Skip to main content

Table 2 Domain architecture and functional predictions for functionally diversified proteins

From: Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins

Gene name (GI numbers)* Domain organization Phyletic distribution Predicted function§
Chlamydia trachomatis-Chlamydia muridarum-Chlamydophila pneumoniae
CT079/CP0424/TC0351 (4376613, 3328474, 7190393) Signal peptide, four transmembrane regions (TMs) Aquifex aeolicus Membrane protein, potential receptor
CT288/CP0709/TC0561 (4376321, 3328702, 7190602) Four TMs, coiled coil Chlamydia-specific, distant additional paralogs Membrane protein, potential receptor
CT656/CP0029/TC0027 (4377021, 3329106, 7190067) NA Chlamydia-specific Unknown
CT006/CP0311/TC0274 (4376725, 3328394, 7190315) Three TMs Chlamydia-specific Membrane protein, potential receptor
CT036/CP0642/TC0306 (4376393, 3328427, 7190347) Two TMs Chlamydia-specific Membrane protein, potential receptor
CT147/CP0623/TC0424 (4376417, 3328548, 7190467) Three-four TMs, coiled coil Chlamydia-specific Membrane protein, potential receptor
CT695/CP0071/TC0067 (4376977, 3329149, 7190102) Low sequence complexity Chlamydia-specific Non-globular protein of unknown function
Pyrococcus horikoshii-abyssi-furiosus
PH0310 (301754, 3256700, 5459075) Cathepsin-like cysteine protease, signal peptide, three to seven TMs Orthologs only in pyrococci; distantly related cathepsins in animals Pyrolysin - hyperthermostable membrane protease
PH1993, PAB1163 (1849588, 3258437, 5459195) Signal peptide, deacetylase superfamily hydrolase domain Methanococcus jannaschii, Pseudomonas aeruginosa, Mycobacterium tuberculosis (COG3233) Predicted secreted deacetylase
PH1708, PAB2041 (76490, 3258139, 5457898) Signal peptide, low-sequence-complexity regions Pyrococcus-specific Secreted, non-globular protein
PH0103, PAB0064 (693117, 3256489, 5457538) Type IV restriction endonuclease, Eco57I homolog Sporadic distribution in archaea and bacteria (COG2810) Predicted restriction endonuclease
PH1340, PAB1824 (1411868, 3257763, 5458235) NA Pyrococcus-specific Unknown
PH0996, PAB0660 (984613, 3257410, 5458405) Signal peptide, coiled coil, low complexity Pyrococcus-specific Secreted, non-globular protein
PH0617, PAB1428 (506618, 3257023, 5458851) Signal peptide, seven TMs Pyrococcus-specific Integral membrane protein
PH0692, PAB0621 (917540, 3257100, 5458351) Signal peptide, low sequence complexity regions Pyrococcus-specific Secreted, non-globular protein
PH0228, PAB0142 (1132938, 3256617, 5457641) Acetate/butyrate kinase domain Conserved orthologs in some archaea (Archaeoglobus, Aeropyrum); poorly conserved orthologs in most bacteria (COG2441) Predicted butyrate kinase
PH1703, PAB0312(1599997, 3258134, 5457902) Signal peptide, low sequence complexity regions Pyrococcus-specific Secreted small protein
PH0538, PAB0257 (396645, 3256944, 5457867) Signal peptide, four TMs Pyrococcus-specific (distant homologs in some archaea and bacteria) Integral membrane protein
Homo sapiens-Mus musculus-Rattus norvegicus
Interferon precursor (32680, 309328, 2317784) Signal peptide, interferon gamma domain Vertebrate-specific Interferon gamma
Interferon-beta-2 (32674, 52702, 204926) Signal peptide, interleukin 6 domain Vertebrate-specific Interleukin 6 (interferon-beta-2)
Glycoprotein 34 (219666, 551081, 3779224) Tumor necrosis factor domain, one TM Mammal-specific OX40 ligand (membrane-associated cytokine)
Uteroglobin (23132, 49691, 206040) Signal peptide, uteroglobin domain Mammal-specific Secreted phospholipid-binding protein
Eotaxin (1280141, 995911, 1707665) Signal peptide, interleukin 8 domain Vertebrate-specific Eotaxin (small inducible CxC cytokine)
Taste receptor T2R1 (9625043, 10048430, 7262627) Signal peptide, seven TMs Mammal-specific Taste receptor
Relaxin, H2 (35927, 414781, 57044) Signal peptide, insulin-like growth factor/relaxin family domain Mammal-specific Relaxin
IgE receptor (34003, 193246, 313673) Lectin C-type domain (CTL), one transmembrane segment, coiled coil domain Orthologs only in mammals, lectin domain in all animals Immunoglobulin E receptor
Lactadherin (1381162, 4586464, 1620007) Signal peptide, epidermal growth factor-like domains, coagulation factor 5/8 C-terminal (discoidin) domain (2) Orthologs in mammals only, discoidin domain animal-specific Lactadherin (secreted integrin- and phospholipid-binding protein, involved in antimicrobial defense)
Secretin preproprotein (11345450, 313711, 206888) Glucagon-like hormone domain Mammal-specific Secretin
C-reactive protein (30213, 50564, 203592) Signal peptide, pentraxin/C-reactive protein family domain Vertebrate-specific C-reactive protein, phosphorylcholine-binding, involved in host defense against bacterial infection
Preproapolipoprotein AI (28772, 50015, 202945) Signal peptide, apolipoprotein A1/A4/E family domain Vertebrate-specific Preproapolipoprotein AI
EDAG-1 (7677357, 11244774, 11140172) Regions of low sequence complexity Mammal-specific Unknown
Deoxyribonuclease II beta (11427442, 6175550, 6470131) Signal peptide, deoxyribonuclease Mammals, nematodes, insects (animal-specific) Deoxyribonuclease (lysosomal enzyme, implicated in apoptosis)
Hydroxysteroid sulfotransferase (306702, 496152, 2104492) Sulfotransferase domain Animals, plants, mycobacteria Hydroxysteroid sulfotransferase
Hydroxy acid oxidase 3 (7208440, 8926328, 311833) FMN-dependent oxidoreductase All eukaryotes, many bacteria Hydroxy acid oxidase (peroxisomal enzyme)
  1. *Global identifiers (Gis) for the selected orthologous protein sets. The first GI of each Pyrococcus orthologous set corresponds to the P. furiosus identifiers used at the sequencers' site. Domain organization was assessed using the SMART and CD-Search servers, and PSI-BLAST search results. TM, predicted transmembrane α-helix; NA (not applicable) indicates that no distinct domains could be identified. Species or taxa in which homologs were detected in BLAST or PSI-BLAST searches. §Functional prediction was based on the domain architecture and comparison of the results of BLAST searches with the protein annotation in Entrez. The COGnitor server was used to query the COG database for Chlamydiaceae and Pyrococcus proteins. Only Pyrococcus proteins grouped into any existing COGs.