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Table 3 Selected functionally uncharacterized protein families with low variability and presence in 85% or more genomes in respective lineage

From: Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions

csCOG Genome number Proteins number Varia-bility COG (arCOG)* Pfam (DUF) Comment
sulfo9.02117 52 52 0.25 COG1698 (arCOG04308)   Essential [42]; PDB: 2QZG, linked to Zn-finger protein
sulfo9.02278 52 52 0.26 (arCOG08212)   
sulfo9.01977 52 52 0.29 (arCOG05886)   Essential [42]
sulfo9.00722 52 52 0.57 COG1888 (arCOG04140)   PDB: 3BPD; ferredoxin fold
sulfo9.01763 52 52 0.61 COG4755 (arCOG04123) DUF2153 Linked to Trm112 RNA methyltransferase activating protein
halo9.02555 37 40 0.36 COG1885 (arCOG02119) DUF555 Single CxxC, weak similarity to CREN7
halo9.01859 37 37 0.38 (arCOG04616) DUF5800  
halo9.01783 37 37 0.39 (arCOG04777)   
halo9.02264 36 36 0.28 (arCOG04587)   Linked to glutaredoxin family protein
halo9.02689 32 32 0.23 (arCOG03655)   Linked to Anion-transporting ATPase ArsA
halo9.02039 37 37 0.49 COG2412 (arCOG04051) DUF424 PDB: 2QYA; linked to TPR repeats containing protein
thermo9.00526 40 40 0.46 (arCOG04849)   Linked to Ribosome biogenesis GTPase A
thermo9.01167 41 41 0.3 COG2412 (arCOG04051) DUF424 linked to NMD protein affecting ribosome stability and mRNA decay
thermo9.01884 41 41 0.32 (arCOG05846)   Linked to Transcription initiation factor IIE, alpha subunit
thermo9.01623 41 41 0.36 COG1885 (arCOG02119) DUF555 Linked to Uncharacterized protein, DUF357 family
thermo9.02768 42 43 0.2 COG1888 (arCOG04140)   Linked to ArsR transcriptional regulators; PDB: 2X3D [69]
thermo9.01533 42 42 0.31 COG1531 (arCOG01302)   Linked to MBL-fold metallohydrolase superfamily; predicted RNA cyclic group end recognition domain [70]
thermo9.01369 42 42 0.42 (arCOG05869)   PDB: 2K4N; linked 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI;
methano7.000565 41 48 0.48 COG4744 (arCOG03208) DUF2149 Membrane protein; linked to biopolymer transport protein TolQ
methano7.001417 41 41 0.48 COG3377 (arCOG04424) DUF1805 PDB: 1QW2; linked to tRNA G10 N-methylase Trm11
methano7.001273 41 41 0.45 COG4050 (arCOG04903) DUF2112 In a conserved context with uncharacterized protein, DUF2102 family and others; single CxxC motif; methanogenesis maker 5
methano7.001697 41 41 0.4 (arCOG04388)   Linked to Uncharacterized protein, DUF2551 family
methano7.001273 41 41 0.45 COG4050 (arCOG04903) DUF2102 Methanogenesis maker 6; linked to DUF2112
flavo9.00782 50 50 0.47 DUF4286 Linked to outer membrane protein assembly factor BamD
flavo9.01459 50 50 0.45   Linked to RuvX, Holliday junction resolvase; SRPBCC domain, Hsp90 cochaperone in yeast [71, 72]; putative hydrophobic ligand binding site
flavo9.00789 50 50 0.45 DUF2797 Linked to GH3 auxin-responsive promoter; contains Zn ribbon
flavo9.01638 50 50 0.30   SRPBCC domain, also see flavo9.01459
flavo9.02618 50 50 0.30 DUF4254 Linked to ADP-heptose:LPS heptosyltransferase, RfaF
deino9.00587 33 33 0.34   Annotated as quinate 5-dehydrogenase; present in Thermus and other bacteria
deino9.01277 33 33 0.35 DUF4385 Linked to DNA-binding ferritin-like protein Dps; present in Thermus
deino9.00288 33 33 0.45   Linked to uncharacterized membrane protein, Outer membrane protein assembly factor BamB, contains PQQ-like beta-propeller repeat; secreted; present in Thermus
deino9.01656 33 33 0.49   
deino9.02309 32 32 0.33 DUF1844 Linked to D-Tyr-tRNA(Tyr) deacylase
paen9.03935 66 66 0.22 COG4472 DUF965 Linked to Alanyl-tRNA synthetase, AlaS; homolog of IreB, acting a negative regulator of cephalosporin resistance [73]
paen9.05835 66 66 0.34   Next uncharacterized protein YrrD, contains PRC-barrel domain and Cysteine sulfinate desulfinase/cysteine desulfurase or related enzyme; Zn ribbon domain
paen9.02641 66 66 0.37   YokU-like protein, putative antitoxin RelE fold family
paen9.02767 66 66 0.39   Linked to uncharacterized membrane protein SpoIIM, required for sporulation
paen9.02361 66 66 0.4 DUF1499  
rhodo7.006964 53 53 0.07 DUF2469 Often found in Actinomycetes clustered with signal peptidase and/or RNAse HII
rhodo7.004823 53 53 0.14 DUF3039 Possibly metal-binding; Hx(20)C…CxxC motif
rhodo7.005227 53 54 0.159 DUF3151 Linked to Uncharacterized membrane protein YgaE, UPF0421/DUF939 family
rhodo7.003034 53 53 0.253 DUF4191 2TM domain, in operon with Lipoate synthase LipA
rhodo7.002008 53 53 0.615 DUF3090 Contain CxxC..HxC motif, putative metal-binding protein