SII-SWORD/CoKE huggingface dataset:
p55, C-terminal domain (p55_CTD)
Type: Domain

This entry corresponds to the C-terminal domain of the p55 protein of emaraviruses (plant-infecting bunyaviruses), a highly conserved domain found in all p55 proteins. The function of these proteins is unknown, but in Rose rosette virus, p55 proteins were dispensable for transcription of a minireplicon [

,

, https://doi.org/10.3390/f13111868]. Structure prediction using AlphaFold colab tool, suggests that this domain may have three α-helices.
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha/beta/delta, EF-hand (P2R3A_B_D_EF-hand)
Type: Domain

This is a EF-hand domain found in Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha/beta/delta (P2R3A/B/D) and similar animal proteins. This proteins may modulate substrate selectivity and catalytic activity.
Major inner capsid protein P1 (P1)
Type: Family

This entry represents a group of proteins from Cystovirus, including Major inner capsid protein P1, which forms the inner T=1 shell of Bacteriophage phi-6, a dodecahedral polymerase complex (PC) that contains the three viral dsRNA segments. The protein folds into a flattened trapezoid shape with a mostly α-helical fold. It was initially though to adopt a funnel-shaped pentameric assembly, but later research has shown dimers of different P1 chains are also present in the virus capsid .
OTU1, Ubl domain (OTU1_Ubl)
Type: Domain

OTU1 is a deubiquitinating enzyme that may play an important regulatory role at the level of protein turnover by preventing degradation. This entry represents the ubiquitin-like (Ubl) domain, which interacts with the N-terminal domain of VCP and removes ubiquitin chains using the OTU domain. This domain is also found in VCIP1, a known UBXL-containing protein that functions in p97/p47-mediated Golgi reassembly .
Oligosaccharyl transferase, peripheral 1 domain (OST_P1)
Type: Domain

This domain is found in Oligosaccharyl transferase from Pyrococcus furiosus (OST, also known as AglB-L) and similar archaeal sequences. OST catalyses the co-translational transfer of an oligosaccharide from a lipid donor to an asparagine residue in nascent polypeptide chains. This protein is organised into four regions: a N-terminal half , the central core (CC) domain that includes the IS (insert) domain (

) and two peripheral domains, P1 (this entry) and P2 (

). This domain, which consists mainly of β-strands, encircles the central core domain .
BTB/POZ domain-containing protein 16, C-terminal domain (BTBD16_C)
Type: Domain

This is the C-terminal domain of BTB/POZ domain-containing protein 16 (BTBD16) which may adopt a β-sandwich structure. The function of BTBD16 is not clear.
Cellulose synthase subunit B-like, C-terminal domain (BscB-like_C)
Type: Domain

This domain is found at the C-terminal of Cellulose Synthase Subunit B (BscB) from Cereibacter sphaeroides and similar sequences from alphaproteobacteria. BscB, involved in bacterial cellulose biosynthesis, is organised into two periplasmic carbohydrate binding domains and two α/β-domains similar to the flavodoxin-fold (FD1 and FD2) . This entry represents FD2.
Stage VI sporulation protein D, N-terminal domain (SPOCS_spoVID_N)
Type: Domain

This is the SPOCS (SpoVID-CotE-SipL) domain consisting of a β-strand-rich sandwich fold with long twisted strands found at the N-terminal of Stage VI sporulation protein D (SpoVID) from Bacillus subtilis (

) and in related proteins primarily found in firmicutes.
Pre-mRNA-splicing helicase BRR2-like, plug domain (BRR2_plug)
Type: Domain

This entry represents the plug domain from the Brr2 RNA helicase from yeast and its homologues, such as U5 small nuclear ribonucleoprotein 200 kDa helicase from human . The Brr2 helicase provides the key remodelling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein) . The plug domain is a small α-helical bundle domain, found near the N-terminal of the Brr2 protein .
Histone H3 binding protein ORF158L-like (ORF158L-like)
Type: Family

This protein family is found in ORF158L from Singapore grouper iridovirus (

) and similar viral proteins. ORF158L interacts with the histone H3/H4 complex and H3. It may play a key role in histone H3 modulation and function as a histone H3 chaperon. It folds into two β-sheets that form an elongated β-sandwich domain, and two short α-helices on one surface of the molecule with several loops between the secondary structures. The β-sheets consist of four antiparallel β-strands and five antiparallel β-strands, respectively .
ORC5, lid domain (ORC5_lid)
Type: Domain

ORC5 is a component of the origin recognition complex (ORC) that binds origins of replication. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication. This entry represents the lid domain, which with the N-terminal RecA-fold domain, constitutes the well-known AAA domain .
Origin recognition complex subunit 1, C-terminal winged HTH domain (ORC1_wHTH)
Type: Domain

This entry represents the C-terminal winged helix-turn-helix domain found in fungal Origin recognition complex subunit 1 proteins .
Putative 8-oxoguanine DNA glycosylase OGG-like protein (OGG-like_put)
Type: Family

This entry represents an uncharacterised family of bacterial proteins that are structurally similar to 8-oxoguanine DNA glycosylase enzymes. These proteins are involved in DNA repair of the base excision repair pathway.
OCRL-1/2, ASH domain (OCRL-1_2_ASH)
Type: Domain

This domain is found in Inositol polyphosphate 5-phosphatase OCRL-1 and Type II inositol 1,4,5-trisphosphate 5-phosphatase (OCRL-2) from humans and similar eukaryotic proteins. OCRL-1 is an enzyme that dephosphorylate the 5' position of the inositol ring. It is thought to help coordinate intracellular membrane traffic through changes in the phosphoinositide composition of associated membranes. Mutations in this protein are responsible for Lowe syndrome. This entry represents a domain found C-terminal to

and N-terminal to

. It is comprised by two layers of β-sheets and is closely related to the members of the family of immunoglobulin-like β-sandwiches .
Minor structural protein 5-like, C-terminal domain (BppU-like_C)
Type: Domain

This domain is found at the C-terminal of the minor structural protein 5 from Lactococcus phage Tuc2009 (BppU,

) and similar proteins from tailed bacteriophages and prophages. BppU is a viral baseplate component. This domain folds into a structure Ig-like β-sandwich .
Bacterial PH domain (PH_7_bact)
Type: Domain

This entry represents a group of bacterial PH domains that contain two transmembrane helices. The function of this family is uncertain, but they may act as antitoxins or as chaperones for membrane bound complexes.
Ribosomal protein bL31m, N-terminal domain (Ribosomal_bL31m_N)
Type: Domain

Ribosomal protein bL31m (also known as 54S ribosomal protein L36), is a component of the mitochondrial ribosome. Overexpression of bL31m suppresses mutations in the COX2 leader peptide-encoding and initiation codon regions . This entry represents the N-terminal domain of yeast bL31m .
BIRC2/3-like, UBA domain (BIRC2-3-like_UBA)
Type: Domain

Baculoviral IAP repeat-containing proteins, also known as c-IAPs, function as ubiquitin E3 ligases that mediate the ubiquitination of the substrates involved in apoptosis, nuclear factor-kappaB (NF-kappaB) signalling, and oncogenesis . This entry represents the UBA domain of BIRC2/3/4/8, E3 ubiquitin-protein ligase XIAP from mammals and BIRC7 from Xenopus tropicalis .
TypA/BipA, C-terminal domain (BipA_C)
Type: Domain

This entry represents the C-terminal domain of the TypA/BipA protein. The C-terminal domain of BipA forms a unique motif with two crossed β-sheets (comprising of two and four β-strands, respectively) wrapped by three short α-helices forming a nearly equilateral triangle .

This family includes the GTP-binding protein BipA or TypA (Tyrosine phosphorylated protein A (TypA), also known as 50S ribosomal subunit assembly factor BipA) from bacteria and its homologue from Arabidopsis (putative elongation factor TypA-like SVR3). BipA is a 50S ribosomal subunit assembly protein with GTPase activity, required for 50S subunit assembly at low temperatures, also functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds the 70S ribosome at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs . The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. This GTPase impacts interactions between enteropathogenic E.coli (EPEC) and epithelial cells and also has an effect on motility . It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defence peptides, flagellum-mediated cell motility, and expression of K5 capsular genes .

TypA-like SVR3 is a putative chloroplastic elongation factor involved in response to chilling stress. It is required for proper chloroplast rRNA processing and/or translation at low temperature and it is also involved in plastid protein homeostasis .
Oxalate Biosynthetic Component A, N-terminal domain (ObcA_N)
Type: Domain

This domain is found at the N-terminal end of Oxalate Biosynthetic Component A from Burkholderia glumae (ObcA,

). ObcA shows a unique structural architecture, with the small N-domain (this entry) inserted into a loop between the first β-strand and the first α-helix of the C-domain barrel fold .
Oxalate biosynthetic component 1, cap domain (Obc1_cap)
Type: Domain

This domain is found in a group of proteins mainly from proteobacteria, including the bifunctional enzyme Oxalate biosynthetic component 1 from Burkholderia pseudomallei (Obc1,

). This entry represents the cap domain of Obc1, which adopts an α-helical fold, with two layers of anti-parallel helices .
Oxalate biosynthetic component 1, C-terminal (Obc1_C)
Type: Domain

This domain is found at the C-terminal end of a group of proteins mainly from proteobacteria, including the bifunctional enzyme Oxalate biosynthetic component 1 from Burkholderia pseudomallei (Obc1,

).
Nucleoporin Nup188, N-terminal subdomain III (Nup188_N-subdom_III)
Type: Domain

Nup188 is one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes . The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of the at least six that make up the NPC, and as such is symmetrically localised on both faces of the NPC at the nuclear end, being integrally bound to the C-terminal of Pom34p . This protein folds into an extended stack of helices where the N-terminal forms a closed ring (subdivided into subdomains I-III in ) and the C-terminal forms a more regular, superhelical structure . This entry represents the helical segment of subdomain III described in , which consists of an array of HEAT and ARM repeats with an inserted SH3-like domain .
Nucleoporin Nup120, helical domain, fungal (Nup120_helical)
Type: Domain

This entry represents the helical domain of Nup120 from S. pombe and similar yeast sequences, referred to as the irregular helical bundle (IHB) , which makes extensive contacts with the propeller and helical bundle at the N-terminal.

Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth . The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export . Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 subcomplex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 subcomplex, but rather that it regulates the association of the subcomplex with the NPC and other proteins .
Bridging integrator 2, C-terminal tail (Bin2_C)
Type: Domain

Bridging integrator 2 (Bin2) is a BAR domain -containing protein that is mainly expressed in haematopoietic cells . It promotes cell motility and migration, probably via its interaction with the cell membrane and with podosome proteins that mediate interaction with the cytoskeleton. Bin2 modulates membrane curvature, mediates membrane tubulation and it plays a role in podosome formation.

This entry represents the C-terminal tail which mediates interactions with SH3 domains, through its proline-rich regions, functioning as an adaptor for SH3 domain-containing proteins at podosomes. This domain is rich in glutamates, serines and prolines. It contains two consensus PxxP sequences (PTSPR and PEKPVR) .
NtrZ-like (NtrZ-like)
Type: Family

This entry represents a family of proteins predominantly found in alphaproteobacteria, including the periplasmic protein NtrZ from Caulobacter crescentus, which functions to regulate the activity of the NtrY-NtrX two-component system . NtrZ inhibits NtrY phosphatase activity.
BibA adhesin-like, stalk domain (BibA_stalk)
Type: Domain

BibA, a group B streptococcus (GBS) surface protein, has been shown to protect the pathogen from phagocytic killing by sequestering a complement inhibitor: C4b-binding protein (C4BP) . This entry represents a three helical repeated domain in this protein.
NSUN5/RCM1, N-terminal domain (NSUN5_RCM1_N)
Type: Domain

28S rRNA (cytosine-C(5))-methyltransferase from mammals (NSUN5), 26S rRNA (cytosine-C(5))-methyltransferase nsun-5 from nematodes, 25S rRNA (cytosine-C(5))-methyltransferase NSUN5 from plants and the homologue from yeast 25S rRNA (cytosine-C(5))-methyltransferase rcm1 are SAM-dependent methyltransferases that specifically methylate the C(5) position of a cytosine . This entry represents the N-terminal globular domain of NSUN5 which is required for targeting to nucleoli .
BH1974-like, central domain (BH1974-like_central)
Type: Domain

This entry represents a domain found in the central region of BH1974 protein from Alkalihalobacillus halodurans and similar bacterial proteins. It is found planked by

and

. It may adopt an α/β structure.
Non-structural protein 3, zinc-binding domain (nsP3_ZBD)
Type: Domain

This domain is found in Non-structural protein 3 (nsP3) from Chikungunya virus (CHIKV) and similar proteins from Alphavirus. nsP3, one of the four products of the polyprotein P1234, displays mono-ADP-ribosylhydrolase activity . This protein consists of three domains: an N-terminal Macro domain (

), a central zinc-binding domain (ZBD, this entry), and a hypervariable-sequence carboxyl terminus. ZBD is essential for viral replication. It has two cysteines in a loop between α-helices and the other two cysteines at the end of two parallel β-strands, which represent a structural scaffold for zinc-ion coordination .
Nrd1/Seb1, domain 2 (Nrd1_Seb1_dom2)
Type: Domain

Nrd1 is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein, part of the Nrd1-Nab3-Sen1 (NNS) complex which is involved in the termination and processing of short RNA polymerase II transcripts . Seb1 is the Nrd1 homologue from S. pombe that is essential for cell viability and binds directly to Rpb7 subunit of RNA polymerase II. It functions in terminating all classes of Pol II-transcribed genes genome-wide. These proteins have a RNA-recognition motif (RRM,

) fused to a second α/β domain described as domain 2 (represented by this entry and also referred to as the split domain, SD, in ) from Nrd1 and Seb1. This domain is essential and forms a rigid body with the canonical RRM that interacts with RNA .
Nuclear pore complex-interacting protein B13-like, MII repeat (NPB13-like_MII_rpt)
Type: Repeat

This entry represents the MII repeat found in a group of proteins specific to Homo sapiens, including Nuclear pore complex-interacting protein family member B13 (NPB13), NPB12, NPB11, NPB3, NPB4 and NPB5. These repeats may arrange in a β-solenoid structure. Members of this entry have the repeated sequence MIISRHLPSV.
Infectious salmon anemia virus nucleoprotein, C-terminal (NCAP_ISAV_C)
Type: Domain

This entry represents a domain found in the nucleoprotein from the orthomyxovirus Infectious salmon anemia virus . This protein is similar to that in Influenza virus and consists of a head and a body domain . This entry represents the tail loop which plays a role in oligomerisation. It folds into an extended β-hairpin that protrudes into a deep pocket in a neighbouring subunit to mediate dimer formation.
MJ0694-like, N-terminal domain (MJ0694-like_N)
Type: Domain

This entry represents the N-terminal domain of the uncharacterised NOP5 family protein MJ0694 from Methanocaldococcus jannaschii and similar archaeal sequences. MJ0694 is an homologue of Nop56/58, which are pre-RNA processing ribonucleoproteins (RNP). This domain is very well conserved and mediates a stable interaction with fibrillarin, playing a role in both RNP assembly and methyltransferase activity .
Nop5/56-related, N-terminal domain (Nop5_56-rel_N)
Type: Domain

This domain is found at the N-terminal end of a group of Nop5/56-related archaeal proteins. This domain interacts with fibrillarin, the other subunit of a complex that is critical to modify and process ribosomal RNAs . This domain shows a highly conserved folded structure despite low sequence similarity among homologs. It shows four β-sheets surrounded by four α-helices and is found associated with

.
Nucleolar protein 11, C-terminal domain (Nol11_C)
Type: Domain

This α-solenoid repeat is found at the C-terminal of human nucleolar protein 11 (NOL11) and similar animal proteins. NOL11 is a ribosome biogenesis factor. It may be required for both optimal rDNA transcription and small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b .
60S ribosomal export protein NMD3, OB-fold domain (NMD3_OB)
Type: Domain

A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. 60S ribosomal export protein NMD3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the third domain in NMD3 which adopts an OB-fold . The OB of Nmd3 does not recognise 25S rRNA. Instead it interacts with two ribosomal proteins, eL42 and uL1 .
60S ribosomal export protein NMD3, SH3 domain (NMD_SH3)
Type: Domain

A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. 60S ribosomal export protein NMD3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. This entry represents the second domain in NMD3 which adopts an SH3-fold denoted as RBDII in . The two short α-helices in RBDII participate in rRNA recognition .
NLR family member X1, C-terminal domain (NLRX1_C)
Type: Domain

This domain is found at the C-terminal end of NLR family member X1 from humans (NLRX1) and similar proteins from vertebrates. NLRX1 is both a proinflammatory activator that stimulates the production of reactive oxygen species (ROS) via TNFalpha activation and is able to down-regulate inflammatory responses through interaction with the mitochondrial antiviral signalling adaptor and TRAF6-IKK. This domain is organised into a three subdomains: an N-terminal helical domain, a central LRR motifs and a C-terminal three-helix bundle. The interaction of this domain with RNA ligands plays a key role in NLRX1-mediated ROS activation .
Cysteine methyltransferase effector NleE/OspZ (NleE/OspZ)
Type: Family

Type III secretion system (T3SS) effector NleE from Escherichia coli is a S-adenosyl-L-methionine (SAM)-dependent methyltransferase that inhibits NF-kappa-B-mediated proinflammatory response in the host. Its structure shows an α-β doubly wound topology with a central three-stranded anti-paralleled β-sheet sandwiched by α-helices . OspZ from Shigella flexneri inhibits host cell NF-kappa-B activation by preventing nuclear translocation of host protein RELA/p65 . This protein family is predominantly found in Enterobacterales.
Phosphoribosyl-dephospho-CoA transferase MdcG, N-terminal (MdcG_N)
Type: Domain

This entry represents the N-terminal SH3-like domain from MdcG which is a phosphoribosyl-dephospho-CoA transferase that is involved in the biosynthesis of the prosthetic group of malonate decarboxylase . Malonate decarboxylase from Klebsiella pneumoniae contains an acyl carrier protein (MdcC) to which a 2'-(5' '-phosphoribosyl)-3'-dephospho-CoA prosthetic group is attached via phosphodiester linkage. MdcG catalyses the following reaction:

2'-(5''-triphosphoribosyl)-3'-dephospho-CoA apo-[acyl-carrier-protein] = holo-[acyl-carrier-protein] diphosphate.
Mcp40H-20-like, sensor (Mcp40H-20-like_sensor)
Type: Domain

This domain is found in Methyl-accepting chemotaxis sensory transducer, class 40H from Geobacter sulfurreducens (Mcp40H-20,

) and similar bacterial proteins. This entry represents the periplasmic c-type heme-containing sensor domain, which is located between two transmembrane helices near the N terminus of the protein. This domain adopts a PAS-type domain fold with two helical segments followed by a four-stranded β-sheet .
Major capsid protein 1/2, C-terminal (Vir_MCP_C)
Type: Domain

This entry represents the C-terminal domain of a major coat protein from Acidianus filamentous virus 1 which adopts a four-helix bundle fold.
MCM, winged-helix (MCM_WH)
Type: Domain

This entry represents the conserved truncated winged helix domain of minichromosome maintenance complex (MCM, a replicative DNA helicase) from archaea, which lacks the two typical 'wings' of canonical WH domains .
Minichromosome maintenance protein MCM, C-terminal domain (MCM_C)
Type: Domain

This entry represents a C-terminal winged helix-turn-helix domain found at the C-terminal of archaeal proteins from the minichromosome maintenance complex (MCM) .
6-fold beta flower protein (Bflower_3)
Type: Family

This family of bacterial proteins have a repetitive structure composed of pairs of β-strands. In this family, the proteins usually have six copies of the β-hairpin repeat with a central α-helix in the barrel.
5-fold beta-flower protein (Bflower_2)
Type: Family

This family of proteins have a repetitive structure composed of pairs of β-strands. In this family, found mainly in bacteria, the proteins usually have five copies of the β-hairpin repeat.
4-fold beta flower domain (Bflower)
Type: Domain

This domain is found in a family of proteins from bacteria which have a repetitive structure composed of pairs of β-strands. Proteins in this entry usually have four copies of the β-hairpin repeat.
Beta-galactosidase 1-like , first all-beta domain (BetaGal1-like_ABD1)
Type: Domain

This entry represents a subset of the glycosyl hydrolase 35 family, including beta-galactosidase (B-gal), B-gal-1, B-gal-1-like, B-gal-8, B-gal-17. Mammalian beta-galactosidase is a lysosomal enzyme (gene GLB1) which cleaves the terminal galactose from gangliosides, glycoproteins, and glycosaminoglycans and whose deficiency is the cause of the genetic disease Gm(1) gangliosidosis (Morquio disease type B).

These proteins consist of a catalytic TIM-barrel and two all-β domains (ABD1 and ABD2) . This entry represents the first all-β domain ABD1.
Beta-galactosidase, galactose-binding domain (BetaGal_gal-bd)
Type: Domain

Beta-galactosidase belongs to Glycoside hydrolase family 35 . This entry represents the galactose-binding domain, found at the C-terminal.