SII-SWORD/CoKE huggingface dataset:
Large ribosomal subunit protein mL55 (Ribosomal_mL55)
Type: Family

This entry represents the large ribosomal subunit protein mL55 from animals. Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins .
Protein GUCD1 (GUCD1)
Type: Family

GUCD1 contains a guanylyl cyclase domain and is found highly expressed in liver during regeneration .
Ima1, N-terminal domain (Ima1_N)
Type: Domain

This domain occurs at the N terminus of the Schizosaccharomyces pombe inner nuclear membrane protein, Ima1. Ima1 interacts with other inner nuclear membrane proteins .
GID complex substrate-recognition subunit 4/10-like (GID4/10-like)
Type: Family

This entry represents yeast GID complex substrate-recognition subunit 4 and 10 (GID4/10) and similar eukaryotic proteins. GID4, also known as Vacuolar import and degradation protein 24, VID24, is required for proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBP1), malate dehydrogenase (MDH2), and other gluconeogenic enzymes, probably by targeting FBP1-containing vesicles to the vacuole, but is not required for FBP1 sequestration in cytoplasmic vesicles . GID10 is required for the adaptation to osmotic or heat stress and for the regulation of protein levels of the adapter protein ART2, a component of the ART-Rsp5 ubiquitin ligase pathway, part of the plasma membrane quality control . These proteins are the substrate-recognition components of the GID E3 ligase complex catalysing ubiquitination of proteins targeted for degradation. GID E3 is regulated through assembly with interchangeable N-degron-binding substrate receptors induced by distinct environmental perturbations .
Hyccin (Hyccin)
Type: Family

This family hyccin proteins (HYCC1/2) which are a component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane and it also regulates phosphatidylinositol 4-phosphate (PtdIns4P) synthesis . HYCC1 plays a key role in oligodendrocytes formation which may explain its importance in myelination of the central and peripheral nervous system . Defects in Hyccin are the cause of hypomyelination with congenital cataracts . This disorder is characterised by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs .
Ubiquitin 3 binding protein But2, C-terminal (Ubiquitin3-bd_protein_But2_C)
Type: Domain

This entry represents a presumed C-terminal domain of ubiquitin 3 binding proteins (But2). But2 is conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway .
Autophagy-related protein 31 (Atg31)
Type: Family

Autophagy is an intracellular degradation system that responds to nutrient starvation. Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae . It functions with Atg17 and Atg29 at the preautophagosomal structure (PAS) in order to form normal autophagosomes under starvation conditions .
DNA damage checkpoint protein, Lcd1 (DNA_damage_chkpnt_Lcd1)
Type: Family

This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe (Fission yeast) this protein is called Rad26 and in Saccharomyces cerevisiae (Baker's yeast) it is called LCD1 .
Translocation protein Sec66 (Sec66)
Type: Family

Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures .
Protein Pet100 (Pet100)
Type: Family

Pet100 is a chaperone required for the assembly of cytochrome c oxidase . The human Pet100 homologue (also known as C19orf79) has been shown to be located in the mitochondrial inner membrane and forms a ~300kDa subcomplex with mitochondrial complex IV subunits .
Protein LCHN/Anr2 (LCHN/Anr2)
Type: Family

This entry include LCHN (also known as DENN domain-containing protein 11) from animals and Anr2 from budding yeasts. LCHN may play a role in neuritogenesis, as well as in neuronal recovery and/or restructuring in the hippocampus following transient cerebral ischemia . The function of Anr2 is not clear.
Elongator complex protein 6 (ELP6)
Type: Family

This entry represents Elongator complex protein 6 (ELP6).

Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The human Elongator six-subunit complex, known as holo-Elongator, has histone acetyltransferase activity directed against histone H3 and H4 . It consists of two subcomplexes, a core subcomplex (ELP1-3), and an accessory subcomplex (ELP4-6) . The elongator complex has been associated with many cellular activities, including transcriptional elongation , but its main function is tRNA modification . It is required for the formation of 5-methoxy-carbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups on uridine nucleosides present at the wobble position of many tRNAs .
Cytochrome c oxidase assembly factor 3, mitochondrial, coiled-coil domain (Coa3_CC)
Type: Domain

This entry represents a coiled-coil domain found in cytochrome c oxidase assembly factor 3 and homologues.

Cytochrome c oxidase assembly factor 3, previously known as coiled coil domain-containing protein 56 (CCDC56), plays a critical role in the biogenesis and activity of cytochrome c oxidase (COX) .
XK-related protein (XK-rel)
Type: Family

This family is represented by the multipass membrane protein XK, which may be involved in sodium-dependent transport of neutral amino acids or oligopeptides. It forms a heterodimer with Kell. In humans, Kell is an 93kDa type II membrane glycoprotein with endothelin-3-converting enzyme activity that is linked by a single disulphide bond to XK, that spans the membrane ten times. An absence of XK leads to clinical symptoms termed the McLeod syndrome , an X-linked multi-system disorder characterised by late onset abnormalities in the neuromuscular and hematopoietic systems . It has been shown that XK recruits the lipid transfer protein VPS13A from lipid droplets to the endoplasmic reticulum (ER) membrane and dysregulation of a VPS13A-XK complex is the common basis for Chorea-Acanthocytosis and McLeod Syndrome .
RZZ complex, subunit Zwilch (Zwilch)
Type: Family

The protein Zwilch is an essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. It is required for the assembly of the dynein-dynactin, Mad2 complexes and spindly/CG15415 onto kinetochores .
AAA-ATPase-like domain (AAA-ATPase-like_dom)
Type: Domain

This entry is predicted to be an AAA-ATPase domain . It is usually found together with

.
C-terminal AAA-associated domain (AAA-associated_dom_C)
Type: Family

This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family

.
Domain of unknown function DUF2357 (DUF2357)
Type: Domain

This entry was previously the N-terminal portion of DUF524 (

) before it was split into two. This domain has no known function. It is predicted to adopt an all β secondary structure pattern followed by mainly α-helical structures .
ChrB, C-terminal domain (ChrB_C)
Type: Domain

This entry represents the C-terminal domain found in protein ChrB from Cupriavidus metallidurans, a protein involved in the reduction of chromate accumulation and essential for chromate resistance . This domain may carry the metal detection motifs that are important for its function .
Uncharacterised protein family UPF0319 (UPF0319)
Type: Family

The proteins in this entry are functionally uncharacterised.
Protein of unknown function DUF2058 (DUF2058)
Type: Family

This protein family represents various prokaryotic proteins, including Uncharacterized protein YaiL fom Escherichia coli (strain K12). It has no known function.
Domain of unknown function DUF2059 (DUF2059)
Type: Domain

This entry represents a domain predominantly found in bacterial proteins, including PA0856 from Pseudomonas aeruginosa (

). It shows an all-α structure.
Domain of unknown function DUF2061, membrane (DUF2061_membrane)
Type: Domain

This domain, found in various prokaryotic proteins, has no known function.
Domain of unknown function DUF2062 (DUF2062)
Type: Domain

This domain, found in various prokaryotic proteins, has no known function. It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.
Putative DNA-binding domain, bacteria (DUF2063)
Type: Domain

This entry represents the N-terminal part of a Neisseria protein (

,

). It runs from residues 31-117 as a helical bundle with 4 main helices. From genomic context and the fold of the C-terminal part, it is suggested that this protein is involved in transcriptional regulation .
Transferase 1, rSAM/selenodomain-associated (Trfase_1_rSAM/seldom-assoc)
Type: Family

Many members of this protein family show strongly correlated phylogenetic distribution, and in most cases co-clustering, with an unusual radical SAM enzyme (

) involved in arsenosugar biosynthesis whose C-terminal domain often contains a selenocysteine residue.

Other members of the conserved gene neighbourhood include another putative glycosyltransferase, an alkylhydroperoxidase family protein (

), and a phosphoesterase family protein (

).
Protein of unknown function DUF2066 (DUF2066)
Type: Family

This entry represents a family of prokaryotic proteins with no known function.
Protein of unknown function DUF2069, membrane (DUF2069_membrane)
Type: Family

This family of prokaryotic proteins has no known function but is thought to be a membrane protein.
Protein of unknown function DUF2071 (DUF2071)
Type: Family

This conserved protein, similar to YgjF, has no known function.
Origin-associated protein OapC-like (OapC-like)
Type: Family

This entry includes archaeal Zinc-ribbon containing proteins which are mostly uncharacterised. Some members of this entry have been described as OapC/ArvC, encoded by oapC gene which is part of the three-gene cluster oapABC (origin-associated proteins), involved in generation of extracellular vesicles (arv, archaeal vesiculating GTAse). Knockout of OapC/ArvC leads to over vesiculation, possibly due to dysregulation of OapA/ArvA, a small GTPase, therefore, it has been suggested that OapC/ArvC may represent a GAP .
Membrane protein of 12 TMs (12TM_1)
Type: Family

This family carries twelve transmembrane regions. It does not have any characteristic nucleotide-binding-domains of the GxSGSGKST type, so it may not be an ATP-binding cassette transporter. However, it may well be a transporter of some description. ABC transporters always have two nucleotide binding domains; this has two unusual conserved sequence-motifs: 'KDhKxhhR' and 'LxxLP'.
Schlafen group 3-like, DNA/RNA helicase domain (SLFN_3-like_DNA/RNA_helicase)
Type: Domain

This domain, found in group 3 of Schlafen proteins from mammals, including Schlafen 5, 8, 9, 11 and 13, represents the helicase domain. Schlafen proteins are involved in the control of cell proliferation, induction of immune responses, and in the regulation of viral replication . These proteins inhibit DNA replication and promote cell death in response to DNA damage. They play a role in genome surveillance to kill cells with defective replication . This domain is also found in various prokaryotic proteins fused to a DNA helicase, GIY-YIG or PD-(D/E)XK catalytic domain or HsdR-N(terminal) domain, which are similar to AAA DNA helicase, Type III restriction enzyme ATPase, RecD and RuvB helicase .
Protein of unknown function DUF2076 (DUF2076)
Type: Family

This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
SHOCT domain (SHOCT)
Type: Domain

The Short C-terminal (SHOCT) domain is widespread in bacteria but is missing from the most commonly studied model organisms, despite being present in closely related species. It's predominantly C-terminal location, co-occurrence with numerous other domains and short size is reminiscent of the Gram-positive anchor motif, however it is present in a much wider range of species. It may be involved in oligomerisation and nucleic acid binding .
Sulfolobus virus STSV1, Orf64 (STSV1_Orf64)
Type: Family

This entry is represented by Sulfolobus virus STSV1, Orf64. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

This entry contains a family of various integral membrane proteins with no known function.
Protein of unknown function DUF2082, nucleic-acid-binding, Zn-ribbon (DUF2082_NA-bd_Znr)
Type: Family

This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Short-chain fatty acyl coenzyme A regulators, C-terminal (ScfR_C)
Type: Domain

This domain is found at the C-terminal end of various short-chain fatty acyl coenzyme A regulators (ScfRs) from bacteria , including HTH-type transcriptional regulators PrpR and RamB from Mycobacterium tuberculosis. PrpR (propionate regulator) plays a key role in the regulation of the expression of enzymes involved in the catabolism of short chain fatty acids (SCFA) via both the glyoxylate (acetyl degradation route) and the methylcitrate cycle (propionate degradation route) . RamB (regulator of acetate metabolism B) negatively controls the expression of the expression of the isocitrate lyase during growth on acetate as the sole carbon source, and therefore the utilization of fatty acids . This region is organised into a GAF-like domain with a central β-sheet and a C-terminal region that consists mainly of loops and short secondary structure elements .
Putative toxin of bacterial toxin-antitoxin pair (YjhX_toxin)
Type: Family

YjhX_toxin is a putative toxin of a bacterial toxin-antitoxin pair .
Protein of unknown function DUF2086 (DUF2086)
Type: Family

This is a family of prokaryotic proteins. They are predicted to catalyse oxidative demethylation of damaged bases in DNA .
Domain of unknown function DUF2087 (DUF2087)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
LarA-like, N-terminal (LarA-like_N)
Type: Domain

This entry represents the N-terminal domain of LarA and related proteins.

LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporation of Ni in the lactate racemase apoprotein .

LarA contains 18 β-strands and 16 α-helices arranged in a novel fold composed of two domains of similar size.
Domain of unknown function DUF2089 (DUF2089)
Type: Domain

This domain is found in various hypothetical prokaryotic proteins. It occurs as a fusion of ZnR+HTH+SHOCT-like
Domain of unknown function DUF2090 (DUF2090)
Type: Domain

This domain, found in various prokaryotic carbohydrate kinases, has no known function.
C-type lysozyme inhibitor (MliC)
Type: Domain

Lysozymes are ancient and important components of the innate immune system of animals that hydrolyse peptidoglycan, the major bacterial cell wall polymer. Various mechanisms have evolved by which bacteria can evade this bactericidal enzyme, one being the production of lysozyme inhibitors. MliC (membrane bound lysozyme inhibitor of c-type lysozyme) of E. coli and Pseudomonas aeruginosa, possess lysozyme inhibitory activity and confer increased lysozyme tolerance upon expression in E. coli . Structural analyses show that the invariant loop of MliC plays a crucial role in the inhibition of the lysozyme by its insertion into the active site cleft of the lysozyme, where the loop forms hydrogen and ionic bonds with the catalytic residues .

Interestingly, lipoprotein LprI has a C-terminal MliC domain, and has been identified only in virulence-associated mycobacterial strains, where it acts as a lysozyme inhibitor .
Protein of unknown function DUF2093 (DUF2093)
Type: Family

This family of various hypothetical prokaryotic proteins has no known function.
Protein of unknown function DUF2095 (DUF2095)
Type: Family

This domain, found in various hypothetical prokaryotic proteins, has no known function.
Protein of unknown function DUF2101, membrane (DUF2101_membrane)
Type: Family

This family of conserved hypothetical proteins has no known function.
Protein of unknown function DUF2103, metal-binding (DUF2103_metal-binding)
Type: Family

This family of various putative metal binding prokaryotic proteins has no known function.
Protein of unknown function DUF2122, RecB-family nuclease-related (DUF2122_RecB-nuclease-rel)
Type: Family

This family of archaeal proteins include RecB nuclease-like proteins as well as proteins of no known function.
Protein of unknown function DUF2125 (DUF2125)
Type: Family

This family of conserved hypothetical proteins has no known function.
Domain of unknown function DUF2126 (DUF2126)
Type: Domain

This domain is found in bacterial transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown.
DNA-binding protein VF530-like (DNA-binding_VF530-like)
Type: Family

This entry includes the DNA-binding protein VF530 from Vibrio fischeri. VF530 contains a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains .
Toxin-antitoxin system, mRNA interferase HigB (Toxin_HigB)
Type: Family

This entry represents mRNA interferase HigB from Escherichia coli and similar bacterial proteins. HigB is the toxin of the HigB-HigA toxin-antitoxin (TA) system, acting as a translation-dependent mRNA interferase. HigB inhibits protein synthesis by cleaving translated mRNAs within the coding region . The crystal structure of this TA complex shows an hetero-tetramer formed by two HigB and two HigA subunits. Each toxin HigB has a microbial RNase T1 fold with a three antiparallel β-sheet core shielded by a few α-helices at either side . Unlike other TA systems, both components make minimal interactions .
Protein of unknown function DUF2138 (DUF2138)
Type: Family

This entry contains uncharacterised proteins found in Proteobacteria, including Uncharacterized protein YfaA from Escherichia coli (strain K12).
Protein of unknown function DUF2140 (DUF2140)
Type: Family

This protein family contains uncharacterised proteins found in Firmicutes, including Uncharacterized protein YpmS from Bacillus subtilis (strain 168).
Protein of unknown function DUF2141 (DUF2141)
Type: Family

This family of conserved hypothetical proteins has no known function.
Protein of unknown function DUF2142, membrane (DUF2142_membrane)
Type: Family

This family of conserved hypothetical proteins has no known function.
Protein of unknown function DUF2149 (DUF2149)
Type: Family

This entry represents a group of uncharacterised proteins from bacteria and archaea.
Domain of unknown function DUF2157 (DUF2157)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, has no known function.
Protein of unknown function DUF2160, transmembrane (DUF2160_TM)
Type: Family

The members of this family of hypothetical prokaryotic proteins have no known function. It is thought that they are transmembrane proteins, but their function has not been inferred yet.
Putative PD-(D/E)XK phosphodiesterase (DUF2161) (DUF2161)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in prokaryotes. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses s have established this family to be a member of the PD-(D/E)XK superfamily.
Protein of unknown function DUF2164 (DUF2164)
Type: Family

This family of various hypothetical prokaryotic proteins has no known function.
Protein of unknown function DUF2165, transmembrane (DUF2165_transmembrane)
Type: Family

This family of various hypothetical prokaryotic proteins has no known function.
Protein of unknown function DUF2167, membrane (DUF2167_membr)
Type: Family

This family of various hypothetical membrane-anchored prokaryotic proteins has no known function.
Domain of unknown function DUF2169 (DUF2169)
Type: Domain

This domain, found in various hypothetical prokaryotic proteins, has no known function.
Protein of unknown function DUF2171 (DUF2171)
Type: Family

This family of various hypothetical prokaryotic proteins has no known function.
Protein of unknown function DUF2173 (DUF2173)
Type: Family

This family of various hypothetical prokaryotic proteins has no known function.
Protein of unknown function DUF2175 (DUF2175)
Type: Family

This family of various hypothetical archaeal proteins has no known function.
Protein of unknown function DUF2177, membrane (DUF2177_membr)
Type: Family

This family of putative membrane proteins has no known function.
Copper chaperone PpoB2-like (PpoB2-like)
Type: Family

This family includes Copper chaperone PpoB2 from Marinomonas mediterranea and similar prokaryotic sequences. PpoB2 is a membrane copper transporter involved in the delivery of this ion to the PpoB1 tyrosinase (

) .
Immunity protein Imm33 domain (Imm33_dom)
Type: Domain

This domain has been identified as a putative family of immunity proteins found in bacterial toxin/antitoxin systems . This domain was previously called DUF2185.
Protein of unknown function DUF2187 (DUF2187)
Type: Family

This family consists of various hypothetical bacterial proteins with unknown function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Protein of unknown function DUF2188 (DUF2188)
Type: Family

DUF3892 is related to the truncated RNaseH fold-containing ribosome hibernation factors. It has been predicted to function as a possible conflict effector domain at the ribosome, based on comparable genome contextual associations with DUF2188, including repeated association with nucleotide-activated effector conflict systems .
Predicted integral membrane protein DUF2189 (DUF2189)
Type: Family

This family includes several hypothetical prokaryotic proteins. Some are described as putative cytochrome c oxidases.
Protein of unknown function DUF2192 (DUF2192)
Type: Family

This family of various hypothetical archaeal proteins has no known function.
Protein of unknown function DUF2193 (DUF2193)
Type: Family

This family of various hypothetical archaeal proteins has no known functio
Protein of unknown function DUF2194 (DUF2194)
Type: Family

This family of prokaryotic proteins has no known function; however it may be a membrane protein.
Protein of unknown function DUF2195 (DUF2195)
Type: Family

This family of various bacterial proteins has no known function.
Protein of unknown function DUF2199 (DUF2199)
Type: Family

This domain has no known function.
VWA-like domain (VWA-like_dom)
Type: Domain

This domain, found in various hypothetical bacterial proteins, has no known function. However, it is clearly related to the VWA domain.
Protein of unknown function DUF2203 (DUF2203)
Type: Family

This family has no known function.
Protein of unknown function DUF2204 (DUF2204)
Type: Family

This family of hypothetical prokaryotic proteins has no known function. However, this family was identified as belonging to the nucleotidyltransferase superfamily [

,

].
Protein of unknown function DUF2206, membrane (DUF2206_membrane)
Type: Family

This family of predicted membrane proteins from archaea has no known function.
Domain of unknown function DUF2207 (DUF2207)
Type: Domain

This domain with no known function is located at the N-terminal domain of a group of uncharacterised prokaryotic proteins, including the predicted membrane protein YciQ from Escherichia coli.