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Formate/glycerate dehydrogenase catalytic domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Flavodoxin-like [ 52171] (15)
Superfamily:   Formate/glycerate dehydrogenase catalytic domain-like [ 52283] (3)
Families:   Formate/glycerate dehydrogenases, substrate-binding domain [ 52284] (7)
  L-alanine dehydrogenase-like [ 52297] (2)
  S-adenosylhomocystein hydrolase [ 52300]


Superfamily statistics
Genomes (2,955) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 18,899 106,999 34
Proteins 18,711 106,387 28


Functional annotation
General category Metabolism
Detailed category Redox

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 cellular process00.0000005387Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00034530.7383Least InformativeInherited
Biological Process (BP)multicellular organismal process0.00052871Least InformativeInherited
Biological Process (BP)biological regulation0.0039421Least InformativeInherited
Biological Process (BP)cellular component assembly0.0000055060.003203Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.0000011680.06655Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.0000023620.1501Moderately InformativeInherited
Biological Process (BP)cell differentiation0.0000051890.01346Moderately InformativeInherited
Biological Process (BP)animal organ development0.0000048570.3544Moderately InformativeInherited
Biological Process (BP)single-organism membrane organization0.0000060930.00000001615InformativeDirect
Biological Process (BP)regulation of cell differentiation0.00000013180.0006015InformativeDirect
Biological Process (BP)regulation of nervous system development0.0000000067570.000002234InformativeDirect
Biological Process (BP)cell development0.00000063240.009463InformativeInherited
Biological Process (BP)generation of neurons0.00000012730.001166InformativeInherited
Biological Process (BP)camera-type eye development0.00000000059390.000000000003355Highly InformativeDirect
Biological Process (BP)cell maturation0.00000000016620.000000000000001925Highly InformativeDirect
Biological Process (BP)neuron development0.000000011240.000002402Highly InformativeDirect
Biological Process (BP)anatomical structure maturation0.000000000008940Highly InformativeDirect

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) single-organism cellular process 0.0000005387 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000005783 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.7383 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.00003287 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0001096 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00001124 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.003203 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.06655 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1501 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.01346 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.0336 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.0115 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1406 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.1859 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.6764 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.05612 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.3544 Moderately Informative Inherited
Biological Process (BP) single-organism membrane organization 0.00000001615 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.0006015 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.00005884 Informative Direct
Biological Process (BP) regulation of nervous system development 0.000002234 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.000008002 Informative Direct
Biological Process (BP) cell development 0.009463 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.003898 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.06319 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.01953 Informative Inherited
Biological Process (BP) generation of neurons 0.001166 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.7814 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.08968 Informative Inherited
Biological Process (BP) camera-type eye development 0.000000000003355 Highly Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.0000002279 Highly Informative Direct
Biological Process (BP) cell maturation 0.000000000000001925 Highly Informative Direct
Biological Process (BP) neuron development 0.000002402 Highly Informative Direct
Biological Process (BP) anatomical structure maturation 0 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.01454 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000004201 Moderately Informative Direct
Molecular Function (MF) coenzyme binding 0.0000000000001673 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.0001714 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.0000000026 Highly Informative Direct
Molecular Function (MF) NAD binding 0.000000000000009279 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.971 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.0177 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1759 Least 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)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Acting on NADH or NADPH1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors0.2181Moderately InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on ether bonds0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000002992InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.08813InformativeInherited
Enzyme Commission (EC)Phosphoglycerate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)NAD(P)(+) transhydrogenase (AB-specific)0Highly InformativeDirect
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.975Moderately InformativeInherited
Biological processOne-carbon metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentEndoplasmic reticulum1Moderately InformativeInherited
Cellular componentMicrosome0.0003861Highly InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0.0000003122Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately 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) · 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 13 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 Formate/glycerate dehydrogenase catalytic domain-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 13 hidden Markov models representing the Formate/glycerate dehydrogenase catalytic domain-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 ]