SII-SWORD/CoKE huggingface dataset:
Bacteriophage PhiKZ vertex-binding protein gp91 (PhiKZ_Gp91)
Type: Family

This entry represents the vertex-binding protein Gp91 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa . This α-helical protein is a component of the vertex-binding complex attached to the inner surface of the viral capsid. Gp91 extends towards the capsid vertex and, unlike other members of the vertex-binding complex that primarily interact with hexameric capsomer 1, this protein mainly interacts with the pentameric capsomer via hydrophobic interactions and several salt bridges. It forms an important bridge between the vertex-binding complex and the pentameric capsomer. Gp91 also interacts with Gp119, which in turn interacts with hexameric capsomer 1, thereby connecting the pentameric capsomer and hexameric capsomer 1. Neighbouring vertex-binding complexes are connected via interactions between gp28 from one complex and gp91 from an adjacent complex. This protein plays a critical role in stabilising the capsid vertex by directly binding to the pentameric capsomer. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses.
Bacteriophage PhiKZ major capsid protein gp120 (PhiKZ_MCP)
Type: Family

This entry represents the major capsid protein (MCP) gp120 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa . It is the main structural component of the viral capsid with a triangulation number T=27 (h=3, k=3). The protein undergoes proteolytic cleavage between residues Glu163 and Asn164, with only residues 164-747 resolved in the structure. The MCP contains an N-terminal arm, a peripheral domain (P domain), an axial domain (A domain), and notably an insertion domain (I domain) that can be seen as an extension of the E-loop found in other phage MCPs like HK97. The A domain of the PhiKZ MCP has ~50 more residues than that of HK97. The I domain creates significant differences in inter-capsomer interactions compared to smaller phages. MCP subunits within hexameric capsomers form a central six-α-helix bundle creating a 9-angstrom-wide pore. The MCP exhibits remarkable structural adaptability, with subunits adopting different conformations depending on their position in the capsid, allowing adaptation to diverse curvatures. The protein shares 43% sequence similarity with the MCP of phage PhiKp24. This MCP is fundamental to the assembly and stability of the large PhiKZ capsid, working in concert with numerous minor capsid proteins.
Bacteriophage PhiKZ vertex-binding protein gp28 (PhiKZ_VTX)
Type: Family

This entry represents the vertex-binding protein gp28 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa . This α-helical protein functions as a component of the vertex-binding complex attached to the inner surface of the viral capsid. Gp28 forms a sandwich structure along with gp85 dimer and gp119 at the centre of the vertex-binding complex. Neighbouring vertex-binding complexes connect via interactions between gp28 from one complex and gp91/gp119 from an adjacent complex. This protein plays an important role in capsid assembly and stabilisation by reinforcing the associations between the pentameric capsomer and the five hexameric capsomers encircling the vertex. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses.
Minor capsid protein P12/P13, Phycodnaviridae (P12/P13)
Type: Family

This entry represents the minor capsid proteins P12 and P13 of the Paramecium bursaria chlorella virus 1 (PBCV-1). P13 is one of the thirteen minor capsid proteins found in the viral capsid. The structure of P13 consists of a helical domain with a region at the N terminus (residues 4-23) predicted to be a transmembrane helix, suggesting a role in associating the viral capsid with the inner viral membrane. Unlike most other minor capsid proteins in PBCV-1, P13 does not serve a cross-linking function between neighbouring capsomers but likely plays a role in membrane association during viral capsid assembly . The protein is conserved among chloroviruses, indicating its importance in the viral life cycle.
Putative capsid protein ORF9, Plectrovirus (Plectro_ORF9)
Type: Family

This protein family includes ORF9 capsid protein from Plectrovirus, and similar prophages from Spiroplasma. These proteins, which are involved in the formation of viral capsids, may self-assemble to form a helical capsid structure, which encapsulates the viral genomic DNA. The process of virion assembly and budding occurs at the host's inner membrane, indicating a role in the viral life cycle and propagation within the host.
Minor capsid protein VP2, Polyomaviruses (Polyoma_VP2)
Type: Family

The polyomaviruses capsid protein VP2 function as a structural component within the viral capsid, residing in the core surrounded by VP1 pentamers. It plays a crucial role in host cell receptor binding in conjunction with VP1. After the virus undergoes endocytosis and reaches the endoplasmic reticulum, VP2 and VP3 oligomerise and integrate into the membrane. This integration may form a viroporin, facilitating the transport of the viral genome across the membrane into the cytoplasm. The nuclear entry of viral DNA involves the exposure and recognition of a nuclear localisation signal shared by VP2 and VP3. Additionally, VP2 contributes to virion assembly within the nucleus, aided by a DNA-binding domain in its C-terminal region. The N-terminal myristoylation of VP2 suggests it may serve as a scaffold during virion assembly.
Double-stranded DNA deaminase toxin A, prePAAR motif (prePAAR_DddA)
Type: Domain

This motif, known as prePAAR motif, is found at the N-terminal of the class I prePAAR effector Rhs1 from Salmonella Typhimurium, Double-stranded DNA deaminase toxin A from Burkholderia cenocepacia (DddA) and related proteins mainly from proteobacteria. prePAAR facilitates PAAR domain

interaction with the VgrG spike . prePAAR is required for PAAR function and effector export by the T6SS .

DddA is the toxic component of a toxin, immunity protein module that functions within a cellular contact-dependent growth inhibition (CDI) system, enabling bacteria to communicate with and inhibit the growth of closely related neighbouring bacteria through direct contact . It contains a deaminase domain with double-stranded DNA cytidine deaminase activity and has been adapted for CRISPR-free mitochondrial base editing, highlighting its potential in genome engineering applications .
QRICH1-like domain (QRICH1_dom)
Type: Domain

This domain is found in human Transcriptional regulator QRICH1 and similar proteins, mainly found in animals, including ZMYM2/3/4. This domain is predicted to adopt a mainly α-structure.

QRICH1 acts as a mediator of the integrated stress response through transcriptional control of protein homeostasis under conditions of ER stress .

Zinc finger MYM-type proteins 2, 3, and 4 (ZMYM2, ZMYM3, ZMYM4) are nuclear proteins involved in chromatin regulation, transcriptional repression, and DNA repair. ZMYM2 participates in retrotransposon silencing and DNA double-strand break repair by interacting with chromatin-modifying complexes and DNA-PK, and is targeted for degradation by cereblon-modulating drugs. ZMYM3 functions as a scaffold protein in gene silencing and DNA repair, facilitating BRCA1 recruitment to damaged chromatin through H2AX binding. ZMYM4 interacts with the transcription factor B-MYB, undergoes SUMOylation, and is essential for early cranial gene expression and craniofacial development. These proteins collectively highlight the importance of MYM-type zinc finger proteins in genome maintenance and developmental processes .
Checkpoint protein RAD24-like, helical bundle (RAD24-like_helical)
Type: Domain

This domain is found in Checkpoint protein RAD24 from Saccharomyces cerevisiae, its orthologue in Schizosaccharomyces pombe Rad17 , and similar sequences mainly found in fungi. RAD24 participates in checkpoint pathways arrest of the cell cycle, a mechanism that allows the DNA repair pathways to act to restore the integrity of the DNA prior to DNA synthesis or separation of the replicated chromosomes . This domain folds into a five-helical bundle.
RamC, N-terminal domain (RamC_N)
Type: Domain

This domain is found at the N-terminal end of RamC.

Probable SapB synthase from Streptomyces coelicolor (RamC) is required for aerial hyphae formation . It is probably involved in processing the precursor of SapB to its mature form. It shows an α-β configuration. This protein is part of the LanC-like protein superfamily represented by

.
Antitoxin, putative (Antitoxin_put)
Type: Family

This entry represents a putative family of bacterial antitoxin proteins that interact with ParE-like toxin proteins.
ERCC6L2-like, ribbon-helix-helix domain (RHH_ERCC6L2)
Type: Domain

This is the ribbon-helix-helix (RHH) domain of human ERCC6L2.

ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) is a member of the DEAD-like helicase superfamily, a diverse group of proteins involved in ATP-dependent RNA or DNA unwinding. ERCC6L2 may contribute to both DNA repair and mitochondrial function, and in humans, mutations in the ERCC6L2 gene are linked to bone marrow failure syndrome 2. This protein plays a role in DNA double-strand break (DSB) repair by restricting DNA end resection, thereby contributing to the maintenance of genomic stability .
Nesprin-1/3, spectrin repeats region (Spectrin_SYNE1_3)
Type: Domain

This entry represents a region of spectrin repeats found in human Nesprin-1/3 (SYNE1/3) and similar proteins from vertebrates.

SYNE1 is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organisation . This protein has been associated with several severe disorders .

SYNE3 plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarisation and directional migration in aortic endothelial cells .
Nesprin-3 domain (SYNE3_dom)
Type: Domain

This region is found in human Nesprin-3 (SYNE3), a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton.

SYNE3 plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarisation and directional migration in aortic endothelial cells .
Spt5, KOW domain repeat 7 (KOW_Spt5_7)
Type: Domain

This entry represents the seventh KOW domain of Spt5 from animals, which is located at the very C-terminal of the sequences .

Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminal. Spt5 is involved in transcription elongation and termination. The KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 . Unlike bacterial NusG with its single KOW motif, eukaryotic Spt5 has multiple KOW domains. There are five KOW motifs in yeast Spt5, whereas animals and plants Spt5 have seven . Spt5 KOW domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases .
Spt5, KOW domain repeat 6, plant (KOW_Spt5_6_plant)
Type: Domain

This entry represents the KOW6 domain found in Spt5 in plants that is located between domains KOW5 and KOW7. It folds into a β-barrel with an SH3-like topology.

Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminal. Spt5 is involved in transcription elongation and termination. The KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 . Unlike bacterial NusG with its single KOW motif, eukaryotic Spt5 has multiple KOW domains. There are five KOW motifs in yeast Spt5, whereas animals and plants Spt5 have seven . Spt5 KOW domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases .
Spt5, KOWx domain (KOWx_Spt5)
Type: Domain

This entry represents the KOWx domain that is located between domains KOW3 and KOW4. The KOWx domain along with KOW4 and KOW5 forms an RNA clamp . The tandem KOWx-4 contacts the wall, stalk, and dock domains of Pol II .

Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminal. Spt5 is involved in transcription elongation and termination. The KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4 . Unlike bacterial NusG with its single KOW motif, eukaryotic Spt5 has multiple KOW domains. There are five KOW motifs in yeast Spt5, whereas animals and plants Spt5 have seven . Spt5 KOW domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases .
Transcription regulator HVO_2718-like (HVO_2718)
Type: Family

This is a family of archaeal transcription regulators, including HVO_2718 from Haloferax volcanii. Members of this family are predicted to show an HTH fold towards the C-terminal end.
TreTu toxin, C-terminal domain (TreTu_C)
Type: Domain

This entry represents the C-terminal domain of TreTu from Salmonella enterica and related bacterial proteins. TreTu is a part of the TreTu/TriTu toxin/antitoxin system and is involved in the ADP-ribosylation of the EF-Tu GTP-bound form. The C-terminal domain of TreTu adopts a typical ADP-ribosyltransferase fold. The TreTu activity is neutralised by TriTu immunity protein which acts like a lid that closes the TreTu catalytic site and traps the NAD+ .
TRF2/HOY1, PH-like domain (TRF2_HOY1_PH)
Type: Domain

This domain is found in Pyriculol/pyriculariol biosynthesis cluster transcription factor 1 (TRF2), Homeobox protein HOY1 (HOY1) and uncharacterised proteins mainly from plants and fungi. TRF2 is a transcription regulator which negatively regulates the expression of a gene cluster responsible for the biosynthesis of pyriculol and pyriculariol . This domain has a detectable similarity to characterised PH domains and is predicted to adopt a similar β-barrel structure.
Tri-helical domain (Tri-helical_dom)
Type: Domain

This domain is found in a group of uncharacterised fungal proteins, including

from Aspergillus niger. This domain, which is often found C-terminal to

, is predicted to adopt a tri-helical configuration.
Transportin-3/Importin-13, second TPR domain (TPR_TNPO3_IPO13_2nd)
Type: Repeat

This entry represents the second TPR domain found in Transportin-3 (TNPO3) from animals, as well as orthologues MTR10 and uncharacterised protein YNR7 from yeast and MOS14 from plant. This entry also includes Importin-13 (IPO3) from animals. This domain is involved in the binding to the globular Ran protein in TNOP3 . In IPO13, this domain is involved in the protein interaction with Ubc9 for nuclear import and with eIF1A for nuclear import .

These proteins are involved in transport of target proteins into the nucleus. TNPO3 mediates the nuclear import of splicing factor serine/arginine (SR) proteins, such as RBM4, SFRS1 and SFRS2, by recognising phosphorylated SR domains .
Transportin-3/Importin-13, third TPR domain (TPR_TNPO3_IPO13_3rd)
Type: Repeat

This entry represents the third TPR domain found in Transportin-3 (TNPO3) from animals, as well as orthologues MTR10 and uncharacterised protein YNR7 from yeast and MOS14 from plants. This entry also includes Importin-13 (IPO3) from animals. This domain is part of TPR structure that binds proteins for nuclear transport .

These proteins are involved in transport of target proteins into the nucleus. TNPO3 mediates the nuclear import of splicing factor serine/arginine (SR) proteins, such as RBM4, SFRS1 and SFRS2, by recognising phosphorylated SR domains .
TSTD2, N-terminal domain (TSTD2_N)
Type: Domain

This entry represents the N-terminal domain found in TSTD2 (thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 2). TSTD2 is involved in the transfer of sulphur from thiosulfate to cyanide, forming thiocyanate. It plays a role in cyanide detoxification and sulphur metabolism. The rhodanese-like domain is crucial for their catalytic activity, facilitating the transfer of sulphur atoms. Low TSTD2 expression correlates with poor prognosis in kidney renal clear cell carcinoma (KIRC), potentially due to disrupted sulfur metabolism promoting tumour growth and metastasis .
ZSWIM8, TPR repeats (TPR_ZSWIM8)
Type: Domain

This is a region of tetratricopeptide (TPR)-like repeats found in human Zinc finger SWIM domain-containing protein 8 (ZSWIM8) and similar proteins mainly found in animals.

ZSWIM8 is a substrate recognition component of a SCF-like E3 ubiquitin-protein ligase complex that promotes target-directed microRNA degradation (TDMD), a process that mediates degradation of microRNAs (miRNAs) .
ZFYVE26-like, TPR repeats (TPR_ZFYVE26)
Type: Domain

This region of tetratricopeptide (TPR)-like repeats is found in ZFYVE26 and similar proteins mainly found in animals.

Zinc finger FYVE domain-containing protein 26 (ZFYVE26, also known as SPG15) is a phosphatidylinositol 3-phosphate-binding protein recruited to the midbody during cytokinesis and required for the abcission step in cytokinesis (cleaving of the midbody in two) . It may also be required for efficient homologous recombination DNA double-strand break repair .

Mutations in ZFYVE26 cause spastic paraplegia 15, autosomal recessive (SPG15), which is a form of spastic paraplegia, a neurodegenerative disorder characterised by a slow, gradual, progressive weakness and spasticity of the lower limbs .
Exportin-7/Ran-binding protein 17, TPR repeats (TPR_XPO7/RBP17)
Type: Domain

This is a region of tetratricopeptide (TPR)-like repeats found in human Exportin-7 (XPO7, also known as RAN binding protein 16), Ran-binding protein 17 (RBP17) and similar eukaryotic proteins. XPO7 mediates the nuclear export of proteins with broad substrate specificity .

Exportins bind cargo molecules in the nuclei and transport them through nuclear pores to the cytoplasm, a process that requires RanGTP. XPO7 mediates the nuclear export of proteins with broad substrate specificity. They bind cooperatively to its cargo and to the GTPase Ran in its active GTP-bound form .
E3 ubiquitin-protein ligase TRIP12-like, TPR repeats (TPR_TRIP12_N)
Type: Domain

This is a region of tetratricopeptide (TPR)-like repeats found at the N-terminal end of human E3 ubiquitin-protein ligase TRIP12 and similar eukaryotic proteins, including Ufd4 from budding yeasts and UPL3/4 from Arabidopsis.

TRIP12 is involved in the ubiquitin fusion degradation pathway and regulation of DNA repair

,

]. This protein plays an important role in nervous system development and function . UPL3 is involved in ubiquitination and subsequent proteasomal degradation of target proteins and in the repression of the endoreduplication process and the cell morphogenesis in the trichomes .
TEX10-like, TPR repeats (TPR_TEX10)
Type: Domain

This is the C-terminal region of human Testis-expressed protein 10 (TEX10), which consists of tetratricopeptide (TPR)-like repeats.

TEX10 functions as a component of the Five Friends of Methylated Chtop complex, which can only be recruited when Chtop is arginine-methylated leading to transactivation of ZNF148 target genes .
RIMB1/RIM3A-C-like, N-terminal domain (RIMB1/RIM3A-C-like_N)
Type: Domain

This domain is found at the N-terminal end of human Peripheral-type benzodiazepine receptor-associated protein 1 (RIMB1), RIMS-binding protein 3A-C (RIM3A-C) and similar proteins mainly found in animals. RIMB1 is required for synaptic transmission regulation and probably controls the recruitment of voltage-gated calcium channels to the presynaptic membrane, and modulates neurotransmitter release. RIM3A-C are thought to be components of the manchette, a microtubule-based structure which plays a key role in sperm head morphogenesis during late stages of sperm development . This domain is predicted to adopt an α-helical configuration and is usually found associated to

and

.

RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2 . RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3 . RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery . RIM-BPs contain three SH3 domains (

) and two to three fibronectin III repeats (

). Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3 . RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis . The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits .
CPSF6/7, RSLD domain, N-terminal region (CPSF6/7_RSLD_N)
Type: Domain

This entry represents the N-terminal region of the (RS)-like domain (RSLD) found in human Cleavage and polyadenylation specificity factor subunit 6/7 (CPSF6/7) and similar animal proteins. This domain is predicted to adopt an all-α fold.

CPSF6/7 are components of the Cleavage Factor Im complex (CFIm) which plays a key role in pre-mRNA 3'-cleavage and polyadenylation . These proteins are components of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs .
Rv2743c-like (Rv2743c-like)
Type: Family

This entry represents Putative envelope-preserving system protein Rv2743c from Mycobacterium tuberculosis and similar proteins from actinomycetes. Rv2743c plays a crucial role in maintaining envelope integrity and tolerance to surface stress . It is part of a four-gene operon that includes clgR, pspA, rv2743c, and rv2742c, which is regulated by the envelope-stress-responsive sigma factor sigmaE and ClgR itself. Rv2743c forms a complex with PspA and Rv2742c, which is targeted to the cell membrane . This protein contains transmembrane helices.
Suppressor APC domain-containing protein 2, N-terminal EF-hand-like domain (SAPC2_N)
Type: Domain

This entry represents the EF-hand-like fold found at the N-terminal end of suppressor APC domain-containing protein 2 (SAPC2) and related proteins in animals .

In humans, SAPC2 plays a role in planar mitotic spindle orientation. It is also involved in positive regulation of cell proliferation and tumour cell growth . The EF-hand fold is a helix-loop-helix motif that binds calcium . SAPC2 is expressed in many primary gastric carcinoma. It is expressed preferentially in M and G1 phases, compared to S and G2 phases .