SII-SWORD/CoKE huggingface dataset:
Zona-pellucida-binding protein 1/2, C-terminal domain (ZPBP1/2_C)
Type: Domain

This entry represents the C-terminal EGF-like domain found in zona-pellucida-binding proteins. These are sperm proteins that bind to the 90 kDa family of zona pellucida glycoproteins in a calcium-dependent manner . These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur .
Zona-pellucida-binding protein 1/2, N-terminal domain (ZPBP1/2_N)
Type: Domain

This entry represents the N-terminal Ig-like domain from a number of zona-pellucida-binding proteins. These are sperm proteins that bind to the 90 kDa family of zona pellucida glycoproteins in a calcium-dependent manner . These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilisation to occur .
Putative peptidoglycan-binding domain (PG-bd)
Type: Domain

This entry represents a putative peptidoglycan binding domain (

) found in a group of proteins from firmicutes.
PG_0320-like, C-terminal domain (PG_0320-like_C)
Type: Domain

This domain is found at the C-terminal end of PG_0320 from Porphyromonas gingivalis (

) and similar bacterial sequences. This domain is usually found associated with DUF1573. It is functionally uncharacterised.
General secretion pathway protein A, peptidase C39-like domain (GspA_C39-like)
Type: Domain

This entry represents a domain of the type II secretion system protein General secretion pathway protein A (GspA) from Escherichia coli (

), which folds into a papain-like fold similar to that in peptidase C39 family .
Baseplate wedge protein gp7, helical domain (Gp7_helical)
Type: Domain

This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 (

) and similar proteins from tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents helix-turn-helix motif that is part of the long linker connecting the second and fourth domains .
Baseplate wedge protein gp7, domain V (Gp7_dom_V)
Type: Domain

This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 (

) and similar proteins from tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain V, which is an insertion into domain IV and consists of an eight-stranded β-barrel followed by two short α-helices .
Baseplate wedge protein gp7, domain VI (Gp7_dom_VI)
Type: Domain

This domain is found in Baseplate wedge protein gp7 from Bacteriophage T4 (

) and similar proteins from tailed bacteriophages. Gp7 provides the primary control of the conformational changes of the viral baseplate during assembly and infection. This protein is organised into six domains connected by flexible linkers. This entry represents Domain VI, which forms a ribbon-like structure that interacts with N-terminal region of the protein Gp10 .
Major capsid protein GP7-like (GP7-like)
Type: Family

This family represents Major capsid protein GP7 from Salmonella phage epsilon15 (

) and similar proteins found in tailed bacteriophages and bacterial prophages. GP7 adopts a canonical phage structure, showing different structural features (an N-arm, an F-loop, an E-loop, a P-domain, a long α-helix, an A-domain and the C-terminal end) .
Period circadian protein homolog 1-3, PAS-A domain (Per1-3_PAS-A)
Type: Domain

This domain is found in Period circadian protein homolog 1-3 from Mus musculus (Per1-3) and similar proteins predominantly found in vertebrates. This entry represents the first PAS domain (PAS-A) present in this protein. This domain shows a five-stranded antiparallel β-sheet covered on one face by α-helices .

PER proteins (PER 1-3) are transcriptional repressors which form the core component of the circadian clock. They play a critical role in rhythm generation, whereas delays imposed by post-translational modifications are important for determining the period of the rhythms. The core clock genes: PER1/2/3 and CRY1/2 form the negative limb of the feedback loop and interact with the CLOCK|NPAS2-BMAL1|BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression .
Sliding-clamp-loader large subunit, AAA+ ATPase lid domain (Gp44_lid)
Type: Domain

This entry represents the AAA ATPase lid domain of Gp44 and similar sequences from tailed bacteriophages and bacterial prophages.

Sliding-clamp-loader large subunit (also known as Gp44) from Bacteriophage T4 forms the sliding-clamp-loader together with the small subunit. These are members of the AAA superfamily of ATPases which form pentameric complexes that load sliding DNA clamps onto the DNA, key for processive chromosomal replication .
M17 aminopeptidase, N-terminal domain (Peptidase_M17_N_1)
Type: Domain

This entry represents a domain found at the N-terminal end of a group of proteobacterial M17 aminopeptidases that contain

at its C-terminal end. This domain has several highly conserved W and Y residues.
Sliding-clamp-loader large subunit, C-terminal domain (Gp44_C)
Type: Domain

This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (

also known as Gp44) and similar proteins from tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module (

) .
BACUNI_00178-like, N-terminal domain, bacteroidetes (BACUNI_00178-like_N)
Type: Domain

This is the PDZ-like domain found in the middle region of a group of proteins from bacteroidetes that belong to the peptidase S41 family, such as Bacteroides uniformis (BACUNI_00178,

). It is found associated with {interpro:IPR028204] at the N-terminal and the peptidase S41 domain at the C-terminal (

).
Xaa-Pro dipeptidase, N-terminal domain (PepQ_N)
Type: Domain

This domain is found in Xaa-Pro dipeptidase from Escherichia coli (PepQ), a metalloprotease that catalyse the cleavage of Xaa-Pro dipeptides. This protein is organised into N-terminal (this entry) and C-terminal (usually

) domains and adopts a dimeric configuration. This domain shows an α-β structure with four helices, one pair flanking each side of the six-stranded mixed β-sheet .
PdeA-like, PAS domain (PdeA-like_PAS)
Type: Domain

This entry represents the PAS domain from phosphodiesterase PdeA from Caulobacter vibrioides and similar bacterial proteins. PAS domains are found in all kingdoms of life and are involved in diverse functions but have an especially strong presence in signalling networks. They often serve as protein-protein interaction modules. In PdeA, the PAS domain serves as an adaptor recognition site needed for regulated proteolysis by the ClpXP protease .
2',5'-phosphodiesterase 12-like, N-terminal domain (PDE12-like_N)
Type: Domain

This domain is found in 2',5'-phosphodiesterase 12 from humans (PDE12) and similar animal proteins. Pde12 cleaves 2',5'- phosphodiester bond linking adenosines of oligoadenylates. It plays a role as a negative regulator of the 2-5A system that is one of the major pathways for antiviral and antitumour functions induced by interferons (IFNs). PDE12 is organised into two clear domains: an N-terminal domain (this entry) and a C-terminal domain (

). This domain is primarily composed of extended loop regions around a core composed of a six β-strand meander that forms a two-layer β-sandwich, showing an immunoglobulin-like fold .
PD-(D/E)XK nuclease-like domain (PDDEXK_13)
Type: Domain

This entry represents a domain present in a group of bacterial uncharacterised proteins. Structure prediction suggests it is likely to be part of endonuclease enzymes related to the PD-(D/E)XK nuclease superfamily.
CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain (Cas3_I-F_Cas2)
Type: Domain

This is the N-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa and similar sequences predominantly found in proteobacteria. In the type I-F CRISPR-Cas system, Cas3 is fused with Cas2 at the N terminus. This entry represents the Cas2 domain of Cas3, which shows a four-stranded β-sheet and two α-helices, in a structure that resembles that of Cas2 from the Escherichia coli. It appears N- terminal to the histidine-aspartate (HD)-type nuclease domain (

) .
CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain (Cas3-like_C)
Type: Domain

This domain is found at the C-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa. Cas3 contains an HD nuclease domain (

), RecA1, RecA2, a long linker region, and this C-terminal domain. AcrF3, and anti-CRISPR protein, forms a homodimer that locks Cas3 in an ADP-bound form, blocking the entrance of the DNA-binding tunnel in the helicase domain. It masks the linker region and C-terminal domain of Cas3, which prevents the recruitment by Cascade and inhibiting the type I-F CRISPR-Cas system . This domain shows two α-helices and two six-stranded β-blades .
Complement component C7, Kazal domain (C7_KAZAL)
Type: Domain

Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C7 contains a FIM pair at the C-terminal, FIM1 ana FIM2, each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain . This entry represents the KAZAL domain of FIM1 .
Complement component C7, FIM2 N-terminal domain (C7_FIM2_N)
Type: Domain

Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C7 contains a FIM pair at the C-terminal, FIM1 and FIM2; each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain . This entry represents the N-terminal of FIM2; it has a FOLN architecture which is a truncated form of the epidermal growth factor domain (EGF) .
Complement component C6, KAZAL domain (C6_KAZAL)
Type: Domain

Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C6 contains a FIM pair at the C-terminal, FIM1 and FIM2, each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain . This entry represents the KAZAL domain of FIM1 .
Pre-mRNA cleavage complex 2 protein Pcf11, RFEGP repeat (PCF11_RFEG_rpt)
Type: Repeat

This entry represents a repeat region found in Pre-mRNA cleavage complex 2 protein Pcf11 from human (

) and similar proteins from vertebrates. This repeat is about thirteen amino acids with a high content of proline and glycine residues, however, it varies in length among the sequences included in this entry. These repeats contain the highly conserved RFE/DG motif, conserved in PCF11 orthologues in vertebrates but not in Drosophila, C. elegans, or yeast . It has been described that human PCF11 has 30 repeats of the RFE/DG motif (referred as FEGP in ) which are necessary for pre-mRNA cleavage complex II (CFII) activity . PCF11 is a subunit and an essential component of CFII (the orthologue of cleavage and polyadenylation factor IA (CFIA) from yeast) which is involved in pre-mRNA 3' end processing and in transcription termination . PCF11 is thought to be one of the scaffold proteins of the processing complex. PCF11-mediated termination is essential for vertebrate development .
Pre-mRNA cleavage complex 2 protein Pcf11, helical domain (PCF11_helical)
Type: Domain

This entry represents the α-helical domain found adjacent the CID domain in Pre-mRNA cleavage complex 2 protein Pcf11 from human and similar animal proteins whose function is unknown . Pcf11 is a subunit and an essential component of CFII (the orthologue of cleavage and polyadenylation factor IA (CFIA) from yeast) which is involved in pre-mRNA 3' end processing and in transcription termination . PCF11 is thought to be one of the scaffold proteins of the processing complex. PCF11-mediated termination is essential for vertebrate development .
Complement components C8A/B/C6, EGF-like domain (C8A_B_C6_EGF-like)
Type: Domain

This domain is found in the alpha and beta chains of complement component C8 (C8A/B) and in complement component C6 (C6) from humans. These are constituents of the membrane attack complex (MAC) that play a key role in the innate and adaptive immune response by forming pores in the plasma membrane of target cells.

This entry represents the rigid, disulfide-rich epidermal growth factor (EGF) domain, which is included in the regulatory segment of these proteins . It is found C-terminal to the membrane attack complex perforin domain (

) and N-terminal to the thrombospondin type 1 repeat (

).
PCF11, charged region (PCF11_charged)
Type: Domain

This entry represents the charged region found in the Pre-mRNA cleavage complex 2 protein (Pcf11) from human and the orthologues from vertebrates . PCF11 is a subunit and an essential component of the pre-mRNA cleavage complex II (CFII), the orthologue of yeast cleavage and polyadenylation factor IA (CFIA), which is involved in pre-mRNA 3' end processing and in transcription termination . PCF11-mediated termination is essential for vertebrate development .
CCA-adding enzyme, C-terminal domain (CAA_C)
Type: Domain

Archaeal CCA-adding enzyme builds and repairs the 3'-end of tRNA . This is the C-terminal domain (tail) of CCA-adding enzyme, which serves as a ruler to ensure that only tRNAs and tRNA-like transcripts are substrates for the enzyme and also contributes to the discrimination between stable and unstable RNA substrates .
SpaA-like, prealbumin fold domain subgroup 3 (SpaA_pre-album)
Type: Domain

This entry represents a stalk domain found in bacterial cell surface proteins. It is likely to adopt a prealbumin-like fold and to contain an isopeptide bond.
Picobirnavirus capsid protein (CP_picobirnavirus)
Type: Family

This entry represents a group of proteins from picobirnavirus, including Capsid protein precursor from Human picobirnavirus.

Picobirnaviruses have a unique layer with icosahedral architecture consisting of 60 quasi-symmetric dimers of a its Capsid protein (CP). This protein is organised into two domains, a shell (S) domain that contains all of the α-helices and two β-sheets, and a projecting (P) domain that includes the remaining β-sheets. The dimer is stabilised by domain swapping .
Polymerase basic protein 2, cap-binding domain (PB2_cap-bd)
Type: Domain

This entry represents the cap-binding domain and includes PB2 from Thogotovirus, which is similar to IAV .

Polymerase basic protein 2 (PB2) is a subunit of the RNA-dependent RNA polymerase of Orthomyxovirus Influenza A virus (IAV) which performs transcription of viral mRNAs by cap-snatching, a processes that generated capped primers by host pre-mRNA binding, mediated by PB2 .
Polymerase basic protein 2, '627' domain (PB2_627_dom)
Type: Domain

This entry represents the so-called '627 domain' of the PB2 of several Thogotovirus. This domain was named because it contains the host specificity residue 627 which is a lysine in human Influenza A virus and a glutamate in avian strains . It contains a large positively charged region, consistent with its ability to bind RNA.

Polymerase basic protein 2 (PB2) is a subunit of the RNA-dependent RNA polymerase of Orthomyxovirus Influenza A virus (IAV) which performs transcription of viral mRNAs by cap-snatching, a processes that generated capped primers by host pre-mRNA binding, mediated by PB2 .
Spermatogenesis-associated protein 2, PUB-like domain (SPATA2_PUB-like)
Type: Domain

This domain is found at the N-terminal of Spermatogenesis-associated protein 2 from humans (SPATA2) (

) and similar proteins from animals. This protein interacts with the deubiquitinase CYLD through its non-canonical PUB domain and activates CYLD-mediated hydrolysis of ubiquitin chains. This entry represents the PUB-like domain which folds into a globular α-helical structure .
Poly(A) polymerase, nucleotidyltransferase domain (PolA_pol_NTPase)
Type: Domain

This entry represents the N-terminal nucleotidyltransferase domain of Poly(A) polymerase and similar eukaryotic proteins.

In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA .
PAN2-PAN3 deadenylation complex catalytic subunit PAN2, N-terminal (PAN2_N)
Type: Domain

This entry represents the N-terminal domain of PAN2 and similar sequences predominantly found in animal and fungi. This domain, the assembly unit, engages in a bipartite interaction with PAN3 dimers .

The poly(A)-specific nuclease (PAN) is a deadenylating enzyme involved in cytoplasmic mRNA turnover consisting of two subunits, PAN2 and PAN3 that form a conserved complex which acts in the initial trimming of poly(A) tails during deadenylation, followed by the processive activity of CCR4-NOT complex . PAN2 has two independent structural units, the C-terminal catalytic unit (including

and

) and the N-terminal assembly unit . This assembly unit contains a WD40 propeller that contacts the PAN3 C-terminal domain and it is connected to an adaptable linker which reinforces the asymmetry of the PAN3 dimer preventing the recruitment of a second PAN2 molecule .
Endo-alpha-N-acetylgalactosaminidase-like, helical bundle domain (GH101_helical)
Type: Domain

This domain is found in endo-alpha-N-acetylgalactosaminidase (GH101) from Bifidobacterium longum subsp. longum and similar bacterial proteins . This protein, belongs to the Glycoside Hydrolase Family 101 (GH101) and is related to endo-alpha-N-acetylgalactosaminidase from Streptococcus pneumoniae, a virulence factor. It hydrolyses the T-antigen disaccharide from extracellular host glycoproteins to aid colonization. This entry represents the helical bundle domain, which consists of three α-helices (

)
Complement component 5, CUB domain (C5_CUB)
Type: Domain

Complement component 5 (C5) is a component of the lytic complex consisting of factors C5-C9 which attack bacterial cell membranes. This entry represents the CUB domain .
LpdD-like, chaperone-like domain (LpdD-like_chaperone-like)
Type: Domain

This entry represents a domain present in LpdD (Swiss:

), a protein found in the gallate decarboxylase operon. Structurally this protein is closely related to eukaryotic proteasome assembling chaperone 4 (PAC4)

. This suggests that the proteins in this family may play a similar role. This domain has three highly conserved histidine residue that may be important for function.
tRNA (uracil(54)-C(5))/23S rRNA (uracil(747)-C(5))-methyltransferase, TRAM domain (RUMT_ARLMC_TRAM_dom)
Type: Domain

This domain is found at the N-terminal end of tRNA (uracil(54)-C(5))- methyltransferase (RUMT) and 23S rRNA (uracil(747)-C(5))-methyltransferase (ARLMC) from Pyrococcus abyssi and similar archaeal proteins. RUMT catalyses the formation of 5-methyl-uridine at position 54 (m5U54) in tRNA. ARLMC catalyses the formation of 5-methyl-uridine at position equivalent to 747 (m5U747) in 23S rRNA . This domain, a TRAM domain, adopts a five-stranded β-barrel architecture characteristic of an oligosaccharide/ oligonucleotide-binding fold (OB-fold) .
Transcriptional repressor PaaX-like, central Cas2-like domain (PaaX-like_central)
Type: Domain

This entry represents the central domain of the Transcriptional repressor PaaX from Escherichia coli and similar bacterial proteins. PaaX is involved in metabolism of phenylacetic acid . This domain is structurally related to the Cas2 ribonuclease domain, suggesting that these proteins may degrade mRNAs to carry out regulation.
Complement C4, MG1 domain (C4_MG1)
Type: Domain

Complement component C4 is a non-enzymatic component of C3 and C5 convertases and essential for the propagation of the classical complement pathway. It covalently binds to immunoglobulins and immune complexes and enhances the solubilization of immune aggregates and clearance through CR1 on erythrocytes. C4 is cleaved into the fragments C4a and C4b by MASP-2 protease. C4A isotype is responsible for effective binding to form amide bonds with immune aggregates or antigens, whereas C4B isotype catalyses the transacylation of the thioester carbonyl group to form ester bonds with carbohydrate antigens.

This entry represents the macroglobulin 1 (MG1) found at the N-terminal of C4 .
Complement component 3, CUB domain, second segment (C3_CUB2)
Type: Domain

Complement C3 is major component in the both the classical and alternative complement activation pathways. C3 is cleaved into two chains (alpha and beta) by C3 convertases. C3 is a multidomain protein. This entry represents the second segment of the CUB domain , which is completed by the first segment of the CUB domain, represented in

. The CUB domain is interrupted by the TE domain (

). The CUB, TE and MG8 domains form a massive, tightly packed super domain.

This domain is also found in venom factors, also known as Complement C3 homologues. These are complement-activating proteins with structural and functional similarities to complement component C3b, the activated form of C3 .
Endolysin PlyC (Endolysin_PlyC)
Type: Family

PlyCB is one of the two components of the potent endolysin PlyC, an enzyme specific for streptococcal species. PlyC consists of a single PlyCA catalytic subunit in complex with eight PlyCB molecules arranged in a planar octameric ring. One surface of the PlyCB octamer is quite planar, whereas the other is more convex in shape. The bacterial cell wall binding is achieved through a cleft on PlyCB, which interacts strongly with phosphatidylserine so that PlyC can cross the epithelial cell membrane
BTH_I2711-like (BTH_I2711-like)
Type: Family

This family represents a group of sequences mainly from Burkholderiaceae, including BTH_I2711 (

) from Burkholderia thailandensis. This protein may adopt a fold consisting of two α-helices and two or three β-sheets.
Stability determinant domain (PaaA2_dom)
Type: Domain

This entry represents a domain that covers most of the protein sequence in Stability determinant from Escherichia coli (PaaA2,

) and similar proteins predominantly found in proteobacteria. PaaA2 is an antitoxin from prokaryotic type II toxin-antitoxin three- component module paaR2-paaA2-parE2 that belongs to the RelB- antitoxin family but lacks a DNA-binding domain. It shows two α-helices and adopts defined loop conformations when it wraps itself around the toxin ParE2 . This domain is also found associated with

in some uncharacterised proteins.
PoNi, N-terminal domain 2 (PoNi_N_2)
Type: Domain

This entry represents the N-terminal helical bundle domain from the Pseudomonas aeruginosa PA2201 protein. This protein also contains a C-terminal

domain.

The PoNe immunity proteins (PoNi) which antagonise the DNAse toxin PoNe (Polymorphic Nuclease effector) . PoNi proteins may directly interact with PoNe .
Anthrax protective antigen, immunoglobulin-like domain (PA_Ig-like)
Type: Domain

Anthrax protective antigen (PA) is one of the three proteins forming the anthrax toxin. It is involved in the first step of toxin entry into host cells, enabling lethal factor (LF) and oedema factor (EF) to cross to the cytosol. PA undergoes cleavage by Furin to generate PA20 and PA63. The latter, which adopts a ring-shaped heptameric assembly, shows four distinct domains. The fourth domain, a carboxy- terminal receptor-binding domain, shows an initial hairpin and helix, followed by a β-sandwich with an immunoglobulin-like fold (this entry) .