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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 (2,950) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,813 101,227 34
Proteins 18,629 101,046 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 process00.000003448Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00029710.642Least InformativeInherited
Biological Process (BP)biological regulation0.0034821Least InformativeInherited
Biological Process (BP)cellular component assembly0.0000030880.0009007Moderately InformativeDirect
Biological Process (BP)regulation of developmental process0.0000011070.03863Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.0000023520.1025Moderately InformativeInherited
Biological Process (BP)cellular developmental process0.0012850.4096Moderately InformativeInherited
Biological Process (BP)system development0.00002490.6878Moderately InformativeInherited
Biological Process (BP)single-organism membrane organization0.0000071480.00000001996InformativeDirect
Biological Process (BP)regulation of cell differentiation0.0000001060.0002196InformativeDirect
Biological Process (BP)generation of neurons0.00000011710.0004872InformativeDirect
Biological Process (BP)regulation of nervous system development0.0000000059760.00000185InformativeDirect
Biological Process (BP)cell development0.00000056820.006042InformativeInherited
Biological Process (BP)camera-type eye development0.00000000054770.000000000001377Highly InformativeDirect
Biological Process (BP)cell maturation0.00000000018760Highly InformativeDirect
Biological Process (BP)neuron development0.000000011140.0000007672Highly 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 0.0000000000005193 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000003448 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.0000000000002055 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.642 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.6575 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.0009007 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.4096 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.03863 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1025 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.1278 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.109 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.01163 Moderately Informative Inherited
Biological Process (BP) sulfur compound metabolic process 0.005032 Moderately Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.2602 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.08873 Moderately Informative Inherited
Biological Process (BP) system development 0.6878 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.003392 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.004775 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.02119 Moderately Informative Inherited
Biological Process (BP) single-organism membrane organization 0.00000001996 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.0002196 Informative Direct
Biological Process (BP) generation of neurons 0.0004872 Informative Direct
Biological Process (BP) regulation of nervous system development 0.00000185 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.00002745 Informative Direct
Biological Process (BP) cell development 0.006042 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.04946 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.3761 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.02065 Informative Inherited
Biological Process (BP) camera-type eye development 0.000000000001377 Highly Informative Direct
Biological Process (BP) cell maturation 0 Highly Informative Direct
Biological Process (BP) neuron development 0.0000007672 Highly Informative Direct
Biological Process (BP) pattern specification process 0.04813 Highly Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0.001298 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 0.000001257 Moderately Informative Direct
Molecular Function (MF) coenzyme binding 0.00000000000005215 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.00000000605 Highly Informative Direct
Molecular Function (MF) NAD binding 0.000000000000003237 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.9093 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.01652 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.005888 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.5457 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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of amino acid metabolism0.0007619InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.3911Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.04815Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.1077Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology0.006631InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0Least InformativeDirect
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect

Document: ZA 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)tissue0Least 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)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0.08514Least InformativeInherited
Plant ANatomical entity (PAN)portion of vascular tissue0.0008174InformativeDirect
Plant ANatomical entity (PAN)vascular bundle0.000004671Highly InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve 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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0.0153InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors0.2206InformativeInherited
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1InformativeInherited
Enzyme Commission (EC)Acting on NADH or NADPH1InformativeInherited
Enzyme Commission (EC)Formate dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Acting on ether bonds0Highly InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.00000000000109Highly 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 componentMicrosome0.0003884Highly InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0.0000000001679InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid degradation0.8565Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0InformativeDirect
UniPathway (UP)L-lysine biosynthesis0.3288InformativeInherited
UniPathway (UP)L-serine biosynthesis0Highly InformativeDirect
UniPathway (UP)alanine degradation0Highly InformativeDirect
UniPathway (UP)L-lysine biosynthesis via AAA pathway0.0000000004192Highly InformativeDirect
UniPathway (UP)L-lysine degradation via saccharopine pathway0.00000001514Highly 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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · 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 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]