SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF6881 (DUF6881)
Type: Domain

This entry represents a domain found in small bacterial proteins of unknown function. Its predicted structure shows a 6 stranded β-sheet with a C-terminal helix packed on one side. In a few proteins this domain is associated with InterPro:

, a presumed immunity protein, which could suggest this domain may have a toxin function or be involved in a toxin/antitoxin system or in phage defence.
Family of unknown function DUF6882 (DUF6882)
Type: Family

This family of bacterial proteins is uncharacterised.
Domain of unknown function DUF6883 (DUF6883)
Type: Domain

This entry represents a domain found in the DUF6866 family. The function of these proteins remains unknown. This domain can be found in various domain architectures, either alone or in association with other domains.
Domain of unknown function DUF6884 (DUF6884)
Type: Domain

This entry represents a domain of unknown function that is found either as a standalone protein or in combination with other domains. Members of this family possess a highly conserved LSAXXG motif that may constitute an active site. This domain may be distantly related to oxidative stress response YaaA proteins.
Family of unknown function DUF6885 (DUF6885)
Type: Family

This entry represents a small family of prokaryotic proteins likely to adopt a papain-like fold. Most members of this family possess conserved residues in equivalent positions to those constituting the active site of cysteine proteases.
Family of unknown function DUF6886 (DUF6886)
Type: Family

This entry represents a family of bacterial proteins whose function is unknown. They may be distantly related to ADP-ribosylating toxins.
Phage tail terminator (Phage_tail_terminator)
Type: Family

These entry represents the homologues of Uncharacterized protein YqbJ from Bacillus subtilis (

) found in bacteria and bacteriophages. Some members of this family may be phage tail terminator proteins which form a hexameric complex that joins the phage neck to the tail.
Anaphase-promoting complex subunit 1, N-terminal domain (Apc1_N)
Type: Domain

Apc1 (anaphase-promoting complex subunit 1) is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes . Infection of human fibroblasts with human cytomegalovirus (HCMV) leads to cell cycle dysregulation, which is associated with the inactivation of the anaphase-promoting complex .

Apc1 consists of an N-terminal WD40 β-propeller domain, a middle domain (Mid-N), a PC domain and a C-terminal domain (Mid-C) that coalesces with Mid-N to form Apc1Mid which connects Apc1-WD40 with Apc1-PC and comprises an α-solenoid capped by a β-sandwich .

This entry represents the N-terminal domain of Apc1, which is essential for APC/C catalytic activity as it mediates the coactivator-induced conformational change of the APC/C which promotes UbcH10 binding .
Get5, C-terminal domain (Get5_C)
Type: Domain

This entry represents the C-terminal domain of Get5 from A. fumigatus (

) and related proteins found primarily in Ascomycetes. This domain folds into helical hairpin that dimerises to form a four helical bundle (

). This entry does not include proteins from Saccharomycetes. The domain found in these species is represented by

.

Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyses the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3 .
Gon4l/CASP8AP2, myb-like domain (Gon4l/CASP8AP2_myb-like)
Type: Domain

This domain is the DNA-binding SANT/myb-like domain of Caspase 8-associated protein 2 (CASP8AP2) / GON-4 like proteins from vertebrates.

CASP8AP2 (also known as Flice-Associated Huge Protein, FLASH) is implicated in numerous gene regulatory roles including roles in embryogenesis, oncogenesis, down-regulation of replication-dependent histone genes, regulation of Caspase 8 activity at the death-inducing signalling complex (DISC), and as a useful marker in leukaemia prognosis. Gon-4 is critical in Caenorhabditis elegans gonadogenesis. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the three α-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins
ODAD1, central coiled coil region (ODAD1_CC)
Type: Domain

This domain, previously know as DUF6872, is found in Outer dynein arm-docking complex subunit 1 (ODAD1, CCDC114) from humans and similar eukaryotic proteins. In mammals, ODAD1 forms a hetero-coiled coil with CCDC151 within the A07/A08 interprotofilament cleft, analogous to the DC1/2 coiled coil of the trimeric ODA-DC observed in C. reinhardtii axoneme . DC2 is a homologue of the human ODAD1 and in C. reinhardtii it is a part of the outer dynein arm docking complex (ODA-DC) that consists of three proteins: DC1, DC2, and DC3. The N-terminal halves of DC1 and DC2 form a microtubule-bound heteromeric coiled-coil .
DNA-binding protein REB1, Myb-associated domain (REB1_MybAD)
Type: Domain

This domain is found in DNA-binding protein REB1 from Schizosaccharomyces pombe and similar proteins from yeast. REB1 mediates transcription termination and is also involved in replication termination and transcription activation. This protein, almost entirely α-helical, is organised into five domains: two Myb-associated domains (MybADs, this entry), each consisting of four α-helices, two Myb repeats (MybRs,

) and a final C-terminal domain .
RecA-like, C-terminal (RecA-like_C)
Type: Domain

This entry represents a small domain located at the C-terminal of RecA. This domain adopts a structure composed of a β-hairpin and three α-helices. It has been shown to bind to dsDNA .

The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response . In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs . RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage .

RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved among eubacterial species. It is also found in the chloroplast of plants . RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, β-strand 3, the loop C-terminal to β-strand 2, and α-helix D of the core domain form one surface that packs against α-helix A and β-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation . The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between β-strand 1 and α-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at β-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at β-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.
ATPTG10-like domain (ATPTG10-like_dom)
Type: Domain

This entry, previously known as DUF6828, represents a domain found in the T. gondii ATP synthase subunit 10 (ATPTG10,

) and related proteins from Apicomplexan species. This domain adopts an α-helical structure consisting of five helices . It contains two highly conserved sequence motifs: FSWxD and MxLWI/LKxRI/L. The formation of the T. gondii ATP synthase hexamer involves two contact sites in the lumenal region. ATPTG10 contributes to the the second site via interaction with ATP synthase subunit 11 (ATPTG11).
Domain of unknown function DUF6833 (DUF6833)
Type: Domain

This domain is found primarily in sequences from tailed bacteriophages and proteobacterial prophages, including Pseudomonas phage LUZ7 (

). It folds into an helical hairpin and forms an obligatory dimeric structure (

). Its function is unknown.
Domain of unknown function DUF6846 (DUF6846)
Type: Domain

This domain is found at the N-terminal of uncharacterised protein AF_2093 from Archaeoglobus fulgidus (

) and similar proteins from archaea. It has structural similarity to winged helix HTH domains

. Its function is unknown.
Domain of unknown function DUF6834 (DUF6834)
Type: Domain

This presumed domain is found at the C terminus of uncharacterised protein AF_2093 from Archaeoglobus fulgidus (

) and similar proteins of unknown function mainly from archaea. This domain has structural similarity to type II restriction endonucleases (

).
AF2093-like, C-terminal domain superfamily (AF2093-like_C_sf)
Type: Homologous_superfamily

This superfamily represents a domain found at the C-terminal of the uncharacterised protein AF_2093 from Archaeoglobus fulgidus (

), whose function is unknown.
Domain of unknown function DUF6835 (DUF6835)
Type: Domain

This domain of unknown function is found in proteins from bacteria, including the product of the gene SO_2669 from Shewanella oneidensis. It adopts an α-helical hairpin structure that self-associates into 16-helical bundle (

,

).
PaaA-like, N-terminal domain (PaaA-like_N)
Type: Domain

This domain is found at the N-terminal end of PaaA from Enterobacter agglomerans (

), an enzyme involved in post-translational modification and host immunity. PaaA is composed of two domains: an N-terminal domain, represented in this entry, which folds into a globular domain and has similarity to RiPP precursor peptide recognition elements or RREs (PDBe:

) and a C-terminal THIF-type NAD/FAD binding fold
(

) .
Domain of unknown function DUF6836 (DUF6836)
Type: Domain

This domain is predominantly found in proteins from bacteria, including CLOLEP_02462 from Clostridium leptum (

). It adopts an α/β structure consisting of eight antiparallel β-sheet and α-helices packed on one side of it with an overside connection (

). The function of this protein is unknown.
Cilia- and flagella-associated protein 58, central coiled coil (CFAP58_CC)
Type: Domain

This domain is found in Cilia- and flagella-associated protein 58 (CFAP58) and related eukaryotic proteins. The human CFAP58 protein has an essential role in the assembly and organisation of the sperm flagellar axoneme . This domain forms a parallel coiled coil that in the C. reinhardtii axonemal structure lays on the doublet microtubule surface and interacts with the N terminus of the MIA coiled coil (

) .
Domain of unknown function DUF6862 (DUF6862)
Type: Domain

This entry represents a small domain that is found in a variety of toxin proteins. The precise function of this domain is uncertain. In some instances, it follows

.
DUF3829-like, N-terminal domain (DUF3829-like_N)
Type: Domain

This domain is found at the N-terminal of uncharacterised DUF3829-like proteins. It might be related to

. Its function is unknown.
LynD/TruD, winged helix-turn-helix-like domain (LynD/TruD_wHTH-like)
Type: Domain

This domain is found at the N terminus of TruD , a protein involved in cyanobactin heterocyclisation. It is also found in the related LynD protein, an ATP-dependent enzyme that heterocycles multiple cysteine residues to thiazolines within peptide substrates . It adopts a winged helix-turn-helix structure. The function of this domain is unclear.
Domain of unknown function DUF6854 (DUF6854)
Type: Domain

This domain is usually found in tandem in a group of uncharacterised bacterial proteins. It consists of a four-stranded β-sheet and two α-helices. It is related to proteins members of the 'dimeric α+β barrel' superfamily

.
Protein of unknown function DUF6853 (DUF6853)
Type: Family

This protein family includes the functionally uncharacterised protein NMB0500 from Neisseria meningitidis (

) and similar bacterial uncharacterised proteins. NMB0500 adopts an all-α structure consisting of three α-helices that self-associates to form a helical bundle (

).
DUF3860-like (DUF3860-like)
Type: Family

This protein family includes

from Rhodopseudomonas palustris, an uncharacterised protein that adopts a structure similar to winged HTH domains (

). It also has some similarity to members of

.
Mechanosensitive ion channel MscS, C-terminal domain (MS_channel_C)
Type: Domain

This entry includes small conductance mechanosensitive channels (MscS), which assembles to a homoheptameric complex . Each monomer consists of an N-terminal transmembrane region and a large cytoplasmic segment composed of a five-stranded antiparallel β-sheet domain (β-domain,

) and a C-terminal α/β-domain .

This is the C-terminal domain of McsS which, together with the middle β-domain, creates a framework that connects to the cytoplasm through distinct openings .

Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya . There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL . The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved.

MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals .

In the fission yeast Schizosaccharomyces pombe the mechanosensitive ion channel proteins are known as msy1 and msy2 .
DUF3108-like (DUF3108-like)
Type: Domain

This is a domain found in uncharacterised proteins from Parabacteroides distasonis (

), Bacteroides fragilis (

) and other bacteria. It adopts a β-barrel fold of the YmcC-like type (

).
Domain of unknown function DUF6852 (DUF6852)
Type: Domain

This domain is found at the C-terminal of BVU_3817 from Phocaeicola vulgatus (

) and similar proteins mostly from Bacteroidetes. This domain shows an α/β structure and is usually found associated with

. Its function is unknown.
BVU_3817-like, C-terminal domain superfamily (BVU_3817-like_C_sf)
Type: Homologous_superfamily

This superfamily represents a domain that is found at the C-terminal of BVU_3817 from Phocaeicola vulgatus (

) and similar proteins mostly from Bacteroidetes. This domain shows an α/β structure and is usually found associated with

. Its function is unknown.
BVU_3817-like, N-terminal domain superfamily (BVU_3817_N_sf)
Type: Homologous_superfamily

This domain is found at the N-terminal of BVU_3817 from Phocaeicola vulgatus (

) and similar proteins mostly from bacteroidetes. This domain adopts a β-barrel with SH3 topology and is usually found associated with

. Its function is unknown.
Domain of unknown function DUF6851 (DUF6851)
Type: Domain

This domain of unknown function is found in the N-terminal region of a group of bacterial proteins, including Vanadium-dependent haloperoxidases such as NapH1 (

) and NapH3 (

) . In some proteins, this domain is found associated to

. Its specific function is unknown.
Protein-L-isoaspartyl O-methyltransferase, C-terminal domain (PIMT_C)
Type: Domain

Protein-L-isoaspartyl O-methyltransferase (PIMT) from Thermotoga maritima is a conserved and nearly ubiquitous enzyme involved in the repair of proteins damaged by age-related isoaspartyl formation. PIMT consists of three domains. This entry represents its C-terminal domain, which shows a five-stranded β meander flanked on both sides by α-helices. Its function is unknown .
DUF4931, C-terminal domain (DUF4931_C)
Type: Domain

This domain is found at the C-terminal of bacterial proteins and is around 270 residues in length. Proteins containing this domain are mainly found in firmicutes, including a di/tripeptide transporter from Lactobacillus helveticus (

). In BCE0241 protein from Bacillus cereus (

), which is structurally but not functionally characterised, this domain adopts an α/β structure that is similar to HIT-like domains (

). It is also similar to the N-terminal domain (

) that also adopts HIT-like structure. The specific function of this domain is unknown.
Domain of unknown function DUF6844 (DUF6844)
Type: Domain

This domain is found predominantly found in proteobacteria and campylobacteria, including the hypothetical protein FTT_1539c from Francisella tularensis (

). It is located in the centre of the proteins included in this entry.
Domain of unknown function DUF6837 (DUF6837)
Type: Domain

This domain is found in 201phi2-1p060 protein from Pseudomonas phage 201phi2-1 (

). It folds into an α/β structure consisting of a five-stranded antiparallel β-sheet and an α-helix packed on one side of it. Its function is unknown.
DUF447, C-terminal domain (DUF447_C)
Type: Domain

This entry represents a spectrin-like domain found in the DUF447 family of bacterial and archaeal proteins. This domain is found C-terminal to the FMN-binding split β-barrel domain

. It consists of a three helical bundle that packs on the β-barrel wall

.
Domain of unknown function DUF6839 (DUF6839)
Type: Domain

This entry represents a domain of unknown function found in a group of bacteria and Thermus phages, such as TTMA177 protein from Thermus thermophilus phage TMA (

) that adopts an open β-barrel structure (

).
TTMA177-like (TTMA177-like)
Type: Homologous_superfamily

This entry represents a domain of unknown function found in a group of bacteria and Thermus phages, such as TTMA177 protein from Thermus thermophilus phage TMA (

) that adopts an open β-barrel structure (

).
Protein of unknown function DUF6840 (DUF6840)
Type: Family

This uncharacterised protein family is predominantly found in Leptospirillum sp. Its function is unknown. There are some conserved motifs: SRD, AGGL and some highly conserved Y, H and W residues.
Domain of unknown function DUF6842 (DUF6842)
Type: Domain

This domain is found in the hypothetical protein lpg2422 from Legionella pneumophila (

) and related proteins from Legionella species. It adopts an α-helical structure consisting of a four-helical bundle (

). This domain is found C-terminal to

and usually in three tandem copies. Its function is unknown.
Domain of unknown function DUF6843 (DUF6843)
Type: Domain

This domain is found in the putative lipoprotein BA_2398 from Bacillus anthracis (

) and similar proteins from bacteria, predominantly firmicutes and bacteroidetes. It folds into an open β-barrel packed on one side with α-helix (

).
Domain of unknown function DUF6848 (DUF6848)
Type: Domain

This domain is found in uncharacterised proteins from bacteria and a few tailed bacteriophages.
Domain of unknown function DUF6849 (DUF6849)
Type: Domain

This domain is found in uncharacterised archaeal proteins. It is found C-terminal to

, in CDC48 proteins. It self-associates to form a twelve-bladed β-propeller, possibly representing the prototypical ancestral propeller fold (

). Its function is unknown.
PARP1-like, PADR1 domain, N-terminal helical subdomain (PARP1-like_PADR1_N)
Type: Domain

This entry represents de N-terminal helical region of PADR1 zinc-binding domain found in poly(ADP-ribose) polymerase-1 (PARP-1) from human and its homologues. The PADR1, known as the third zinc-binding domain (Zn3) localises between the N-terminal PARP-type zinc fingers (Zn1 and Zn2) and the central BRCT domain; it is involved in protein-protein interactions that orchestrate PARP-1 activation and are critical to the DNA-dependent stimulation of PARP-1 .

Poly(ADP-ribose) polymerase-1 (PARP-1) is a chromatin-associated enzyme involved in multiple cellular processes including DNA repair, cell cycle control, apoptotic signalling, and transcriptional regulation. Stimulated by binding to nicked DNA, PARP-1 catalyses poly(ADP-ribosyl)ation of the acceptor proteins using NAD as a substrate. PARP-1 has a modular architecture composed of multiple, independently folded domains that can be generally described in three major segments representing the biochemical activities and functional roles of the enzyme: the DNA-binding domain (DBD), the automodification domain which contains a BRCT fold, and the catalytic domain, which consists of the helical (HD) and the ART subdomains. The catalytic domain of PARP-1 is located at the C-terminal end of the protein. The DNA-binding domain is located at the N terminus of PARP-1 and contains two zinc fingers that bind to various DNA structures, a nuclear localization signal, and a caspase-3 cleavage site. The two N-terminal zinc fingers of PARP-1 bind to DNA structures to trigger activation of the C-terminal catalytic domain of PARP-1. The DBD of human PARP-1 contains yet a third zinc-binding domain, referred to as PADR1, located between the N-terminal PARP-type zinc fingers and the central BRCT domain and it is required to mediate interdomain contacts essential for the efficient assembly of PARP-1 domains .

The fold of the PADR1 zinc-binding domain consists of an N-terminal helical region, a central zinc ribbon fold, and a C-terminal tail. Three α-helices form a subdomain at the N terminus, with the first helix extending away from the subdomain. The zinc-binding region forms a separate subdomain, making primarily water-mediated contacts with the N-terminal helical subdomain. The zinc-binding subdomain resembles a zinc ribbon fold with four Cys ligands. The spacing between the four Cys residues is strongly conserved among all organisms, following the pattern C-x(2)-C-x(11,12)-C-x(9)-C where C is cysteine and x(n) is the number of amino acids between the Cys
residues. The zinc-binding subdomain contains a three-stranded antiparallel β-sheet, with the first pair of zinc ligands located in the loop running over the top of the sheet. The other pair of zinc ligands is centrally located within β-strands, a result of a long (nine-amino acid) insertion between the third and fourth cysteines. An α-helix on the C-terminal tail of the PADR1 zinc-binding domain contributes to the fold of the N-terminal helical region, and the remainder of the C terminus extends away from the N-terminal subdomain .
Tail fiber protein, third domain (Gp63_dom_3)
Type: Domain

This domain is found in Tail fiber protein from Escherichia virus G7C (Gp63,

) and similar proteins from tailed bacteriophages and prophages from enterobacterales. Gp63 is a receptor-binding protein (RBP) that emanate from the phage particle in the form of fibres for the virus to recognise and bind to their host. It deacetylates surface polysaccharides of E. coli leaving the backbone of the polysaccharide intact. This entry represents domain 3 of Ggp63, which shows structural similarity to a small domain that connects the sialidase domain with the N-terminal particle-binding domain in phage tailspikes with sialidase activity (

). It shows two β-helical rungs capped by an N-terminal α-helix oriented perpendicular to the rungs' axis .