Table 2
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The top 15 phyletic patterns in proteins from archaea |
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Pattern*
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Number of COGs (and of the complementary pattern, CP)
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Comments and examples
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313 (0) |
Archaeal core, including 200 COGs present in both B† and E, 34 present in at least one B, 63 present in at least one E, 16 unique for A CP: Only COG0564, pseudouridylate synthase, 23S RNA-specific pseudouridylate synthase present in all E (in which it has an apparently mitochondrial origin) and B, but not in A. In all A another specific pseudouridylate synthase is present (COG1258) |
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163 (3) |
This pattern reflects a large number of genes acquired via HGT† in Mac (see [55]), including F0F1-type ATP synthase and NADH:ubiquinone oxidoreductase, and a specific signal transduction system based on several apoptosis-related domains CP: The small number of such COGs indicates that the archaeal core is almost fully conserved in Mac |
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79 (14) |
This pattern reflects a substantial amount of HGT in Hsp; see [125] |
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47 (7) |
This pattern consists of COGs including four methanogens and Afu; these organisms specifically share several metabolic pathways (see [45]). The set includes subunits of coenzyme F420-reducing hydrogenase, formylmethanofuran dehydrogenase, CO dehydrogenase/acetyl-CoA synthase and other enzymes of energy metabolism These might have originally evolved in methanogens and subsequently transferred to Afu. CP: Sugar ABC transporter and some fatty acid biosynthesis enzymes are missing from methanogens and Afu |
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40 (2) |
This pattern is specific for four methanogens, including unique pathways for coenzyme M biosynthesis and reduction and 14 uncharacterized proteins, many of which are likely to be unique enzymes involved in biosynthesis of other specific coenzymes and their utilization CP: COG2096, cob(I)alamin adenosyltransferase and COG1058, predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA, for which functional substitutes remain to be identified |
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33 (16) |
A pattern specific for thermophilic methanogens (Mth, Mja and Mka), comprising mostly uncharacterized COGs, it includes a specific membrane complex EhaA-EhaP (approximately 18 components) involved in hydrogen production and possibly electron transfer [45,134] CP: Specific gene loss: peptide ABC-type transporter, NADH: ubiquinone oxidoreductase, malic enzyme (COG0281), and cysteinyl-tRNA synthetase (COG0215; see text) |
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28 (6) |
This pattern reflects a substantial amount of HGT in Sso, including several enzymes of carbohydrate metabolism (beta-glucosidase, alpha-L-fucosidase, and malto-oligosyl trehalose synthase) [97] |
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27 (1) |
This reflects a substantial amount of HGT in Afu CP: COG0449, glucosamine 6-phosphate synthetase, which catalyzes the first step in hexosamine metabolism. A functional substitute remains to be identified |
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25 (4) |
A pattern specific for two mesophilic archaea, probably resulting from independent HGT |
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23 (7) |
This pattern includes genes that might have been acquired via HGT in Mja, in particular three enzymes of biotin biosynthesis: pimeloyl-CoA synthetase (COG1424), dethiobiotin synthetase (COG0132), and adenosylmethionine-8-amino-7-oxononanoate aminotransferase (COG0161) |
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21 (13) |
A crenarchaea-specific pattern, including 11 COGs that do not have orthologs outside this lineage. Among genes shared with bacteria but not euryarchaeota are three subunits of aerobic-type CO dehydrogenase and CO dehydrogenase maturation factor. Genes specifically shared with eukaryotes are three ribosomal proteins (S30, S25 and L13E) CP: Euryarchaea-specific pattern, including two subunits of archaeal DNA polymerase II and ERCC4-like helicase, division GTPase FtsZ (COG0206) and ATP-dependent protease LonB (COG1067) plus six COGs that do not have orthologs outside this lineage |
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20 (0) |
Apparent independent HGT to Mac and Afu |
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19 (16) |
Apparent specific gene loss in the Thermoplasma lineage: two subunits of topoisomerase VI (COG1389, 1697), adenylate cyclase of class 2 (COG1437), and predicted exosome subunits (COG1325, COG1931) CP: genes apparently acquired via HGT in Thermoplasma, including bacterial nucleoid DNA-binding protein HU (COG0776). See also [96] |
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18 (6) |
Apparent gene loss in Ape, including 9 enzymes of purine biosynthesis [135]. |
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17 (11) |
Apparent HGT in Pyrococci. Includes two subunits of allophanate hydrolase (COG1984, 2049), two enzymes of carbohydrate metabolism, β-galactosidase (COG1874) and endoglucanase (COG2730) CP: Specific gene loss in the Pyrococcus lineage includes five enzymes of heme biosynthesis |
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*The pattern of appearance within the 13 sequenced archaeal species currently available in the COG database. Species abbreviations are as given in Table 1 and are written vertically. †Abbreviations: A, archaea; B, bacteria; E, eukaryotes; CP, complementary pattern; HGT, horizontal gene transfer. | ||
Makarova and Koonin Genome Biology 2003 4:115 doi:10.1186/gb-2003-4-8-115 |
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