SII-SWORD/CoKE huggingface dataset:
ARMC9, LIS1 homology motif (ARMC9_LisH)
Type: Conserved_site

This entry represents the Lis1H motif found in the ARMC9 protein family. The ARMC9 protein plays a role in ciliogenesis, being essential for the proper acetylation and polyglutamylation of ciliary microtubules, as well as for the control of cilium length .
Polysaccharide lyase 14 (Polysacc_lyase_14)
Type: Domain

This protein family includes Alginate lyase from the mollusc Aplysia kurodai (AkAly30) and similar proteins from all cellular organisms. AkAly30 degrades alginate by cleaving the glycosidic bond through a β-elimination reaction. This enzyme adopts a β-jelly roll fold comprising two antiparallel β-sheets. Some β strands of the first sheet twist to form an electropositive-rich cavity where the substrates are believed to be located .
LisH domain-containing protein ARMC9, ARM repeat domain (ARMC9_ARM_dom)
Type: Domain

ARMC9 is localised to the basal body of a cilium and is upregulated during ciliogenesis . It is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length . This entry represents a domain consisting of armadillo repeats found towards the C-terminal of ARMC9 .
POLQ-like, helical domain (POLQ-like_helical)
Type: Domain

DNA polymerase theta (Pol Theta, encoded the POLQ gene) is one of ~15 DNA polymerases in the human genome. PolQ is distinct among human DNA polymerases, exhibiting not only a C-terminal DNA polymerase domain but also an N-terminal domain exhibiting similarity and motifs typical of superfamily 2 (SF2) helicases . This entry corresponds to the helical domain . This entry also includes mammal Helicase POLQ-like (HELQ, ) and Helicase and polymerase-containing protein TEBICHI (TEB, ).
E3 ubiquitin-protein ligase ARIH1-like, UBA-like domain (ARIH1-like_UBL)
Type: Domain

This entry represents the UBA-like (UBL) domain from the Human Homologue of Ariadne (HHARI) and its homologues, which are Ariadne subfamily E3 ubiquitin ligase proteins . This domain binds to Ubiquitin and NEDD8 .
Arginine dihydrolase ArgZ/ArgE-like, C-terminal, second subdomain (ArgZ/ArgE-like_C_2nd)
Type: Domain

This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein and Ornithine cyclodeaminase), ArgE from Synechocystis sp and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (

) and a C-terminal uncharacterised region that can be divided in two subdomains. This entry represents the most C-terminal region, which forms a large Rossmann fold domain. Its specific function is unknown .
Arginine dihydrolase ArgZ/ArgE-like, C-terminal, first subdomain (ArgZ/ArgE-like_C_1st)
Type: Domain

This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein and Ornithine cyclodeaminase), ArgE from Synechocystis sp and similar prokaryotic sequences. ArgZ is involved in an ornithine-ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (

) and a C-terminal uncharacterised region that can be divided in two subdomains. This entry represents the small first subdomain of the C-terminal domain, which folds into β-strands. Its specific function is unknown .
Activity-regulated cytoskeleton-associated protein, capsid domain (Arc_capsid_dom)
Type: Domain

This domain is found in Activity-regulated cytoskeleton-associated protein from humans (Arc), a master regulator of synaptic plasticity that promotes endocytosis of AMPA receptors and a postsynaptic mediator of activity-dependent synapse elimination in the developing cerebellum. This protein is associated with cognitive diseases. This Gag-like protein has the topology of a retroviral Gag protein, with a central capsid domain (this entry) with two globular subdomains, the N-lobe and the C-lobe, consisting of four and five α-helices, connected by a short non-helical segment .
RNA helicase aquarius, beta-barrel (Aquarius_b-barrel)
Type: Domain

This entry represents the β-barrel domain found adjacent the N-terminal domain of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly .
RNA helicase aquarius, insertion domain (Aquarius_insert)
Type: Domain

This entry represents the insertion domain of RNA helicase aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly .
Anaphase-promoting complex subunit 5, N-terminal domain (Apc5_N)
Type: Domain

This domain is found at the N-terminal of Anaphase-promoting complex subunit 5 from human (Apc5), a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This domain has an α-helical fold [1-4]. It is normally found in association with

.
FACT complex subunit SPT16, C-terminal domain (FACT_SPT16_C)
Type: Domain

This entry represents the C-terminal domain of SPT16, which wraps around the DNA binding surface of H2A-H2B .

SPT16 is a component of the FACT (facilitator of chromatin transcription) complex, a general chromatin factor that acts to reorganise nucleosomes . In budding yeasts, the N-terminal domain (NTD) of SPT16 includes a smaller N-terminal lobe (residues 1-175) and a larger C-terminal lobe (residues 176-447).
Single-stranded DNA binding protein Ssb-like, OB fold (Ssb-like_OB)
Type: Domain

This entry represents the OB fold domain of single-stranded DNA binding protein Ssb from archaea and its homologues from mammals and plants such as the SOSS complex subunits B1 and B2. Members of this entry have a simple domain organisation consisting of a single DNA-binding OB fold coupled to a flexible C-terminal tail (

) . The ssDNA recognition is modulated by base-stacking of three key aromatic residues in archaeal Ssb, in contrast with the OB domain of the human homologue hSSB1 (

) .
Anaphase-promoting complex subunit 1, beta-sandwich domain (Apc1_3rd)
Type: Domain

This domain is found close to the C-terminal of the Apc1 (anaphase-promoting complex subunit 1) protein which is a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle .
PMI1/PMIR1-2, C-terminal domain (PMI1_PMIR1-2_C)
Type: Domain

This entry represents a presumed domain found towards the C-terminal of plant proteins, such as PMI1 (PLASTID MOVEMENT IMPAIRED 1 and PMIR1/2 (PMI1 related 1 and 2) from Arabidopsis. PMI1 and PMIR1 are required for efficient chloroplast photorelocation movement, while PMIR2 seems not necessary for this . PMI1 is a mobile signal that initiates coordinated changes in protein-protein and protein-plasma membrane interactions for chloroplast movement in response to light, which determines where in the cell chloroplasts are able to anchor o the plasma membrane . PMI1 has been found to mediate ABA sensitivity during germination .
Bacteriophage PM2 P3 protein-like (PM2_P3-like)
Type: Family

Viral membrane protein P3 assemblies into dimers. Each P3 subunit comprise a core of two perpendicular α-helices, and subunits are bound together by a parallel two-stranded β sheet. 120 asymmetric dimers form a layer below the outer capsid shell in an almost planar structure. This protein family is found in Bacteriophage PM2 and similar sequences from virus and gammaproteobacteria.
PlyCA, N-terminal domain (PlyCA_N)
Type: Domain

This domain is found at the N-terminal end of PlyCA from Fischettivirus C1, the catalytic subunit of the potent lysin PlyC that is specific for streptococcal virus. PlyCA contains three distinct domains. This domain, which folds into a loose bundle of α-helices, is considered as a putative glycosyl hydrolase (GyH) domain, as it has similarity to class IV family 19 chitinases .
Apoptotic protease-activating factor 1, winged-helix domain (APAF1_WHD)
Type: Domain

This domain is found in Apoptotic protease-activating factor 1 (APAF-1), responsible to ignite the downstream cascade of caspases in the mitochondrial pathway of apoptosis. This entry represents the winged-helix domain (WHD) .
PKMT, C-terminal winged helix domain (PKMT_C)
Type: Domain

This entry represents the C-terminal winged helix domain of PKMTs. PKMTs are protein-lysine methyltransferases that catalyse the methylation of lysine residues on many different proteins. They consist of N-terminal S-adenosylmethionine binding domain, a middle domain and a C-terminal domain. The middle and the C-terminal domain share significant structural similarity and are both distantly related to HTH winged helix DNA-binding domains .
SsfX3-like, N-terminal domain (SsfX3-like_N)
Type: Domain

This domain is found at the N-terminal of SsfX3 (

) from Streptomyces sp. and in similar bacterial proteins. SsfX3 is an acyltransferase involved in the biosynthesis of the anticancer natural product SF2575. This protein is organised into two distinct domains (

): an N-terminal β-sandwich, represented in this entry, and a C-terminal catalytic domain (

). The N-terminal domain resembles the β-sandwich of the carbohydrate-binding module (CBM) and is critical for substrate binding .
AP-5 complex subunit beta-1, N-terminal domain (AP5B1_N)
Type: Domain

AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport . This entry represents the N-terminal domain which adopts an α-solenoid structure.
AP5B1, middle domain (AP5B1_middle)
Type: Domain

AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport . This entry represents the central domain which consists of an α-solenoid arrangement.
AP-5 complex subunit beta-1, beta-barrel domain (AP5B1_barrel)
Type: Domain

AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport . This entry represents a β-barrel domain found towards the C-terminal region of AP5B1. Structure predictions suggests that it contains seven antiparallel β-strands.
AP5B1, C-terminal domain (AP5B1_C)
Type: Domain

AP5B1 is part of the AP-5 adaptor protein complex, which may be involved in endosomal transport . This entry represents a presumed α/β domain found at the C-terminal of AP5B1 proteins. Structure predictions suggest that it consists of five β-strands with three α-helices around them.
PirA-like (PirA-like)
Type: Family

This family includes PirA from Vibrio parahaemolyticus. PirA is a plasmid-encoded homologue of a Photorhabdus insect-related (Pir) protein. It folds into an eight-stranded antiparallel β-barrel with jelly-roll topology .
Alpha-11 giardin, fourth annexin domain (Alpha11G_Annexin_4)
Type: Domain

This entry represents the fourth annexin domain of of Alpha-11 giardin, an unusual annexin from Giardia lamblia . Alpha-11 giardin is a member of the multi-gene alpha-giardin family in the intestinal protozoan, Giardia lamblia. This gene family shares an ancestry with the annexin super family, whose common characteristic is calcium-dependent binding to membranes that contain acidic phospholipids .
Secreted effector protein PipB2, N-terminal domain (PipB2_N)
Type: Domain

This domain is found at the N-terminal end of Secreted effector protein PipB2 from Salmonella typhimurium and similar sequences from gammaproteobacteria. PipB2 is involved in the reorganisation of late endosome/lysosome compartments in host mammalian cells. It is required for virulence. This domain shows a two-layer α-β structure.
FACT complex subunit SSRP1, C-terminal domain (SSRP1_C)
Type: Domain

FACT (facilitates chromatin transactions) is a general chromatin factor that acts to reorganise nucleosomes. SSRP1 is a subunit of this complex that is conserved among higher eukaryotes. This entry represents the C-terminal domain of SSRP1, which is highly likely to be disordered .
Protein D-63 (SSV1_D-63)
Type: Family

This entry includes protein D-63 (

) from Sulfolobus spindle-shape virus 1, which folds into an α-hairpin with the two helices running antiparallel to each other. It adopts a dimeric assembly and forms an antiparallel four-helical bundle. It might be involved in macromolecular assembly as an adaptor protein .
PIN domain associated with the TPR-GreAB-C-PIN system (PIN-TPR-GreABC)
Type: Domain

This is a divergent PIN domain present in the TPR-GreAB-C-PIN type conflict system from prokaryotes. These proteins have a constant module comprising of TPR-repeats, the GreA/B-C-terminal domain and the PIN domain. The N-terminal domain is variable and usually contains effector domains or EADs. The PIN domain is predicted to cleave emerging nascent transcripts .
Signal transducer and activator of transcription, linker domain (STAT_linker)
Type: Domain

This domain is found in signal transducer and activator of transcription proteins (STAT) from animals. These proteins are activated in response to extracellular signals such as cytokines, growth factors and hormonal factors and translocate to the nucleus, where they bind to specific promoter sequences in target genes.

This entry represents the α-helical linker domain that connects the DNA binding domain (

) and the SH2 domain (

) .
Metalloprotease StcE, beta-sandwich domain (StcE_b-sandwich)
Type: Domain

This domain is found in metalloprotease StcE (

) from Escherichia coli and similar proteins predominantly found in gammaproteobacteria.

StcE is a virulence factor that contributes to intimate adherence to host cells. This enzyme is organised into three distinct globular domains, IG, M and C, that are packed against each other to show an overall T-shape (

). This entry represents a region that is located within the domain IG. This region folds independently as a mixed, eight-stranded β-sandwich and contains an additional β-strand followed by a perpendicular arrangement of two α-helices in its N terminus. It is also known as the INS domain. This entry also covers a disordered region that has been described as D1 .
PHA01746-like domain (PHA01746-like_dom)
Type: Domain

This entry represents a domain found in an uncharacterised protein from a sulfolobus phage and similar sequences from Tokiviricetes. ECOD notes structural similarity to

, which includes the YkuJ protein from Bacilli .
Stereocilin, LRR domain (Stereocilin_LRR)
Type: Domain

Stereocilin is expressed in the sensory hair cells and is associated with the stereocilia, the stiff microvilli forming the structure for mechanoreception of sound stimulation . It is essential for the formation of horizontal top connectors in hair cells, which leads to deafness when it is defective . This is a large secreted protein containing a large leucine-rich region .
FACT complex subunit SSRP1-like, first PH domain (SSRP1-like_PH1)
Type: Domain

SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. This entry represents the first of two PH-like domains in these proteins . This group of proteins also include its fungal homologue FACT complex subunit POB3 .
STL11/RBM22-like, N-terminal domain (STL11/RBM22-like_N)
Type: Domain

This entry represents the N-terminal domain of STL11 from yeast and its homologues , such as RBM22 from human (

). This domain comprises a FYVE/PHD-type zinc finger (

). Members of this entry are involved in pre-mRNA splicing.
PGRS repeats (PGRS_rpt)
Type: Repeat

This entry represents a region of repeats present in a group of proteins from Mycobacteriales named PE_PGRSs, with members implicated in tuberculosis (TB) pathogenesis. Proteins of this family show a modular structure: the N-terminal PE domain (

), highly homologous to the domain found in tens of other PE proteins and whose structure has been already solved by crystallography; a C-terminal domain that is unique for each protein; and a central polymorphic glycine-rich repeat (PGRS) that varies in length from few tens to more than 1,000 amino acids .
Stonustoxin-like, helical domain (Stonustoxin-like_helical)
Type: Domain

This entry represents the Stonustoxin helical domain (

). Stonustoxin is a large pore forming toxin found in stonefish. This entry contains Stonustoxin as well as a variety of other toxin proteins such as Veruccotoxin and Neoverrucotoxin.
STPR domain (STPR)
Type: Domain

The silkgland-specific transcription factor FMBP-1 (

) from the silkworm Bombyx mori contains a unique DNA-binding domain of four tandem STPRs, namely the Score and Three amino acid Peptide Repeats . In the presence of target DNA, STPRs adopts a zig-zag structure of three or four tandem α-helices that run along the major groove of DNA (

) .
STT3/PglB/AglB, core domain (STT3-PglB_core)
Type: Domain

This entry represents the C-terminal core domain found in the oligosaccharyl transferase STT3 subunit and related proteins, such as bacterial PglB and archaeal AlgB. STT3 is part of the oligosccharyltransferase (OTase) complex and required for its activity, which transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER. In the archaea, STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines . This is a globular domain adopts a mixed α/β fold and contains the highly conserved WWDYG motif, in which the aspartate residue is thought to function as a catalytic residue .
Virulence plasmid protein pGP3-D, N-terminal domain (PGP3-D_N)
Type: Domain

This domain is found in Virulence plasmid protein pGP3-D, a virulence protein from Chlamydia trachomatis involved in stimulating host immune responses and thought to be required for growth within mammalian cells. Pgp3 consists of globular N- and C-terminal domains (

is the latter) connected by a triple-helical coiled coil (THCC). The N-terminal domain (this entry), which includes several structural motifs typically found in trimeric viral proteins, folds into a fairly flat surface .
Putative adhesin Stv domain (Stv)
Type: Domain

This entry represents a putative adhesin domain found predominantly in Gram-negative bacteria.
PgaA, membrane beta barrel domain (PgaA_barrel)
Type: Domain

The partially de-N-acetylated poly-beta-1,6-N-acetyl-d-glucosamine (dPNAG) polymer serves as an intercellular biofilm adhesin that plays an essential role for the development and maintenance of integrity of biofilms of diverse bacterial species. Translocation of dPNAG across the bacterial outer membrane is mediated by a tetratricopeptide repeat-containing outer membrane protein, PgaA . This entry represents the PgaA membrane β-barrel domain .
Scytovirin-like domain (SVN-like_dom)
Type: Domain

Scytovirin (

) is a protein from the cyanobacteria Scytonema varium with anti cytopathic activity against some strains of HIV. It binds to HIV gp120, HIV gp160 and to a lesser extent HIV gp41 . The protein, which adopts a monomeric assembly, has two repeats that form similarly structured domains (

). Remarkably, it has a high percentage of cysteine residues, all participating in disulfide bonds . This domain is also found in proteins from a few proteobacteria species and plants.
Major structural protein 1, jelly-roll domain (MSP1_barrel)
Type: Domain

This entry represents a β-barrel domain found towards the N-terminal of phage Tuc2009 receptor binding protein (RBP) which forms the head domain, involved in carbohydrate recognition .
Selenoprotein methionine sulfoxide reductase A, helical domain (MsrA_helical)
Type: Domain

This entry represents a domain from 1-Cys type selenoprotein methionine sulfoxide reductase A from the bacteria Clostridium oremlandii (MsrA,

), a repair enzyme for proteins that have been inactivated by oxidation that is found both in prokaryotes and eukaryotes. MsrA catalyses the reduction of methionine sulfoxide in proteins to methionine. This enzyme is organised into a catalytic domain (

) and a helical domain (this entry) absent in most of the known MsrA structures. It consists of five helices, interacts with the catalytic domain and is essential for the active site formation . This domain is only found in proteins from some bacterial species and animals.
Myosin A tail domain interacting protein, EF-hand domain (MTIP_EFh)
Type: Domain

This domain is found at the N-terminal end of Myosin A tail domain interacting protein from Plasmodium falciparum (MTIP) and in similar sequences mainly found in Apicomplexa. MTIP is one of the proteins that empower host cell invasion. This domain adopts an EF hand configuration .
Protein arginine N-methyltransferase 3, C2H2 zinc finger (ANM3_Znf-C2H2)
Type: Domain

This entry represents the C2H2-type zinc finger from arginine N-methyltransferase 3 (ANM3). It catalyses both the monomethylation and asymmetric dimethylation of the guanidino nitrogens of arginine residues in target proteins.
Anamorsin, N-terminal domain, metazoan-type (Anamorsin_N_metazoan)
Type: Domain

Anamorsin (also named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1), is the human homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis . It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) . Anamorsin is found to be up-regulated in hepatocellular cancer. It is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis . In addition, it mediates the anti-apoptotic effects of various cytokines . This entry represents the N-terminal domain of metazoan-type anamorsin, which has a S-adenosylmethionine methyltransferase-like fold.
Mutator-like transposase domain (Mutator_transp_dom)
Type: Domain

This is a transposase domain found in a group of proteins from the mutator superfamily mainly found in animals.
MxiC, C-terminal (MxiC_C)
Type: Domain

This entry represents the domain found at the C-terminal of Shigella flexneri type III secretion protein MxiC and similar sequences from Enterobacterales. It is composed of three domains, each possessing a four-helix X-bundle fold.
Transcriptional protein SWT1, C-terminal domain (SWT1_C)
Type: Domain

This entry represents the C-terminal domain of transcriptional protein SWT1 from Saccharomyces cerevisiae and similar fungal proteins.

SWT1 is an RNA endonuclease involved in quality control of nuclear messenger ribonucleoprotein particles (mRNPs). It consists of three domains: N-terminal, middle (

), and C-terminal domains. This domain shows three long antiparallel α-helices and three shorter ones

. It shares characteristics with members of the HEPN domain (

) .
Myosin VI, lever arm (MYO6_lever)
Type: Domain

This entry represents the lever arm from the unconventional myosin 6 proteins, the only class of myosin that has been shown to move toward the minus-end of actin filaments. This domain comprises an insert (Insert2) that binds the structural calmodulin (CaM) followed by the IQ motif and a proximal tail domain described as the lever arm extension . The lever arm amplifies the conformational changes in the motor into a movement on the order of nanometres known as the powerstroke.
Nab2, type CCCH zinc finger 4 (Nab2_Znf4)
Type: Domain

This entry represents the CCCH-type fourth zinc finger of Nab2p (Znf4), which is also found in similar fungal sequences. It doesn't participate in RNA binding .

Poly(A)-binding proteins (PABPs) protect against nuclease activity and are co-transcriptionally recruited to the nascent poly(A) tail. Nab2 belongs to one of the three major families of PABPs. It contains seven CCCH-type zinc fingers (Znf1-7) that are found in three structurally independent tandems, Nab2p Znf1-2, Nab2p Znf3-4 and Nab2p Znf5-7 .