SII-SWORD/CoKE huggingface dataset:
C381 turret protein, C-terminal (C381_turret_C)
Type: Domain

This entry represents the C-termina jelly roll domain of the Sulfolobus turreted icosahedral virus (STIV) turret protein. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbours two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions .
A223 penton protein, C-terminal (A223_penton_C)
Type: Domain

This entry represents the C-terminal second jelly roll domain of the Sulfolobus turreted icosahedral virus (STIV) penton protein (

,

). STIV is a virus that infects the archaeon Sulfolobus solfataricus and was isolated in acidic hot springs. The virus has a unique architecture based on a pseudo T = 31d capsid symmetry with each icosahedral asymmetric unit consisting of 15 copies of the coat subunit (B345), one copy of the A223 penton base protein, one copy of the C381 turret protein, and one copy of the A55 membrane protein. The pentameric penton base protein is a crucial component of the virus as it forms the vertices of the capsid shell and decorates the penton base structure forming the first floor of the turret. The penton protein contains three different layers, with the N termini forming a 10-stranded β-pore, the middle layer comprising a canonical viral jelly-roll forming a pentameric ring, and the C-terminal forming a second pentameric ring of jelly-rolls.
Putative tail fiber protein gp53-like, C-terminal (Gp53-like_C)
Type: Domain

This entry represents a domain found at the C-terminal end of putative tail fiber protein gp53 from Acinetobacter phage AP22 (

,

, gp53) and similar uncharacterised sequences from tailed bacteriophages and prophages mainly found in proteobacteria. It shows structural similarities to other phage/virus host cell-binding fibres.
Zuotin-like, zuotin homology domain (ZUO1-like_ZHD)
Type: Domain

This domain is found in Zuotin from Saccharomyces cerevisiae (ZUO1) and in similar eukaryotic sequences. ZUO1 is a component of the ribosome-associated complex (RAC), a heterodimeric chaperone complex involved in the regulation of accurate translation termination and in folding or maintaining nascent polypeptides in a folding-competent state. This entry represents its zuotin homology domain (ZHD), which is functionally important for association with ribosomes. It folds into four helices, including a three helix bundle . It is normally found C-terminal to the DnaJ domain (

).
TMEM181, GOLD domain (TMEM181_GOLD)
Type: Domain

This is the N-terminal domain of TMEM181, also known as a Golgi-dynamics (GOLD) domain . TMEM181 mediates action of cytolethal distending toxins (CDT), which are secreted by many pathogenic bacteria . It is homologous to GPR180, TMEM145, and WLS which, together with TMEM87A/B, GPR107 and GPR108, they have been grouped as GOLD domain seven-transmembrane helix (GOST) proteins as they share the same domain architecture .
BRF2-like, C-terminal (BRF2-like_C)
Type: Domain

This domain is found in human Transcription factor IIIB 50 kDa subunit (BRF2) and similar sequences mainly found in eukaryotes. BRF2 is a general activator of RNA polymerase III transcription. This protein consists of an N-terminal zinc ribbon (

), a core domain consisting of two cyclin fold imperfect repeats and a C-terminal domain. This entry represents the second or C-terminal cyclin repeat .

This domain is also found in Plant-specific TFIIB-related protein PTF2 which is a plant-specific TFIIB-related protein that plays important roles in pollen germination and embryogenesis, possibly by regulating gene expression through interaction with TBP2 and the subunits of RNA polymerases .
RhiE, branching domain (RhiE_branching_dom)
Type: Domain

This entry represents the branching domain of RhiE, part of a non-canonical polyketide synthase (PKS) module found in Mycetohabitans rhizoxinica (

,

), and in similar sequences from proteobacteria. Unlike typical PKS modules, RhiE catalyses a Michael-type acetyl addition to generate a branch in the carbon chain, expanding the biosynthetic scope of polyketide biosynthesis. The module consists of a ketosynthase domain, an acyl carrier protein domain, and a cryptic branching ('B') domain in between, featuring a double hot dog (DHD) fold that is structurally homologous to the product template domain of a fungal PKS. The RhiE B domain alone is not sufficient to catalyse the Michael addition, and mutagenesis experiments revealed a crucial role of the ketosynthase domain in branching the carbon chain.
TPR1-like, CTLH-containing domain (TPR1-like_2nd)
Type: Domain

This domain is found in Protein TPR1 from Oryza sativa, also known as Topless-related protein 1/2, and in similar sequences predominantly found in plants and some fungal species. TPR1 is thought to be a downstream regulator of strigolactones signalling. This entry represents the second part of the N-terminal domain of TPR1, which contains the C-terminal to LisH (CTLH) motif, responsible for the binding to the auxin-responsive protein 12 (IAA12) . This domain shows an all-alpha configuration.
Lin-28A-like, second zinc knuckle (Lin-28A-like_Znf-CCHC_2)
Type: Domain

This domain is found at the C-terminal of human protein lin-28 homolog A and B (Lin-28A/B). Lin28A is an RNA-binding protein that inhibits processing of pre-let-7 miRNAs and regulates translation of mRNAs that control developmental timing, pluripotency and metabolism. This interaction requires the zinc-knuckle domains of Lin-28A . Lin-28B is also a suppressor of miRNA biogenesis, including that of let-7 and possibly of miR107, miR-143 and miR-200c. It binds primary let-7 transcripts (pri-let-7), including pri-let-7g and pri-let-7a-1, and sequester them in the nucleolus, away from the microprocessor complex, hence preventing their processing into mature miRNA . This entry represents the second zinc-knuckle domain.
Talin, IBS2B domain (Talin_IBS2B)
Type: Domain

Talin is an adaptor protein that activates integrin family of cell adhesion molecules and couples them to the actin cytoskeleton. The integrin activation is known to involve binding of the Talin FERM domain to membrane proximal sequences in the cytoplasmic domain of the integrin beta-subunit. IBS2 is a second integrin-binding site that has been identified near the C-terminal end of the Talin rod. The crystal structure of IBS2 reveals two five-helix bundles, IBS2A and IBS2B, connected by a continuous helix. The Talin IBS2B domain, represented in this entry, is essential for integrin binding, binding to acidic phospholipids, and targeting to focal adhesions. The domain comprises a tandem pair of five-helix bundles with the same topology, comprising five antiparallel α-helices .
Sarcolamban A/B (SclA/B)
Type: Family

This entry represents Sarcolamban A and B from Drosophila melanogaster (SclA/B) and similar sequences from Drosophila species. SclA and SclB play an essential role in the regulation of calcium transport at the sarcoplasmic reticulum (SR), which is secondarily required for regular muscle contraction .
Tarsal-less AA (Tal-AA)
Type: Family

This entry represents Peptide tarsal-less AA from Drosophila melanogaster and simal sequences from Drosophilidae. This protein is required in early stages of leg development for the intercalation of the tarsal segments during the mid-third instar stage and later for tarsal joint formation . It is one of four peptides (tal-1A, tal-2A, tal-3A and tal-AA) produced from a polycistronic gene that function redundantly in several developmental processes .
Cep192-like, domain 1 (Cep192-like_D1)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the first domain found in the metazoan Cep192 homologues.
Cep192-like, domain 2 (Cep192-like_D2)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the second domain found in the metazoan Cep192 homologues.
Cep192-like, domain 7 (Cep192-like_D7)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the seventh domain found in the metazoan Cep192 homologues.
Cep192-like, domain 8 (Cep192-like_D8)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the eighth domain found in the metazoan Cep192 homologs.
Cep192-like, domain 3 (Cep192-like_D3)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the third domain found in the metazoan Cep192 homologues.
Cep192/Spd-2-like domain (Cep192_Spd-2-like_dom)
Type: Domain

Human Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the fourth domain of the metazoan Cep192 homologues. This domain along with domain 5 constitutes the so-called Spd2 domain that is ubiquitously present in all SPD2/CEP192 homologues beyond Metazoa and represents the most conserved region amongst them .

This domain is also found centrally located in Spindle-defective protein 2 from Caenorhabditis elegans (Spd-2), which is required for centrosome duplication and maturation and for pericentriolar material (PCM) recruitment .
Cep192-like, domain 5 (Cep192-like_D5)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the fifth domain of the metazoan Cep192 homologues. This domain along with domain 4 constitutes the so-called Spd2 domain that is the most conserved region amongst metazoa .
Cep192-like, domain 6 (Cep192-like_D6)
Type: Domain

Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation . Most of the metazoan Cep192 homologues consist of eight ASH/PapD-like domains, which are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion . This entry represents the sixth domain of the metazoan Cep192 homologues.
Androglobin, domain II (Androglobin_II)
Type: Domain

Androglobin is a protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility. Androglobin contains an N-terminal cysteine protease domain that lacks the catalytic cysteine, a tandem of three β-sandwich domains (domains II, IV, V) and a circularly permuted globin-like domain (domain III) that is inserted between domain II and IV . This entry represents domain II. This domain is predicted to adopt a jelly-roll topology that is observed in galactose-binding domains. It has a significant sequence similarity to domains found in ciliary protein FAP42 and to domain III in calpains.
Androglobin, domain IV (Androglobin_IV)
Type: Domain

Androglobin is a protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility. Androglobin contains an N-terminal cysteine protease domain that lacks the catalytic cysteine, a tandem of three β-sandwich domains (domains II, IV, V) and a circularly permuted globin-like domain (domain III) that is inserted between domain II and IV . This entry represents domain IV. This domain is predicted to adopt a jelly-roll topology that is observed in galactose-binding domains. It has a significant sequence similarity to domains found in ciliary protein FAP42 and to domain III in calpains.
Androglobin, domain V (Androglobin_V)
Type: Domain

Androglobin is a protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility. Androglobin contains an N-terminal cysteine protease domain that lacks the catalytic cysteine, a tandem of three β-sandwich domains (domains II, IV, V) and a circularly permuted globin-like domain (domain III) that is inserted between domain II and IV . This entry represents domain V. This domain is predicted to adopt a jelly-roll topology that is observed in galactose-binding domains. It has a significant sequence similarity to domains found in ciliary protein FAP42 and to domain III in calpains. This domain is predicted to contain two large, nearly 80 residues long insertions in the loops both of which are likely to be disordered.
FAP42-like, domain B2 (FAP42-like_B2)
Type: Domain

FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection of the ciliary central apparatus (CA). This protein forms a complex with FAP413 and FAP246, which is essential for a stable assembly of the C1b, C1f and C2b projections, and loss of these proteins leads to ciliary motility defects. FAP42 structure has been determined along with other components of the Chlamydomonas reinhardtii ciliary central apparatus . FAP42 contains cysteine peptidase domain, adenylate kinase domain, five guanylate kinase domains and three β-sandwich domains. The latter adopt a jelly-roll topology and have a significant sequence and structural similarity to domain III in calpains and the predicted β-sandwich domains in androglobin. This entry represents the second FAP42 β-sandwich domain B2.
FAP42-like, domain B3 (FAP42-like_B3)
Type: Domain

FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection of the ciliary central apparatus (CA). This protein forms a complex with FAP413 and FAP246, which is essential for a stable assembly of the C1b, C1f and C2b projections, and loss of these proteins leads to ciliary motility defects. FAP42 structure has been determined along with other components of the Chlamydomonas reinhardtii ciliary central apparatus . FAP42 contains cysteine peptidase domain, adenylate kinase domain, five guanylate kinase domains and three β-sandwich domains. The latter adopt a jelly-roll topology and have a significant sequence and structural similarity to domain III in calpains and the predicted β-sandwich domains in androglobin. This entry represents the third FAP42 β-sandwich domain B3.
NGO1945-like, C-terminal domain (NGO1945-like_C)
Type: Domain

This entry represents the C-terminal domain of a Neisseria protein, NGO1945 (

). This domain shows a β-sheet containing three antiparallel β-strands and three α-helices (

). From genomic context and the fold of the C-terminal part, it is suggested that this protein is involved in transcriptional regulation . The N-terminal domain of NGO1945 is represented in

. Members of this group are mainly found in proteobacteria.
Oxygen-evolving enhancer protein 3, plants (PSII_PsbQ_pln)
Type: Family

In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants .

This family represents the PSII OEC protein PsbQ from plants. Both PsbQ and PsbP (

) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII .

Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product .

PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane . Within the core of the complex, the chlorophyll and β-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection .
Membrane protein of 12 TMs, archaea (12TM_1_arc)
Type: Family

This entry represents a family of archaeal proteins that carry twelve transmembrane regions. It does not have any characteristic nucleotide-binding-domains of the GxSGSGKST type, so it may not be an ATP-binding cassette transporter. However, it may well be a transporter of some description. ABC transporters always have two nucleotide binding domains.
TMEM87A/B, GOLD domain (TMEM87A/B_GOLD)
Type: Domain

This entry represents the GOLD (Golgi-dynamics) domain of TMEM87A and TMEM87B.

Members of this entry are evolutionary related to GPR107 and GPR108. Together with GPR180, TMEM145, TMEM181 and WLS, they have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) given they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain . TMEM87s localise to the Golgi and have suggested roles in protein trafficking to and from the Golgi. TMEM87 has been proposed to act as mechanosensitive ion channels, however, structural and functional analysis suggest that they do not act as ion channels or G-protein coupled receptors .
BDI_0842-like (BDI_0842-like)
Type: Domain

This entry represents the C-terminal region of BDI_0842 from Parabacteroides distasonis and similar sequences, for which there is a known structure

. The structure has similarity to the alpha-lytic protease prodomain-like fold. Proteins in this family have an N-terminal lipoprotein attachment motif. The function of these proteins is unknown.
CAND6/7, N-terminal domain (CAND6-7_N)
Type: Domain

This entry represents the N-terminal domain found in CAND6/7 from Arabidopsis and related sequences. These proteins have been predicted to be G-protein coupled receptors that play a role in plant and microbe interactions . They consist of two domains, a GOLD-like domain represented in this entry and a seven transmembrane domain, an architecture shared with GOST (GOLD seven-transmembrane helix) proteins . CAND7 has been described as a G-protein coupled receptor involved in root growth mediated by the bacterial quorum-sensing signals N-acyl-homoserine lactones (AHLs) .
Nsp1alpha, N-terminal zinc finger (Nsp1alpha_Znf)
Type: Domain

Porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV), a positive-strand RNA virus that belongs to the Arteriviridae family of Nidovirales, has been identified as the causative agent of PRRS. Nsp1alpha is the amino (N)-terminal protein in a polyprotein encoded by the PRRSV genome and is reported to be crucial for subgenomic mRNA synthesis, presumably by serving as a transcription factor. Before functioning in transcription, nsp1alpha proteolytically releases itself from nsp1beta.

Nsp1alpha contains a zinc finger domain (Znf, represented in this entry), a papain-like cysteine protease (PCP) domain with a zinc ion unexpectedly bound at the active site (which is essential for proteolytic self-release of nsp1alpha), and a carboxyl-terminal extension (which occupies the substrate binding site of the PCP domain).
NrtR, DNA-binding winged helix domain (NrtR_WHD)
Type: Domain

This entry represents the C-terminal DNA-binding domain of transcriptional regulator NrtR from Acinetobacter baylyi and similar bacterial proteins. NrtR is involved in regulating the transcription of NAD biosynthetic genes. This domain has a winged helix-turn-helix structure .
CEP-1, C-terminal SAM domain (CEP-1_C)
Type: Domain

This entry represents the C-terminal domain of the CEP-1 protein which is a p53 homologue found in C. elegans . The CEP-1 C-terminal is composed of two sub-domains, an oligomerisation domain (OD) followed by a SAM domain (this entry) that closely interacts with the oligomerisation. The OD domain of CEP-1 forms a dimer instead of the usual tetramer observed in human p53 .
Cel124-like, catalytic domain (Cel124_cat)
Type: Domain

This entry represents the catalytic domain of endo-acting cellulase Cel124 (

), found at its C-terminal, and related proteins. The active site architecture of this cellulase shares significant structural similarity to GH23 enzymes, a family that contains inverting lysozymes and lytic transglycosylases . These proteins adopt typical lysozyme (muramidase)-like fold.