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Table 4 Some frequently populated Pfam-A families with origin at different evolutionary nodes.

From: Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level

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
  1. * N is the number of protein sequences containing those Pfam-A families in the left column.