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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.

From: Evaluating the protein coding potential of exonized transposable element sequences

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