SII-SWORD/CoKE huggingface dataset:
Straight fiber protein PB4, spike domain (PB4_spike)
Type: Domain

This entry represents the Straight fiber protein PB4 spike found in Escherichia phage T5 and other tailed bacteriophages and some bacterial prophages. The T5 PB4 spike forms a hetero trimer containing several small distinct subdomains some of which defining a β-helix, others are β-prism .

PB4 along with PB3, forms the central straight fibre, bearing the receptor binding protein PB5 at its C-terminal . Upon PB5 binding to the host receptor FhuA, the central fibre reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring . In this process the PB4 spike undergoes structural rearrangement as well.
Straight fiber protein PB4, first Fn3-like domain (Fn3-I_PB4)
Type: Domain

This entry represents the N-terminal Fn3-like domain of the Straight fiber protein PB4 found in in Escherichia phage T5 and other tailed bacteriophages.

PB4 along with PB3, forms the central straight fibre, bearing the receptor binding protein PB5 at its C terminus . Upon PB5 binding to the host receptor FhuA, the central fibre reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring . The PB4-PB3 interactions are ensured by the proximal loops of the first and the distal loops of the second of the three PB4 Fn3-like domains. These interactions are disrupted upon binding to the host receptor and the string of the three PB4 Fn3-like domains undergoes drastic conformational changes.
Straight fiber protein PB4, second Fn3-like domain (Fn3-II_PB4)
Type: Domain

This entry represents the second Fn3-like domain of the Straight fiber protein PB4 found in in Escherichia phage T5 and other tailed bacteriophages.

PB4 along with PB3, forms the central straight fibre, bearing the receptor binding protein PB5 at its C terminus . Upon PB5 binding to the host receptor FhuA, the central fibre reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring . The PB4-PB3 interactions are ensured by the proximal loops of the first and the distal loops of the second of the three PB4 Fn3-like domains. These interactions are disrupted upon binding to the host receptor and the string of the three PB4 Fn3-like domains undergoes drastic conformational changes.
Straight fiber protein PB4, third Fn3-like domain (Fn3-III_PB4)
Type: Domain

This entry represents the third Fn3-like domain of the Straight fiber protein PB4 found in in Escherichia phage T5 and other tailed bacteriophages.

PB4 along with PB3, forms the central straight fibre, bearing the receptor binding protein PB5 at its C terminus . Upon PB5 binding to the host receptor FhuA, the central fibre reorganises and undergoes structural rearrangements that lead to its bending, bringing PB3 close to the host membrane for anchoring . The PB4-PB3 interactions are ensured by the proximal loops of the first and the distal loops of the second of the three PB4 Fn3-like domains. These interactions are disrupted upon binding to the host receptor and the string of the three PB4 Fn3-like domains undergoes drastic conformational changes.
SAC9, second GBDL domain (SAC9_GBDL_2nd)
Type: Domain

This domain is found toward the C-terminal of the SAC9 from Arabidopsis thaliana. It is the second of the three GBDL domains. It is predicted to contain a large insertion (~40 residues long) before the last β-strand.

SAC9 is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response . SAC9 is critical for regulating lipid signaling and endocytic trafficking. SAC9 acts as a lipid "gatekeeper," ensuring PI(4,5)P2 is confined to the plasma membrane to support endocytosis and cellular homeostasis. Its interplay with SH3P2 and clathrin underscores the integration of lipid metabolism and membrane trafficking in plants . SAC9 contains three domains (GBDL) with topology similar to the galactose binding domains (GBD), in particular to the anaphase promoting complex subunit 10. These domains are located in the second half of the protein.
SAC9, C-terminal domain (SAC9_C)
Type: Domain

This domain is found at the C-terminal of SAC9 from Arabidopsis thaliana. It is predicted to fold into a β-sandwich with a similarity to the anaphase promoting complex subunit 10.

SAC9 is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response . SAC9 is critical for regulating lipid signaling and endocytic trafficking. SAC9 acts as a lipid "gatekeeper," ensuring PI(4,5)P2 is confined to the plasma membrane to support endocytosis and cellular homeostasis. Its interplay with SH3P2 and clathrin underscores the integration of lipid metabolism and membrane trafficking in plants . SAC9 contains three domains (GBDL) with topology similar to the galactose binding domains (GBD), in particular to the anaphase promoting complex subunit 10. These domains are located in the second half of the protein.
SAC9, first GBDL domain (SAC9_GBDL_1st)
Type: Domain

This domain is found toward the C terminus of the SAC9 from Arabidopsis thaliana. It is the first of the three GBDL domains.

SAC9 is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response . SAC9 is critical for regulating lipid signaling and endocytic trafficking. SAC9 acts as a lipid "gatekeeper," ensuring PI(4,5)P2 is confined to the plasma membrane to support endocytosis and cellular homeostasis. Its interplay with SH3P2 and clathrin underscores the integration of lipid metabolism and membrane trafficking in plants . SAC9 contains three domains (GBDL) with topology similar to the galactose binding domains (GBD), in particular to the anaphase promoting complex subunit 10. These domains are located in the second half of the protein.
Surface lipoprotein assembly modifier, N-terminal TPR repeats region (TPR_Slam)
Type: Domain

This is a region of tetratricopeptide repeats (TPR) found at the N-terminal of Surface lipoprotein assembly modifier from the proteobacteria Pasteurella multocida (Slam) and similar sequences. Slam plays a role in the export to the cell surface of some cell outer membrane lipoproteins . This domain is usually found N-terminal to

.
SAC9, C8D domain (SAC9_C8D)
Type: Domain

This domain is found in the SAC9 protein from Arabidopsis thaliana. It contains four pairs of highly conserved cysteine residues that are probably involved in metal coordination.

SAC9 is a probable phosphoinositide phosphatase that is involved in modulating phosphoinositide signals during the stress response . SAC9 is critical for regulating lipid signaling and endocytic trafficking. SAC9 acts as a lipid "gatekeeper," ensuring PI(4,5)P2 is confined to the plasma membrane to support endocytosis and cellular homeostasis. Its interplay with SH3P2 and clathrin underscores the integration of lipid metabolism and membrane trafficking in plants . SAC9 contains three domains (GBDL) with topology similar to the galactose binding domains (GBD), in particular to the anaphase promoting complex subunit 10. These domains are located in the second half of the protein.
SWR1-complex protein 3 domain (Swc3_dom)
Type: Domain

This domain sis found in SWR1-complex protein 3 from Saccharomyces cerevisiae (Swc3) and similar proteins from ascomycetes.

Swc3 is a component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling . SWC3 has been used to refer to both SWC3/YAL011W, whose gene product is involved in chromatin remodeling and ER biogenesis, and ALR1/YOL130W, a plasma membrane transporter.
SAM-like domain (SAM_6)
Type: Domain

This entry represents a SAM-like domain found close to the C terminus of a variety of long proteins. This domain is often associated with

. The function of this domain unknown.
SCAN domain-containing protein 3-like, zinc finger (Znf_SCAND3)
Type: Domain

This zinc finger domain is found in human SCAN domain-containing protein 3 (SCAND3) and similar animal proteins. SCAND3 is a candidate prognostic marker for non-small cell lung cancer .
NAD glycohydrolase, translocation F5/8 type C domain (NADase_transloc)
Type: Domain

This entry represents the N-terminal translocation domain of NAD+-glycohydrolase from Streptococcus pyogenes (

) that is required for secretion through the SLO pore. The domain spans residues 38-190 and adopts a jelly roll fold with structural similarity to carbohydrate binding modules (CBMs) . However, it is found in a much wider range of bacterial uncharacterised proteins where its function is not known.
Tli3-like domain (Tli3-like_dom)
Type: Domain

This entry represents a domain found in the type VI secretion system (T6SS) Tli3 immunity protein from adherent-invasive Escherichia coli and related proteobacterial proteins. Some members have a lipoprotein lipid attachment site.

Tli3 is an outer membrane lipoprotein and a cognate immunity protein of T6SS Tle3 phospholipase effector. Tli3 and Tle3 form a stable complex in which a loop of Tli3 inserts deeply in the Tle3 substrate-binding pocket and thus inhibiting its function . Tli3 folds into an all-β structure composed of three stacked β-sheets, two of which are resembling a β-sandwich while the third packs on its edge .
Sema5A/B-like, TSP-1 type 1 (Sema5A/B-like_TSP-1)
Type: Domain

This is a TSP-1 type 1 domain found in human Semaphorin-5A (Sema5A) and Semaphorin-5B (Sema5B), Semaphorin 5c from Drosophila melanogaster and similar sequences mainly found in animals.

In mice, Sema5A has been identified as a protein that induces inhibitory responses during optic nerve development . It also has been identified as a candidate gene for causing idiopathic autism in humans . Plexin B3 functions as a binding partner and receptor for Sema5A . Sema5A is highly expressed in human pancreatic cancer cells and is associated with tumor growth, invasion and metastasis . Sema5A belongs to class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterised by unique thrombospondin specific repeats in the extracellular region of the protein .

Sema5B acts as an axonal guidance cue and regulates the development and maintenance of synapse size and number in hippocampal neurons .
Serine/threonine-protein kinase ATR-like, HEAT repeats (HEAT_ATR)
Type: Domain

This region of HEAT repeats is found towards the C-terminal of the FAT domain in human Serine/threonine-protein kinase ATR and similar eukaryotic proteins.

ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal α-solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain (

), a kinase domain (

), and a C-terminal short segment referred to as FATC (

). N-terminal part has two continuous HEAT repeat regions, the N-HEAT and the M-HEAT. The FAT domain contains TPR (tetratricopeptide) repeats followed by a HEAT repeat domain .
Transcription elongation regulator 1-like, third WW domain (WW_TCRG1_3rd)
Type: Domain

This entry corresponds to the third WW domain of human Transcription Elongation Regulator 1 (TCRG1) and similar animal proteins. The WW domains within these proteins are responsible for binding to Pro-rich domains, facilitating further protein-protein interactions.

TCRG1 (also known as CA150) contains three N-terminal WW domains and six consecutive FF domains (

). WW and FF domains are versatile modules that mediate protein-protein interactions . TCRG1 is a transcription elongation factor that interacts with the splicing factor SF1 and with the phosphorylated C-terminal repeat domain (CTD) of RNA polymerase II (RNAPII) through its WW and FF domains, respectively . It regulates transcription elongation in a TATA box-dependent manner . They bind the phosphorylated C-terminal of RNA polymerase II and mediate interactions with other proteins such as HTATSF1.
TTI1, N-terminal TPR domain (TPR_TTI1_N)
Type: Domain

This entry represents the TPR domain found at the N-terminal of TELO2-interacting protein 1 homologue (TTI1) from animals and yeast. This domain interacts with the FAT domain of the PIKK ATM .

TTI1 binds to TELO2 and TTI2 proteins to form the TTT complex, which plays a role in the assembly and stability of all phosphatidylinositol 3-kinase-related protein kinases (PIKKs) , pivotal proteins in various pathways related to cell metabolism, proliferation and differentiation . The TTT complex is involved in the cellular resistance to DNA damage stresses, like ionizing radiation (IR), ultraviolet (UV) and mitomycin C (MMC) . Budding yeast TTI1 is a subunit of the ASTRA complex, which is involved in chromatin remodelling .
TTI1, C-terminal TPR domain (TPR_TTI1_C)
Type: Domain

This entry represents the TPR domain found at the C-terminal of TELO2-interacting protein 1 homologue (TTI1) from animals and yeast. This domain binds to HEAT repeats of the ATM PIKK .

TTI1 binds to TELO2 and TTI2 proteins to form the TTT complex, which plays a role in the assembly and stability of all phosphatidylinositol 3-kinase-related protein kinases (PIKKs) , pivotal proteins in various pathways related to cell metabolism, proliferation and differentiation . The TTT complex is involved in the cellular resistance to DNA damage stresses, like ionizing radiation (IR), ultraviolet (UV) and mitomycin C (MMC) . Budding yeast TTI1 is a subunit of the ASTRA complex, which is involved in chromatin remodelling .
CortBP2/NAV1-like, AAA+ ATPase lid domain (CortBP2_NAV1-like_AAA_lid)
Type: Domain

This ATPase lid domain is found towards the C-terminal end of human Cortactin-binding protein 2 (CortBP2), Neuron navigator 1 (NAV1) and similar animal proteins.

CortBP2 regulates the dendritic spine distribution of CTTN/cortactin in hippocampal neurones and thus controls dendritic spinogenesis and dendritic spine maintenance . NAV1 may be involved in neuronal migration and neurite outgrowth .
C2 domain, nematode (C2_nem)
Type: Domain

This entry represents a specific C2 domain found in uncharacterised nematode proteins, including C05B5.4 and R10E12.2 from Caenorhabditis elegans. C2 domains are protein modules that can bind calcium and phospholipids.
NOL9, C-terminal domain (NOL9_C)
Type: Domain

This domain is found at the C-terminal end of human Polynucleotide 5'-hydroxyl-kinase NOL9 and similar proteins from eukaryotes. This domain is predicted to adopt an α-β configuration.

NOL9 and its orthologue Gre3 are polynucleotide 5'-kinases involved in rRNA processing . NOL9 can phosphorylate single-stranded and double-stranded RNA and DNA substrates .
SDR PhqE-like (SDR_PhqE-like)
Type: Family

Short-chain dehydrogenase/reductase (SDR) MalC and PhqE (its homologue from the paraherquamide pathway) are bifunctional enzymes that function as both a reductase and an intramolecular [4+2] Diels-Alderase in the paraherquamide biosynthetic pathway. MalC and PhqE contain a classical SDR fold with a nucleotide-binding subdomain that includes the invariant "TGX3GXG" motif (P-loop), and a C-terminal substrate binding region that is less conserved and largely hydrophobic. Unlike typical SDRs, MalC and PhqE lack the characteristic Tyr and Lys catalytic amino acids, with the SDR catalytic Tyr and Lys replaced by shorter, non-polar residues (Ile and Cys). A distinctive "PDPGW" motif positions the essential Asp166 closer to the substrate compared to canonical SDRs .
Non-GDSL lipase-like (NonGDSL)
Type: Family

This entry represents a family of α/β hydrolase enzymes. These presumed enzymes are most similar to the GDSL lipases. However the GDSL motif has been lost suggesting they may have lost their lipase activity. Members are mainly found in proteobacteria.
NOL9, N-terminal domain (NOL9_N)
Type: Domain

This domain is found toward the N-terminal end of human Polynucleotide 5'-hydroxyl-kinase NOL9 and similar eukaryotic sequences. This domain is predicted to adopt a cupin fold.

NOL9 and its orthologue Gre3 are polynucleotide 5'-kinases involved in rRNA processing . NOL9 can phosphorylate single-stranded and double-stranded RNA and DNA substrates .
Novel STAND NTPase 5 domain (nSTAND_NTPase5_dom)
Type: Domain

This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in prokaryotic conflict systems . It can be found in association with

.
Novel STAND NTPase 6 domain (nSTAND6_dom)
Type: Domain

This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases, found in bacterial conflict systems .
NUCB1-like, N-terminal domain (NUCB1_N)
Type: Domain

This domain is found at the N-terminal end of rat Nucb1/2 and similar animal proteins predicted to also have an EF-hand domain. This domain is predicted to adopt an all-α configuration.

Nucb2 is a calcium-binding protein that may have a role in calcium homeostasis . It can be cleaved into an isoform named nesfatin-1, which is an anorexigenic peptide that seems to play an important role in hypothalamic pathways regulating food intake and energy homeostasis, acting in a leptin-independent manner . Nucb1 is a major calcium-binding protein of the Golgi, which may have a role in calcium homeostasis . Nucb1/2 act as non-receptor guanine nucleotide exchange factors which bind to and activate alpha subunits of guanine nucleotide-binding proteins (G proteins) . Nucb1 is expressed in pancreatic islets and other endocrine tissues and may have a role in in Ca(2+) handling/sensing in secretory cells . Nucleobindin-1 encodes a nesfatin-1-like peptide that stimulates insulin secretion .
Nucleoprotein, TPR/MPL1 domain (Nucleoprot-TPR/MLP1_dom)
Type: Domain

This domain is found in human Nucleoprotein TPR and its orthologue in fungi MLP1. This domain is predicted to adopt an α-helical configuration.

TPR and MLP1/2 share several features; for example, they have coiled-coil regions and are associated with nuclear pores . TPR is thought to be a component of nuclear pore complex-attached intranuclear filaments , and is implicated in nuclear protein import . Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex . MLP1 acts as a docking platform for heterogeneous nuclear ribonucleoproteins that are required for mRNA export .
Nucleoside diphosphate kinase 7, DM10 domain (DM10_NDK7)
Type: Domain

This entry represents the DM10 domain in nucleoside diphosphate kinase 7 (NDK7) proteins. This domain is found preceding either one or two nucleoside diphosphate kinase (NDK) catalytic domains. DM10 domains might act as flagellar NDK regulatory modules or as units specifically involved in axonemal targeting or assembly . DM10 domains have the same organisation of secondary structural elements, a pleckstrin homology (PH)-like fold, which includes seven β strands, with a short 3-4 residue helix after the first strand, and a more extended α helical region at the C-terminal .

Human NDK7 is a functional component of the gamma-tubulin ring complex, implicated in the regulation of the microtubule-nucleating activity of the gamma-tubulin ring complex in centrosomes, in a kinase activity-dependent manner . It is part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating .
Putative cytidine deaminase, C-terminal domain (Deam_C)
Type: Domain

This domain is found at the C-terminal end of a group of sequences from proteobacteria. Foldseek predicts high structure similarity of this domain with Cytidine deaminases.
Putative phage ssDNA-binding domain (Phage_ssDNA_bind)
Type: Domain

This entry represents an OB fold domain in a small group of phage proteins that show structural similarity to other phage ssDNA-binding proteins. Structure prediction shows a plausible ssDNA binding pocket on the surface of the domain.
Putative phage tail tube protein (Phage_TTP_15)
Type: Family

This entry shows structural similarity to the Afp1 tail tube protein from the AFP antifeeding prophage of Serratia. This suggests that this family is also likely to form the inner tail tube.
PYCO1, Rubisco-binding repeat (PYCO1_repeat)
Type: Repeat

This entry represents a repeat found in the pyrenoid component 1 (PYCO1) protein from diatoms.

PYCO1 is an intrinsically disordered repeat protein that plays a crucial role in the formation of the pyrenoid, a microcompartment within chloroplasts that concentrates CO2 for more efficient carbon fixation. This entry represents a repeat that binds to the Rubisco small subunit. Four KWSPR/Q motifs can form a tetrad that binds to the small subunits lining Rubisco's central solvent channel. The repeats enable PYCO1 to undergo liquid-liquid phase separation, forming condensates that specifically partition diatom Rubisco. This phase separation is crucial for the formation and function of the pyrenoid in diatoms, which are responsible for a significant portion of marine carbon fixation .
RDM3, beta-solenoid (RDM3_C)
Type: Domain

This entry represents a β-solenoid domain found at the C-terminal region of Protein RNA-directed DNA methylation 3 (RDM3) from Arabidopsis thaliana and similar proteins from plants. This entry also includes putative helicases from bacteria.

RNA-directed DNA methylation (RdDM) initiates and re-establishes silencing of transposable elements through de novo methylation of cytosines .
Tetratricopeptide repeat domain, fungi (TPR_dom_fungi)
Type: Domain

This region of Tetatricopeptide-like (TPR) repeats is found in a group of uncharacterised fungal proteins.

The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins . It mediates protein-protein interactions and the assembly of multiprotein complexes . The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding .
NUP210-like, Ig-like domain 16 (Ig_NUP210_16th)
Type: Domain

This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210) and similar animal proteins.

NUP210 is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as for its structural integrity. NUP210 is composed of multiple immunoglobulin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen . There are eight copies of NUP210 per spoke. NUP210 is the only NUP that primarily resides in the NE lumen. This protein is not required for faithful NPC assembly .
Tip attachment protein J, second Ig-like domain (GpJ_Ig_second)
Type: Domain

This is the second Ig-like domain found in Tip attachment protein J from Escherichia phage lambda (GpJ) and similar sequences from tailed bacteriophages and bacterial prophages.

The Tip attachment protein J (GpJ) from Escherichia phage lambda is a crucial tail fibre protein responsible for recognising and binding the host cell's LamB receptor, thereby initiating infection. Structurally, GpJ forms the central tail fibre at the phage tip and undergoes conformational changes upon receptor engagement, which are essential for triggering DNA injection into the host . It interacts with other tail proteins during assembly, serving as a scaffold for tail tube formation and coordinating with the tape measure protein to regulate genome delivery . Mutations in GpJ can alter host specificity and affect phage stability, while its exposed position makes it a target for neutralising antibodies .