SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF5904 (DUF5904)
Type: Domain

This entry represents a domain of unknown function found mostly in Prasinovirus proteins.
Contractile injection system tube protein, N-terminal domain (CIS_tube_prot_N)
Type: Domain

Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. This entry represents a domain found in the tube proteins of the extracellular CISs present in bacteria and archaea. Proteins containing this domain include Pvc7, which is part of the Photorhabdus asymbiotica virulence cassette (PVC). Pvc7 is a tube protein with an additional LysM domain. The equivalents of these two parts in T4 phage are gp48 and gp53, respectively .
Contractile injection system spike tip protein (CIS_spike_tip)
Type: Family

Contractile injection systems (CISs) are cell-puncturing nanodevices that share ancestry with contractile tail bacteriophages. This entry represents the spike tip protein from a extracellular CIS present in bacteria. This protein family includes the Pvc10 (the homologue of T4 gp5.4). This monomeric protein was part of a CryoEM structure and although not resolved at atomic resolution in the map, it was observed to form the sharp conical tip on the Pvc8 spike .
Ceramide kinase, C-terminal domain (CERK_C)
Type: Domain

This domain is found at the C-terminal of ceramide kinases (CERKs) from eukaryotes. This domain is related to the β-sandwich domain of NAD kinases. Along with the N-terminal domain, it catalyses specifically the phosphorylation of ceramide to form ceramide 1-phosphate .

The Ceramide kinase proteins are responsible for the phosphorylation of ceramide to produce ceramide 1-phosphate. This enzymatic activity is specific to ceramides, including both natural and analogue forms such as C6, C8, C16 ceramides, and C8-dihydroceramide. The proteins exhibit a preference for the D-erythro isomer of ceramides and show reduced activity on C2-ceramide and C6-dihydroceramide. Notably, they do not act on other lipid types, such as various sphingosines. Additionally, members of this group have the ability to bind phosphoinositides, which may play a role in their function or regulation. Ceramide is a critical sphingolipid metabolite that induces programmed cell death (PCD), while ceramide-1-phosphate has a PCD suppressive effect. Thus, ceramide phosphorylation plays a role in the modulation of PCD, and the CERK activity is crucial for the maintenance of cell viability .
Protein of unknown function DUF5883 (DUF5883)
Type: Family

This is a family of uncharacterised proteins of unknown function found in Chlorovirus.
Protein of unknown function DUF5884 (DUF5884)
Type: Family

This is a family of uncharacterised proteins of unknown function found in Mimivirus.
Protein of unknown function DUF5905 (DUF5905)
Type: Family

This is a family of uncharacterised proteins of unknown function found in Marseillevirus.
Protein of unknown function DUF5885 (DUF5885)
Type: Family

This is a family of uncharacterised proteins of unknown function found in Pandoravirus.
Protein of unknown function DUF5886 (DUF5886)
Type: Family

This entry represents a group of proteins of unknown function predominantly found in Mimivirus.
Protein of unknown function DUF5887 (DUF5887)
Type: Family

This is a family of uncharacterised proteins of unknown function predominantly found in viruses. This entry includes proteins that are thought to have acetyltransferase activity in Betabaculovirus.
Protein of unknown function DUF5888 (DUF5888)
Type: Family

This is a family of uncharacterised proteins mainly found in Pandoravirus and Mollivirus.
ADAMTS/ADAMTS-like, cysteine-rich domain 3 (ADAMTS_CR_3)
Type: Domain

This cysteine rich domain (CRD) is found in a variety of ADAMTS and ADAMTS-like endopeptidases widely spread in animals . It is a well-conserved cysteine-rich sequence containing 10 cysteine residues .

Proteolysis of the extracellular matrix plays a critical role in establishing tissue architecture during development and in tissue degradation in diseases such as cancer, arthritis, Alzheimer's disease and a variety of inflammatory conditions . The proteolytic enzymes responsible for this process are members of diverse protease families, including the secreted zinc metalloproteases (MPs) .

ADAM-TS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) is closely related to the ADAM family (A Disintegrin and Metalloproteinase) and is a subfamily of the MP family, consists of at least 20 members sharing a high degree of sequence similarity and conserved domain organisation . The defining domains of the ADAM-TS family are (from N- to C-termini) a pre-pro metalloprotease domain of the reprolysin type, a snake venom disintegrin-like domain, a thrombospondin type-I (TS) module, a cysteine-rich region, and a cysteine-free (spacer) domain . Domain organisation following the spacer domain C terminus shows some variability in certain ADAM-TS members, principally in the number of additional TS domains. These enzymes have a wide-spectrum role in vascular biology and cardiovascular pathophysiology .

Members of the ADAM-TS family have been implicated in a range of diseases . For instance, members of this family have been found to participate directly in processes in the central nervous system (CNS) such as the regulation of brain plasticity . ADAM-TS1 is reported to be involved in inflammation and cancer cachexia , whilst recessively inherited ADAM-TS2 mutations cause Ehlers-Danlos syndrome type VIIC, a disorder characterised clinically by severe skin fragility . ADAM-TS4 is an aggrecanase involved in arthritic destruction of cartilage .

ADAM-TS-like proteins lack a metalloprotease domain. They resides in the ECM and have regulatory roles . Examples of ADAM-TS-like proteins are papilin and punctin .
YidB-like protein (YidB)
Type: Family

This entry includes the uncharacterised protein YidB from E. coli. This entry was previously a subset of the DUF937 family.
Domain of unknown function DUF5889 (DUF5889)
Type: Domain

This entry represents a domain of unknown function mostly found in uncharacterised proteins from Mimivirus.
Cas5fv helical domain (Cas5fv_helical)
Type: Domain

This entry represents the Cas5fv helical domain .
Putative radical SAM, N-terminal (Put_radical_SAM-like_N)
Type: Domain

This entry represents a domain found in a group of putative radical SAM proteins mostly from bacteria.
Glycosyltransferase Maf, N-terminal (Maf_N)
Type: Domain

This entry represents the N-terminal Rossmann-like domain found in the flagellin glycosyltransferase Maf .
Flagellin glycosyltransferase Maf, helical bundle domain (Maf_C)
Type: Domain

This entry represents the helical bundle domain found in flagellin glycosyltransferase Maf .
Apolipoprotein N-acyltransferase, N-terminal (LNT_N)
Type: Domain

This domain represents the N-terminal transmembrane region of the apolipoprotein N-acyltransferase enzyme. Proteins containing this domain also include bifunctional apolipoprotein N-acyltransferase/polyprenol monophosphomannose synthase from Mycobacterium tuberculosis.

Apolipoprotein N-acyltransferase (Lnt) transfers the acyl group to lipoproteins and is involved in lipoprotein biosynthesis in Gram-negative bacteria. It is an integral membrane protein . In the last step of lipoprotein maturation, N-acylation by apolipoprotein N-acyltransferase of the plasma membrane is required for recognition of the outer membrane lipoproteins by the Lol system, which transports the lipoproteins from the plasma to the outer membrane . This is a reverse amidase (i.e. condensation) reaction.
Crinkler effector protein, N-terminal (Crinkler_N)
Type: Domain

Phytophthora sojae encodes hundreds of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling- and necrosis-inducing proteins (CRN) or Crinkler. CRNs have been functionally characterised in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity . This entry represents the N-terminal domain of Crinkler. It contains an ubiquitin-like fold.

Proteins containing this domain also include Rhizophagus irregularis RiCRN1 (crinkler effector protein 1). Similar to other CRNs, RiCRN1 can be found in host nucleus. However, it is involved in arbuscule development .
L,D-transpeptidase, scaffold domain (LD_TPept_scaffold_dom)
Type: Domain

This entry represents the scaffolding domain of L,D-transpeptidases, such as YcbB from E. coli .
Brassinosteroid receptor BRI1, island domain (BRI1_island_dom)
Type: Domain

The island domain in BRI1 corresponds to a large insertion in the regular repeat-structure between LRRs 21 and 22. The resulting 70-residue segment forms a small domain that folds back into the interior of the LRR superhelix, where it makes extensive polar and hydrophobic interactions with LRRs 13-25. The domain fold is characterised by an anti-parallel β-sheet, which is sandwiched between the LRR core and a 3-10 helix and stabilized by a disulphide bridge. The insertion of a folded domain into the LRR repeat has not been observed in other LRR receptor structures, and is probably an adaptation to the challenge of sensing a small steroid ligand (rather than larger ligands, such as proteins, nucleic acids, or lipids) .
Protein of unknown function DUF6529 (DUF6529)
Type: Family

This is a group of uncharacterised proteins found in bacteria.
Protein of unknown function DUF6528 (DUF6528)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes.
Protein of unknown function DUF6527 (DUF6527)
Type: Family

This family of proteins is functionally uncharacterised. They are found mostly in bacteria.
Protein of unknown function DUF6526 (DUF6526)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6525 (DUF6525)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. There are two conserved sequence motifs: AALPWSP and RAE.
Protein of unknown function DUF6524 (DUF6524)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein HHL1-like (HHL1-like)
Type: Family

This entry represents a group of proteins from plants and Cyanobacteria, including HHL1 from Arabidopsis. HHL1 functions in protecting photosystem II against photodamage .
Protein of unknown function DUF6522 (DUF6522)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
ABC-three component system, Middle Component 3 (ABC-3C_MC3)
Type: Family

Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses .
Protein of unknown function DUF6520 (DUF6520)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6519 (DUF6519)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6518 (DUF6518)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Alpha/beta hydrolase domain (Abhydrolase_dom)
Type: Domain

This entry represents a group of proteins that belong to the alpha/beta hydrolase superfamily.
ALTTAQ repeat (ALTTAQ_rpt)
Type: Repeat

This repeat is called after the short repeat ALTTAQ found in uncharacterised proteins mostly from Proteobacteria.
Protein of unknown function DUF6517 (DUF6517)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in archaea.
Toxin TumE-like (TumE-like)
Type: Family

This entry represents a family of proteins found in archaea and bacteria. These proteins have been recently described as the toxin component TumE from the novel toxin-antitoxin system TumE-TumA, which constitutes a translation-targeting toxic effector . These proteins are predicted to adopt a conserved α+β fold, where two α-helices pack against an antiparallel β-sheet with seven strands .
Protein of unknown function DUF6515 (DUF6515)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Trypanosoma Tc-38 (p38) protein (Tc-38)
Type: Domain

This domain can be found in multiple copies in kinetoplastid-specific minicircle binding proteins that evolved from a prokaryotic ArdCN domain .
Wolframin, cysteine-rich domain (Wolframin_Cys-rich)
Type: Domain

Located N-terminal to the wolframin OB-fold domain, this region could represent an extension to the core of the OB fold domain. The observed conserved cysteine residues could contribute to disulfide-bond-mediated cross-linking in calcium-stores regulation .

Wolframin, a multi-pass membrane protein found in the endoplasmic reticulum, is expressed by the Wolfram syndrome 1 gene (WFS1) . The detailed molecular function of the protein is not known, but it is believed to participate, at least in part, in the regulation of cellular calcium homeostasis by modulating the filling state of the endoplasmic reticulum calcium store.

Defects in WFS1 cause Wolfram Syndrome (WFS), also referred to as DIDMOAD - this syndrome is characterised by diabetes insipidus, childhood-onset diabetes mellitus, gradual loss of vision owing to optic atrophy, and deafness . It is a rare autosomal recessive disorder, and may give rise to other complications affecting the bladder and nervous system.

Wolframin homologues have been identified in a range of species, from mammals and amphibia to insects. Notwithstanding regions of high similarity, vertebrate and invertebrate wolframins exhibit characteristic lineage- specific differences. This entry represents the Wolframin family, and includes homologues from invertebrates.
GTPase-associated protein 1, middle domain (GAP1-M)
Type: Domain

GTPase-associated protein 1 (GAP1) is part of the GTPase-centric systems, a class of NTP-dependent biological conflict systems. It is comprised of three clearly distinguishable globular domains: GAP1-N, GAP1-M and GAP1-C. GAP1 occurs in two distinct subtypes that are readily distinguished by versions of the GAP1-N domain: GAP1-N1 and GAP1-N2 .

This entry represents the middle domain (GAP1-M) found in GAP1 .
GTPase-associated protein 1, N-terminal domain type 2 (GAP1-N2)
Type: Domain

GTPase-associated protein 1 (GAP1) is part of the GTPase-centric systems, a class of NTP-dependent biological conflict systems. It is comprised of three clearly distinguishable globular domains: GAP1-N, GAP1-M and GAP1-C. GAP1 occurs in two distinct subtypes that are readily distinguished by versions of the GAP1-N domain: GAP1-N1 and GAP1-N2 .

This entry represents the N2 domain (GAP1-N2) found in GAP1. This domain is predicted to mediate effector-GAP1 interactions.
Helix-turn-helix domain, Firmicutes-type (HTH_59_Firmicutes_type)
Type: Domain

This helix-turn-helix domain can be found in proteins mostly from Firmicutes.
Major capsid protein 13-like (Gp13-like)
Type: Family

This entry represents a group of phage capsid/coat-related proteins, including Gp13 from Bacillus phage SPP1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Gp13 is part of the icosahedral capsid together with the auxiliary protein gp12, which are organized in a T=7 lattice . This family contains some conserved motifs: GD, GxxxxV/IxxD and NW.
Peptidase S80 family (Peptidase_S80)
Type: Family

This family represents the protease responsible for the proteolysis of head proteins, a critical step in the morphogenesis of many tailed phages. Cleavage facilitates the conversion of the prohead to the mature capsid. All these cleavages are carried out by action at consensus S/A/G-X-E recognition sequences at 39 cleavage sites. Evidence of multiple processing sites in nine phiKZ proteins appears to represent a built-in mechanism by which the phage ensures that the majority of the propeptide regions are removed, and emphasizes the essential nature of processing in phiKZ-head morphogenesis . The family is classified by MEROPS as a serine peptidase.
Domain of unknown function DUF6513 (DUF6513)
Type: Domain

This presumed domain is functionally uncharacterised. This domain can be found in bacterial and archaeal proteins.
Protein of unknown function DUF6512 (DUF6512)
Type: Family

This family of proteins is functionally uncharacterised. Members of this entry are mainly found in bacteria.
Protein of unknown function DUF5890 (DUF5890)
Type: Family

This entry represents a family of uncharacterised Avipoxvirus proteins, which presumably contain a Host Targeting (HT) motif. This motif is involved in targeting host proteins as part of the infection process in several organisms .
Protein of unknown function DUF5891 (DUF5891)
Type: Family

This entry represents a family of uncharacterised proteins predominantly found in Pimascovirales. Members of this group are predicted to be RNA methyltransferases.
Zinc finger domain-containing protein (Zn_finger_prot)
Type: Family

This family of proteins is predominantly found in Iridoviridae. Members of this group contain a zinc finger domain.
Protein of unknown function DUF5892 (DUF5892)
Type: Family

This entry represents a family of proteins of unknown function predominantly found in Ranavirus.
Protein of unknown function DUF5893 (DUF5893)
Type: Family

This entry represents a family of proteins of unknown function predominantly found in Marseillevirus.
Domain of unknown function DUF5894 (DUF5894)
Type: Domain

This entry represents a domain of unknown function predominantly found in proteins from Mimivirus.
Domain of unknown function DUF5895 (DUF5895)
Type: Domain

This entry represents a domain of unknown function predominantly found in proteins from Cyanobacteria.
Protein of unknown function DUF5896 (DUF5896)
Type: Family

This entry represents a family of proteins of unknown function predominantly found in Marseillevirus.
Domain of unknown function DUF5897 (DUF5897)
Type: Domain

This entry represents a domain of unknown function found in uncharacterised proteins from Pandoravirus. In most of its members, this domain is located at the C terminus.
Domain of unknown function DUF5898 (DUF5898)
Type: Domain

This entry represents a domain of unknown function found in proteins mostly from Amoebozoa, Filasterea and Pandoravirus.
Minor capsid protein P2-like, DUF5899 (P2_DUF5899)
Type: Domain

This entry represents a domain of unknown function found in Minor capsid protein P2 from Paramecium bursaria Chlorella virus 1 and related sequences from Mimiviridae and Phycodnaviridae.

Minor capsid protein P2 is one of the minor capsid proteins that constitute a network internal to the major capsid proteins and outside the lipid membrane . The minor capsid proteins glue and stabilize the capsomers . It also acts as a molecular tape measure protein that determines the size of the viral capsid .
Domain of unknown function DUF5900 (DUF5900)
Type: Domain

This entry represents a domain of unknown function predominantly found in uncharacterised proteins from Pandoravirus. Some members of this entry are thought to be F-box domain-containing proteins. The conserved F-box domain, present in numerous proteins, is involved in protein-protein interaction.
Domain of unknown function DUF5901 (DUF5901)
Type: Domain

This entry represents a domain of unknown function predominantly found in uncharacterised proteins from Chlorovirus.
Domain of unknown function DUF5902 (DUF5902)
Type: Domain

This entry represents a domain of unknown function found in uncharacterised proteins from Pandoravirus.
Protein of unknown function DUF6511 (DUF6511)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
Protein of unknown function DUF6510 (DUF6510)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. There is a conserved RCP sequence motif.
Protein of unknown function DUF6509 (DUF6509)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. There are two conserved sequence motifs: DPTGI and ILA.
Protein of unknown function DUF6508 (DUF6508)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria.
ADYC domain (ADYC)
Type: Domain

This domain is named ADYC after the most conserved motif. Proteins containing this domain are found in proteobacteria and cyanobacteria. These proteins have 7 conserved cysteines and one conserved histidine which might indicate a zinc-binding function.
MoxR domain (MoxR)
Type: Domain

This is the core MoxR component domain of the MoxR-vWA-β-propeller ternary systems, a class of NTP-dependent biological conflict systems .
Effector Associated Constant Component 1 (EACC1)
Type: Family

Effector Associated Constant Component 1 (EACC1) is a component of a membrane-associated two-gene conflict system, a class of NTP-dependent biological conflict systems. It is found either a standalone domain or fused to Effector-associated domains EAD1 or EAD2. It is comprised of a single conserved TM helix with short, N- and C-terminal extensions. It is predicted to insert into the membrane and protrude beyond both the outer and inner layers of the bilayer .
Effector-associated domain 10 (EAD10)
Type: Domain

This entry represents the effector-associated domain 10 (EAD10) found in cyanobacteria with a predicted mixed α+β character .

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.
Effector-associated domain 1 (EAD1)
Type: Domain

This entry represents the effector-associated domain 1 (EAD1). This domain is one of the most prevalent EADs, widely distributed across bacteria. EAD1 is primarily linked to effector domains that also occur directly fused to the vWA component in MoxR-vWA ternary systems or GAP1 in the case of the GAP1-N1 GTPases systems which suggests that it primarily recruits other effectors to the systems . It is predicted to be an all α-helical domain.

Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminal, of a core component of a biological conflict system; examples include VMAP (vWA-MoxR associated protein), iSTAND (inactive STAND (iSTAND) NTPase system), or GAP1 (GTPase-associated protein 1). Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling approximates the advantages of collinear transcription . EADs are all small domains with no enzymatic features.