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Table 2 Proteins that are specific for all Archaea

From: Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

(a) Proteins specific to all Archaea
PAB0063 [NP_125796] Cca COG1746 PAB0247 [NP_126062] DNA binding COG1571
PAB0252 [NP_126069] RNA-binding CDD16214 PAB0439 [NP_126328]   COG1308
PAB0316 [NP_126166] DNA primase COG0358 PAB0475 [NP_126376] regulator COG1709
PAB1633 [NP_126790] PilT ATPase COG1855 PAB1040 [NP_127251] SpoU CDD6631
PAB1716 [NP_126666] NMD3 CDD16276 PAB1106 [NP_127361]   CDD9578
PAB2291 [NP_125771]   CDD6629 PAB1706 [NP_126677]   COG1634
PAB0018a [NP_125721] RNA binding COG2888 PAB2062 [NP_126118]   CDD16190
PAB00751 [NP_125817] dehydratase CDD23288 PAB2104 [NP_126058] HTH COG1395
(b) Archaea-specific proteins with gene loss in few species
PAB0301 [NP_126142] SK COG1685 PAB7388 [NP_127197] Ribosomal_LX CDD2437
PAB0654 [NP_126650]   CDD8168 PAB0469.1n [NP_877631]   CDD8674
PAB0950 [NP_127106] TFIIE CDD480 PAB0547 [NP_126484]   COG1759
PAB1112 [NP_127373]   CDD5727 PAB0552 [NP_126501] Hjr CDD29957
PAB1135 [NP_127406]   CDD8168 PAB0623 [NP_126611]   CDD9586
PAB1241 [NP_127355]   CDD9682 PAB1272 [NP_127310]   COG1759
PAB1387 [NP_127161] flaJ COG1955 PAB1429 [NP_127105]   COG2433
PAB1715 [NP_126667]   CDD9801 PAB1721 [NP_126657]   COG2248
PAB1906 [NP_126377]   CDD2531 PAB23422 [NP_125707]   CDD15774
PAB7094 [NP_126085] Alba CDD25844 PAB7309 [NP_126897]   CDD2523
  1. These proteins were identified by BLASTP searches and their specificity is further confirmed by PSI-BLAST searches. For details, see method section. The protein ID number starting with PAB represents query protein from the genome of P. abyssi GE5, which was used as probe to perform the blast search. Accession numbers for these proteins are shown in square brackets. The possible cellular functions and COG or CDD number of some proteins are noted. For other proteins, the cellular functions are not known.
  2. Note 1. Two low-scoring homologs to PAB0075 were also found in Dehalococcoides ethenogenes 195 (Chloroflexi) and Dehalococcoides sp. CBDB1.
  3. Note 2. A homolog to PAB2342 is also found in Oenococcus oeni PSU-1, Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Clostridium perfringens str. 13.