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 (1,049) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 6,943 48,485 17
Proteins 6,856 48,390 17


Functional annotation
General category Processes_IC
Detailed category Protein modification

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

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GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) localization 0.06342 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.644 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3494 Least Informative Inherited
Biological Process (BP) response to stimulus 0.4624 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.02383 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1437 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.00005419 Moderately Informative Direct
Biological Process (BP) cellular localization 0.00008242 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.002186 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.1327 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.03465 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.004148 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.003294 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.004132 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.02574 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2011 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.01043 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.102 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.1762 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.004004 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.111 Moderately Informative Inherited
Biological Process (BP) cation homeostasis 0.0006567 Informative Direct
Biological Process (BP) cellular chemical homeostasis 0.0005166 Informative Direct
Biological Process (BP) regulation of transferase activity 0.001982 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.09447 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.3408 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.007631 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.00107 Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.000009036 Highly Informative Direct
Biological Process (BP) ER-nucleus signaling pathway 0.00000000000001587 Highly Informative Direct
Biological Process (BP) response to endoplasmic reticulum stress 0.000000001957 Highly Informative Direct
Biological Process (BP) modification of morphology or physiology of other organism 0.00000006128 Highly Informative Direct
Biological Process (BP) response to topologically incorrect protein 0.000000000002095 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0.000001702 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.000001169 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0000002297 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.0001057 Highly Informative Direct
Molecular Function (MF) binding 0.3365 Least Informative Inherited
Molecular Function (MF) cytoskeletal protein binding 0.0002623 Informative Direct
Molecular Function (MF) enzyme binding 0.000869 Informative Direct
Molecular Function (MF) protein dimerization activity 0.000007289 Informative Direct
Molecular Function (MF) tubulin binding 0.00000001442 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.000975 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.323 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.008719 Least Informative Inherited
Cellular Component (CC) membrane 0.001008 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1559 Least Informative Inherited
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0.0000005945 Moderately Informative Direct
Cellular Component (CC) membrane region 0.00001816 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.0000000001273 Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

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

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

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WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0.00001968Least 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 progeny0.0000008764Moderately InformativeDirect
Worm Phenotype (WP)larval lethal0.000001443Moderately InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.00000002937InformativeDirect

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)

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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)

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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)

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KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUnfolded protein response0.00000000000722Highly InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.000000000004316Moderately InformativeDirect
Cellular componentPeriplasm0InformativeDirect
DomainSignal0.00000000001933Least InformativeDirect
DomainTransmembrane0.6285Least InformativeInherited
DomainCoiled coil0.0002512Moderately 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 ]