Table 4 Some frequently populated Pfam-A families with origin at different evolutionary nodes.
Pfam-A family | N* | Functional description |
|---|---|---|
Archaea_only (131 sequences) | ||
Ribosomal proteins | 25 | Involved in catalyzing mRNA-directed protein synthesis |
RNA polymerase | 20 | Catalyse the DNA dependent polymerisation of RNA |
Translation initiation factor | 12 | Required for maximal rate of protein biosynthesis, in directing ribosome to proper start state of translation |
DNA polymerase | 5 | Required in replication of DNA |
Diphthamide_syn | 5 | Putative diphthamide synthesis protein |
Bacteria_only (1102 sequences) | ||
Sulfotransferases | 67 | Responsible for the transfer of sulphate groups to specific compounds |
Tubulin | 35 | Major component of microtubules, involved in polymer formation |
DAGAT | 23 | The enzyme diacylglycerol acyltransferase involved in the catalysis of terminal step of triacylglycerol |
Carb_anhydrase | 23 | Carbonic anhydrase, catalyze reversible hydration of carbon dioxide |
2OG-FeII_Oxy | 21 | 2-oxoglutarate and Fe(II)-dependent oxygenase superfamily |
Ribosomal protein | 17 | Involved in catalyzing mRNA-directed protein synthesis |
Eukaryota (2928 sequences) | ||
K_tetra | 120 | K+ channel cytoplasmic tetramerisation domain |
Ocular_alb | 113 | X-linked disorder characterized by severe impairment of visual acuity, retinal hypopigmentation and the presence of macromelanosomes |
CH | 109 | Calponin homology domain, found in both cytoskeletal and signal transduction protein |
Histone | 68 | Core Histone H2A/H2B/H3/H4, involved in histone-histone and histone-DNA interactions |
7 tm_3 | 65 | 7 transmembrane receptor (metabotropic glutamate family), coupled to G-proteins and stimulate the inositol phosphate/Ca2+ intracellular signalling pathway |
Actin | 62 | Involved in formation of filament, major component of cytoskeleton |
Fork_head | 59 | A transcription factor that promotes terminal rather than segmental development, involved in early developmental decisions of cell fates during embryogenesis |
UQ_con | 59 | Ubiquitin-conjugating enzyme, involved in catalytic activity or assist in poly-ubiquitin chain formation |
Metazoa (1362 sequences) | ||
Zf-C4 | 88 | DNA binding domain of a nuclear hormone receptor |
PID | 67 | Phosphotyrosine interaction domain |
RA | 51 | Ras association domain |
sema | 48 | The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance |
Ets | 37 | Erythroblast transformation specific domain, required for induction of erythroblastosis |
Wnt | 25 | Role in intercellular communication, possible role in central nervous system |
T-box | 24 | Perform DNA-binding and transcriptional activation/repression roles |
Chordata (470 sequences) | ||
Connexin | 22 | Gap junction protein |
Interferon | 19 | Produce antiviral and antiproliferative responses in cells |
Protocadherin | 17 | Cadherin-related molecules in central nervous system |
MHC_II_alpha | 15 | Related with cell-mediated immune responses |
Fn2 | 14 | Fibronectin type II domain, involved in a number of important functions e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis |
Mammalia (146 sequences) | ||
Gag_p10 | 21 | The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding |
GP41 | 16 | The GP41 subunit of the envelope protein complex mediates membrane fusion during viral entry |
Bim_N | 11 | Bim protein N terminus, essential initiators of apoptotic cell death |
Primates (21 sequences) | ||
SPAN-X | 14 | Human sperm proteins associated with the nucleus and mapped to the X chromosome, they are cancer-testis antigens. |
Homo sapiens (120 sequences) | ||
GP120 | 9 | Envelope glycoprotein GP120 |
BAGE | 5 | B melanoma antigen family |