PANDIT+

KeywordFamilyClanGene   

Entry: AfaD (PF05775) * this family does not contain any human sequence in the seed alignment although some of the annotation data are human specific [read more]

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Pfam summary

Description

Enterobacteria AfaD invasin protein

This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells [1].
 
Literature1. Garcia MI, Jouve M, Nataro JP, Gounon P, Le Bouguenec C; FEBS Lett 2000;479:111-117.Characterization of the AfaD-like family of invasins encoded by pathogenic Escherichia coli associated with intestinal and extra-intestinal infections. PUBMED:10981717
 
 
InterPro entry IPR008394
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 8 aligned sequences:

  AFAD_ECOLI/5-143   AGGB_ECOLI/3-141   Q53997_SALEN/5-146   Q8KWG5_ECOLI/3-142   Q93IN7_SALTI/5-150   Q9X4L4_ECOLI/2-142   Q9XDG6_ECOLI/6-144   Q9XDG7_ECOLI/1-139  

The full alignment for this family in the Pfam database contains 52 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Escherichia coli (6);   Salmonella enteritidis (1);   Salmonella typhi (1);  

The full alignment covers 5 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-3134.86-3111.669831-3111.669831-3108.862815-3106.731691

Tree Length  

16.8316.8348916.8348916.8348916.83489

κ  

2.502.6034282.6034282.5814942.583905

ω-ratio  

ω=0.19111p0=0.810277 ~ ω0=0.180364
p1=0.189723 ~ ω1=1
p0=0.810277 ~ ω0=0.180364
p1=0.105365 ~ ω1=1
p2=0.084358 ~ ω2=1
ω~Β(1.613868,4.739375)p0=0.910726 ~ ω~Β(2.463539,9.017316)
p1=0.089274 ~ ω=1

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=0.118704
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-3478.14046-3475.59451

Mean ω-ratio  

ω = 0.29787ω = 0.33928

Coeff. of variation  
of ω-ratio  

CVω = 0.75518CVω = 1.00298
 

Annotations

InteractionsThis family has 0 known interactions:

StructuresThis family has 4 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Cellular component
 fimbrium[GO:0009289]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Propanoate metabolism [KEGG]
Butanoate metabolism [KEGG]
Energy Metabolism
Nitrogen metabolism [KEGG]
Sulfur metabolism [KEGG]
Lipid Metabolism
Fatty acid metabolism [KEGG]
Amino Acid Metabolism
Glutamate metabolism [KEGG]
Methionine metabolism [KEGG]
Valine, leucine and isoleucine degradation [KEGG]
Lysine degradation [KEGG]
Tryptophan metabolism [KEGG]
Metabolism of Other Amino Acids
beta-Alanine metabolism [KEGG]
Selenoamino acid metabolism [KEGG]
Metabolism of Cofactors and Vitamins
Riboflavin metabolism [KEGG]
Porphyrin and chlorophyll metabolism [KEGG]
Biosynthesis of Secondary Metabolites
Limonene and pinene degradation [KEGG]
Xenobiotics Biodegradation and Metabolism
Geraniol degradation [KEGG]
Benzoate degradation via CoA ligation [KEGG]
Caprolactam degradation [KEGG]
Genetic Information Processing
Translation
Aminoacyl-tRNA biosynthesis [KEGG]
Environmental Information Processing
Membrane Transport
ABC transporters [KEGG]
Signal Transduction
Two-component system [KEGG]
Cellular Processes
Cell Motility
Bacterial chemotaxis [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

none


HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data
 
Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment
 
Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment