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.