Table 2.

Amino acid similarities between E.  coli and self-proteins in patients with primary biliary cirrhosis (PBC).  There are three major targets of cross-reactive autoantibodies directed against an epitope located at the inner lipoyl domain (ILD) of human pyruvate dehydrogenase E2 complex (PDC-E2), a cross-reactive one at the outer lipoyl domain (OLD), and one mimic on the PDC E3-binding protein (E3BP). Amongst six PDC-E2 mimics originated from various E.  coli proteins, four are targets of cross-reactive responses while three are unreactive, including the E.  coli PDC-E2 mimic which is a weak target. Amino acids appear in standard single letter code. Sequence alignment has been performed using the BLAST2p protein-protein comparison programmes. + indicates conserved or semiconserved substitutions.

															Protein	Identity	Similarity	Reactivity
G	Q	A	M	V	D	L	L	A	E	Y	E	K	V	G	E.  coli nitrate reductase 2	6	53% (8/15)	No
K	A	S	E	G	E	L	L	A	Q	V	E	P	E	D	E.  coli ATP-dependent Clp-X	8	93% (14/15)	No
K	V	A	A	E	Q	S	L	I	T	V	E	G	D	K	E.  coli PDC-E2	5	73% (11/15)	Weak
K	L	S	E	G	D	L	L	A	E	I	E	T	D	K	Human PDC-E2 ILD
L	M	T	D	G	I	L	L	A	E	I	Q	Q	D	R	E.  coli ATP-dependent helicase	7	80% (12/15)	Yes
G	Y	A	Q	S	G	L	L	A	E	I	T	P	D	K	E.  coli periplasmic maltose-binding	7	73% (11/15)	Yes
D	A	A	V	E	D	L	L	A	E	V	S	Q	P	K	E.  coli fatty acid oxidation-α	6	60% (9/15)	Yes
L	A	T	L	D	D	L	L	A	E	I	G	L	G	N	E.  coli (P) ppGpp synthetase II	6	60% (9/15)	Yes
A	V	S	A	G	D	A	L	C	E	I	E	T	D	K	Human PDC-3BP	10	80% (12/15)	Yes (strong)