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].

Literature

1. 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

Download: AA alignments DNA alignments

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	16.83	16.83489	16.83489	16.83489	16.83489
κ	2.50	2.603428	2.603428	2.581494	2.583905
ω-ratio	ω=0.19111	p₀=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 = 0.29787	ω = 0.33928
Coeff. of variation of ω-ratio	CV_ω = 0.75518	CV_ω = 1.00298

Annotations

Interactions

This family has 0 known interactions:

Structures

This family has 4 structures:

Notation: PDB_ID (PDB chain, PDB residues)

2axw (A, 1-117)
2axw (B, 1-117)
2ixq (A, 2-118)
2fvn (A, 2-118)

Gene Ontologies

Cellular component

fimbrium[GO:0009289]

KEGG Pathways - for genes coding for sequences from full alignment

Metabolism

Carbohydrate Metabolism

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]

Pfam summary

Enterobacteria AfaD invasin protein

Alignment

Species in the seed alignment

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

Model name

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score

Tree Length

κ

ω-ratio

P-value for testing positive selection

Model name

Model Nonsynonymous

Model Dual

Log-likelihood score

Mean ω-ratio

Coeff. of variation of ω-ratio

Annotations

Expression data (explanation)

Human disease association

P-value for testing
positive selection

Coeff. of variation
of ω-ratio