SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


MurD-like peptide ligases, catalytic domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribokinase-like [ 53612] (3)
Superfamily:   MurD-like peptide ligases, catalytic domain [ 53623] (2)
Families:   MurCDEF [ 53624] (4)
  Folylpolyglutamate synthetase [ 53629]


Superfamily statistics
Genomes (3,070) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 16,241 101,459 12
Proteins 16,169 101,142 12


Functional annotation
General category Processes_IC
Detailed category Proteases

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) biosynthetic process 0.0000001172 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00000000004052 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.2096 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 0.2277 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.004342 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.003586 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.3568 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.207 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.000006742 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.0005046 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.0000000008994 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000007412 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.1008 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.07046 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.005042 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.1721 Moderately Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0 Informative Direct
Biological Process (BP) coenzyme biosynthetic process 0.009499 Informative Inherited
Biological Process (BP) aminoglycan biosynthetic process 0 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 0.000000001315 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 0 Highly Informative Direct
Biological Process (BP) pteridine-containing compound biosynthetic process 0.0000000000001356 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 0 Informative Direct
Molecular Function (MF) acid-amino acid ligase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.3081 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)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-lysin0.0000132Highly InformativeDirect
Enzyme Commission (EC)UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanin0.0008424Highly InformativeDirect

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 biosynthesis0.000000003209Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013221 SSF53623 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 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].


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) · 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 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, catalytic 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, catalytic 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) · UniProtKB KeyWords (KW) · Internal database links ]