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 (1,865) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,614 34,237 7
Proteins 7,656 31,268 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 4.107e-07 Least Informative Direct
Biological Process (BP) multicellular organismal process 4.121e-12 Least Informative Direct
Biological Process (BP) developmental process 4.081e-10 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0004765 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000303 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0005041 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) localization 0.1624 Least Informative Inherited
Biological Process (BP) response to stimulus 0.4029 Least Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.0005463 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0.0003237 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0003209 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 1.97e-06 Moderately Informative Direct
Biological Process (BP) response to abiotic stimulus 0.02024 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9161 Moderately Informative Inherited
Biological Process (BP) organ development 0.01632 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.04385 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.04676 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1246 Moderately Informative Inherited
Biological Process (BP) reproduction 0.1082 Moderately Informative Inherited
Biological Process (BP) tissue development 0.03391 Moderately Informative Inherited
Biological Process (BP) proteolysis 2.26e-10 Informative Direct
Biological Process (BP) cellular component movement 8.66e-05 Informative Direct
Biological Process (BP) organ morphogenesis 8.482e-05 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.0001976 Informative Direct
Biological Process (BP) locomotion 1.526e-06 Informative Direct
Biological Process (BP) regulation of locomotion 1.089e-09 Informative Direct
Biological Process (BP) embryonic morphogenesis 0.0001168 Informative Direct
Biological Process (BP) regulation of cellular component movement 2.518e-10 Informative Direct
Biological Process (BP) localization of cell 1.263e-09 Informative Direct
Biological Process (BP) embryo development ending in birth or egg hatching 0.4799 Informative Inherited
Biological Process (BP) embryonic organ development 0.01108 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.03783 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.003968 Informative Inherited
Biological Process (BP) response to lipid 0.02544 Informative Inherited
Biological Process (BP) single organism reproductive process 0.05176 Informative Inherited
Biological Process (BP) multicellular organismal reproductive process 0.7317 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.2736 Informative Inherited
Biological Process (BP) tube development 0.009596 Informative Inherited
Biological Process (BP) reproductive system development 0.8318 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.01465 Informative Inherited
Biological Process (BP) epithelium development 0.785 Informative Inherited
Biological Process (BP) skeletal system development 1.083e-14 Highly Informative Direct
Biological Process (BP) ossification 1.592e-13 Highly Informative Direct
Biological Process (BP) response to hypoxia 1.53e-05 Highly Informative Direct
Biological Process (BP) protein processing 4.349e-10 Highly Informative Direct
Biological Process (BP) cellular component disassembly 0 Highly Informative Direct
Biological Process (BP) ovulation cycle process 1e-05 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0 Highly Informative Direct
Biological Process (BP) respiratory tube development 3.283e-05 Highly Informative Direct
Biological Process (BP) response to amino acid stimulus 2.333e-05 Highly Informative Direct
Biological Process (BP) multicellular organismal metabolic process 0 Highly Informative Direct
Biological Process (BP) development of primary female sexual characteristics 3.234e-06 Highly Informative Direct
Biological Process (BP) branching morphogenesis of an epithelial tube 4.284e-08 Highly Informative Direct
Biological Process (BP) respiratory system development 5.905e-07 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.8873 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.04942 Highly Informative Inherited
Biological Process (BP) gonad development 0.01488 Highly Informative Inherited
Biological Process (BP) post-embryonic organ development 0.2537 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 4.622e-11 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.03418 Moderately Informative Inherited
Molecular Function (MF) enzyme activator activity 0.0003607 Informative Direct
Molecular Function (MF) peptidase activity 0 Informative Direct
Molecular Function (MF) zinc ion binding 0 Informative Direct
Molecular Function (MF) endopeptidase activity 4.722e-07 Highly Informative Direct
Molecular Function (MF) metallopeptidase activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0.653 Least Informative Inherited
Cellular Component (CC) extracellular region part 2.654e-11 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.00201 Moderately Informative Inherited
Cellular Component (CC) cell projection 0.1958 Moderately Informative Inherited
Cellular Component (CC) extracellular space 7.184e-05 Informative Direct
Cellular Component (CC) neuron projection 0.01491 Informative Inherited
Cellular Component (CC) dendrite 0.0001281 Highly Informative Direct
Cellular Component (CC) anchored to membrane 7.567e-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 cancer0.01219Least InformativeInherited
Disease Ontology (DO)immune system disease0.02337Least InformativeInherited
Disease Ontology (DO)nervous system disease0.1471Least InformativeInherited
Disease Ontology (DO)lung disease2.578e-06Moderately InformativeDirect
Disease Ontology (DO)mouth disease0.0001364Moderately InformativeDirect
Disease Ontology (DO)artery disease0.0003728Moderately InformativeDirect
Disease Ontology (DO)skin disease0.0006686Moderately InformativeDirect
Disease Ontology (DO)cell type cancer0.001633Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.003268Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.00347Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.01662Moderately InformativeInherited
Disease Ontology (DO)muscular disease0.02183Moderately InformativeInherited
Disease Ontology (DO)musculoskeletal system cancer0.03423Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.03886Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.05604Moderately InformativeInherited
Disease Ontology (DO)connective tissue disease0.3008Moderately InformativeInherited
Disease Ontology (DO)female reproductive system disease8.68e-09InformativeDirect
Disease Ontology (DO)chondrosarcoma8.422e-08InformativeDirect
Disease Ontology (DO)myopia5.059e-07InformativeDirect
Disease Ontology (DO)prostate cancer1.365e-06InformativeDirect
Disease Ontology (DO)Kawasaki disease2.982e-06InformativeDirect
Disease Ontology (DO)atherosclerosis3.97e-06InformativeDirect
Disease Ontology (DO)endometrial cancer7.256e-06InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease8.741e-05InformativeDirect
Disease Ontology (DO)myeloma9.653e-05InformativeDirect
Disease Ontology (DO)integumentary system cancer0.0001275InformativeDirect
Disease Ontology (DO)arthritis0.0002934InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.000328InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.0004064InformativeDirect
Disease Ontology (DO)rheumatic disease0.001655InformativeInherited
Disease Ontology (DO)collagen disease0.004237InformativeInherited
Disease Ontology (DO)urinary system cancer0.007031InformativeInherited
Disease Ontology (DO)heart disease0.01552InformativeInherited
Disease Ontology (DO)malignant glioma0.01556InformativeInherited
Disease Ontology (DO)esophageal disease0.02438InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.06026InformativeInherited
Disease Ontology (DO)myositis0.07586InformativeInherited
Disease Ontology (DO)gastrointestinal system cancer0.2218InformativeInherited
Disease Ontology (DO)adult astrocytic tumour6.455e-08Highly InformativeDirect
Disease Ontology (DO)ovary epithelial cancer7.68e-07Highly InformativeDirect
Disease Ontology (DO)abdominal aortic aneurysm1.254e-06Highly InformativeDirect
Disease Ontology (DO)dermatomyositis2.494e-05Highly InformativeDirect
Disease Ontology (DO)bronchiectasis0.000285Highly InformativeDirect
Disease Ontology (DO)pancreatic ductal adenocarcinoma0.0005889Highly 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 skeletal morphology0.3107Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of long bone morphology0.006068InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the metaphyses0.0002202Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the epiphyses0.0008931Highly 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 phenotype0.01936Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.05524Least InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.03475Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1266Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1503Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.2606Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.4409Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.7493Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.9367Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0004211InformativeDirect
Mammalian Phenotype (MP)abnormal cartilage morphology0.001697InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton physiology0.003549InformativeInherited
Mammalian Phenotype (MP)abnormal appendicular skeleton morphology0.01234InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.01277InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.01618InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.04142InformativeInherited
Mammalian Phenotype (MP)abnormal limb morphology0.04893InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.05539InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.09872InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to bacterial infection4.788e-06Highly InformativeDirect
Mammalian Phenotype (MP)overexpanded pulmonary alveoli6.082e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased angiogenesis0.0001053Highly InformativeDirect
Mammalian Phenotype (MP)decreased tumor growth/size0.0001843Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.0004205Highly InformativeDirect
Mammalian Phenotype (MP)aneurysm0.001392Highly InformativeInherited
Mammalian Phenotype (MP)abnormal maxilla morphology0.002642Highly InformativeInherited
Mammalian Phenotype (MP)abnormal hindlimb morphology0.004691Highly InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton development0.004905Highly InformativeInherited
Mammalian Phenotype (MP)abnormal limb long bone morphology0.3186Highly 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 system0.5628Least InformativeInherited
Xenopus ANatomical entity (XAN)head0.8051Least InformativeInherited
Xenopus ANatomical entity (XAN)surface structure0.1168Moderately InformativeInherited
Xenopus ANatomical entity (XAN)visual system0.9348Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage3.25e-05Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage5.275e-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 bonds0.9807Moderately InformativeInherited
Enzyme Commission (EC)Metalloendopeptidases0InformativeDirect
Enzyme Commission (EC)In linear amides8.308e-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 processSporulation4.149e-15InformativeDirect
Biological processAngiogenesis3.954e-12InformativeDirect
Biological processCell wall biogenesis/degradation9.351e-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 modificationGlycoprotein9.235e-13Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues4.61e-16Moderately InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationAutocatalytic cleavage1.114e-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 ]