SII-SWORD/CoKE huggingface dataset:
Septum site-determining protein Ssd-like (Ssd-like)
Type: Family

This entry represents a family of proteins from actinomycetes, including Rv3660c from Mycobacterium tuberculosis (Septum site determining protein, Ssd), which plays a role in septum formation . Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins .
Flagellar motor stator, MotA (Flagellar_motor_stator_MotA)
Type: Family

The MotA protein, along with its partner MotB, comprises the stator complex of the bacterial flagellar motor. MotAB span the cytoplasmic membrane and undergo conformational changes powered by the translocation of protons. These conformational changes in turn are communicated to the rotor assembly, producing torque .

This family represents MotA proteins found in proteobacteria.
Flagellar regulator, FliZ (Flagellar_regulator_FliZ)
Type: Family

FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype . FliZ interacts with the flagellar translational activator FlhCD complex.
Flagellar assembly FliH, Bacilli (FliH_Bacilli)
Type: Family

This entry represents a bacillus clade of FliH proteins. Sequences in this entry are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Beta-lysine N-acetyltransferase (GNAT_AblB)
Type: Family

Members of this protein family are GNAT family acetyltransferases, based on a seed alignment in which every member is associated with a lysine 2,3-aminomutase family protein, usually as the adjacent gene. This family includes AblB, the enzyme beta-lysine acetyltransferase that completes the two-step synthesis of the osmolyte (compatible solute) N-epsilon-acetyl-beta-lysine; all members of the family may have this function . Note that N-epsilon-acetyl-beta-lysine has been observed only in methanogenic archaea (e.g. Methanosarcina) but that this model, paired with Lysine-2,3-aminomutase (

), suggests a much broader distribution.
F420-dependent oxidoreductase, Rv3093c (F420_Rv3093c)
Type: Family

This entry describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN.
Sucrose phosphorylase (Sucrose_phospho)
Type: Family

This family includes glycoside phosphorylases that act on alpha-glucosides. Characterised representatives from Streptococcus mutans and Bifidobacterium adolescentis are sucrose phosphorylases. In the forward direction, sucrose phosphorylase uses phosphate to cleave sucrose into D-fructose + alpha-D-glucose 1-phosphate . This family also includes glucosylglycerol phosphorylase, an enzyme that catalyses the reversible phosphorolysis of 2-O-alpha-D-glucosylglycerol .
6-phosphogluconolactonase, YbhE-like (6PGL_YbhE-like)
Type: Family

This entry refers to the 6-phosphogluconolactonase YbhE type proteins found mainly in enterobacteriaceae organisms.

6-phosphogluconolactonases (6PGL)

are cytosolic enzymes found in all organisms that catalyse the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconic acid in the oxidative phase of the pentose phosphate pathway. Trypanosoma brucei and other characterised 6PGL proteins [

] share an α/β hydrolase fold, with both parallel and anti-parallel β-sheets surrounded by eight α-helices . In Escherichia coli (strain K12), 6PGL (YbhE) is characterised by a 7-bladed β-propeller fold

(

) .
Protein of unknown function DUF3530 (DUF3530)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
RNA-directed RNA polymerase L, PA-C-like domain (L_PA-C-like)
Type: Domain

This domain is found in RNA-directed RNA polymerase L from Bunyavirales. This has been described as the PA-C like domain, which forms a narrow and positively charged cleft with the thumb domain, where the 3' RNA is likely bound .
Domain of unknown function DUF3696, C-terminal (DUF3696)
Type: Domain

This domain is found in bacteria and archaea, and is approximately 50 amino acids in length.
Cox20 (Cox20)
Type: Family

Complex IV (CIV) is a copper-heme oxidase that couples electron transfer from cytochrome c to oxygen with proton extrusion across the inner membrane to contribute to the proton gradient required for ATP generation. This entry includes fungal mitochondrial complex IV assembly factor Cox20 and its homologues (also known as (FAM36A) in metazoa .

Human CIV is formed by three catalytic core subunits (COX1/2/3). COX20 has been found to form a complex with SCO1, SCO2, and newly synthesized COX2. It may act as a chaperone in the early steps of COX2 maturation .
Protein of unknown function DUF2563 (DUF2563)
Type: Family

This entry represents a family of proteins with unknown function that are predominantly found in Mycobacterium.
Golgi pH regulator, conserved domain (Golgi_pH-regulator_cons_dom)
Type: Domain

This conserved domain is found in the Golgi pH regulator family, including human Golgi pH Regulators (GPHR) and GPCR-type G proteins (GTG1 and GTG2) from Arabidopsis .
ESX-1 secretion-associated protein EspC (EspC)
Type: Family

This is a family of exported virulence proteins from largely Acinetobacteria and a few Fimicutes, Gram-positive bacteria. It is exported in conjunction with EspA as an interacting pair .
TRSP domain (TRSP_dom)
Type: Domain

This domain occurs C-terminal to phosphoribosyl transferase domain

, and has a highly conserved GXXE and TRSP signatures . It is found in bacteria. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo- nucleoside involved in stress response .
Protein of unknown function DUF2570 (DUF2570)
Type: Family

This is a family of proteins with unknown function.
Picornavirus VP1, conserved C-terminal region (VP1_C)
Type: Conserved_site

This region is found in VP1 structural proteins of picornaviruses, and is approximately 20 amino acids in length. It is located C-terminal to

. This region constitutes the part of VP1 that is unstructured and interacts with VP0/VP2 structural protein . It contains an invariant tyrosine that engages in interaction with VP0/VP2.
Protein of unknown function DUF2556 (DUF2556)
Type: Family

This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
FicA antitoxin homologue YhfG (YhfG)
Type: Family

This protein family includes proteins predominantly found in Gammaproteobacteria, such as YhfG from Escherichia coli. YhfG is a FicA antitoxin homologue (also known as antitoxin EcFicA) that interacts with EcFiT and forms a complex with it. YhfG shows a unique conformation, forming two parallel α-helices linked by a 10-residues loop. The structure of the complex shows a highly conserved extended ligand-binding pocket .
Focadhesin/RST, DUF3730 (FOCAD/RST1_DUF3730)
Type: Domain

This domain of unknown function is found in Focadhesin from animals and RST1 (RESURRECTION 1) from plants. Focadhesin (FOCAD) is a focal adhesion protein with potential tumour suppressor function in gliomas . RST1 was originally identified in a genetic screen for factors involved in the biosynthesis of epicuticular waxes . Later, RST1 and RST1 INTERACTING PROTEIN (RIPR) have been shown to act as cofactors of the cytoplasmic exosome and the Ski complex in plants . RST1 is involved in the suppression of siRNA-mediated silencing of transgenes and certain endogenous transcripts .
Protein of unknown function DUF2572 (DUF2572)
Type: Family

This bacterial family of proteins has no known function.
Bacteriophage P22, Orf80 (Phage_P22_Orf80)
Type: Family

This entry is represented by Bacteriophage P22, Orf80. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Human herpesvirus, UL121 (HHV_UL121)
Type: Family

Members in this family are represented by human cytomegalovirus UL121 proteins of unknown function.
Uncharacterised protein family Ycf68 (Uncharacterised_Ycf68)
Type: Family

This family of plant proteins represent Ycf58 a chloroplast encoded protein that is restricted to the monocots and conifers. The proteins have no known function but as the family is exclusively found in the chloroplasts of phototrophic organisms it may play a role in photosynthesis.
ATPase, RavA, C-terminal (ATPase_RavA_C)
Type: Domain

This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) . RavA consists of three domains: the N-terminal domain is the AAA+ module, which is composed of two subdomains, the α-β-α subdomain with a Rossmann-type fold commonly found in nucleotide binding proteins and the all-α subdomain consisting of four antiparallel α-helices; the second domain is a discontinuous triple-helical domain which has a rigid structure stabilised by hydrophobic interactions localised at the interface between the three helices; and the third domain, named the LARA domain which forms a compact antiparallel β-barrel-like structure consisting of six β-strands and one α-helix . RavA forms an hexamer in which the triple helical domain mediates the lateral interactions between neighbouring RavA monomers .
Domain of unknown function DUF2846 (DUF2846)
Type: Domain

Some members of this group of proteins with unknown function are annotated as lipoproteins, although this has not been experimentally confirmed.
Domain of unknown function DUF3627 (DUF3627)
Type: Domain

This domain is found in bacteria and viruses, and is approximately 90 amino acids in length. The domain is found C-terminal to

.
Nucleotidyltransferase 8 (NTP_transf_8)
Type: Family

This is a family of bacterial proteins that have a nucleotidyltransferase fold. The fold-prediction is backed up by conservation of three highly characteristic sequence motifs found in all other nucleotidyl transferases: i) pDhDhhh(h/p), where p is a polar residue and h is a hydrophobic residue; ii) upstream of the first, a GG/S; iii) a conserved D/E in a hydrophobic surround. In the classification of nucleotidyltransferases proposed in this is a group XVIII NTP-transferase. Many of these sequences were classified in the COG database as COG5397. The exact function is not known.
BrxC (BrxC)
Type: Family

Bacillithiol (BSH) functions as a general thiol reductant, analogous to glutathione, in a wide range of bacterial species. Bacilliredoxins reduce those proteins that are modified by disulfide bond formation with BSH (S-bacillithiolation) .

This entry represents BrxC from Bacillus subtilis (formerly known as YtxJ) and similar bacterial proteins related to BSH. BrxC is a monothiol bacilliredoxin responsible for the removal of BSH from oxidized cytosolic proteins. It can also debacillithiolate the mixed disulfide form of the bacilliredoxin BrxB . It has a similar fold to thioredoxin.

The homologue in Deinococcus radiodurans, named AbxC, plays a role in the response to oxidative stress .
Uncharacterised protein family Ycf55 (UPF_Ycf55)
Type: Family

This entry represents proteins annotated as Ycf55. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown, though there are two completely conserved residues (L and D) that may be functionally important. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Protein of unknown function DUF2645 (DUF2645)
Type: Family

This entry represents a family of proteins predominantly found in Enterobacterales. Some members in the family are annotated as inner membrane protein YjeO and YgiZ. However no function is currently known.
Respiratory growth induced protein 1 (RGI1)
Type: Family

This family of fungal proteins includes RGI1, standing for respiratory growth induced 1. RGI1 is involved in aerobic energetic metabolism .
Protein of unknown function, DUF2577 (DUF2577)
Type: Family

This entry represents a family of proteins with no known function, including Phage-like element PBSX protein XkdR from Bacillus subtilis (strain 168).
Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf5 (AcMNPV_Orf5)
Type: Family

The function of this viral family of proteins is unknown. The entry contains Orf5 from Autographa californica nuclear polyhedrosis virus (AcMNPV).
Smad anchor for receptor activation-like, C-terminal (SARA-like_C)
Type: Domain

This entry represents a domain, previously known as DUF3480, that is found in a group of Zinc finger FYVE domain-containing proteins such as Zinc finger FYVE domain-containing protein 9, also known as SARA, and Zinc finger FYVE domain-containing protein 16 (KIAA0305) from humans and similar sequences present in animals. This domain is involved in the interaction with the TGF-beta receptor .

Smad proteins mediate transforming growth factor-beta (TGF-beta) signalling from the transmembrane serine-threonine receptor kinases to the nucleus. SARA (Smad anchor for receptor activation) recruits Smad2 to the TGF-beta receptors for phosphorylation .

KIAA0305 may be involved in regulating membrane trafficking in the endosomal pathway. Its overexpression induces endosome aggregation. It is required to target TOM1 to endosomes .
Protein of unknown function DUF2654 (DUF2654)
Type: Family

This entry represents a family of viral proteins whose function is not known.
Protein SUP-1-like (SUP-1-like)
Type: Family

SUP-1 is a transmembrane protein that may be involved in trafficking or stabilization of the vesicular acetylcholine transporter unc-17 .
Domain of unknown function DUF3473 (DUF3473)
Type: Domain

This domain, found in bacteria and archaea, is functionally uncharacterised. It is about 130 amino acids in length and is found C-terminal to

. It contains two completely conserved residues (P and H) that may be functionally important.
Protein of unknown function DUF3466 (DUF3466)
Type: Family

This family of bacterial proteins are functionally uncharacterised. Proteins in this family are typically between 564 to 612 amino acids in length.
Domain of unknown function DUF3463 (DUF3463)
Type: Domain

This functionally uncharacterised domain is found in bacteria and archaea, which is about 140 amino acids in length and is found C-terminal to

. It contains two conserved sequence motifs: CTPWG and PCYL. This domain is associated with hopanoid biosynthesis associated radical SAM proteins.
Protein of unknown function DUF2678 (DUF2678)
Type: Family

This family of proteins has no known function.
Protein of unknown function DUF2608 (DUF2608)
Type: Family

This entry represents a group of proteins predominantly found in Bacteria. The function is not known.
Protein of unknown function DUF2613 (DUF2613)
Type: Family

This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known.
Glycosyl hydrolase, C-terminal (DUF3459) (DUF3459)
Type: Domain

This entry represents a conserved domain found at the C-terminal of a subset of the glycosyl hydrolase 13 family members, including

from Xanthomonas campestris, which consists of two antiparallel β-sheets . The function of this domain is not clear.
Protein of unknown function DUF2824 (DUF2824)
Type: Family

This family of proteins has no known function. Members of the family are found in P22-like viruses and bacteria. Some of the phage members have been annotated as head assembly proteins, but this has not been confirmed.
Ferredoxin, C-terminal (Fd_C)
Type: Domain

This functionally uncharacterised domain is found in bacteria and is about 50 amino acids in length. It is found C-terminal to

. It contains a single completely conserved residue N that may be functionally important.
NSP1, betacoronavirus lineage A (B-CoV_A_NSP1)
Type: Family

This entry represents the N-terminal region of the betacoronavirus polyprotein, which contains non-structural protein 1 (Nsp1) from betacoronavirus lineage A. This protein is important for viral replication and pathogenesis . It suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling.
Magnesium chelatase, subunit H, N-terminal (Mg_chelatase_H_N)
Type: Domain

This functionally uncharacterised domain, found N-terminal to

, occurs in magnesium chelatase subunit H, which is involved in chlorophyll biosynthesis. It is found in bacteria, green plants and archaea. It is around 160 amino acids in length.
DNA replication/recombination mediator RecO, N-terminal (DNA_rep/recomb_RecO_N)
Type: Domain

This entry represents the N-terminal domain of the bacterial recombination protein O (RecO). This domain of RecO adopts a typical OB-fold DNA-binding structure; it contains two three-stranded β sheets with strand B1 common between both sheets . The RecO OB-fold is unusual in that it interacts primarily with the DNA backbone and is capable of binding ss and dsDNA . It is found in association with

.
Protein of unknown function DUF2887 (DUF2887)
Type: Family

This bacterial group of proteins has no known function.
Protein of unknown function DUF2623 (DUF2623)
Type: Family

This entry represents a group of proteins predominantly found in the Enterobacteriaceae family. Several members are named as YghW. The function is not known.
Neurogenic differentiation factor, domain of unknown function (NeuroD_DUF)
Type: Domain

This domain is found in Neurogenic differentiation factor 1 from Mus musculus (NeuroD1) and similar proteins from animals. Neuronal basic helix-loop-helix (bHLH) transcription factors such as neuroD and neurogenin have been shown to play important roles in neuronal development and its absence leads to serious diseases . This domain is found C-terminal to the less specific helix-loop-helix DNA binding domain

.
Protein YfgG (YfgG)
Type: Family

This entry represents Protein YfgG from Escherichia coli (strain K12) and similar proteins from Gammaproteobacteria. YfgG may be related to the resistance to the iron analogue gallium nitrate (Ga(NO3)3), and to the tolerance to nickel and cobalt stress . However, the exact function is still unknown.
Tubulin-folding cofactor D, C-terminal domain (TBCD_C)
Type: Domain

This region is found in TBCD and its paralogues in eukaryotes. It is typically between 182 and 199 amino acids in length. There is a single completely conserved residue R that may be functionally important.

Tubulin-folding cofactor D (TBCD) can interact with beta tubulin, which is regulated via its interaction with ARL2 (ADP ribosylation factor-like protein 2), a small monomeric G protein. ARL2 inhibits the beta-tubulin GTPase activating protein (GAP) activity of TBCD, and its interaction with native tubulin dimers . TBCD does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alpha/beta-heterodimers in microtubules .

The tubulin heterodimer consists of one alpha- and one beta-tubulin polypeptide. In humans, five tubulin-specific chaperones termed TBCA/B/C/D/E are essential for bring the alpha- and beta-tubulin subunits together into a tightly associated heterodimer. Following the generation of quasi-native beta- and alpha-tubulin polypeptides (via multiple rounds of ATP-dependent interaction with the cytosolic chaperonin), TBCA and TBCB bind to and stabilise newly synthesised beta- and alpha-tubulin, respectively. The exchange of beta-tubulin between TBCA and TBCD, and of alpha-tubulin between TBCB and TBCE, resulting in the formation of TBCD/beta and TBCE/alpha. These two complexes then interact with each other and form a supercomplex (TBCE/alpha/TBCD/beta). Interaction of the supercomplex with TBCC causes the disassembly of the supercomplex and the release of E-site GDP-bound alpha/beta tubulin heterodimer, which becomes polymerization competent following spontaneous exchange with GTP .
Flagellin, D2 domain (Flagellin_D2_dom)
Type: Domain

This entry represents the variable D2 domain found in uncharacterised proteins from Betaproteobacteria, including Flagellin from Burkholderia pseudomallei (FliC,

), an important subunit vaccine candidate for the serious infectious disease melioidosis. FliC assembles to form the flagellar filament that supports bacterial motility . This domain is found in association with

,

.
Neuropilin, C-terminal (Neuropilin_C)
Type: Domain

This domain of unknown function is located in the C terminus of the eukaryotic neuropilin receptors. There are two completely conserved residues (Y and E) that may be functionally important.

Neuropilins are essential multifunctional vertebrate cell surface receptors . They function as receptors for axon guidance factor semaphorin class 3 (Sema3), vascular endothelial growth factor (VEGF) and placenta growth factor-2 (PLGF-2).
Protein of unknown function DUF2639 (DUF2639)
Type: Family

This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Spt5 transcription elongation factor, N-terminal (Spt5_N)
Type: Domain

This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 . The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 , nor is it essential for RNA polymerase II binding .
T-box transcription factor 2/3, transcription activation domain (TBX2/3_TAD)
Type: Domain

This region is found C-terminal to the T-box DNA binding domain

in T-box transcription factors 2 and 3, which are highly homologous . This region may be a transcription activation domain (TAD) and contains two completely conserved residues (S and P) that may be functionally important . T-box genes are highly conserved and encode transcription factors that are involved in morphogenesis and organogenesis of both invertebrates and vertebrates . However, TBX2 is strongly re-expressed in adults which suggests a role in non-developmental processes .
Microcystin synthetase, domain of unknown function (Microcystin_synth_DUF)
Type: Domain

This domain of unknown function is found in cyanobacteria and is approximately 40 amino acids in length. It is found in association with

,

,

, and

and contains a conserved YAN motif. This region is found in microcystin synthetase, which is one of a number of proteins involved in microcystin toxin synthesis . Microcystins form a large family of small cyclic heptapeptides harbouring extensive modifications in amino acid residue composition and functional group chemistry. These peptide hepatotoxins contain a range of non-proteinogenic amino acids and unusual peptide bonds, and are typically N-methylated. They are synthesized on large enzyme complexes consisting of non-ribosomal peptide synthetases and polyketide synthases .
Protein of unknown function DUF2937 (DUF2937)
Type: Family

This family of proteins with unknown function appears to be found mainly in Proteobacteria.
TraD coupling protein, N-terminal (TraD_N)
Type: Domain

This domain of unknown function is found in bacteria, and is typically between 96 and 107 amino acids in length. It is probably periplasmic and is found N-terminal to the DNA binding domain

.

TraD is a hexameric ring ATPase that is part of the bacterial F sex factor complex and involved in bacterial conjugation , , .
Swinepox virus, C51 (Swinepox_virus_C51)
Type: Family

This entry represents viral proteins with unknown function. The entry contains ORF C51 from Swinepox virus (strain Kasza).