Table 4

Pfam domains enriched in up- and down-regulated genes

Pfam domain IDa

Pfam domain description

Domains in genomeb

Domains in subsetc

P-valued


Up-regulated at 8 h encystation (compared to trophozoite)

PF00962

Adenosine/AMP deaminase

10

4

1.00 × 10-4

PF01370

NAD dependent epimerase/dehydratase family

7

3

6.45 × 10-4

PF01380

Sugar isomerase domain

3

2

2.20 × 10-3

PF01416

tRNA pseudouridine synthase

5

2

6.92 × 10-3

PF06978

Ribonucleases P/MRP protein subunit POP1

2

2

7.52 × 10-4

PF02463

Structural maintenance of chromosomes superfamily

9

3

1.46 × 10-3

PF08221

RNA polymerase III subunit RPC82 helix-turn-helix domain

3

2

2.20 × 10-3

PF00620

RhoGAP domain

97

10

2.61 × 10-4

PF00566

Rab-GTPase-TBC domain

62

6

5.48 × 10-3

PF08743

DNA repair

3

2

2.20 × 10-3

PF03114

Protein dimerisation domain

12

3

3.53 × 10-3

PF09777

Osteopetrosis-associated transmembrane protein 1 precursor

2

2

7.52 × 10-4

PF00888

Cullin family ubiquitin ligase scaffold protein

11

3

2.72 × 10-3

PF10557

Cullin protein neddylation domain

12

3

3.53 × 10-3

PF00643

B-box zinc finger

15

3

6.72 × 10-3

PF00578

Alkyl hydroperoxide reductase and thiol specific antioxidant

17

3

9.50 × 10-3

PF12796

Ankyrin repeats

87

9

5.03 × 10-4

PF03197

Bacteriophage FRD2 protein

3

2

2.20 × 10-3

PF07534

unknown function

210

19

4.34 × 10-6

Up-regulated at 24 h encystation (compared to trophozoite)

PF06045

Rhamnogalacturonate lyase family

6

5

2.74 × 10-6

PF00704

Glycosyl hydrolases family 18

7

5

9.07 × 10-6

PF07651

Phosphatidylinositol 4,5-bisphosphate binding

8

4

4.96 × 10-4

PF07653

Variant SH3 domain

21

6

6.16 × 10-4

PF00018

SH3 domain: protein-protein interaction

32

7

1.19 × 10-3

PF00614

Phospholipase D active site motif

2

2

2.98 × 10-3

PF00069

Protein kinase domain

510

41

3.42 × 10-3

PF00806

Pumilio-family RNA binding repeat

60

12

6.48 × 10-5

PF06978

Ribonucleases P/MRP protein subunit POP1

2

2

2.98 × 10-3

PF00352

Transcription factor TFIID (or TATA-binding protein, TBP)

11

4

1.98 × 10-3

PF00620

RhoGAP domain

97

18

3.50 × 10-6

PF00225

Kinesin motor domain

6

3

2.75 × 10-3

PF03953

Tubulin C-terminal domain

6

3

2.75 × 10-3

PF00443

Ubiquitin carboxyl-terminal hydrolase

29

6

3.45 × 10-3

PF13476

ATPase domain

10

4

1.33 × 10-3

PF04506

Integral membrane protein, possible sugar transporter

2

2

2.98 × 10-3

PF12796

Ankyrin repeats

87

13

6.03 × 10-4

PF07534

Unknown function

210

31

3.07 × 10-7

Up-regulated at 72 h encystation (compared to trophozoite)

PF00128

Alpha amylase, catalytic domain

24

7

5.95 × 10-5

PF02784

Pyridoxal-dependent decarboxylase, pyridoxal binding domain

5

3

8.37 × 10-4

PF12697

Alpha/beta hydrolase family

8

3

4.08 × 10-3

PF00614

Phospholipase D active site motif

2

2

2.04 × 10-3

PF00806

Pumilio-family RNA binding repeat

60

12

1.05 × 10-5

PF00773

Catalytic domain of ribonuclease II

10

4

6.58 × 10-4

PF01885

RNA 2'-phosphotransferase, Tpt1/KptA family

3

2

5.83 × 10-3

PF06978

Ribonucleases P/MRP protein subunit POP1

2

2

2.04 × 10-3

PF04054

CCR4-Not complex component - global regulator of transcription

5

3

8.37 × 10-4

PF00145

C-5 cytosine-specific DNA methylase

2

2

2.04 × 10-3

PF08221

RNA polymerase III subunit RPC82 helix-turn-helix domain

3

2

5.83 × 10-3

PF08743

DNA repair

3

2

5.83 × 10-3

PF02144

Repair protein Rad1/Rec1/Rad17

3

2

5.83 × 10-3

PF02145

Rap/ran-GAP

33

6

2.67 × 10-3

PF00620

RhoGAP domain

97

11

2.92 × 10-3

PF04506

Integral membrane protein, possible sugar transporter

2

2

2.04 × 10-3

PF01436

NHL repeat

8

3

4.08 × 10-3

PF05237

MoeZ/MoeB domain: unknown function

3

2

5.83 × 10-3

PF07534

Unknown function

210

20

8.17 × 10-4

Up-regulated at 2 h excystation (compared to 72 h cyst)

PF00723

Glycosyl hydrolases family 15

6

4

4.71 × 10-4

PF00534

Glycosyl transferases group 1

4

3

1.75 × 10-3

PF01592

Iron-sulfur cluster assembly

148

24

2.86 × 10-4

PF00076

RNA recognition motif (aka RRM, RBD, or RNP domain)

36

9

1.11 × 10-3

PF00270

DEAD/DEAH box helicase

12

5

1.29 × 10-3

PF00565

Staphylococcal nuclease homolog

5

3

4.03 × 10-3

PF01416

Pseudouridine synthesis

4

3

1.75 × 10-3

PF04719

hTAFII28-like protein conserved region

9

4

3.10 × 10-3

PF01926

50S ribosome-binding GTPase

2

2

6.08 × 10-3

PF02270

Transcription initiation factor IIF (TFIIF)

22

7

8.81 × 10-4

PF00226

DnaJ domain

4

3

1.75 × 10-3

PF08423

DNA repair and recombination

19

6

2.12 × 10-3

PF02450

Lecithin:cholesterol acyltransferase

2

2

6.08 × 10-3

PF06728

GPI transamidase subunit

2

2

6.08 × 10-3

PF01238

Phosphomannose isomerase type I

46

10

1.81 × 10-3

PF00112

Papain family cysteine protease

6

3

7.44 × 10-3

PF01067

Calpain large subunit, domain III (protease)

28

20

1.03 × 10-16

PF00630

Filamin/ABP280 repeat

24

9

4.09 × 10-5

PF01602

Adaptin N-terminal region

9

6

1.47 × 10-5

PF04324

BFD-like [2Fe-2S] binding domain

4

3

1.75 × 10-3

PF02777

Iron/manganese superoxide dismutases, C-terminal domain

8

4

1.87 × 10-3

PF00400

WD domain, G-beta repeat

263

51

7.47 × 10-10

PF13115

YtkA-like: unknown function

12

7

9.20 × 10-6

PF06229

FRG1-like family: unknown function

4

3

1.75 × 10-3

PF08238

Sel1 repeat

21

6

3.60 × 10-3

Down-regulated at 72 h encystation (compared to trophozoite)

PF00723

Glycosyl hydrolases family 15

6

4

5.42 × 10-4

PF00106

Short chain dehydrogenase

12

6

1.55 × 10-4

PF01663

Type I phosphodiesterase/nucleotide pyrophosphatase

19

7

4.13 × 10-4

PF02878

Phosphoglucomutase/phosphomannomutase domain I

3

3

5.29 × 10-4

PF02880

Phosphoglucomutase/phosphomannomutase domain III

3

3

5.29 × 10-4

PF00408

Phosphoglucomutase/phosphomannomutase, C-terminal domain

3

3

5.29 × 10-4

PF00349

Phosphorylates hexoses

2

2

6.54 × 10-3

PF01467

Cytidylyltransferase

9

6

1.82 × 10-5

PF09334

tRNA synthetases class I (M)

3

3

5.29 × 10-4

PF00432

Prenyltransferase and squalene oxidase repeat

4

4

4.27 × 10-5

PF00630

Filamin/ABP280 repeat

28

25

1.10 × 10-24

PF00307

Calponin homology (CH) domain

50

13

9.75 × 10-5

PF06268

Actin cross-linking

6

5

1.90 × 10-5

PF01602

Adaptin N-terminal region

24

9

5.41 × 10-5

PF04324

BFD-like [2Fe-2S] binding domain

9

6

1.82 × 10-5

PF00248

Aldo/keto reductase family

4

4

4.27 × 10-5

PF02777

Iron/manganese superoxide dismutases, C-terminal domain

4

4

4.27 × 10-5

PF00081

Iron/manganese superoxide dismutases, alpha-hairpin domain

5

4

1.96 × 10-4

PF13115

YtkA-like: unknown function

12

8

6.40 × 10-7

PF00501

AMP-binding enzyme

26

11

2.08 × 10-6

PF12796

Ankyrin repeats

87

20

1.15 × 10-5


aSelected Pfam domains that were significantly enriched (P <0.05) in genes up- or down-regulated at 8 h, 24 h and 72 h post-encystation, and at 2 h post-excystation. bNumber of a Pfam domain in the whole E. invadens genome. cNumber of a Pfam domain among the subset of regulated genes. dP-value for Pfam domain enrichment.

Ehrenkaufer et al. Genome Biology 2013 14:R77   doi:10.1186/gb-2013-14-7-r77

Open Data