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)

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Superfamily statistics

	Genomes (1,057)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	6,984	30,049	17
Proteins	6,898	29,731	17

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Functional annotation

• General category: Processes_IC
• Detailed category: Protein modification

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Worm Phenotype (WP)

Highlighted in gray are those with FDR_all>0.001

	WP term	FDR (all)	IC level	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	development variant	0	0.001706	--	DIRECT
Worm Phenotype (WP)	morphology variant	0	0.06117	--	DIRECT
Worm Phenotype (WP)	organism development variant	0	0.004279	--	DIRECT
Worm Phenotype (WP)	organism morphology variant	0	0.2011	--	DIRECT
Worm Phenotype (WP)	linker cell migration variant	0.0000003125	2.407	--	DIRECT
Worm Phenotype (WP)	fat content variant	0.00001128	1.594	--	DIRECT
Worm Phenotype (WP)	progeny variant	0.00002136	0.7582	--	DIRECT
Worm Phenotype (WP)	cell migration variant	0.0001423	1.327	--	DIRECT
Worm Phenotype (WP)	postembryonic development variant	0.0002618	0.3347	--	DIRECT
Worm Phenotype (WP)	slow growth	0.0003997	0.5903	--	DIRECT
Worm Phenotype (WP)	larval arrest	0.0004395	0.5677	--	DIRECT
Worm Phenotype (WP)	developmental growth variant	0.0004795	0.5677	--	DIRECT
Worm Phenotype (WP)	dauer lifespan variant	0.0005337	2.23	--	DIRECT
Worm Phenotype (WP)	dauer metabolism variant	0.0006205	2.23	--	DIRECT
Worm Phenotype (WP)	developmental timing variant	0.0009646	0.5373	--	DIRECT
Worm Phenotype (WP)	organism physiology variant	0.009043	0.1405	--	INHERITED FROM: larval arrest || dauer metabolism variant || lipid metabolism variant || slow growth || larval growth variant || fat content variant || developmental growth variant || dauer lifespan extended || dauer lifespan variant
Worm Phenotype (WP)	growth variant	0.01998	0.4022	--	INHERITED FROM: larval arrest || slow growth || larval growth variant || developmental growth variant
Worm Phenotype (WP)	larval physiology variant	0.06983	1.594	--	INHERITED FROM: dauer lifespan variant || dauer metabolism variant || dauer lifespan extended
Worm Phenotype (WP)	reproductive system physiology variant	0.2375	0.07209	--	INHERITED FROM: sterile progeny
Worm Phenotype (WP)	organ system physiology variant	0.2415	0.05921	--	INHERITED FROM: sterile progeny
Worm Phenotype (WP)	fertility reduced	0.5125	0.09267	--	INHERITED FROM: sterile progeny
Worm Phenotype (WP)	lethal	0.9757	0.01121	--	INHERITED FROM: larval lethal
Worm Phenotype (WP)	fertility variant	1	0.08329	--	INHERITED FROM: sterile progeny
Worm Phenotype (WP)	physiology variant	1	0	--	INHERITED FROM: developmental growth variant || fat content variant || retarded heterochronic variations || dauer lifespan variant || larval lethal || cell migration variant || sterile progeny || progeny variant || slow growth || linker cell migration variant || development variant || developmental timing variant || lipid metabolism variant || larval growth variant || general pace of development variant || dauer lifespan extended || postembryonic development variant || larval arrest || dauer metabolism variant || organism development variant
Worm Phenotype (WP)	organism homeostasis metabolism variant	1	0.1501	--	INHERITED FROM: lipid metabolism variant || larval arrest || slow growth || larval growth variant || developmental growth variant || fat content variant
Worm Phenotype (WP)	sterile	1	0.161	--	INHERITED FROM: sterile progeny
Worm Phenotype (WP)	larval lethal	0.00008177	0.6947	Least Informative	DIRECT
Worm Phenotype (WP)	larval growth variant	0.0004433	0.5677	Least Informative	DIRECT
Worm Phenotype (WP)	general pace of development variant	0.0005409	0.5708	Least Informative	DIRECT
Worm Phenotype (WP)	retarded heterochronic variations	0.0008037	0.5373	Least Informative	DIRECT
Worm Phenotype (WP)	larval development variant	0.1535	0.5007	Least Informative	INHERITED FROM: larval arrest
Worm Phenotype (WP)	cell development variant	0.9163	0.632	Least Informative	INHERITED FROM: cell migration variant || linker cell migration variant
Worm Phenotype (WP)	organism metabolism processing variant	1	0.4572	Least Informative	INHERITED FROM: lipid metabolism variant || fat content variant
Worm Phenotype (WP)	sterile progeny	0.00001993	0.7582	Moderately Informative	DIRECT
Worm Phenotype (WP)	lipid metabolism variant	0.00002589	1.429	Informative	DIRECT
Worm Phenotype (WP)	life span variant	0.9409	1.276	Informative	INHERITED FROM: dauer lifespan variant || dauer lifespan extended
Worm Phenotype (WP)	dauer larva physiology variant	1	1.594	Informative	INHERITED FROM: dauer lifespan variant || dauer metabolism variant || dauer lifespan extended
Worm Phenotype (WP)	dauer lifespan extended	0.0004248	2.23	Highly Informative	DIRECT

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Fly Phenotype (FP)

Highlighted in gray are those with FDR_all>0.001

	FP term	FDR (all)	IC level	SDFP level	Annotation (direct or inherited)
Fly Phenotype (FP)	phenotype	0	0.05522	--	DIRECT
Fly Phenotype (FP)	viable	0	0.735	Least Informative	DIRECT
Fly Phenotype (FP)	fertile	0	0.981	Moderately Informative	DIRECT

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Fly Anatomy (FA)

Highlighted in gray are those with FDR_all>0.001

	FA term	FDR (all)	IC level	SDFA level	Annotation (direct or inherited)
Fly Anatomy (FA)	organism	0	0.07918	--	DIRECT
Fly Anatomy (FA)	multicellular structure	0	0.009143	--	DIRECT
Fly Anatomy (FA)	anatomical structure	1	0	--	INHERITED FROM: organism || cell || multicellular structure
Fly Anatomy (FA)	material anatomical entity	1	0	--	INHERITED FROM: multicellular structure || cell || organism
Fly Anatomy (FA)	cell	0	0.4937	Least Informative	DIRECT

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Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	trunk region	0	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	genital system	0	0.5909	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1442	--	DIRECT
Xenopus ANatomical entity (XAN)	organism subdivision	0	0.1871	--	DIRECT
Xenopus ANatomical entity (XAN)	compound organ	0	0.24	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical region	0	0.193	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical system	1	0.3094	--	INHERITED FROM: urogenital system || genital system
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: urogenital system || genital system || anatomical group || cavitated compound organ || multicellular anatomical structure || compound organ || trunk || anatomical region || trunk region || organism subdivision
Xenopus ANatomical entity (XAN)	urogenital system	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	trunk	0	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0	0.3033	Least Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT

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Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	shoot system	0	0.05747	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01577	--	DIRECT
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: collective plant structure || shoot system
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: shoot system
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	1 main shoot growth stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf production stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.2036	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2833	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.03771	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.4754	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.4754	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.07083	--	INHERITED FROM: corolla development stage || flowering stage || floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || LP.10 ten leaves visible stage || E expanded cotyledon stage || LP.12 twelve leaves visible stage || F mature embryo stage || LP.04 four leaves visible stage || D bilateral stage || LP.06 six leaves visible stage || LP.08 eight leaves visible stage || LP.02 two leaves visible stage || plant embryo stage || leaf production stage || 1 main shoot growth stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.04053	--	INHERITED FROM: phyllome development stage || reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || flowering stage || corolla development stage || plant organ development stage || 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.2022	--	INHERITED FROM: LP.08 eight leaves visible stage || LP.12 twelve leaves visible stage || E expanded cotyledon stage || LP.10 ten leaves visible stage || LP.06 six leaves visible stage || sporophyte vegetative stage || leaf production stage || 1 main shoot growth stage || D bilateral stage || F mature embryo stage || LP.04 four leaves visible stage || plant embryo stage || LP.02 two leaves visible stage
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.353	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.4088	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.3729	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	0.5666	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	0.586	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	0.5603	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	0.4338	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	0.5243	Least Informative	DIRECT

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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 [10859353].

  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 [15372038]. 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 [12051923, 15388931]. Major sperm proteins are central components in molecular interactions underlying sperm motility, with many isoforms existing in Caenorhabditis elegans.

InterPro database

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