Table 4 Pfam domains enriched in up- and down-regulated genes
From: The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation
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 |