SUPERFAMILY 1.75 HMM library and genome assignments server


MurD-like peptide ligases, peptide-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   MurD-like peptide ligases, peptide-binding domain [ 53243]
Superfamily:   MurD-like peptide ligases, peptide-binding domain [ 53244] (2)
Families:   MurCDEF C-terminal domain [ 53245] (4)
  Folylpolyglutamate synthetase, C-terminal domain [ 53250]


Superfamily statistics
Genomes (2,995) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 15,062 89,313 12
Proteins 15,008 89,156 12


Functional annotation
General category Metabolism
Detailed category Other enzymes

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) nitrogen compound metabolic process 5.376e-07 Least Informative Direct
Biological Process (BP) biosynthetic process 1.554e-09 Least Informative Direct
Biological Process (BP) single-organism metabolic process 3.308e-10 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.2797 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.2504 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.1682 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02654 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 9.127e-08 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 2.041e-06 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 8.581e-10 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0001117 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.259e-13 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.00171 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.002094 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.00379 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.003434 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.002968 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.006169 Moderately Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 7.029e-05 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0001291 Informative Direct
Biological Process (BP) aminoglycan biosynthetic process 1.922e-15 Highly Informative Direct
Biological Process (BP) folic acid-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 1.206e-09 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 6.969e-14 Highly Informative Direct
Biological Process (BP) pteridine-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) cell wall macromolecule metabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 0 Highly Informative Direct
Molecular Function (MF) ligase activity, forming carbon-nitrogen bonds 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Forming carbon-nitrogen bonds0Moderately InformativeDirect
Enzyme Commission (EC)Acid--D-amino-acid ligases (peptide synthases)0InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramate--L-alanine ligase0Highly InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-dia0Highly InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase0Highly InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysin1.32e-05Highly InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanin0.0008424Highly InformativeDirect

Document: EC annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Acid--amino-acid ligases (peptide synthases)0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processPeptidoglycan synthesis0Highly InformativeDirect
Biological processFolate biosynthesis4.886e-06Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)organic acid metabolism3.503e-05Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect
UniPathway (UP)organic acid biosynthesis0InformativeDirect
UniPathway (UP)pteridine biosynthesis3.142e-10InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR004101 SSF53244 Protein matches
Abstract

This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes the C-terminal domain of folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [PubMed9652408].

The C-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases, N-terminal domain (see ).


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-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 7 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 MurD-like peptide ligases, peptide-binding domain 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 7 hidden Markov models representing the MurD-like peptide ligases, peptide-binding domain 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-coverage) · Enzyme Commission (EC) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]