SII-SWORD/CoKE huggingface dataset:
Phage tail assembly chaperone 18 (Phage_TAC_18)
Type: Family

This entry represents a putative phage tail assembly chaperone protein protein family found primarily in viruses that infect bacteria. Members are typically around 100 amino acids in length. Tail assembly chaperones are known to assist in forming and attaching phage tails. This entry is found in caudoviruses of several families including Myoviridae, Podoviridae and Siphoviridae, but is not universal in phages.
PRTase-CE (PRTase-CE)
Type: Domain

This entry represents PRTase-like domain found in experimentally uncharacterised bacterial proteins. It is predicted to act as an effector in multiple antiviral immunity systems by targeting nucleotides .
TARBP1 domain (TARBP1_dom)
Type: Domain

This domain is found in the human probable methyltransferase TARBP1 and similar animal proteins. TARBP1 methylates RNA molecules such as tRNAs . This domain is often found associated with

.
SUPPRESSOR-OF-WHITE-APRICOT-like, C-terminal (SWAP1_C)
Type: Domain

This domain is found at the C-terminal end of SUPPRESSOR-OF -WHITE-APRICOT from Arabidopsis thaliana (SWAP1), a member of the SWAP1-SFPS-RRC1 splicing factor complex that modulates photomorphogenesis by regulating the gene expression and pre-messenger RNA alternative splicing of a large number of genes, including those involved in plant responses to light signalling .
Minor tail protein gp31, C-terminal (Minor_tail_gp31_C)
Type: Domain

This small region is found at the C terminus of a Minor tail protein gp31 from mycobacteriophages such as D29, Bxb1, L5 and related proteins from tailed bacteriophages and some bacterial prophages. According to structure predictions these proteins form homotrimers. Presumably this domain mediates interaction with either the host cell or with another phage tail fibre protein. The structure of this region forms three β-strands and up to two small α-helices, with one of the β-strands in the trimeric structure strand swapping between the monomers. In some phage we find this domain in isolation in rather short 60 residue proteins.
Tf2-1-like, SH3-like domain (SH3_Tf2-1)
Type: Domain

This domain is found towards the C-terminal end of Transposon Tf2-1 polyprotein from Schizosaccharomyces pombe (Tf2-1), a retrotransposon that belong to the gypsy-like elements. Members of this group are found in eukaryotes.
ParE-like toxin domain (ParE-like)
Type: Domain

This entry represents a ParE-like domain found in bacteria, bacteriophages and bacterial prophages. It is predominantly present in RelE/HigB/ParE toxins and some DNA-binding proteins such as transposases and endonucleases. The ParE-like domain is located at the C-terminal in proteins with an N-terminal zinc-binding domain IPR056099. Members of the family that lack the zinc finger appear to form confident homodimers based on structure prediction and are often associated with likely antitoxin proteins.

ParE is the toxin of the ParDE toxin/antitoxin system. ParE toxin binds to DNA gyrase in the absence of the ParD protein
Fluoroquinolones export permease (FLQE3_permease)
Type: Family

This entry represents the Fluoroquinolones export permease protein family, which is involved in the export of fluoroquinolones as part of an ABC transporter complex. This family is likely responsible for the translocation of substrates across the membrane and confers resistance to various fluoroquinolones, including ciprofloxacin, norfloxacin, moxifloxacin, and sparfloxacin. A member of this family, Fluoroquinolones export permease protein Rv2687c (

), is part of the ABC transporter complex Rv2686c/Rv2687c/Rv2688c involved in fluoroquinolones export and confers resistance to ciprofloxacin .
Phage tail assembly chaperone protein (Phage_TAC)
Type: Family

This family represents phage tail assembly chaperone proteins.
Podophage GP4 fiber-tail adaptor protein gp77-like (Gp77-like)
Type: Family

This entry represents the Podophage GP4 fiber-tail adaptor protein gp77 and related phage proteins. This circular fibre-tail adaptor consists of 15 copies of protein gp77. Gp77 folds into a β-sandwich with an Ig-like topology (

) .

Bacteriophage tail fibres play a critical role in the early stage of infection by binding to the bacterial surface. In Podophage GP4, five fibre I, each composed of five dimers of gp80 and linked by rope protein, are attached to the five edges of the tail vertex of the icosahedral head of the phage . The fibre-tail adaptor acts as a fulcrum, encircling the dodecameric adaptor I and providing the anchoring sites for the 5-fold symmetric fibres I and II.
RING zinc finger-like domain (Znf_RING-like)
Type: Domain

This domain is found in uncharacterised fungal proteins. It is predicted to fold into a structure with significant similarity to RING/U-box domains. It contains four highly conserved pairs of cysteine residues.
Transposon Tf2-1-like, C-terminal (Tf2-1-like_C)
Type: Domain

This is the C-terminal region of Transposon Tf2-1 polyprotein from Schizosaccharomyces pombe (Tf2-1) and similar fungal sequences. Tf2-1 is a retrotransposon that belong to the gypsy-like elements. This region is predicted to adopt an all-α structure. Members of this group are specific to Schizosaccharomyces.
Phage T5 D14-like (D14-like)
Type: Family

This entry represents a family of phage proteins that are structurally related to the PD-(D/E)XK nuclease superfamily, including Protein D14 from Escherichia phage T5. The highest structural similarity is to Holliday junction resolvase Hjc proteins. The exact function of this protein family is unknown.
Separase-like, second TPR repeats region (TPR_ESP1_2nd)
Type: Domain

This region of tetratricopeptide (TPR)-like repeats is found in Separase from Arabidopsis thaliana (ESP1) and similar plant proteins. ESP1 is essential for embryo and endosperm development and may play a role in centromeric heterochromatin structure/formation during early meiosis, non-homologous centromere association and radial microtubule system .
Separase-like, TPR repeats region (TPR_ESP1)
Type: Domain

This region of tetratricopeptide (TPR)-like repeats is found in Separase from Arabidopsis thaliana (ESP1) and similar plant proteins. ESP1 is essential for embryo and endosperm development and may play a role in centromeric heterochromatin structure/formation during early meiosis, non-homologous centromere association and radial microtubule system .
Histone acetyltransferase Rv0428c-like, SH3 domain (SH3_Rv0428c)
Type: Domain

This entry represents the SH3 domain found at the N terminus of Rv0428c, a probable histone acetyltransferase from Mycobacterium tuberculosis. It may be involved in survival under stress conditions . Members of this entry are specific to actinomycetes.
Histone acetyltransferase Rv0428c-like, C-terminal (Rv0428c-like_C)
Type: Domain

This entry represents the GNAT (GCN5-related N-acetyltransferase) domain found at the C terminus of Rv0428c from Mycobacterium tuberculosis and Cgl2740 from Corynebacterium glutamicum (cg3035,

), in association with

. Rv0428c is a probable histone acetyltransferase that may be involved in survival under stress conditions . Cgl2740 uses acetyl-CoA for acetylation of glutamate, the first step of arginine biosynthesis .

This domain is also found covering the full length of the protein in the Uncharacterized N-acetyltransferase YobR from Bacillus subtilis.
YqbQ/XkdQ (YqbQ/XkdQ)
Type: Domain

This entry represents a domain found standalone in the Uncharacterized protein YqbQ, Phage-like element PBSX protein XkdQ and other related proteins. This domain is also found N-terminal in Clostridioides difficile endolysin (Ecd09610,

), diffocin CD1368 . In diffocin CD1368, it adopts a globular structure comprised mainly of two β-barrels arranged in a head-to-tail manner and decorated with two small subdomains (

). CD1368 is a component of the diffocin baseplate inner section that connects to the tube and an outer section that connects to the sheath . Three copies of this protein sit below the tube tail, enclosing the N-terminal α-helices of the spike trimer. The exact function of this domain is unknown but in CD1368 it precedes the hydrolase domain and forms a barrel with C3 symmetry, which functions as a 6-to-3-fold symmetry adapter between the tube tail and the central spike .
Vacuolar protein sorting-associated protein 8, C-terminal domain (Vps8_C)
Type: Domain

This domain is found towards the C-terminal end of Vacuolar protein sorting-associated protein 8 from Schizosaccharomyces pombe (Vps8), which is involved in the retention of proteins to the late-Golgi. Members of this group are specific to Schizosaccharomyces.
Vps8, RING finger (Znf_RING_Vps8)
Type: Domain

Vps8 is one of the Golgi complex components necessary for vacuolar sorting. It is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes . These proteins consist of a β-propeller at the N-terminal followed by a long, central TPR domain and a RING zinc finger at the C-terminal. This entry represents the RING zinc finger found in Vps8 from mammals and similar sequences mainly found in vertebrates.
PEX18/PEX21, C-terminal domain (PEX18_PEX21_C)
Type: Domain

This domain is found C-terminal in Peroxisomal membrane proteins PEX18 and PEX21 from Saccharomyces cerevisiae. PEX18/PEX21 are involved in peroxisome biogenesis and import of peroxisomal matrix proteins that contain the peroxisomal targeting sequence PTS2 . The crystal structure of the heterotrimeric PTS2-recognition complex from S. cerevisiae revealed the molecular mechanism of PTS2 recognition . It showed that the C-terminal domain of PEX21 directly covers the hydrophobic surfaces of both PEX7 and PTS2, and the resulting hydrophobic core is the primary determinant of the stable complex formation.
RpoH-modulating protein-like (Mrh-like)
Type: Family

This entry represents RpoH-modulating protein from Enterobacteria phage T4 (Mrh), the uncharacterised Y01F from bacteriophage T4 and similar sequences from tailed bacteriophages. Mrh plays a role in transcriptional regulation of late T4 genes. It modulates the phosphorylation status of host heat shock sigma factor RpoH which is an initiation factor that promotes the attachment of host RNA polymerase to specific initiation sites . Structure prediction suggests that this protein may oligomerise with the C terminus contacting the next subunit in a cyclic homo-oligomer.
Phage head-tail joining protein (Phage_H_T_join)
Type: Domain

This entry is related to

which is a phage protein that acts as a stopper to retain phage DNA in the capsid as well performing a head tail connector function.
Pikachurin, EGF-like domain (EGF_Pikachurin)
Type: Domain

This EFG-like domain is found in mouse Pikachurin, which is involved in both the retinal photoreceptor ribbon synapse formation and physiological functions of visual perception . The fold of this domain consists of a two stranded β-sheet followed by a loop and a short two-stranded sheet.
Tubby, C-terminal domain-like (Tubby_C-like)
Type: Domain

This entry represents a bacterial protein domain that is structurally similar to the C-terminal domain of the tubby protein. It consists of 12 β-strands organised into a barrel with a central C-terminal α-helix. It shows distant sequence similarity to both the Tubby C-terminal domain and the LURP 1 family. This domain is found in a group of uncharacterised proteins from bacillales, often covering most of the length of the protein sequence.
YmcF-like (YmcF-like)
Type: Family

This protein family includes Protein YmcF from Escherichia coli and similar sequences from gammaproteobacteria. YmcF is a 62-residues long cold shock-regulated micropeptide encoded by an small open reading frame (smORF) .
Pepco domain (Pepco_dom)
Type: Domain

This entry represents a small domain co-occurring with peptidases like Trypsin, Caspase, and MPTase. The domain is homologous to Trypco1 and Trypco2 from MoxR-vWA-based ternary systems typically seen in multicellular bacteria. Peptidase cleavage of Pepco superfamily domains may trigger assembly into multimeric complexes, leading to cell suicide akin to processes seen in metazoan apoptosis .
Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A, N-terminal (PNGaseA_N)
Type: Domain

This domain is found at the N-terminal end of almond Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase A, a protein capable of hydrolysing glycopeptides with an alpha-1,3-fucosylated asparagine-bound N-acetylglucosamine . This domain is related to Peptide-N-glycosidases .
CD59 glycoprotein (CD59)
Type: Family

This entry represents the human CD59 glycoprotein and related proteins. CD59 is a cell-surface glycoprotein that protects host cells from complement-mediated lysis. It binds to and prevents the normal functioning of the complement proteins C8 and C9 which form part of a membrane penetrating assembly called the membrane attack complex. CD59 folds into a compact domain with a central three-stranded antiparallel β-sheet and a two-stranded antiparallel β-sheet located on one side of it. This structure is stabilised by disulphide bonds and has a significant similarity to the snake venom neurotoxins and other members of the uPAR/Ly6/CD59/snake toxin-receptor superfamily . CD59 binds the pore-forming β-hairpins of C8 to form an intermolecular β-sheet that prevents membrane perforation. While bound to C8, CD59 deflects the cascading C9 β-hairpins, rerouting their trajectory into the membrane .
Phage tail termination protein (Phage_tail_terminator_3)
Type: Family

This entry represents the phage tail termination protein found in a variety of tailed phages that infect Enterobacter and prophages. These proteins form a hexameric ring that caps the tail tube at the neck of these bacteriophage.
Phage connector protein (Phage_connect_2)
Type: Family

This entry represents a family of phage proteins that are structurally related to the HK97 gp6 protein that forms a head to tail connection. It is likely that these proteins form large homo-oligomeric rings.
Phage T4 Cef protein (T4_Cef)
Type: Family

This entry represents proteins that are related to the phage T4 Protein Cef (also known as MotC,

). This protein adopts a compact globular domain composed of 5 β-strands and one α-helix. The β-strands adopt the order 1-5-4-3-2 with the α-helix found between strands 1 and 2. This family shows structural similarity to

. T4 Cef plays a role in the processing of a cluster of viral tRNAs .
Cuticlin, N-terminal domain (CUT_N)
Type: Domain

This entry represents the N-terminal Ig-like domain of cuticlins 1/3-6 from C. elegans.

Cuticlin is a component of the cuticles, which contributes to the formation of extracellular envelopes protecting the organism from the environment . It also plays a role in alae formation in dauer larvae .
ORC-CDC6-like (ORC-CDC6-like)
Type: Family

This entry represents a group of sequences that belong to the ORC-CDC6-family of AAA+ ATPases associated with prokaryotic antiviral immunity. Members are commonly found with double CARF, methylase and protein containing variable effector domains .
YnaL-like (YnaL-like)
Type: Family

This protein family includes Protein YnaL from Escherichia coli (

) , a 57-residues long protein encoded by a small open reading frame (smORF).
Pam3 phage gp34-like protein (Pam3_Gp34-like)
Type: Family

This entry represents a family of proteins related to PAM3 gp34-like protein found in tailed bacteriophages, bacterial prophages and some bacteria. In Pseudomonas phage Pa193, gp34 has been characterised as a baseplate protein. Both gp34 and gp35 decorate the cap complex, with six copies of each present. These copies do not make direct contact with one another, suggesting that these proteins function as adapters rather than discrete structural components of the baseplate .
Phage tail tube initiator protein, putative (Phage_tail_tube_init_put)
Type: Family

This entry represents a family of uncharacterised proteins mainly found in phages and some bacterial species. Based on structure prediction these proteins show similarity to the Pam3 gp17 the tail tube initiator protein. Six gp17 subunits form a hexameric ring that initiates tail tube polymerisation from the baseplate.
RIIA.1-like (RIIA1-like)
Type: Family

This entry represents a family of small uncharacterised proteins found in phages, including T4 RIIA.1 . Structure prediction suggests the small proteins adopt a three helical bundle structure.
Phage termination protein (SP10_terminator)
Type: Family

This entry represents a likely phage terminator protein which terminates the elongation of the phage tail tube. This protein shows structural similarity to the PAM3 terminator protein which forms a hexameric ring. This protein has a β-sandwich domain nested within the terminator-like domain.
Pseudouridylate synthase PUS7L, R3H domain (R3H_PUS7L)
Type: Domain

This R3H domain is found in human Pseudouridylate synthase PUS7L and related proteins from vertebrates.

Human PUS7L catalyses pseudouridylation of RNAs , acting also as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs). The pseudouridylated tRFs inhibit translation by targeting the translation initiation complex .
Phage blade protein (Phage_blade)
Type: Family

This entry represents a small family of short uncharacterised phage proteins including Uncharacterized 7.2 kDa protein in alt-Gp30 intergenic region from Bacteriophage T4 (

). Structure prediction of

suggests the protein adopts a four stranded β-sheet that can form homo-oligomers, with a homohexamer forming a β-propeller structure (iPTM=0.93). The function of these proteins is unknown.
Pseudouridylate synthase PUS7L, N-terminal domain (PUS7L_N)
Type: Domain

This domain is found N-terminal in the human Pseudouridylate synthase PUS7L and related proteins from vertebrates, ascomycetes and plants. This domain is predicted to adopt a globular structure consisting of a three-stranded antiparallel β-sheet with two α-helices packed on one side of it.

Human PUS7L catalyses pseudouridylation of RNAs , acting also as a regulator of protein synthesis in embryonic stem cells by mediating pseudouridylation of RNA fragments derived from tRNAs (tRFs). The pseudouridylated tRFs inhibit translation by targeting the translation initiation complex .
Putative phage holin 2 (Phage_holin)
Type: Family

This entry represents a family of putative holin proteins found in various phages infecting actinobacterial hosts, particularly Gordonia, Mycobacterium, Arthrobacter, and Microbacterium. Holins are small membrane proteins involved in the timing of host cell lysis during bacteriophage infection. Members of this family typically range from 94 to 151 amino acids in length and contain 3 to 4 predicted transmembrane helices. While some members have an N-terminal signal peptide or lipoprotein signal, most do not. It is unclear where the annotation for these proteins as holins arose. However it appears plausible based on their sequence features. This entry shows similarity to

, a bacterial family of unknown function.
CDCP1, fourth CUB domain (CUB_CDCP1_4th)
Type: Domain

This domain is found in the human CUB domain-containing protein 1 (CDCP1) and related proteins. This entry represents the fourth of the tandem of CUB domains.

CDCP1 may be involved in cell adhesion and cell matrix association. It also plays a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation . CDCP1 contains a tandem of CUB domains.
Dep-1, fifth Fn3-like domain (Fn3_Dep-1_5th)
Type: Domain

This entry represents the fifth Fn3-like domain.

This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the β-integrin subunit pat-3. It is involved in the regulation of the cell fate during the development of the vulva and the excretory system . It is also involved indirectly in the negative regulation of let-23 signalling and vulval induction . Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem.
Dep-1, first Fn3-like domain (Fn3_Dep-1_1st)
Type: Domain

This entry represents the first Fn3-like domain.

This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the β-integrin subunit pat-3. It is involved in the regulation of the cell fate during the development of the vulva and the excretory system . It is also involved indirectly in the negative regulation of let-23 signalling and vulval induction . Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem.
Dep-1, second Fn3-like domain (Fn3_Dep-1_2nd)
Type: Domain

This entry represents the second Fn3-like domain.

This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the β-integrin subunit pat-3. It is involved in the regulation of the cell fate during the development of the vulva and the excretory system . It is also involved indirectly in the negative regulation of let-23 signalling and vulval induction . Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem.
Dep-1, sixth Fn3-like domain (Fn3_Dep-1_6th)
Type: Domain

This entry represents the sixth Fn3-like domain.

This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the β-integrin subunit pat-3. It is involved in the regulation of the cell fate during the development of the vulva and the excretory system . It is also involved indirectly in the negative regulation of let-23 signalling and vulval induction . Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem.
Dep-1, fourth Fn3-like domain (Fn3_Dep-1_4th)
Type: Domain

This entry represents the fourth Fn3-like domain.

This domain is found in the Receptor-type tyrosine-protein phosphatase Dep-1 from Caenorhabditis elegans and related proteins. Dep-1 is involved in the dephosphorylation of the receptor let-23 and the β-integrin subunit pat-3. It is involved in the regulation of the cell fate during the development of the vulva and the excretory system . It is also involved indirectly in the negative regulation of let-23 signalling and vulval induction . Dep-1 is a multidomain protein which is predicted to contain a number of Fn3-like domains arranged in tandem.
C2HC zinc finger, plants (Znf-C2HC_3)
Type: Domain

This domain is found at the C-terminal of uncharacterised plant proteins. It has three invariant cysteine residues and a histidine that are likely involved in metal coordination. It is probably a variant of the classical C2H2 zinc fingers and is predicted to adopt similar structure.
Ribbon-helix-helix domain containing protein (RHH_dom-containing)
Type: Family

This entry represents a family of phage Ribbon-Helix-Helix (RHH) domain containing proteins and proteobacterial prophages. Members of the RHH superfamily are often parts of toxin/antitoxin systems, suggesting these proteins may form part of a phage immunity response.
Phage L5 gene 47 protein-like (Phage_L5_Gp47)
Type: Family

This entry represents the gene 47 protein found in Mycobacterium phage L5 and related proteins from tailed bacteriophages. This protein forms a small globular β-barrel domain that is related to LSM superfamily proteins such as Hfq. AlphaFold modelling suggests this protein forms an unusual octameric arrangement. Based on similarity to LSM proteins these proteins may bind to RNA.