SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,948) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 18,789 101,227 34
Proteins 18,604 101,046 28


Functional annotation
General category Metabolism
Detailed category Redox

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) single-organism metabolic process 2.387e-11 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.006443 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) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.9775 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 6.371e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.5268 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.7046 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.9095 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.9637 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04259 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.793 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02155 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.564 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.3626 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.3328 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.2713 Moderately Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.0007058 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.0005248 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0003163 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.0005252 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.05436 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.3151 Informative Inherited
Biological Process (BP) carbohydrate derivative catabolic process 0.3717 Informative Inherited
Biological Process (BP) glycosyl compound catabolic process 0.3793 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.008409 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.004126 Informative Inherited
Biological Process (BP) negative regulation of transcription, DNA-dependent 8.145e-05 Highly Informative Direct
Biological Process (BP) purine ribonucleoside catabolic process 0.4097 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) nucleotide binding 4.462e-08 Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 7.07e-05 Informative Direct
Molecular Function (MF) cofactor binding 3.482e-13 Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0.0002879 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor 0 Highly Informative Direct
Molecular Function (MF) NAD binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.03925 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 0.4396 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on NAD(P)H 0.2879 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1365 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) membrane 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.0001102 Moderately Informative Direct
Cellular Component (CC) organelle envelope 0.001962 Moderately Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.04883 Moderately Informative Inherited
Cellular Component (CC) nucleoplasm part 0.1714 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 acceptor2.992e-08InformativeDirect
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) Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.3082Least InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system development0.03455Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal neural tube morphology/development0.004133InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Moderately 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

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of 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 plant0.08496Least InformativeInherited
Plant ANatomical entity (PAN)vascular system0.004609InformativeInherited
Plant ANatomical entity (PAN)vascular bundle4.291e-06Highly 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 donors0.03722InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors0.1932InformativeInherited
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 acceptor1.239e-12Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0.9794Moderately InformativeInherited
Biological processOne-carbon metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP2.075e-11InformativeDirect
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 degradation0.8194Moderately InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis1Moderately InformativeInherited
UniPathway (UP)nonprotein amino-acid biosynthesis0InformativeDirect
UniPathway (UP)L-lysine biosynthesis0.321InformativeInherited
UniPathway (UP)L-serine biosynthesis0Highly InformativeDirect
UniPathway (UP)alanine degradation0Highly InformativeDirect
UniPathway (UP)L-lysine biosynthesis via AAA pathway4.181e-10Highly InformativeDirect
UniPathway (UP)L-lysine degradation via saccharopine pathway1.435e-08Highly InformativeDirect

Document: UP annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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-coverage) · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]