SII-SWORD/CoKE huggingface dataset:
NXPE, C-terminal (NXPE4_C)
Type: Domain

This domain is found at the C-terminal of NXPE and similar proteins, mainly from animals. This domain is predicted to adopt an α/β structure with similarity to hydrolase domains.

Neurexophilins (NXPE) are secreted neuropeptide-like glycoproteins originally discovered as alpha-neurexin ligands and later found to bind to the LNS2 domain of alpha-neurexins. NXPE are encoded by four genes that are highly conserved in vertebrates but absent from invertebrates .
ORF20A (ORF20A)
Type: Family

This protein family includes ORF20A from Fowl aviadenovirus 4 .
ORF28 (ORF28)
Type: Family

This protein family includes ORF28 from Fowl aviadenovirus 4 .
ORF68, C-terminal (ORF68_C)
Type: Domain

This entry describes the C-terminal domain in ORF68 from Staphylococcus phage K and similar viral proteins. This domain adopts an all-β configuration.
Phage cement protein (Phage_cement)
Type: Family

This entry represents a small family of phage proteins. These proteins form a trimeric arrangement which stabilises the phage capsid. The proteins have what is known as a β-tulip fold.
Phage g100-like protein (Phage_g100)
Type: Family

This entry includes Yersinia phage phiR1-RT g100 protein

which shows a partial β-barrel topology according to AlphaFold prediction. The function of members of this family is unknown.
Putative phage head-tail joining protein, N-terminal domain (Phage_H_T_join_N)
Type: Domain

This entry represents a domain found at the N-terminal end of a group of putative phage head to tail joining proteins. It is found associated with

.
Putative phage head-tail joining protein, C-terminal domain (Phage_H_T_join_C)
Type: Domain

This entry represents the C-terminal domain found associated with phage head to tail connector domains

, which suggests this domain is part of the phage structure. This region forms a large mainly α-helical domain.
Phage lipoprotein (Phage_lipoprotein)
Type: Family

This entry represents a small family of uncharacterised phage proteins that have an N-terminal lipoprotein attachment motif. This suggests that these proteins are expressed on the host bacterial cell membrane.
Phage Pam3 gp32-like (Pam3_gp32)
Type: Family

This entry represents a family of uncharacterised proteins from phages and bacterial prophages that includes the Pam3 phage gp32 protein (

). Structure prediction shows that the protein is composed of a small globular domain. This protein forms a confident dimer according to structure prediction.
Phage Pam3 gp59-like (Pam3_gp59)
Type: Family

This entry represents a small family of phage proteins, including phage Pam3 gp59 (

). The function of this protein is unknown.
Ring protein 1-like (R1-like)
Type: Family

This entry includes the Ring protein 1 (R1) from Bacteroides phage crAss001, also known as gp43, which is part of the tail assembly in CrAss-like phages (crassviruses). R1 forms one of five stacked dodecameric rings that make up the tail barrel. These proteins share a conserved fold consisting of two domains: an α-helical domain and a β-sandwich domain. The extended tail barrel formed by these ring proteins is a distinctive feature of crassviruses and may assist the tail muzzle in reaching the outer cell membrane through the compact capsular polysaccharide layer of the host bacteria.
Phage tail tube protein 14 (Phage_TTP_14)
Type: Family

This entry represents a family of bacteriophage tail tube proteins. The tail tube forms the inner channel of the contractile tail which is used for DNA transfer from the capsid to the host during infection. The family is found in a wide variety of phages that infect bacteria.
Phage tail tube protein 2 (Phage_TTP_2)
Type: Family

This entry represents a family of phage proteins that by structural similarity are highly likely to be phage tail tube proteins that oligomerise to make the phage tail. These proteins are composed of a distinctive β-barrel structure.
Phage tudor domain-like protein (Phage_tudor-like)
Type: Family

This entry represents a small family of uncharacterised phage proteins that are structurally similar to tudor domains. Structure prediction suggests these proteins form a dimer arrangement.
Non-contractile tail sheath, TIM barrel (TIM-barrel_NCTSP)
Type: Domain

This entry represents the TIM-barrel domain found in the non-contractile tail sheath protein of Bacteriophage N4 (BPN4). This protein is essential for BPN4 infectivity and it is hypothesized that it mediates binding with target cell receptors . The function of this domain is unknown. This entry also includes sequences from bacteria, predominantly from Sphingomonadales.
STAND NTPase 4, small alpha/beta domain (STAND_NTPase4_dom)
Type: Domain

This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems .
Nuclear elongation and deformation protein 1-like, middle domain (Ned1-like_M)
Type: Domain

This domain is centrally located in Nuclear elongation and deformation protein 1 from Schizosaccharomyces pombe (Ned1) and similar fungal proteins. Ned1 may have a role in the maintenance of the nuclear envelope structure and in minichromosome stability .

This domain is also found in Phosphatidic acid phosphohydrolase 1 (PAH1) from Saccharomyces cerevisiae which is involved in plasmid maintenance, in respiration and in cell proliferation . PAH1 is a Mg2+-dependent phosphatidate (PA) phosphatase which catalyses the dephosphorylation of PA to yield diacylglycerol .

This domain is predicted to adopt an α-β structure.
NXF1/2/3/5-like, leucine-rich repeat domain (NXF1/2/3/5-like_LRR)
Type: Domain

This entry represents the leucine-rich repeats (LRR) domain found in nuclear RNA export factor 1, 2, 3 and 5 (NXF1, NXF2, NXF3 and NXF5, respectively) from animals and their yeast orthologues mRNA export factor 67 (MEX67). These proteins are involved in the nuclear export of mRNA from the nucleus to the cytoplasm . NXFs are used by type D retroviruses to export their unspliced genomic RNA to the cytoplasm through this LRR domain, which binds to constitutive transport element of retroviral RNAs . Additionally, cellular mRNA transport is affected when this domain is mutated . In the case of MEX67, this domain is found within a region of the protein that allows MEX67 to act as an accessory factor in Rae1p-dependent mRNA export and is devoid of RNA-binding .
Neuron navigator 1-like, ubiquitin-like domain (NAV1-like_ubiquitin-like)
Type: Domain

This domain is found in human Neuron navigator 1 (NAV1) and similar sequences from animals. NAV1 may be involved in neuronal migration. It is predicted to adopt a ubiquitin-like fold.
MEX67-like, NTF2-like domain (NTF2_MEX67)
Type: Domain

This entry represents a NTF2-like domain of approximately 220 residues long found in a set of uncharacterised kinetoplasts proteins.
MgtT (MgtT)
Type: Family

This protein family includes the uncharacterised protein MgtT from Escherichia coli, a 34-residues micropeptide encoded by a small open reading frame (smORF) that lies just downstream of mgtS and is encoded antisense of the mgrR small regulatory RNA gene. Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms .
Micropeptide inhibiting actin cytoskeleton (MIAC)
Type: Family

This protein family includes human Micropeptide inhibiting actin cytoskeleton (MIAC) and similar sequences from vertebrates. MIAC is a 51-residues long protein that reduces filamentous actin fibres by interacting with aquaporin AQP2. It also inhibits the activation of the EREG/EGFR signalling pathway. Low expression of this micropeptide is associated with poor survival of head and neck squamous cell carcinoma (HNSCC) .
Myosin VII, N-terminal domain (Myosin_VII_N)
Type: Domain

This entry represents a small 5-stranded β-barrel domain found at the N-terminal end of some animal myosin VII proteins. Myosin-VII proteins are actin-based motor molecules with ATPase activity, playing crucial roles in intracellular movements and cellular projections. They function as single-molecule cargo transporters, maintaining tension in actin filaments. In the retina, they are involved in the renewal of photoreceptor disks and the regulation of opsin transport . In the inner ear, they contribute to the differentiation, morphogenesis, and organisation of cochlear hair cell bundles, essential for normal hearing. Additionally, they play roles in epithelial brush border differentiation and microvilli organisation [

.

,

,

].
Fibronectin type-III domain, nematodes (Fn3_nem)
Type: Domain

This entry represents a fibronectin type-III domain found primarily in nematode proteins. The proteins contain several conserved cysteine residues that may either form disulphide bridges or possibly a zinc binding site. Many members of this family also contain a predicted transmembrane region following the FN3 domains, suggesting they may be membrane-anchored proteins.
Nuclear anchorage protein 1, spectrin repeat domain (ANC1_spectrin_dom)
Type: Domain

This entry represents a region of spectrin repeats found in Nuclear anchorage protein 1 from Caenorhabditis elegans and similar proteins from worms.

Nuclear anchorage protein 1 (ANC-1) is a key protein in Caenorhabditis elegans that plays a central role in nuclear and mitochondrial anchoring . ANC-1 has a role in positioning of the cell body of the PVQ lumbar interneuron . It may connect nuclei to the cytoskeleton by interacting with unc-84 at the nuclear envelope and with F-actin in the cytoplasm, creating a bridge across the nuclear envelope between the cytoskeleton and the nucleus . ANC-1 has a complex structure composed of several key domains: actin-binding calponin homology (CH) domains at the N terminus; a long spectrin-like region with multiple repeats, a KASH domain at the C-terminal end and a transmembrane (TM) span near the C terminus.
Nuclear anchorage protein 1, spectrin repeat domain 2 (Spectrin_Anc-1_2)
Type: Domain

This entry represents spectrin-like repeats found in Nuclear anchorage protein 1 from Caenorhabditis elegans and similar proteins from worms.

Nuclear anchorage protein 1 (ANC-1) is a key protein in Caenorhabditis elegans that plays a central role in nuclear and mitochondrial anchoring . ANC-1 has a role in positioning of the cell body of the PVQ lumbar interneuron . It may connect nuclei to the cytoskeleton by interacting with unc-84 at the nuclear envelope and with F-actin in the cytoplasm, creating a bridge across the nuclear envelope between the cytoskeleton and the nucleus . ANC-1 has a complex structure composed of several key domains: actin-binding calponin homology (CH) domains at the N terminus; a long spectrin-like region with multiple repeats, a KASH domain at the C-terminal end and a transmembrane (TM) span near the C terminus.
Nuclear anchorage protein 1, spectrin-like repeat domain 3 (Spectrin_Anc-1_3)
Type: Domain

This entry represents spectrin-like repeats found in Nuclear anchorage protein 1 from Caenorhabditis elegans and similar proteins from worms.

Nuclear anchorage protein 1 (ANC-1) is a key protein in Caenorhabditis elegans that plays a central role in nuclear and mitochondrial anchoring . ANC-1 has a role in positioning of the cell body of the PVQ lumbar interneuron . It may connect nuclei to the cytoskeleton by interacting with unc-84 at the nuclear envelope and with F-actin in the cytoplasm, creating a bridge across the nuclear envelope between the cytoskeleton and the nucleus . ANC-1 has a complex structure composed of several key domains: actin-binding calponin homology (CH) domains at the N terminus; a long spectrin-like region with multiple repeats, a KASH domain at the C-terminal end and a transmembrane (TM) span near the C terminus.
Disease resistance protein At4g27190-like, leucine-rich repeats (At4g27190-like_LRR)
Type: Domain

This entry represents a region of leucine-rich repeats found in Disease resistance protein At4g27190 from Arabidopsis thaliana and similar proteins predominantly from plants.
At2g35280-like, TPR domain (At2g35280_TPR_dom)
Type: Domain

This entry represents the predicted tetratrico peptide repeat (TPR) domain found in F-box proteins At2g35280, At5g50450 and At1g67340 from Arabidopsis thaliana and similar plant proteins. This entry is found associated with

in some members of this family.
Plastid division protein CDP1-like, 2nd alpha solenoid domain (CDP1-like_a_solenoid_2)
Type: Domain

This entry represents the second α-helical solenoid domain of Plastid division protein CDP1, chloroplastic and Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic (ARC6) from Arabidopsis thaliana and similar sequences mainly from plants and cyanobacteria. This domain is usually found next

.

Armadillo/beta-catenin-like (ARM) repeat is a specific subclass of α-helical solenoid domains. ARM repeats are composed of tandem three-helix bundles that form a superhelical structure, primarily facilitating protein-protein interactions . ARM repeats are predominantly found in plastid division regulators (PDR), where they play a crucial role in the coordination and regulation of plastid division in plants .

This group of proteins function as key components of the plastid division machinery, which is responsible for the constriction and division of plastids, including chloroplasts and non-green plastids . It includes proteins such as FtsZ, ARC6, DRP5B, and MinE. ARC6 and PARC6 are essential for the chloroplast replication process , which implies the assembly and constriction of the tubulin-like FtsZ ring on the stromal surface of the inner envelope membrane (IEM) and the dynamin-like ARC5 ring on the cytosolic surface of the outer envelope membrane (OEM). They are also involved in stromule biogenesis and may contribute to plant gravitropism. ARC6 facilitates FtsZ ring assembly and promotes the recruitment of MCD1, which is essential for forming the chloroplast Z-ring. CDP1, on the other hand, is required for the localisation of PDV1 and the correct formation of the FtsZ ring in non-green plastids .
Platelet endothelial aggregation receptor 1-like, EGF domain (EGF_PEAR1L-like)
Type: Domain

This domain is found in human Platelet endothelial aggregation receptor 1 (PEAR1L) and related proteins such as Multiple epidermal growth factor-like domains protein 10 and 11 (MEGF10 and MEGF11).

Platelet Endothelial Aggregation Receptor 1 (PEAR1) is a type I transmembrane protein that plays a significant role in both platelet and endothelial cell functions. PEAR1 is required for SVEP1-mediated platelet activation, via its interaction with SVEP1 and subsequent activation of AKT/mTOR signaling . PEAR1 influences endothelial cell migration and angiogenesis. Knockdown of PEAR1 enhances endothelial cell proliferation, migration, and tube formation via Akt/PTEN pathways . PEAR1 also plays a role in stabilising platelet thrombi during vascular injury .

MEGF10 is a membrane receptor involved in phagocytosis by macrophages and astrocytes of apoptotic cells.
P-granule-associated protein DEPS-1, first OB-fold (OB_DEPS-1_1st)
Type: Domain

This domain is found in the P-granule-associated protein DEPS-1 from C. elegans and related proteins. DEPS-1 is predicted to contain six OB-fold-like β-barrel domains. This entry represents the first of these domains.

DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells . This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes .
P-granule-associated protein DEPS-1, second OB-fold (OB_DEPS-1_2nd)
Type: Domain

This domain is found in the P-granule-associated protein DEPS-1 from C. elegans and related proteins. DEPS-1 is predicted to contain six OB-fold-like β-barrel domains. This entry represents the second of these domains.

DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells . This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes .
P-granule-associated protein DEPS-1, sixth OB-fold (OB_DEPS-1_6th)
Type: Domain

This domain is found in the P-granule-associated protein DEPS-1 from C.elegans and related proteins. DEPS-1 is predicted to contain six OB-fold-like β-barrel domains. This entry represents the sixth of these domains.

DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells. This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes .
P116 (P116)
Type: Family

The structure of P116 (MPN213 or MG075), solved by cryo-electron microscopy, reveals a novel protein fold consisting of a homodimeric core region with a large hydrophobic cavity that binds and extracts lipids. Each monomer also contains an N-terminal domain. Conformational changes between the lipid-bound and lipid-free states suggest a mechanism for lipid uptake and delivery into the mycoplasma membrane. P116 orthologs are found in several other Mycoplasma species. The P116 protein from Mycoplasma pneumoniae is an essential cell surface protein that extracts lipids, including cholesterol, phosphatidylcholine and sphingomyelin, from the host environment for incorporation into the bacterial membrane .
P-granule-associated protein DEPS-1, third OB-fold domain (OB_DEPS-1_3rd)
Type: Domain

This domain is found in the P-granule-associated protein DEPS-1 from Caenorhabditis elegans and related proteins from worms. DEPS-1 is predicted to contain six OB-fold-like β-barrel domains. This entry represents the third of these domains.

DEPS-1 is a component of the P-granules and is required for their formation and integrity in adult germ cells . This protein is also involved in RNA-mediated silencing (RNAi) of germline-expressed genes .
Repeat of unknown function DUF7826 (DUF7826)
Type: Repeat

This entry represents a family of small uncharacterised bacterial alpha solenoid proteins.
Domain of unknown function DUF7827 (DUF7827)
Type: Domain

This domain of unknown function is found in a group of uncharacterised archaeal proteins. It is predicted to adopt an all-beta structure.
Domain of unknown function DUF7828 (DUF7828)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It contains highly conserved cysteine and histidine residues that are likely involved in zinc coordination.
Domain of unknown function DUF7829 (DUF7829)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold into an alpha- helical structure.
Domain of unknown function DUF7830 (DUF7830)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It has three highly conserved cysteine residues and a histidine that may be involved in zinc coordination.
Domain of unknown function DUF7831 (DUF7831)
Type: Domain

This entry represents a family of uncharacterised proteins which form a compact domain. Structure prediction of

suggests a highly confident homodimer (iPTM=0.93). This protein is found in a mixture of bacteria and phage.
Domain of unknown function DUF7832 (DUF7832)
Type: Domain

This entry represents an uncharacterised bacterial protein domain. This domain is found in single domain proteins as well as in large multidomain proteins that contain immunity related domains. This suggests that this family may play a role in a toxin/antitoxin system. The domain contains two structural sites that contain two conserved histidines and an aspartate that may be functionally important.
Domain of unknown function DUF7833 (DUF7833)
Type: Domain

This entry represents a small family of protein domains related to

.
Domain of unknown function DUF7834 (DUF7834)
Type: Domain

This entry represents an uncharacterised domain found at the C terminus of proteins that contain a

domain at the N terminus. This domain is composed of multiple α-helices.
Domain of unknown function DUF7835 (DUF7835)
Type: Domain

This entry represents a small family of uncharacterised proteins found in Halobacteria. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
Domain of unknown function DUF7836 (DUF7836)
Type: Domain

This entry represents a small family of uncharacterised proteins found in Halobacteria. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
Domain of unknown function DUF7837 (DUF7837)
Type: Domain

This entry represents a small family of uncharacterised proteins found in Halobacteria. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
Domain of unknown function DUF7838 (DUF7838)
Type: Domain

This entry represents a small family of uncharacterised proteins found in Halobacteria. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
Domain of unknown function DUF7839 (DUF7839)
Type: Domain

This domain is found at the C-terminal end of a group of uncharacterised archaeal proteins. This domain is predicted to adopt an α-helical structure. Members of this family have an HTH domain at the N terminus.
Domain of unknown function DUF7840 (DUF7840)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold onto a meander β-barrel and it is likely associated with the membrane. It is frequently found in combination with

.
Domain of unknown function DUF7841 (DUF7841)
Type: Domain

This entry represents an uncharacterised bacteriophage family of proteins. Structure prediction with

suggests that members of this family will form homodimeric complexes (iPTM=0.87 and pTM=0.89).
Domain of unknown function DUF7842 (DUF7842)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold onto an α-helical bundle consisting of five α-helices. It is frequently found in combination with

and

.
Domain of unknown function DUF7843 (DUF7843)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold into an α-helical array. It is frequently found in combination with

and

.
Domain of unknown function DUF7844 (DUF7844)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is predicted to fold onto a structure with significant similarity to Glucose-regulated metallo-peptidase M90. This domain is frequently found in combination with

.
Domain of unknown function DUF7845 (DUF7845)
Type: Domain

This entry represents a domain of unknown function. In some proteins the is a C-terminal HTH domain that presumably binds to DNA. This domain may bind to an as unyet identified ligand to enable regulation of bacterial genes. This domain contains a large β sheet composed of 11 β strands with helices packed on the convex face. There is some evidence from structure prediction that this domain may dimerise and form a large structure that has a large hole through it that might accommodate DNA.
Domain of unknown function DUF7846 (DUF7846)
Type: Domain

This is a domain of unknown function, mainly found in a group of archaeal sequences such as HVO_1708 (

). This domain may have a fold related to glycosyltransferases.
Domain of unknown function DUF7847 (DUF7847)
Type: Domain

This is a domain of unknown function found in a group of archaeal and bacterial sequences, including HVO_0229 (

). This domain may consist of several transmembrane helices.
Domain of unknown function DUF7848 (DUF7848)
Type: Domain

This entry represents a likely zinc binding domain that according to structural modelling may form homodimers. The domain is primarily found in actinobacteria as well as a small range of bacteriophage. The function of this domain is unknown.
Domain of unknown function DUF7849 (DUF7849)
Type: Domain

This domain is found in uncharacterised proteins from Gram-negative bacteria. It has a detectable similarity to OmpA-like transmembrane domains and it is predicted to adopt a similar β-barrel structure.