SII-SWORD/CoKE huggingface dataset:
Major capsid protein V20, C-terminal domain (MCP_V20_C)
Type: Domain

This is the C-terminal domain of major capsid protein V20 from Sputnik virophage. This domain folds into a β-sandwich with a jelly-roll topology . V20 is a major capsid protein from Sputnik virophage. This is a dsDNA virus, referred to as a virophage, that is co-assembled with Mimivirus in the host amoeba. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double jelly-roll major capsid proteins creating pseudohexameric capsomer symmetry.
MRM3-like, substrate binding domain (MRM3-like_sub_bind)
Type: Domain

MRM3 catalyses the formation of 2'-O-methylguanosine at position 1370 Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA . This entry represents the substrate binding domain of MRM3 from animals and related sequences from bacteria .
Major capsid protein V20, N-terminal domain (Sputnik_MCP_N)
Type: Domain

This entry represents the N-terminal domain of the major capsid protein V20 from Sputnik virophage, which adopts a jelly roll fold . Sputnik is a dsDNA virus, referred to as a virophage, that is co-assembled with Mimivirus in the host amoeba. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double jelly-roll major capsid proteins creating pseudohexameric capsomer symmetry.
Hen1-like, N-terminal domain (Hen1-like_N)
Type: Domain

This entry represents the N-terminal domain of Hen1 from Capnocytophaga gingivalis and related proteins. This protein is a component of the bacterial RNA repair complex composed of three proteins: Pnkp1, Rnl and Hen1. This complex neutralises the damage inflicted by ribotoxins which is essential for cell survival. The Pnkp-Hen1 RNA repair complex carries out methylation of the 2'-OH group that is responsible for the RNA cleavage and thus the repaired RNA resists future RNA damage by the same ribotoxin. The N-terminal domain of Hen1 activates the ligase activity of Pnkp by locking the insertion domain of Pnkp into a conformation that allows access to the ligase pocket .
Shisa, N-terminal domain (Shisa_N)
Type: Domain

Shisa is a transmembrane, transcription factor-type protein that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface. Vertebrate homologues play roles in development, cancer and apoptosis .

This entry represents a domain found in the N-terminal region, which contains six conserved cysteines. Members of this family are found mainly in vertebrates but also in other animal species.
MoaF-like (MoaF-like)
Type: Domain

This domain consists mainly of uncharacterised bacterial proteins that are related to MoaF and adopt very similar β-barrel structure. In some instances, this domain appears twice.
Polycomb protein EED-like, insertion domain (PRC2_EED-like_ins)
Type: Domain

EED (

) is one of the core subunits of Polycomb Repressive Complex 2 (PRC2) that is involved in histone methylation. EED consists of two domains: a seven-bladed β-propeller and a small α/β domain that is inserted into the sixth blade . EED specifically binds to histone tails carrying trimethyl-lysine residues associated with repressive chromatin marks, and this leads to the allosteric activation of the methyltransferase activity of PRC2 . This entry represents the insertion domain.
Out at first protein, BRICHOS-like domain (OAF_N)
Type: Domain

This entry represents the BRICHOS-like domain found at the N-terminal of Out at first protein (OAF) protein family .

OAF is vital for proper neuronal development and hatching . The gene that encodes this protein, has a promoter which may help mediate regulation of neighbouring genes . An alternative name for this protein is HCV NS5A-transactivated protein 13 target protein 2, which stands for Hepatitis C virus nonstructural 5A-transactivated protein 13 target protein 2. NS5A inhibits double-stranded-RNA-activated protein kinase (PKR) activity, which is thought to allow Hepatitis C Virus replication to continue in the presence of an alpha interferon (IFN) induced antiviral response .
Domain of unknown function DUF7011 (DUF7011)
Type: Domain

This domain of unknown function is found in a group of proteins predominantly from proteobacteria. It has a LxHDGK/RRL motif and a highly conserved W residue. It is usually found C-terminal to

and N-terminal to

.
Butyrophilin subfamily 3 member A2-like, Ig-C domain (BTN3A2-like_Ig-C)
Type: Domain

This domain is found in proteins from B7 family, including Butyrophilin subfamily 3 member A1/A2 (BTN3A1/A2) and similar proteins . BTN3A2 is a protein that plays a role in T-cell responses in the adaptive immune response . BTN3A2 shows two extracellular domains: an N-terminal Ig-V like domain (

) and a C-terminal Ig-C type domain that is located in the centre of the protein sequence .
Out at first, C-terminal (Oaf_C)
Type: Domain

This entry represents the putative C-terminal cysteine-rich mature peptide found in Out at first (Oaf) animal proteins . Oaf is vital in for proper neuronal development and hatchin .
Shieldin complex subunit 1, C-terminal domain (SHLD1_C)
Type: Domain

SHLD1, also known as RINN3, is a component of the shieldin complex, a vertebrate-specific protein complex which functions as a downstream effector in the 53BP1 pathway, that regulates NHEJ (non-homologous end joining) . This entry represents a conserved helical domain found at the C-terminal of SHLD1.
C5orf34-like, second domain (C5orf34-like_2nd)
Type: Domain

This entry represents a domain located C-terminal to

in a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavorable prognosis of patients from a variety of human malignancies . This domain is predicted to show an α/β structure.
C5orf34-like domain (C5orf34-like_dom)
Type: Domain

This entry represents a domain found in a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavorable prognosis of patients from a variety of human malignancies . This domain appears C-terminal to

and

and N-terminal to

. This domain is predicted to show an α/β configuration with high structural similarity to a polo box.
C5orf34-like (C5orf34-like)
Type: Family

This entry represents a family of eukaryotic proteins, including the human uncharacterised protein C5orf34, which has been reported to be correlated with an unfavorable prognosis of patients from a variety of human malignancies .
Interleukin 33, C-terminal (IL33_C)
Type: Domain

This entry represents a β-trefoil-related domain found at the C-terminal of interleukin-33 (IL33) from vertebrates. This protein binds to and signals through IL1RL1/ST2 and its stimulation leads to the recruitment of MYD88, IRAK1, IRAK4, and TRAF6, followed by phosphorylation of MAPK3/ERK1 and/or MAPK1/ERK2, MAPK14, and MAPK8 . It also serves as a warning signal between cells at times of injury or cell death .
CATSPERB, head domain (CATSPERB_head)
Type: Domain

CATSPERB (Cation channel sperm-associated protein subunit beta) is an auxiliary subunit of the CatSper complex which is involved in sperm cell hyperactivation, a process needed for sperm motility which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which consists of an N-terminal domain (

), followed by a β-propeller (

) that is also present in the other auxiliary subunits gamma, delta and epsilon. This entry represents the head domain, only present in the beta subunit .
CATSPERB, Ig-like domain (CATSPERB_Ig-like)
Type: Domain

CATSPERB (Cation channel sperm-associated protein subunit beta) is an auxiliary subunit of the CatSper complex which is involved in sperm cell hyperactivation, a process needed for sperm motility which is essential late in the preparation of sperm for fertilisation. This is a multi-domain protein which consists of an N-terminal domain (

), followed by a β-propeller (

) that is also present in the other auxiliary subunits gamma, delta and epsilon. This entry represents the Ig-like domain of CATSPERB , which seals the top of the channel together with the Ig-like domains of the other auxiliary subunits .
Elongation factor G-like, domain II (EF-G-like_DII)
Type: Domain

This entry represents a domain found in the bacterial group of Elongation factor G (EF-G) proteins, which catalyse the translocation step of translation. It consists of five structural domains, this entry represents the second domain which adopts a β-barrel structure. This entry also includes other translation factors such as translation initiation factor IF-2, peptide chain release factor 3 (RF3), mitochondrial ribosome-releasing factor 2 (also known as EFG2 mitochondrial) , among others.
Domain of unknown function DUF6935 (DUF6935)
Type: Domain

This is a domain, found in uncharacterised bacterial proteins and in some archaeal sequences, either as standalone or in combination with other domains. It is remotely related to soluble lipid-binding protein MlaC and it is predicted to adopt a similar structure with a typical NTF2-like topology (

).
Chloramphenicol halogenase CmlS, C-terminal domain (CmlS_C)
Type: Domain

Chloramphenicol halogenase CmlS (

) belongs to the large and diverse superfamily of flavin-dependent halogenases. CmlS is one of the few enzymes known to halogenate an alkyl group.

This entry represents the C-terminal domain of CmlS that resembles an arch-like structure above a central α-helix. This domain creates a T-shaped tunnel leading to the halogenation active site and thus likely directs substrates into the active site to achieve the desired specificity .
Enoyl-acyl carrier protein reductase FabMG (FabMG)
Type: Family

This entry, previously known as DUF6936, represents FabMG enoyl-acyl carrier protein reductase (ENR) and related proteins. This enzyme is a FabI-type ENR that employs NADH as a coenzyme and mediates resistance to triclosan. FabMG (

,

) adopts an α/β structure, with a central parallel β-sheet elaborated with α-helices on both sides (

). FabMG differs from other related ENRs in sequence and structure. These differences, in particular in the substrate-binding loop and pocket regions in which triclosan binds, could be responsible for the triclosan resistance .
RsmI, HTH domain (RsmI_HTH)
Type: Domain

This entry represents a small α-helical domain at the C terminus of RsmI mainly from proteobacteria and actinomycetes, that folds into a typical three helical DNA/RNA binding bundle containing an HTH motif. This domain is found in Ribosomal RNA small subunit methyltransferase I (RsmI) and related proteins. RsmI is an S-adenosyl-L-methionine-dependent methyltransferase that catalyses the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. It may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity. In vitro, it is active on the assembled 30S subunit, but not naked 16S rRNA or 70S ribosomes .
PGAP2IP, second transmembrane domain (PGAP2IP_TM_2nd)
Type: Domain

This domain is found in the human PGAP2-interacting protein (PGAP2IP) and its homologues in yeast CWH43. PGAP2IP is composed of three domains. Two of these domains are predicted to adopt very similar structure consisting of six transmembrane helices, which suggests a possible duplication event in these proteins. Its yeast homologue CWH43 is involved in the remodeling of the lipid moiety of GPI anchors to ceramides .
PGAP2IP, first transmembrane domain (PGAP2IP_TM_1nd)
Type: Domain

This domain is found in the human PGAP2-interacting protein (PGAP2IP) and its homologues in yeast CWH43. PGAP2IP is composed of three domains. Two of these domains are predicted to adopt very similar structure consisting of six transmembrane helices, which suggests a possible duplication event in these proteins. These two domains have significant similarity to domains belonging to major facilitator superfamily (MFS). The PGAP2IP yeast homologue, CWH43, is involved in the remodeling of the lipid moiety of GPI anchors to ceramides .
DarT1-associated NADAR antitoxin (NADAR-DarT1)
Type: Family

This entry, previously known as DUF6977, represents DarT1-associated NADAR antitoxin and related proteins. The DarT-NADAR system is a TA system catalysing the specific and reversible ADP-ribosylation of guanosine bases in which DarT1-associated NADARs reverse guanine ADP-ribosylation catalysed by DarT1. DarT1-associated NADAR antitoxin adopts an α/β globular structure characterised by an α-helical core that forms the active site flanked by two small β-sheet regions, comprising two and three strands . Its structural core is globally similar to the structure of E.coli protein YbiA, a member of the NADAR domain family (

).
Dispersed gene family protein 1, N-terminal domain (DGF-1_N)
Type: Domain

This entry represents the N-terminal domain present in DGF-1 (Dispersed gene family protein 1) from Trypanosoma, one of the most abundant proteins in T. cruzi genome . It seems to have a preferential expression in amastigotes (intracellular replicative forms that develop in the mammalian host) . The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction .
Dispersed gene family protein 1, beta-sheet domain (DGF-1_b-sheet_dom)
Type: Domain

This entry represents a β-sheet domain present in DGF-1 from Trypanosoma proteins, one of the most abundant proteins in T. cruzi genome . This domain adopts a pectin lyase-like fold. The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction.
Protein of unknown function DUF6978 (DUF6978)
Type: Family

This is a family of uncharacterised proteins. They are predicted to adopt a globular α/β structure consisting of a meander β-sheet and two α-helices packed on one side on the sheet. These proteins contain three highly conserved histidines that in the predicted structure cluster close in space and could potentially form a metal binding site.
Protein of unknown function DUF6979 (DUF6979)
Type: Family

This is a family of uncharacterised proteins. They are predicted to fold into a globular structure consisting mainly of α-helices.
Domain of unknown function DUF6980 (DUF6980)
Type: Domain

This is a domain found in uncharacterised bacterial proteins. This domain occurs either standalone or in combination with other domains. It contains conserved cysteines and histidine that may be involved in Zn2 coordination.
Treslin, N-terminal domain (Treslin_N)
Type: Domain

This entry represents the N-terminal domain of Treslin, the metazoan counterpart of Sld3 from yeast, which are the hub proteins mediating protein associations critical for the helicase formation .

Treslin, as Sld3, interacts with TopBP1 in a Cdk2-dependent manner, which then collaborate in the Cdk2-mediated loading of Cdc45 onto replication origins. Treslin and Sld3 differ in their molecular sizes and amino acid sequences, however, they share a conserved Sld3/Treslin domain (STD) . According to their similarities, it has been suggested that helicase activation in mammals has diverged in complexity during evolution from that in yeasts and may involve additional partners that interact with TopBP1 . This N-terminal domain is also referred to as conserved in Treslins (CIT), which has a von Willebrand factor type A (vWA) fold and its function in replication is not clear .
Treslin, STD domain (Treslin_STD)
Type: Domain

This entry represents the STD (Sld3-Treslin domain) domain from Treslin, the metazoan counterpart of Sld3 from yeast, which are the hub proteins mediating protein associations critical for the helicase formation .

Treslin, as Sld3, interacts with TopBP1 in a Cdk2-dependent manner, which then collaborate in the Cdk2-mediated loading of Cdc45 onto replication origins. Treslin and Sld3 differ in their molecular sizes and amino acid sequences, however, they share this conserved Sld3/Treslin domain (STD), essential for replication origin firing . According to their similarities, it has been suggested that helicase activation in mammals has diverged in complexity during evolution from that in yeasts and may involve additional partners that interact with TopBP1 .
MKRN2 opposite strand protein-like, C-terminal (MKRN2OS-like_C)
Type: Domain

This domain is functionally uncharacterised and is found in animals, including the functionally uncharacterised human MKRN2 opposite strand protein (MKRN2OS). There is a single completely conserved residue C that may be functionally important. This domain is predicted to be structurally similar to peptidase C97 domain (

) .
MKRN2 opposite strand protein-like, N-terminal (MKRN2OS-like_N)
Type: Domain

This cysteine-rich domain is functionally uncharacterised and is found in animals, including the functionally uncharacterised human MKRN2 opposite strand protein (MKRN2OS). It is predicted to adopt a mainly β-configuration and is found associated to (

).
Replication protein RepB, C-terminal domain (RepB_C)
Type: Domain

This entry represents the C-terminal oligomerisation domain (OD) of plasmid replication proteins, such as RepB. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence . They consist of an N-terminal origin binding domain (OBD,

) which is the DNA-binding/catalytic domain that belongs to the HUH endonuclease superfamily and this C-terminal helical domain, which is responsible for the hexameric state of the protein .
RecX, second three-helical domain (RecX_HTH_2nd)
Type: Domain

This entry represents the second three-helical domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells . RecX protein is known to inhibit the activity of RecA protein in DNA recombination . It contains three HTH-like domains, first (

), second, represented by this entry, and third (

).
RecX, third three-helical domain (RecX_HTH_3rd)
Type: Domain

This entry represents the third three-helical domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells . RecX protein is known to inhibit the activity of RecA protein in DNA recombination . It contains three HTH-like domains, first (

), second (

), and third, represented by this entry.
RecX, first three-helical domain (RecX_HTH_1st)
Type: Domain

This entry represents the first three-helix domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells . RecX protein is known to inhibit the activity of RecA protein in DNA recombination . It contains three HTH-like domains, first represented by this entry, second (

) and third (

).
Flagellar hook-associated protein FlgK, helical domain (FlgK_helical)
Type: Domain

This entry represents a mainly helical domain found in flagellar hook-associated protein FlgK (also called Flagellar hook-associated protein 1) and related proteins mostly from bacteria. FlgK is one of three hook associated proteins that form the hook-filament junction. This domain adopts a broken antiparallel helical bundle comprising six helical segments .
Nonstructural protein NS-S, N-terminal, bunyaviral (NS-S_N_bunyaviral)
Type: Domain

This entry represents the N-terminal domain of Nonstructural protein NS-S from the tospovirus Tomato spotted wilt virus and related sequences from related Bunyavirales. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. NS-S, present in infected cells, but absent from purified virus particles , is not essential for virus replication, but contributes substantially to pathogenesis . It has been shown to inhibit the production of alpha/beta interferons, and to inhibit interferon regulatory factor-mediated cell death . It is a viral suppressor of host RNAi and viral inducer of host attractiveness to insect vectors. NSS acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing, a mechanism of plant viral defence that limits the accumulation of viral RNAs .
Nonstructural protein NS-S, WIV domain, bunyaviral (NS-S_WIV_bunyaviral)
Type: Domain

This entry represents the WIV domain of Nonstructural protein NS-S from the tospovirus Tomato spotted wilt virus and related sequences from related Bunyavirales. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. Tospoviruses infect plants and arthropods (such as thrips), which serve as vectors for plant transmission.

NS-S, present in infected cells, but absent from purified virus particles , is not essential for virus replication, but contributes substantially to pathogenesis . It has been shown to inhibit the production of alpha/beta interferons, and to inhibit interferon regulatory factor-mediated cell death . It is a viral suppressor of host RNAi and viral inducer of host attractiveness to insect vectors. NSS acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing, a mechanism of plant viral defence that limits the accumulation of viral RNAs . The WIV domain probably facilitates viral infection of arthropods. WIV stands for 'Widespread, Intriguing, Versatile'.
RapZ-like, N-terminal domain (RapZ-like_N)
Type: Domain

This entry represents the N-terminal P-loop kinase domain of RNase adapter protein RapZ and related proteins. RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism . It is a RNA-binding protein that recruits the major endoribonuclease RNase E to sRNAs GlmZ .
RapZ, C-terminal domain (RapZ_C)
Type: Domain

This entry represents the C-terminal domain of RapZ which belongs to the Rhodanese-Phosphatase superfamily. It has been shown to bind multiple ligands as part of the regulation of glucosamine-6-phosphate (GlcN6P) levels, which is a precursor to the bacterial cell wall polymer peptidoglycan. Assignment to the greater Rhodanese-Phosphatase superfamily has led to the prediction that, as part of this regulation, it functions as a sugar phosphorylation-dephosphorylation switch .
Glabrous enhancer-binding protein-like, DBD domain (GeBP-like_DBD)
Type: Domain

This entry represents the DNA binding domain (DBD) present in GLABROUS1 enhancer-binding protein (GeBP) and GeBP-like proteins, such as storekeeper and storekeeper-like (STKL) transcription factors. GeBP and GeBP-like proteins play a redundant role in cytokinin hormone pathway regulation . Storekeeper was identified as a B-box motif binding factor that regulates expression of patatin, a storage protein in potato . Storekeeper-like transcription factors STKL1 and STKL2 function as transcription factors in the glucose signalling pathway . The overall predicted structure of this DNA binding domain (DBD) reveals a bundle of four helices, with helices α1 to α3 making up a single myb-type helix-turn-helix (HTH) domain.