SUPERFAMILY 1.75 HMM library and genome assignments server


Carbamate kinase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Carbamate kinase-like [ 53632]
Superfamily:   Carbamate kinase-like [ 53633] (3)
Families:   Carbamate kinase [ 53634]
  N-acetyl-l-glutamate kinase [ 75297]
  PyrH-like [ 142721] (3)


Superfamily statistics
Genomes (3,168) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 15,474 41,738 19
Proteins 15,363 41,669 19


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

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)nitrogen compound metabolic process0.00022120Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.025670Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.00052070Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups4.54e-073.684e-07Moderately InformativeDirect
Molecular Function (MF)kinase activity1.436e-070InformativeDirect

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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 8.253e-12 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
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 amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.02048 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4519 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.4826 Moderately Informative Inherited
Biological Process (BP) phosphorylation 0.000995 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.2103 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.00155 Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 3.684e-07 Moderately Informative Direct
Molecular Function (MF) oxidoreductase activity 0.004069 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.431 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0.08785 Informative Inherited
Molecular Function (MF) acetyltransferase activity 1.154e-08 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 1.211e-06 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the aldehyde or oxo group of donors 1.202e-08 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.7476 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.002547 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1823 Least Informative Inherited
Cellular Component (CC) plastid 1.403e-06 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0.06739Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce0InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a carboxyl group as accep0InformativeDirect
Enzyme Commission (EC)Amino-acid N-acetyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Glutamate 5-kinase0Highly InformativeDirect
Enzyme Commission (EC)Homoserine dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Aspartate kinase9.14e-06Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP 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 structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a carboxyl group as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processArginine biosynthesis0Highly InformativeDirect
Biological processArginine metabolism0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processDiaminopimelate biosynthesis8.855e-05Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Coding sequence diversityAlternative initiation1.119e-05Moderately InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately 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)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)L-arginine biosynthesis0InformativeDirect
UniPathway (UP)metabolic intermediate degradation1.869e-12InformativeDirect
UniPathway (UP)L-lysine biosynthesis1InformativeInherited
UniPathway (UP)L-methionine biosynthesis1InformativeInherited
UniPathway (UP)L-proline biosynthesis0Highly InformativeDirect
UniPathway (UP)CTP biosynthesis0Highly InformativeDirect
UniPathway (UP)L-lysine biosynthesis via AAA pathway3.34e-13Highly InformativeDirect
UniPathway (UP)L-threonine biosynthesis0.0008785Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001048 SSF53633 Protein matches
Abstract

This entry contains proteins with various specificities and includes the aspartate, glutamate and uridylate kinase families. In prokaryotes and plants the synthesis of the essential amino acids lysine and threonine is predominantly regulated by feed-back inhibition of aspartate kinase (AK) and dihydrodipicolinate synthase (DHPS). In Escherichia coli, thrA, metLM, and lysC encode aspartokinase isozymes that show feedback inhibition by threonine, methionine, and lysine, respectively [PubMed10220897]. The lysine-sensitive isoenzyme of aspartate kinase from spinach leaves has a subunit composition of 4 large and 4 small subunits [PubMed9584993].

In plants although the control of carbon fixation and nitrogen assimilation has been studied in detail, relatively little is known about the regulation of carbon and nitrogen flow into amino acids. The metabolic regulation of expression of an Arabidopsis thaliana aspartate kinase/homoserine dehydrogenase (AK/HSD) gene, which encodes two linked key enzymes in the biosynthetic pathway of aspartate family amino acids has been studied [PubMed9501134]. The conversion of aspartate into either the storage amino acid asparagine or aspartate family amino acids may be subject to a coordinated, reciprocal metabolic control, and this biochemical branch point is a part of a larger, coordinated regulatory mechanism of nitrogen and carbon storage and utilization.


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) · Yeast Phenotype (YP) · 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 16 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 Carbamate kinase-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 16 hidden Markov models representing the Carbamate kinase-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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]