SUPERFAMILY 1.75 HMM library and genome assignments server


PGBD-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   PGBD-like [ 47089]
Superfamily:   PGBD-like [ 47090] (2)
Families:   Peptidoglycan binding domain, PGBD [ 47091] (2)
  MMP N-terminal domain [ 63427] (4)


Superfamily statistics
Genomes (1,835) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 8,436 16,740 7
Proteins 7,475 15,003 7


Functional annotation
General category Processes_EC
Detailed category Cell adhesion

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) protein metabolic process 1.189e-08 Least Informative Direct
Biological Process (BP) multicellular organismal process 5.132e-08 Least Informative Direct
Biological Process (BP) developmental process 0.0001391 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) localization 0.1053 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.002378 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.008813 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.009799 Least Informative Inherited
Biological Process (BP) response to stimulus 0.4742 Least Informative Inherited
Biological Process (BP) response to endogenous stimulus 5.426e-05 Moderately Informative Direct
Biological Process (BP) organ development 0.0005356 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0008851 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.1046 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.002487 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.01229 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.0133 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01466 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.02521 Moderately Informative Inherited
Biological Process (BP) reproduction 0.05761 Moderately Informative Inherited
Biological Process (BP) tissue development 0.02382 Moderately Informative Inherited
Biological Process (BP) localization of cell 2.576e-09 Informative Direct
Biological Process (BP) proteolysis 7.05e-09 Informative Direct
Biological Process (BP) regulation of cellular component movement 8.703e-09 Informative Direct
Biological Process (BP) regulation of locomotion 2.708e-08 Informative Direct
Biological Process (BP) locomotion 5.92e-06 Informative Direct
Biological Process (BP) cellular component movement 4.636e-05 Informative Direct
Biological Process (BP) organ morphogenesis 0.0001379 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0001972 Informative Direct
Biological Process (BP) tissue morphogenesis 0.000317 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.002602 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.08151 Informative Inherited
Biological Process (BP) embryonic organ development 0.002407 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.003886 Informative Inherited
Biological Process (BP) response to lipid 0.02562 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.03658 Informative Inherited
Biological Process (BP) single organism reproductive process 0.01469 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.7236 Informative Inherited
Biological Process (BP) reproductive structure development 0.3408 Informative Inherited
Biological Process (BP) epithelium development 0.1669 Informative Inherited
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) multicellular organismal catabolic process 0 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) collagen metabolic process 0 Highly Informative Direct
Biological Process (BP) ossification 3.114e-14 Highly Informative Direct
Biological Process (BP) skeletal system development 2.236e-11 Highly Informative Direct
Biological Process (BP) protein processing 2.33e-10 Highly Informative Direct
Biological Process (BP) lung development 1.328e-06 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 2.316e-06 Highly Informative Direct
Biological Process (BP) ovulation cycle process 3.81e-06 Highly Informative Direct
Biological Process (BP) response to acid 6.694e-06 Highly Informative Direct
Biological Process (BP) response to hypoxia 1.287e-05 Highly Informative Direct
Biological Process (BP) response to drug 0.0006538 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0009864 Highly Informative Direct
Biological Process (BP) morphogenesis of a branching epithelium 0.01772 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.7419 Highly Informative Inherited
Biological Process (BP) post-embryonic development 0.6103 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.008353 Highly Informative Inherited
Biological Process (BP) gonad development 0.002285 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.05461 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) cation binding 2.036e-08 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.02494 Moderately Informative Inherited
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) transition metal ion binding 6.808e-12 Informative Direct
Molecular Function (MF) enzyme activator activity 0.0002402 Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Molecular Function (MF) endopeptidase activity 6.575e-06 Highly Informative Direct
Cellular Component (CC) membrane 0.4624 Least Informative Inherited
Cellular Component (CC) extracellular region part 1.405e-12 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.003117 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.1338 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.008751 Informative Inherited
Cellular Component (CC) anchored to membrane 3.777e-05 Highly Informative Direct
Cellular Component (CC) dendrite 6.73e-05 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)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)In linear amides6.703e-07Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect
Enzyme Commission (EC)Gelatinase B1.086e-05Highly InformativeDirect
Enzyme Commission (EC)Gelatinase A1.086e-05Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.017Least InformativeInherited
Disease Ontology (DO)immune system disease0.04628Least InformativeInherited
Disease Ontology (DO)nervous system disease0.235Least InformativeInherited
Disease Ontology (DO)gastrointestinal system disease3.976e-06Moderately InformativeDirect
Disease Ontology (DO)lung disease1.479e-05Moderately InformativeDirect
Disease Ontology (DO)artery disease0.001281Moderately InformativeInherited
Disease Ontology (DO)musculoskeletal system disease0.001474Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.002156Moderately InformativeInherited
Disease Ontology (DO)cell type cancer0.002628Moderately InformativeInherited
Disease Ontology (DO)skin disease0.002904Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.009383Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.01106Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.01552Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.04273Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.08204Moderately InformativeInherited
Disease Ontology (DO)female reproductive system disease9.794e-08InformativeDirect
Disease Ontology (DO)myopia2.491e-07InformativeDirect
Disease Ontology (DO)prostate cancer8.234e-07InformativeDirect
Disease Ontology (DO)Kawasaki disease2.174e-06InformativeDirect
Disease Ontology (DO)renal carcinoma3.959e-05InformativeDirect
Disease Ontology (DO)myeloma6.049e-05InformativeDirect
Disease Ontology (DO)integumentary system cancer8.092e-05InformativeDirect
Disease Ontology (DO)arthritis0.0001674InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0002744InformativeDirect
Disease Ontology (DO)connective tissue cancer0.0006175InformativeDirect
Disease Ontology (DO)large intestine cancer0.0006649InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.000729InformativeDirect
Disease Ontology (DO)liver carcinoma0.0009292InformativeDirect
Disease Ontology (DO)rheumatic disease0.004194InformativeInherited
Disease Ontology (DO)malignant glioma0.01017InformativeInherited
Disease Ontology (DO)esophageal disease0.01736InformativeInherited
Disease Ontology (DO)cardiomyopathy0.02365InformativeInherited
Disease Ontology (DO)muscular disease0.04519InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.04767InformativeInherited
Disease Ontology (DO)connective tissue disease0.271InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.8521InformativeInherited
Disease Ontology (DO)chondrosarcoma4.115e-08Highly InformativeDirect
Disease Ontology (DO)adult astrocytic tumour6.088e-08Highly InformativeDirect
Disease Ontology (DO)abdominal aortic aneurysm9.493e-07Highly InformativeDirect
Disease Ontology (DO)ovary epithelial cancer7.835e-06Highly InformativeDirect
Disease Ontology (DO)dermatomyositis2.077e-05Highly InformativeDirect
Disease Ontology (DO)bile duct adenocarcinoma6.183e-05Highly InformativeDirect
Disease Ontology (DO)adenoid cystic carcinoma6.384e-05Highly InformativeDirect
Disease Ontology (DO)bronchiectasis0.0001519Highly InformativeDirect
Disease Ontology (DO)Lyme disease0.0003319Highly InformativeDirect
Disease Ontology (DO)lichen disease0.0003862Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.3358Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of long bone morphology0.006334InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the metaphyses0.0002109Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the epiphyses0.0009665Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.01949Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.05336Least InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to infection9.707e-05Moderately InformativeDirect
Mammalian Phenotype (MP)tumorigenesis0.01853Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.03253Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1304Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.15Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.2575Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.2717Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7493Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.001745InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton physiology0.003514InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.0127InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.01473InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.01482InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.0419InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.04858InformativeInherited
Mammalian Phenotype (MP)pathological neovascularization0.05564InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.09641InformativeInherited
Mammalian Phenotype (MP)decreased susceptibility to bacterial infection2.279e-07Highly InformativeDirect
Mammalian Phenotype (MP)overexpanded pulmonary alveoli6.444e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased tumor growth/size0.0001727Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.0003787Highly InformativeDirect
Mammalian Phenotype (MP)aneurysm0.001424Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.002684Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hindlimb morphology0.004799Highly InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.005116Highly InformativeInherited
Mammalian Phenotype (MP)abnormal retinal vasculature morphology0.01271Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.2039Highly InformativeInherited

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)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)pericellular component development variant0Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant0InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)central nervous system0.5587Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.8051Least InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.1159Moderately InformativeInherited
Xenopus ANatomical entity (XAN)visual system0.9311Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage3.237e-05Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage5.316e-05Least 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)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.964Moderately InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)In linear amides5.583e-07InformativeDirect
Enzyme Commission (EC)N-acetylmuramoyl-L-alanine amidase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSporulation4.148e-15InformativeDirect
Biological processAngiogenesis4.026e-12InformativeDirect
Biological processCell wall biogenesis/degradation9.766e-10InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentExtracellular matrix0InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationMetalloprotease0InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein9.964e-13Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues4.617e-16Moderately InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage1.216e-09InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002477 SSF47090 Protein matches
Abstract

This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [PubMed9555893, PubMed7121588, PubMed1683402]. Examples are:

  • Muramoyl-pentapeptide carboxypeptidase
  • N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, )
  • Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, )
  • Membrane-bound lytic murein transglycosylase B
  • Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX [PubMed6743245].

Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.

Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [PubMed10190290], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [PubMed12810425, PubMed12888258], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism [PubMed12950257]. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [PubMed11956636].


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) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · 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 6 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 PGBD-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 6 hidden Markov models representing the PGBD-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-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]