SUPERFAMILY 1.75 HMM library and genome assignments server


LDH C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   LDH C-terminal domain-like [ 56326]
Superfamily:   LDH C-terminal domain-like [ 56327] (2)
Families:   Lactate & malate dehydrogenases, C-terminal domain [ 56328] (4)
  AglA-like glucosidase [ 90050] (4)


Superfamily statistics
Genomes (2,862) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,961 45,513 56
Proteins 7,942 45,503 56


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)
Cellular Component (CC)cytoplasmic part03.806e-08Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle00.1287Least 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 2.08e-10 Least Informative Direct
Biological Process (BP) biosynthetic process 0.08221 Least Informative Inherited
Biological Process (BP) nitrogen compound 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) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.8483 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 8.23e-05 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.0002744 Moderately Informative Direct
Biological Process (BP) organic hydroxy compound metabolic process 1.92e-11 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.003296 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.1225 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.1657 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.181 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.05395 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.3844 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.0003033 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 6.405e-07 Informative Direct
Biological Process (BP) carbohydrate catabolic process 4.938e-05 Informative Direct
Biological Process (BP) hexose metabolic process 3.776e-10 Informative Direct
Biological Process (BP) monocarboxylic acid biosynthetic process 1.358e-05 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 3.451e-07 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 1.675e-12 Informative Direct
Biological Process (BP) energy derivation by oxidation of organic compounds 0.00853 Informative Inherited
Biological Process (BP) lactate metabolic process 0 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 3.787e-09 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 1.378e-07 Highly Informative Direct
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) oxidoreductase activity, acting on CH-OH group of donors 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.0002015 Informative Direct
Molecular Function (MF) cofactor binding 6.766e-05 Informative Direct
Molecular Function (MF) nucleotide binding 0.01218 Informative Inherited
Molecular Function (MF) NAD binding 8.528e-09 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.4418 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 3.806e-08 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.8476 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1287 Least Informative Inherited
Cellular Component (CC) cell projection 0.001032 Moderately Informative Inherited
Cellular Component (CC) plastid 0.02663 Informative Inherited
Cellular Component (CC) cilium part 1.191e-11 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)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0.09514Moderately InformativeInherited

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.05316Least InformativeInherited
Disease Ontology (DO)myeloma0.0005146InformativeDirect

Document: DO 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)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ovary0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)tail0InformativeDirect
Xenopus ANatomical entity (XAN)oviduct0InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least 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)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 structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)seed development stage1.711e-05InformativeDirect

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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases0.1554Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Alpha-glucosidase0.0004219Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Cellular componentPeroxisome1.388e-05InformativeDirect
DomainTransit peptide7.827e-07Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycosidase2.214e-05InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015955 SSF56327 Protein matches
Abstract

This entry represents a structural motif found at the C-terminal of lactate dehydrogenase and malate dehydrogenases , as well as at the C-terminal of family 4 glycoside hydrolases . These domains have an unusual fold consisting of segregated alpha-helical and beta-sheet regions, although they contain predominantly anti-parallel beta-sheets [PubMed11276087, PubMed8117664, PubMed12588867].

L-lactate dehydrogenases are metabolic enzymes that catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle.

O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [PubMed7624375, PubMed8535779]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 4 comprises enzymes with several known activities; 6-phospho-beta-glucosidase ; 6-phospho-alpha-glucosidase ; alpha-galactosidase .


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 33 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 LDH C-terminal 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 33 hidden Markov models representing the LDH C-terminal 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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]