Table 2

Pfam domains in HGT candidates

Accession ID

Description

N

Enrichment

p-value


PF00078.20

Reverse transcriptase (RNA-dependent DNA polymerase)

58

14.0×

<10-49

PF03372.16

Endonuclease/Exonuclease/phosphatase family

27

18.8×

<10-26

PF00096.19

Zinc finger, C2H2 type

14

5.1×

<10-5

PF00067.15

Cytochrome P450

11

2.5×

<0.01

PF00069.18

Protein kinase domain

9

0.9×

1

PF07714.10

Protein tyrosine kinase

9

1.0×

0.9

PF00097.18

Zinc finger, C3HC4 type (RING finger)

8

3.1×

<0.01

PF00089.19

Trypsin

6

6.4×

<0.01

PF08036.4

Diapausin family of antimicrobial peptide

6

38.3×

<10-8

PF08953.4

Domain of unknown function (DUF1899)

6

25.6×

<10-6

PF00076.15

RNA recognition motif (RRM)

5

1.6×

0.3

PF00644.13

Poly(ADP-ribose) polymerase catalytic domain

5

24.0×

<10-5

PF00856.21

SET domain

5

5.8×

<0.01

PF03732.10

Retrotransposon gag protein

5

24.0×

<10-5

PF12171.1

Zinc-finger double-stranded RNA-binding

5

3.8×

<0.05

PF00092.21

von Willebrand factor type A domain

4

3.2×

0.06

PF00106.18

short chain dehydrogenase

4

1.4×

0.4

PF00178.15

Ets-domain

4

8.5×

<0.01

PF00005.20

ABC transporter

3

1.4×

0.6

PF00098.16

Zinc knuckle

3

3.7×

<0.05


The 20 most abundant Pfam domains (e-value <0.001) in 509 HGT candidates defined by cross-species homology are shown. Enrichments factors and FDR corrected p-values were calculated relative to all P. pacificus genes with annotated PFAM domains.

Rödelsperger and Sommer BMC Evolutionary Biology 2011 11:239   doi:10.1186/1471-2148-11-239

Open Data