SUPERFAMILY 1.75 HMM library and genome assignments server


PapD-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Immunoglobulin-like beta-sandwich [ 48725] (28)
Superfamily:   PapD-like [ 49354] (2)
Families:   Pilus chaperone [ 49355] (5)
  MSP-like [ 49360] (4)


Superfamily statistics
Genomes (1,048) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,938 48,485 17
Proteins 6,851 48,390 17


Functional annotation
General category Processes_IC
Detailed category Protein modification

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) single-organism cellular process 0.001159 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7821 Least Informative Inherited
Biological Process (BP) response to stimulus 0.4606 Least Informative Inherited
Biological Process (BP) localization 0.05483 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3248 Least Informative Inherited
Biological Process (BP) developmental process 0.02171 Least Informative Inherited
Biological Process (BP) cellular response to stress 4.75e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0002361 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.005919 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.08999 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01809 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.1113 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.07902 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.1284 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.005576 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.003761 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.03243 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.003332 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.1887 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.01031 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.003006 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.6361 Moderately Informative Inherited
Biological Process (BP) metal ion homeostasis 0.0002224 Informative Direct
Biological Process (BP) cellular cation homeostasis 0.000255 Informative Direct
Biological Process (BP) regulation of kinase activity 0.001145 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.004658 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.05752 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.001476 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.00105 Informative Inherited
Biological Process (BP) ER-nucleus signaling pathway 1.784e-14 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 2.205e-12 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 1.537e-09 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 1.899e-08 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 2.64e-07 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 3.8e-07 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 7.547e-07 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 9.362e-06 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 9.828e-05 Highly Informative Direct
Molecular Function (MF) binding 0.3095 Least Informative Inherited
Molecular Function (MF) protein dimerization activity 7.558e-06 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.0002762 Informative Direct
Molecular Function (MF) enzyme binding 0.0007795 Informative Direct
Molecular Function (MF) tubulin binding 1.508e-08 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0009715 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.3554 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.2063 Least Informative Inherited
Cellular Component (CC) membrane 0.00103 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.008735 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 3.815e-08 Moderately Informative Direct
Cellular Component (CC) organelle membrane 2.664e-05 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 1.611e-10 Informative Direct
Cellular Component (CC) Golgi apparatus 0.0001621 Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)muscle phenotype0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant1.968e-05Least InformativeDirect
Worm Phenotype (WP)growth variant0.0004392Least InformativeDirect
Worm Phenotype (WP)larval development variant0.01701Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.9751Least InformativeInherited
Worm Phenotype (WP)sterile progeny8.764e-07Moderately InformativeDirect
Worm Phenotype (WP)larval lethal1.443e-06Moderately InformativeDirect
Worm Phenotype (WP)lipid metabolism variant2.937e-08InformativeDirect

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

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FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon 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)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUnfolded protein response6.351e-12Highly InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum3.853e-12Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
DomainSignal1.964e-11Least InformativeDirect
DomainTransmembrane0.6297Least InformativeInherited
DomainCoiled coil0.0002461Moderately InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008962 SSF49354 Protein matches
Abstract

The PapD-like superfamily of periplasmic chaperones directs the assembly of over 30 diverse adhesive surface organelles that mediate the attachment of many different pathogenic bacteria to host tissues, a critical early step in the development of disease. PapD, the prototypical chaperone, is necessary for the assembly of P pili. P pili contain the adhesin PapG, which mediates the attachment of uropathogenic Escherichia coli to Gal(alpha) Gal receptors present on kidney cells and are critical for the initiation of pyelonephritis. The PapD-like chaperones consist of two Ig-like domains oriented toward each other, forming L-shaped molecules. In the chaperone-subunit complex, the G1beta strand of the chaperone completes an atypical Ig fold in the subunit by occupying the groove and running parallel to the subunit C-terminal F strand. This donor strand complementation interaction simultaneously stabilizes pilus subunits and caps their interactive surfaces, preventing their premature oligomerisation in the periplasm. During pilus biogenesis, the highly conserved N-terminal extension of one subunit has been proposed to displace the chaperone G1beta strand from its neighbouring subunit in a mechanism termed donor strand exchange [PubMed10859353].

This entry represents the immunoglobulin (Ig)-like beta-sandwich domain found in PapD, as well as in other periplasmic chaperone proteins that include FimC and SfaE from Escherichia coli, and Caf1m from Yersinia pestis [PubMed15372038]. In addition, major sperm proteins (MSP) and other related sperm proteins (such as WR4 and SSP-19) contain an Ig-like domain with a similar structural fold to PapD [PubMed12051923, PubMed15388931]. Major sperm proteins are central components in molecular interactions underlying sperm motility, with many isoforms existing in Caenorhabditis elegans.


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 10 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 PapD-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 10 hidden Markov models representing the PapD-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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]