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

sulfo9.02117

COG1698 (arCOG04308)

Essential [42]; PDB: 2QZG, linked to Zn-finger protein

sulfo9.02278

(arCOG08212)

sulfo9.01977

(arCOG05886)

Essential [42]

sulfo9.00722

COG1888 (arCOG04140)

PDB: 3BPD; ferredoxin fold

sulfo9.01763

COG4755 (arCOG04123)

DUF2153

Linked to Trm112 RNA methyltransferase activating protein

halo9.02555

COG1885 (arCOG02119)

DUF555

Single CxxC, weak similarity to CREN7

halo9.01859

(arCOG04616)

DUF5800

halo9.01783

(arCOG04777)

halo9.02264

(arCOG04587)

Linked to glutaredoxin family protein

halo9.02689

(arCOG03655)

Linked to Anion-transporting ATPase ArsA

halo9.02039

COG2412 (arCOG04051)

DUF424

PDB: 2QYA; linked to TPR repeats containing protein

thermo9.00526

(arCOG04849)

Linked to Ribosome biogenesis GTPase A

thermo9.01167

COG2412 (arCOG04051)

DUF424

linked to NMD protein affecting ribosome stability and mRNA decay

thermo9.01884

(arCOG05846)

Linked to Transcription initiation factor IIE, alpha subunit

thermo9.01623

COG1885 (arCOG02119)

DUF555

Linked to Uncharacterized protein, DUF357 family

thermo9.02768

COG1888 (arCOG04140)

Linked to ArsR transcriptional regulators; PDB: 2X3D [69]

thermo9.01533

COG1531 (arCOG01302)

Linked to MBL-fold metallohydrolase superfamily; predicted RNA cyclic group end recognition domain [70]

thermo9.01369

(arCOG05869)

PDB: 2K4N; linked 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI;

methano7.000565

COG4744 (arCOG03208)

DUF2149

Membrane protein; linked to biopolymer transport protein TolQ

methano7.001417

COG3377 (arCOG04424)

DUF1805

PDB: 1QW2; linked to tRNA G10 N-methylase Trm11

methano7.001273

COG4050 (arCOG04903)

DUF2112

In a conserved context with uncharacterized protein, DUF2102 family and others; single CxxC motif; methanogenesis maker 5

methano7.001697

(arCOG04388)

Linked to Uncharacterized protein, DUF2551 family

methano7.001273

COG4050 (arCOG04903)

DUF2102

Methanogenesis maker 6; linked to DUF2112

flavo9.00782

–

DUF4286

Linked to outer membrane protein assembly factor BamD

flavo9.01459

–

Linked to RuvX, Holliday junction resolvase; SRPBCC domain, Hsp90 cochaperone in yeast [71, 72]; putative hydrophobic ligand binding site

flavo9.00789

–

DUF2797

Linked to GH3 auxin-responsive promoter; contains Zn ribbon

flavo9.01638

–

SRPBCC domain, also see flavo9.01459

flavo9.02618

–

DUF4254

Linked to ADP-heptose:LPS heptosyltransferase, RfaF

deino9.00587

–

Annotated as quinate 5-dehydrogenase; present in Thermus and other bacteria

deino9.01277

–

DUF4385

Linked to DNA-binding ferritin-like protein Dps; present in Thermus

deino9.00288

–

Linked to uncharacterized membrane protein, Outer membrane protein assembly factor BamB, contains PQQ-like beta-propeller repeat; secreted; present in Thermus

deino9.01656

–

deino9.02309

–

DUF1844

Linked to D-Tyr-tRNA(Tyr) deacylase

paen9.03935

COG4472

DUF965

Linked to Alanyl-tRNA synthetase, AlaS; homolog of IreB, acting a negative regulator of cephalosporin resistance [73]

paen9.05835

–

Next uncharacterized protein YrrD, contains PRC-barrel domain and Cysteine sulfinate desulfinase/cysteine desulfurase or related enzyme; Zn ribbon domain

paen9.02641

–

YokU-like protein, putative antitoxin RelE fold family

paen9.02767

–

Linked to uncharacterized membrane protein SpoIIM, required for sporulation

paen9.02361

–

DUF1499

rhodo7.006964

–

DUF2469

Often found in Actinomycetes clustered with signal peptidase and/or RNAse HII

rhodo7.004823

–

DUF3039

Possibly metal-binding; Hx(20)C…CxxC motif

rhodo7.005227

–

DUF3151

Linked to Uncharacterized membrane protein YgaE, UPF0421/DUF939 family

rhodo7.003034

–

DUF4191

2TM domain, in operon with Lipoate synthase LipA

rhodo7.002008

–

DUF3090

Contain CxxC..HxC motif, putative metal-binding protein