphokinase0Highly InformativeDirect
Enzyme Commission (EC)3',5'-cyclic-nucleotide phosphodiesterase0Highly InformativeDirect
Enzyme Commission (EC)Guanosine-3',5'-bis(diphosphate) 3'-diphosphatase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processProtein biosynthesis0InformativeDirect
Biological processNitrogen fixation0.000001146InformativeDirect
Biological processSensory transduction0.000523InformativeDirect
Biological processVision0.0000003874Highly InformativeDirect
Biological processAntiviral defense0.0000006402Highly InformativeDirect
Cellular componentMembrane0.00001401Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
DomainRepeat0.0000000003554Least InformativeDirect
DomainTransmembrane0.0000000008647Least InformativeDirect
Molecular functionNucleotide-binding0.000000000003457Least InformativeDirect
Molecular functionMagnesium0.00000001928Least InformativeDirect
Molecular functioncAMP0Highly InformativeDirect
Molecular functioncGMP0Highly InformativeDirect
Molecular functioncGMP-binding0Highly InformativeDirect
Molecular functioncAMP-binding0.00008012Highly InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding0.000001143Moderately InformativeDirect
Post-translational modificationAminoacyl-tRNA synthetase0InformativeDirect
Post-translational modificationEndonuclease0.0000000000004262InformativeDirect
Post-translational modificationCalmodulin-binding0.00003991InformativeDirect
Post-translational modificationPrenylation0.000000000000001916InformativeDirect

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) · 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 24 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 HD-domain/PDEase-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 24 hidden Markov models representing the HD-domain/PDEase-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 · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]