From: A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
KOG number | (Predicted) function | Multiprotein complex | Functional class* | Prokaryotic homologs | Fitness class†| Comments | |
---|---|---|---|---|---|---|---|
 |  |  |  |  | Yeast‡ | Worm§ |  |
Genes experimentally or computationally characterized previously | |||||||
0392 | SNF2 family DNA-dependent ATPase | TBP-DNA complex | Â | Many bacteria and archaea (COG0553) | 0 | 1 | Involved in regulation of transcription from POL II promoters [104] |
0121 | Nuclear cap-binding protein complex, subunit CBP20 (RRM-domain-containing RNA-binding protein) | Cap-binding complex | A | Several bacteria (COG0724) | 1 | X | RRM-domain proteins show scattered presence in bacteria and might have been horizontally transferred from eukaryotes |
0213 | U2-snRNP associated splicing factor 3b, subunit 1 | Spliceosome | A | None | 0 | 0 | Â |
0227 | snRNA-associated protein, splicing factor 3a, subunit b (Prp11p) | Spliceosome | A | None | 0 | 0 | Â |
2268 | Predicted nucleic-acid-binding protein kinase of the RIO1 family; 40S ribosomal subunit biogenesis/18S rRNA processing | Pre-40S subunit | A | Orthologs in most archaea but not in bacteria (COG0478) | 0 | X | One of the very small number of protein kinases that show a clear-cut orthologous relationship between all eukaryotes and most archaea, and, apparently, the only one containing a helix-turn-helix nucleic-acid-binding domain. [105] Associated with yeast pre-40S subunit and required for its maturation. [106] |
3031 | Protein required for 60S ribosomal subunit biogenesis; [107] contains the IMP4 domain, which is involved in rRNA processing [108]; paralog of KOG3095 and KOG3292, which are also represented in all analyzed genomes. | Processosome | A | Distantly related to COG2136, represented by orthologs in most archaea, but not in bacteria (KSM, unpublished) | 0 | X | The COG2136 proteins appear to be subunits of the predicted archaeal exosome [109]. Apparently, this gene has undergone at least two ancient duplications in eukaryotes |
3045 | Predicted RNA methylase involved in rRNA processing | Processosome? | A | Distantly related to numerous Rossmann-fold methylases but prokaryotic orthologs could not be confidently identified | 1 | 1 | This protein (Rrp8p in yeast) has been shown to participate in the processing of rRNA and sequence analysis reveals the presence of a Rossmann-fold methylase domain [110]. Therefore Rrp8p probably methylates either snoRNA or rRNA itself. |
3064 | RNA-binding nuclear protein containing a distinct C4 Zn-finger; implicated in the biogenesis of 60S ribosomal subunits [111] | Processosome | A | None | 0 | 0 | Initially identified in yeast as the MAK16 protein required for dsRNA virus reproduction [112] |
0291, 0302, 0306, 310, 0319, 0650, 1272 | WD40-repeat proteins, subunits of rRNA processing complexes [69, 70] | Processosome | A | WD40-repeat proteins are present in several bacterial lineages and are particularly abundant in cyanobacteria but are missing in most archaea; none of them appear to be obvious orthologs of this protein (COG2319) | all 0 | X,X,1,X,1,1,1 | Â |
0284 | Polyadenylation factor I complex, subunit PFS2, WD40-repeat protein | Poly-adenylation complex | A | Same as above (COG2319) | 0 | X | Â |
0337 | RNA helicase involved in 28S rRNA processing | Processosome | A | Most of the archaea and bacteria (COG0513) | 0 | X | Â |
0343 | RNA helicase involved in 28S rRNA processing | Processosome | A | Most of the archaea and bacteria (COG0513) | 0 | X | Â |
1069 | 3'-5' exoribonuclease (RNAse PH), exosome subunit Rrp46 | Exosome | A | Most bacteria and archaea (COG0689) | 0 | 1 | Â |
1070 | Exosome subunit Rrp5 (RNA-binding S1 domain fused to TPR repeats) | Exosome | A | Most bacteria (COG0539, COG0457) | 0 | 1 | Â |
1135 | mRNA cleavage and polyadenylation complex subunit CFT2 (CPSF) | Cleavage and polyadenylation complex | A | Most archaea and some bacteria (COG1236) | 0 | 0 | Â |
1914 | mRNA cleavage and polyadenylation factor I complex, subunit RNA14 | Cleavage and polyadenylation complex | A | None | 0 | X | Â |
1975 | RNA (guanine-7-) methyltransferase (capping enzyme subunit) | Capping enzyme | A | Numerous methyltrans-ferases (COG0500) but no ortholog | 0 | 1 | Â |
2051 | Nonsense-mediated mRNA decay complex, subunit 2 | NMD complex | A | None | 1 | X | Â |
2554 | Pseudouridylate synthase | ? | A | Most archaea and bacteria (COG0101) | 1 | 1 | Â |
2613 | Upf1p-interacting protein, NMD complex subunit Nmd3p | NMD complex | A | All archaea, no bacteria (COG1499) | 0 | X | Â |
2771 | tRNA-specific adenosine-34 deaminase subunit Tad3p | Heterodimeric RNA-specific deaminase | A | Most bacteria and some archaea (COG0590) | 0 | X | Â |
2780 | Protein involved in ribosomal large subunit assembly (RPF1), contains IMP4 domain | Processosome | A | Most archaea, no bacteria (COG2136) | 0 | 1 | Â |
2781 | Subunit of the small (ribosomal) subunit (SSU) processosome (snoRNP), IMP4 | Processosome | A | Most archaea, no bacteria (COG2136) | 0 | 1 | Â |
2874 | Protein involved in rRNA processing and ribosomal assembly | ? | A | All archaea, no bacteria (COG1094) | 0 | 1 | Predicted RNA-binding protein containing KH domain |
3013 | Exosome subunit Rrp4 | Exosome | A | Most archaea, on bacteria (COG1097) | 0 | X | Â |
3031 | Protein involved in large ribosome subunit assembly and 28S rRNA processing (Rrf2) | Processosome | A | None | 0 | X | Contains the BRIX domain |
3322 | RNAse P/MRP subunit, involved in processing of pre-tRNAs and the 5.8S rRNA | RNAse P/MRP holoenzyme | A | None | 0 | 1 | Â |
3448 | Predicted snRNP core protein | Spliceosome | A | All archaea, no bacteria (COG1958) | 0 | 1 | Â |
3482 | Small nuclear ribonucleoprotein (snRNP) SMF subunit | Spliceosome | A | All archaea, no bacteria (COG1958) | 0 | 0 | Â |
2463 | Predicted RNA-binding protein, consisting of a PIN domain and a Zn-ribbon. Involved in 26S proteasome assembly | 26S proteasome, pre-40S subunit | A,O | Represented by orthologs in all archaea but no bacteria (COG1349) | 0 | X | PIN domain has been detected in exosome subunits and is thought to have RNA-binding properties or even nuclease activity [113, 114]. The demonstration of the role of this protein (Nob1p) in proteasome assembly [115], 40S ribosome subunit assembly, and the processing of 18S rRNA 3'-end [116] supports the connection between degradation of RNA and proteins that seems to have been established already in archaea [109]. |
3273 | Predicted RNA-binding protein containing KH domain, interacts with Nob1p | 26S proteasome, pre-40S subunit | A,O | Orthologs in all archaea but no bacteria (COG1094) | 0 | 0 | This is the second predicted RNA-binding protein involved in proteasome assembly, [115] which emphasizes the aforementioned link between RNA and protein processing |
1831 | Deadenylating 3'-5' exonuclease, negative regulator of PolII transcription | CCR4-NOT core complex | AK | None | 0 | 0 | Â |
1159 | NADP-dependent flavoprotein reductase, probably sulfite reductase subunit | ? | CL | Many bacteria (COG0369) | 0 | X | Genetic evidence of a role in DNA replication [117] |
1800 | Ferredoxin/adrenodoxin reductase | ? | C | Most bacteria and some archaea (COG0493) | 0 | X | Â |
1173 | Anaphase-promoting complex (APC), Cdc16 subunit (TPR-repeat protein) | APC | D | Most of archaea and bacteria have TPR-repeat proteins (COG0457) but no orthologs of Cdc16 | 0 | 0 | Â |
3437 | Anaphase-promoting complex (APC), subunit 10 | APC | D | None | 1 | 1 | Â |
1358 | Serine palmitoyltransferase | ? | I | Most bacteria and some archaea (COG0156) | 0 | 0 | Â |
1511 | Mevalonate kinase | ? | I | Most archaea and some bacteria (COG1577) | 0 | X | Â |
3059 | N-acetylglucosaminyltransferase complex, subunit PIG-C/GPI2, involved in phosphatidylinositol biosynthesis | N-acetylglucos-aminyltransferase complex | I | None | 0 | 1 | Â |
0467 | Translation elongation factor 2 paralog (GTPase) | ? | J | All (COG0480) | 0 | X | Involved in 60S ribosomal subunit maturation [118] |
1147 | Glutamyl-tRNA synthetase | Multispecificity aminoacyl-tRNA synthetase complex | J | All (COG0008) | 0 | X | Â |
2784 | Phenylalanyl-tRNA synthetase, beta subunit | Heterodimeric phenylalanyl-tRNA synthetase | J | All (COG0016) | 0 | X | Â |
3123 | Diphtamide synthase (methyltransferase) | ? | J | All archaea, no bacteria (COG1798) | 1 | 1 | Â |
0261 | RNA polymerase III, largest subunit | RNAPIII holoenzyme | K | All (COG0086) | 0 | X | Â |
0262 | RNA polymerase I, largest subunit | RNAPI holoenzyme | K | All (COG0086) | 0 | X | Â |
0215 | RNA polymerase III, second largest subunit | RNAPIII holoenzyme | K | All (COG0085) | 0 | X | Â |
0216 | RNA polymerase I, second largest subunit | RNAPI holoenzyme | K | All (COG0085) | 0 | X | Â |
1063 | RNA polymerase II elongator complex, subunit ELP2, WD repeat protein | RNA polymerase II elongator complex | K | WD40-repeat proteins are present in several bacterial lineages and are particularly abundant in cyanobacteria but are missing in most archaea; none of them appear to be obvious orthologs of this protein (COG2319) | 1 | X | Â |
1131 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 | RNAPII holoenzyme | K | Most archaea and bacteria (COG1199) | 0 | X | Â |
1920 | RNA polymerase II Elongator subunit | RNAP II elongator complex | K | None | 1 | X | Â |
1932 | TBP-associated factor (Taf2p) | TFIID complex | K | None | 0 | X | Â |
2009 | Transcription initiation factor TFIIIB, Bdp1 subunit (Myb domain) | TFIIIB | K | None | 0 | 0 | Â |
2076 | RNA polymerase III transcription factor TFIIIC, TPR-repeat-containing protein | TFIIIC | K | Most of archaea and bacteria have TPR-repeat proteins (COG0457) but no orthologs of TFIIC | 0 | X | Â |
2487 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 | TFIIH | K | None | 0 | 1 | Â |
2691 | RNA polymerase II subunit 9 | RNAP II holoenzyme | K | Most archaea, no bacteria (COG1594) | 1 | X | Â |
2807 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, SSL1 subunit | TFIIH | K | No orthologs although von Willebrand A domains are present in a variety of prokaryotic proteins | 0 | 0 | Consists of a von Willebrand A domain most closely related to those in the proteasome subunit RPN10 [119] and a Zn-finger domain |
2907 | RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 | TFIIS | K | All archaea, no bacteria (COG1594) | 1 | 0 | Â |
3169 | RNA polymerase II transcriptional regulation mediator | Mediator complex [120] | K | None | 0 | X | Â |
3233 | RNA polymerase III subunit C34 | RNAP III holoenzyme | K | None | 0 | 1 | Â |
3297 | RNA polymerase III subunit C25 | RNAP III holoenzyme | K | All archaea, no bacteria (COG1095) | 0 | 0 | Â |
3438 | Subunit common to RNA polymerases I (A) and III (C); Rpc19p | RNAP I and III holoenzymes | K | Â | 0 | 1 | Â |
3471 | RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 | TFIIH | K | None | 0 | X | Â |
3490 | Transcription elongation factor SPT4, Zn-ribbon protein | Chromatin-associated transcription complexes | K | None | 1 | 1 | Â |
3497 | RNA polymerase II subunit; Rpb10p | RNAP II holoenzyme | K | All archaea, no bacteria (COG1644) | 0 | X | Â |
3901 | Transcription initiation factor IID subunit (Taf13p) | TFIID | K | None | 0 | X | Â |
3949 | RNA polymerase II elongator complex, subunit ELP4 | RNAP II elongator complex | K | None | 1 | 1 | Â |
4086 | SOH1 protein potentially involved in Pol II transcription regulation and repair | SMCC complex [121] | K | None | 1 | X | Â |
1532 | Predicted GTPase of the XAB1 family [122] | TBP-free TAF(II) complex | L | All archaea and several bacteria (COG1100) | 0 | 0 | XP-A-binding protein in humans, thus implicated in repair ([122] and references therein). |
1533 | Predicted GTPase of the XAB1 family (paralog of KOG1757) [122] | TBP-free TAF(II) complex? | L | All archaea and several bacteria (COG1100) | 0 | X | Might have a function in repair given the paralogous relationship with KOG1757. |
1625 | DNA polymerase α processivity subunit, inactivated phosphatase | DNA polymerase α holoenzyme | L | Small subunit of archaeal DNA polymerase II (COG1311) | 0 | 0 | The small, regulatory subunit of DNA polymerase α also forms a pan-eukaryotic KOG3044, which is a paralog of KOG0861 (the only recent duplication in KOG3044 is seen in vertebrates). In contrast, another paralog, the small subunit of DNA polymerase ε, is represented in animals, fungi and the early-branching protozoan Plasmodium, but not in plants or Microsporidia. Thus, the history of this polymerase subunit apparently involved inactivation of the phosphatase (or nuclease) inherited from archaea, with subsequent duplications at early stages of eukaryotic evolution [123] |
0479 | DNA replication licensing factor MCM3 | Pre-replication complex | L | All archaea, no bacteria (COG1241) | 0 | X | Â |
0481 | DNA replication licensing factor MCM5 | Pre-replication complex | L | All archaea, no bacteria (COG1241) | 0 | X | Â |
0482 | DNA replication licensing factor MCM7 | Pre-replication complex | L | All archaea, no bacteria (COG1241) | 0 | 0 | Â |
0964 | Structural maintenance of chromosome protein 3 (cohesin subunit SMC3) | Sister chromatid cohesion complex | L | Many archaea and bacteria (COG1196) | 0 | X | Â |
0979 | Structural maintenance of chromosome protein 5 (cohesin subunit SMC5) | Sister chromatid cohesion complex | L | Many archaea and bacteria (COG1196) | 0 | X | Â |
1942 | TBP-interacting protein TIP49 (DNA helicase) | chromatin remodeling complex | L | Most of the archaea, no bacteria (COG1224) | 0 | 0 | Â |
1979 | DNA mismatch repair ATPase, MLH1 | Mismatch repair complex | L | Most bacteria and some archaea (COG0323) | 1 | 1 | Â |
2267 | DNA primase, large subunit | DNA polymerase α:primase complex | L | All archaea, no bacteria (COG2219) | 0 | 0 |  |
2299 | Ribonuclease HI | Replisome | L | All archaea, most bacteria (COG0164) | 1 | X | Â |
2310 | DNA repair exonuclease MRE11 | MRN complex involved in double-strand break repair | L | All archaea, most bacteria (COG0420) | 1 | 1 | Â |
2929 | Origin recognition complex, subunit 2 (ORC2) | ORC | L | None | 1 | 1 | Â |
0179 | 20S proteasome, regulatory subunit beta type PSMB1/PRE7 (paralog of KOG0185) | 20S proteasome | O | All archaea but only actinomycetes among bacteria (COG0638) | 0 | 0 | Â |
0185 | 20S proteasome, regulatory subunit beta type PSMB4/PRE4 (paralog of KOG0179) | 20S proteasome | O | All archaea but only actinomycetes among bacteria (COG0638) | 0 | 0 | Â |
2708 | Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [124] | Putative complex involved in translation regulation [125] | O | Represented by orthologs in all archaea and bacteria (COG0533) | 0 | X | One of the few remaining uncharacterized proteins that are universally conserved in all cellular life forms. The only experimentally demonstrated activity is that of sialoglycoprotease but fusion with a distinct protein kinase in several archaea and analysis of gene neighborhood suggest a fundamental role in signal transduction, possibly translation regulation. [125] |
0301 | Protein required for normal rates of ubiquitin-dependent proteolysis, contains WD40 repeats | Proteasome? | O | Same as above (COG2319) | 1 | X | Â |
0358 | Chaperonin complex component, TCP-1 delta subunit (CCT4) | TCP-1 | O | All archaea and nearly all bacteria (COG0459) | 0 | 0 | Â |
0363 | Chaperonin complex component, TCP-1 beta subunit (CCT2) | TCP-1 | O | All archaea and nearly all bacteria (COG0459) | 0 | 0 | Â |
0687 | 26S proteasome regulatory complex, subunit RPN7/PSMD6 | 26S proteasome | O | None | 0 | 0 | Â |
1299 | Vacuolar sorting protein VPS45/Stt10 (Sec1 family) | t-SNARE complex | O | None | 1 | X | Involved in t-SNARE complex assembly [126] |
1349 | GPI-anchor transamidase complex, GPI8 subunit | GPI-anchor transamidase complex | O | Distantly related proteases in some bacteria (no COG) | 0 | 1 | Â |
1943 | Beta-tubulin folding cofactor D, involved in chromosome segregation | ? | O | None | 1 | 1 | Â |
2015 | NEDD8-activating complex, UBA3 subunit | NEDD8-activating complex | O | Most bacteria and some archaea (COG0476) | 1 | 1 | Â |
2126 | Phosphoethanolamine N-methyltransferase involved in GPI-anchor biosynthesis | ? | O | Several bacteria and archaea (COG1524) | 0 | X | Â |
2884 | 26S proteasome regulatory complex, subunit RPN10/PSMD4 | 26S proteasome regulatory complex | O | No orthologs although von Willebrand A domains are present in a variety of prokaryotic proteins | 1 | 1 | Contains von Willebrand A domain |
2908 | 26S proteasome regulatory complex, subunit RPN9/PSMD13 | 26S proteasome regulatory complex | O | None | 0 | 0 | Contains PINT domain |
0209 | Endoplasmic reticulum membrane P-type ATPase | ? | P | Many bacteria and some archaea (COG0474) | 1 | X | Â |
3379 | Uncharacterized member of the histidine triad superfamily of nucleotide hydorlases | ? | R | Most archaea and bacteria (COG0537) | 1 | X | Only biochemical function predicted. |
2635 | Coatomer (COPI) complex delta subunit | COPI complex | U | None | 0 | 0 | Â |
2927 | Membrane component of ER protein translocation apparatus (Sec62) | Sec complex | U | None | 0 | 1 | Â |
2978 | Dolichol-phosphate mannosyltransferase | ? | U | All archaea, most bacteria (COG0463) | 0 | X | Â |
3198 | Signal recognition particle, subunit Srp19 | Signal recognition particle | U | All archaea, no bacteria (COG1400) | 0 | X | Â |
3315 | Subunit of the targeting complex (TRAPP) involved in ER to Golgi trafficking | TRAPP | U | None | 0 | X | Â |
3369 | Subunit of the targeting complex (TRAPP) involved in ER to Golgi trafficking | TRAPP | U | None | 0 | X | Â |
1992 | Nuclear export receptor CSE1/CAS (importin beta) | ? | YU | None | 0 | X | Â |
New functional predictions | Â | Â | Â | Â | Â | Â | |
2316 | PP-loop family ATP pyrophosphatase domain, which in fungi, plants and insects is fused to a duplicated translation inhibitor domain. The fusion, along with the phyletic pattern of the PP-ATPase domain, suggests an essential function in translation regulation | ? | A | Orthologs of the PP-loop domain are present in all archaea (COG2102) but not in bacteria. Orthologs of the translation inhibitor domain are found in most bacteria and several archaea (COG0251) | 1 | X | PP-loop ATPases have been previously implicated in base thiolation in various RNAs [127] and proteins in this K/COG might have a similar function, which is likely to be conserved in eukaryotes and archaea. However, the fusion with translation inhibitor, which has been reported to have endoribonuclease activity [128] is a eukaryote-specific feature |
2523 | Predicted RNA-binding protein containing a PUA domain, probable role in RNA modification [129] | Putative novel RNA modification complex | A | Orthologs present in all archaea (COG2016) but not in bacteria | 1 | X | Several of the archaeal orthologs of this protein form fusions with a PP-loop ATPase domain implicated in base thiolation [127]. Thus, the proteins of this KOG might interact with those of KOG2840 (pan-eukaryotic, duplications in Arabidopsis and worm) or KOG2594 (missing in humans and microsporidia) to form a novel enzymatic complex involved in RNA modification |
0270, 0271, 1539 | WD40-repeat proteins | Processosome | A | WD40-repeat proteins are present in several bacterial lineages and are particularly abundant in cyanobacteria but are missing in most archaea; none of them appear to be obvious orthologs of this protein (COG2319) | all 0 | X,1,X | By analogy with other conserved WD40-repeat proteins, predicted to be subunits of rRNA processing/ribosome assembly complexes |
2321 | Nucleolar protein, contains WD40 repeats | rRNA processosome? | A | WD40-repeat proteins are present in several bacterial lineages and are particularly abundant in cyanobacteria but are missing in most archaea; none of them appear to be obvious orthologs of this protein (COG2319) | 0 | 1 | Probable subunit of an rRNA-processing complex |
1763 | Uncharacterized conserved protein containing a CCCH Zn-finger; possible role in RNA processing or splicing | ? | A | None | 1 | 1 | CCCH fingers have been shown to bind 3' untranslated regions in various mRNAs [130, 131] |
2837 | Protein containing a U1-type, RNA-binding C2H2 Zn-finger. Probable role in RNA splicing/processing | Spliceosome? | A | None | 0 | 0 | U1-type fingers are essential for the assembly of U1 RNP [132] |
3073 | Predicted RNA-binding protein containing PIN domain and involved in 18S rRNA processing | Pre-40S subunit | A | Most archaea, no in bacteria (COG1412) | 0 | 1 | Interacts with Nop14p and is required for 40S subunit biogenesis and 18S rRNA maturation (11694595). The presence of the PIN domain suggests RNA-binding and, possibly, RNAse activity |
3154 | Uncharacterized protein with potential function in translation or ribosomal biogenesis | Pre-40S subunit? | A? | Most archaea, no bacteria (COG2042) | 1 | X | The general functional prediction stems from the observation that the gene for this protein forms a predicted conserved operon with the gene for ribosomal protein L40E in several archaeal genomes |
3214 | Small protein containing a Zn-ribbon, possibly RNA-binding; potential role in RNA processing or transcription regulation | ? | A? | Conserved in Crenarchaeota (COG4888) | 1 | 1 | Â |
3800 | Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor | TFIIH | KO | None | 0 | X | Â |
3176 | Predicted α-helical protein, possibly involved in replication/repair; paralog of KOG3636 | A novel complex with PCNA involved in replication? | L? | Conserved in most (possibly all) archaea but not in bacteria (COG1711) | 0 | X | A function in DNA replication/repair and/or transcription is suggested by the analysis of the genome context of archaeal orthologs which form an evolutionarily conserved association with the genes for replication sliding clamp (PCNA ortholog) (K.S.M. and E.V.K., unpublished work) |
3303 | Predicted α-helical protein, possibly involved in replication/repair transcription; paralog of KOG3508 | A novel complex with PCNA involved in replication? | L? | Conserved in most (possibly all) archaea but not in bacteria (COG1711) | 0 | 0 | A function in DNA replication/repair and/or transcription is suggested by the analysis of the genome context of archaeal orthologs which form an evolutionarily conserved association with the genes for replication sliding clamp (PCNA ortholog) (K.S.M. and E.V.K., unpublished.work) |
0396 | Predicted E3 ubiquitin ligase | Ub ligase | O | None | 1 | 1 | The proteins in this KOG contain a modified RING domain, which might not be capable of metal-binding similarly to the U-box domain [133] that has been shown to function as E3 [134] |
1443 | Multitransmembrane protein, predicted drug/metabolite transporter | ? | R | Most archaea and bacteria (COG0697) | 1 | X | Â |
2647 | Multitransmembrane protein, potential transporter | ? | R | Most bacteria and some archaea (COG0628) | 0 | 1 | Â |
2488 | Predicted N-acetyltransferase | ? | R | Most archaea and bacteria (COG0454) | 1 | X | Putative role in ribosomal maturation? |
3347 | Predicted nucleotide kinase; nuclear protein (Fap7p) | ? | R | Conserved in all archaea but not in bacteria (COG1936) | 0 | 1 | Involved in oxidative stress reponse in yeast [135] |
3974 | Predicted sugar kinase | Putative novel complex with KOG2585 proteins | R | All archaea and most bacteria (COG0063) | 1 | 1 | Based on fusions seen in prokaryotes, predicted to interact functionally and, possibly, physically with uncharacterized proteins of KOG2585 (represented in all eukaryotes but includes paralogs in some species) |
No functional prediction | Â | Â | Â | Â | Â | Â | |
2318 | Uncharacterized conserved protein | ? | S | None | 0 | 1 | Â |
3237 | Uncharacterized conserved protein containing coiled-coil domain | ? | S | None | 0 | 1 | Coiled-coil domains are often involved in complex assembly; this could be an uncharacterized component of the chromatin or the spliceosome |