Table 5.

Analysis of the qualified set of TE-associated domain containing proteins. Twelve PDB/Swiss-Prot proteins with TE-associated Pfam domains detected by HMMER (GA and TC cut-offs) are shown. The results from BLAST and RepeatMasker analysis are compared (√ = found, X = not found TE-related sequence). The cut-off E-value of 0.01 was used as the detection criteria.

Accession	Name	Organism	Pfam domain	BLASTN	BLASTP	BLASTX	TBLASTN	TBLASTX	RM
2jm3	Hypothetical protein	C. elegans	THAP	X	X	X	X	X	X
1a0p, XERD_ECOLI	Tyrosine recombinase xerD	E. coli	Phage_integrase	X	X	X	X	X	X
1bw6, 1hlv	Centromere protein B	H. sapiens	CENP-B_N	√	√	√	√	√	X
1uhu	retroviral Gag MA-like domain of RIKEN cDNA 3110009E22	M. musculus	Gag_MA	N/A	√	N/A	√	N/A	N/A
1y4m	Syncytin-2	H. sapiens	TLV_coat	√	√	√	√	√	√
2a3v	Site-specific recombinase IntI4	V.cholerae	Phage_integrase	X	X	X	X	X	X
2cqf	Lin-28 homolog A (Zinc finger CCHC domain-containing protein 1)	H. sapiens	zf-CCHC	X	√	√	√	√	X
2ct5	Zinc finger BED domain-containing protein 1	H. sapiens	zf-BED	X	√	√	√	√	X
2d8r	THAP domain-containing protein 2	H. sapiens	THAP	X	√	√	√	√	X
2djr	Zinc finger BED domain-containing protein 2	H. sapiens	zf-BED	X	√	√	√	√	X
CBH1_SCHPO	CENP-B homolog protein 1	S. pombe	DDE	X	√	√	√	√	X
XERC_ECOLI	Tyrosine recombinase xerC	E. coli	Phage_integrase	X	X	X	X	X	X