SII-SWORD/CoKE huggingface dataset:
Dec-1 repeat (DEC-1_REPEAT)
Type: Repeat

The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing . Cleavage products include S80 (80kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60kDa).

This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown. Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats .
DEC-1 protein, N-terminal (DEC-1_N)
Type: Domain

The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing . Cleavage products include S80 (80kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60kDa).

This domain is present at the N-terminal of these proteins.
Dec-1 protein, C-terminal (DEC-1_C)
Type: Domain

The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing . Cleavage products include S80 (80kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60kDa).
ATP synthase, F1 complex, epsilon subunit, mitochondrial (ATP_synth_F1_esu_mt)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This family constitutes the mitochondrial ATP synthase epsilon subunit, which is distinct from the bacterial epsilon subunit (the latter being homologous to the mitochondrial delta subunit,

). The mitochondrial epsilon subunit is located in the stalk region of the F1 complex, and acts as an inhibitor of the ATPase catalytic core. The epsilon subunit can assume two conformations, contracted and extended, where the latter inhibits ATP hydrolysis. The conformation of the epsilon subunit is determined by the direction of rotation of the gamma subunit, and possibly by the presence of ADP. The extended epsilon subunit is thought to become extended in the presence of ADP, thereby acting as a safety lock to prevent wasteful ATP hydrolysis .

In Drosophila, the protein Stunted which activates the G-protein coupled receptor Methuselah in vitro, leading to increased intracellular calcium ion levels, is embryonically lethal .
Trafficking protein particle complex subunit 2 (Sedlin)
Type: Family

Trafficking protein particle complex subunit 2, also known as Sedlin, is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport . Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder .
Islet cell autoantigen Ica1, C-terminal (Islet_autoAg_Ica1_C)
Type: Domain

This entry represents a C-terminal domain found in islet cell autoantigen Ica1. Ica1 has been identified as an islet cell autoantigen in type I diabetes mellitus . Its precise function is unknown, though it may play a role in neurotransmitter secretion .
Phage tail tube protein 1 (Phage_TTP)
Type: Family

This is a family of phage tail tube proteins from virus .
Per os infectivity factor 2 (PIF2)
Type: Family

This family includes several baculoviral proteins, with predicted molecular weights of approximately 44kDa. The per os infectivity factor 2 (PIF2) is included in this entry. PIF2 forms a stable complex with PIF1, PIF3, PIF4 which is essential for oral infectivity of Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) in insect larvae, and P74 is also associated with this complex .
Para-hydroxybenzoic acid efflux pump subunit AaeB/fusaric acid resistance protein (PHBA_efflux_AaeB/fusaric-R)
Type: Family

This entry represents the p-hydroxybenzoic acid efflux pump subunit AaeB (pHBA efflux pump protein B) whose substrates are p-hydroxybenzoic acid (pHBA), 6-hydroxy-2-naphthoic and 2-hydroxycinnamate. It could function as a metabolic relief valve, allowing to eliminate certain compounds when they accumulate to high levels in the cell . This family also includes fusaric acid resistance proteins , which are likely to be membrane transporter proteins, and uncharacterised transporter YdhK.
Herpesvirus BMRF2 protein (Herpes_BMRF2)
Type: Family

This is a family of unknown function found in the Herpes viruses.
Immunity protein YezG-like (YezG-like)
Type: Family

Proteins in this entry include the Immunity protein YezG from Bacillus subtilis and Type VII secretion system protein EsaG from Staphylococcus aureus. YezG is the antitoxin component of a LXG toxin-antitoxin (TA) module that promote kin selection, mediate competition in biofilms, and drive spatial segregation of different strains, probably helping to avoid warfare between strains in biofilms . EsaG is part of toxin-antitoxin system that counteracts the toxic effect of EssD via direct interaction .
Sestrin (Sestrin)
Type: Family

Sestrins (Sesns) are involved in ROS (reactive oxygen species) regulation. In mammals, there are three Sestrins (Sesn1, Sesn2, and Sesn3), while in Drosophila melanogaster and C. elegans, there is only one Sesn . The N-terminal of Sesns shares protein sequence and structural similarity with the C-terminal α-helical domain of the AhpD protein from Mycobacterium tuberculosis. Interestingly, AhpD is a component of alkyl-hydroperoxide reductase participating in defense against ROS and ROS produced by host immune cells .
Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) (Herpes_pp85)
Type: Family

This family includes UL25 proteins from human cytomelagovirus (HCMV), as well as U14 proteins from the human herpesviruses HHV-6 and HHV-7. These 85kDa phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown. This entry also includes protein M35 from Murid herpesvirus 1. M35 is released by murine cytomegalovirus immediately upon infection in order to deftly inhibit the antiviral type I IFN response by targeting NF-kappaB-mediated transcription .
Poxvirus O1 (Poxvirus_O1)
Type: Family

This entry represents Protein O1 found in poxvirus. This protein is also known as Protein OPG074. It seems to be involved in binding to the host receptors. It comprises an N-terminal annular (ring) and a C-terminal globular (head) domains .
Baculovirus occlusion-derived virus envelope, E56 (Baculo_ODV-E56)
Type: Family

This family represents the E56 protein, which is localized to the occlusion derived virus (ODV) envelope, but not to the budded virus (BV) envelope . Signals necessary for transport and/or retention into this structure are believed to be found within the C-terminal portion of ODV-E56. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ODV-E56 is a per os infectivity factor required for primary midgut infection at a point before or after virion binding and fusion .
PLATZ transcription factor (PLATZ)
Type: Family

This family represents plant AT-rich sequence and zinc-binding proteins (PLATZ), which are zinc dependent DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression . Included in this family is the protein RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), a transcription factor that plays a central role in mediating RGF1 hormone peptide signalling, leading to the production of reactive oxygen species (ROS) in roots to modulate meristem size and root growth, probably via oxidative post-translational modification of the transcription factor PLETHORA .
Replication termination factor 2 (Rtf2)
Type: Family

This entry represents Replication termination factor 2 from Schizosaccharomyces pombe (Rtf2) and similar eukaryotic proteins .

The site-specific replication barrier RTS1 terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 was thought to stabilise the replication fork stalled at the RTS1 element by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin . However, this protein has been later reported to be associated with mRNA processing and splicing factors, and essential for the correct splicing of the rtf1 transcript, necessary for a functional Rtf1 protein (Replication Termination Factor 1) and thus for RTS activity . Its human homologue has been reported essential for the ability of cells to manage replication stress .
Protein of unknown function DUF601 (DUF601)
Type: Family

This family consists of several uncharacterised plant proteins which share a conserved region.
Motilin/ghrelin-associated peptide (Motilin_assoc)
Type: Domain

Motilin is a gastrointestinal regulatory polypeptide produced by motilin cells in the duodenal epithelium. It is released into the general circulation at about 100-min intervals during the inter-digestive state and is the most important factor in controlling the inter-digestive migrating contractions. Motilin also stimulates endogenous release of the endocrine pancreas .

This domain is also found in ghrelin, a growth hormone secretagogue synthesised by endocrine cells in the stomach. Ghrelin stimulates growth hormone secretagogue receptors in the pituitary. These receptors are distinct from the growth hormone-releasing hormone receptors, and thus provide a means of controlling pituitary growth hormone release by the gastrointestinal system .

This domain represents a peptide sequence that lies C-terminal to motilin/ghrelin (

) on the respective precursor peptide. Its function is unknown.
Motilin/ghrelin (Motilin_ghrelin)
Type: Domain

Motilin is a gastrointestinal regulatory polypeptide produced by motilin cells in the duodenal epithelium. It is released into the general circulation at about 100-min intervals during the inter-digestive state and is the most important factor in controlling the inter-digestive migrating contractions. Motilin also stimulates endogenous release of the endocrine pancreas .
Protein of unknown function DUF603 (DUF603)
Type: Family

This family includes several uncharacterised proteins from Borrelia species.
Protein of unknown function DUF604 (DUF604)
Type: Family

This family includes a conserved region found in several uncharacterised plant proteins.
Mating factor alpha, C-terminal repeat (Mating_factor_alpha_C)
Type: Repeat

This repeated sequence,WHWLQLKPGQPMY, characterises the mating factor alpha-1 or alpha-1 mating pheromone. The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A) by binding to a cognate G-protein coupled receptor which is coupled to a downstream signal transduction pathway. It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process.
Poxvirus A12 (Poxvirus_A12)
Type: Family

This family represents Protein A12 from Vaccinia virus, also known as 25 kDa core protein OPG138, and similar proteins from poxvirus. A12 is a component of the virion core that undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition. It is essential for the formation of a structurally normal core .
26S proteasome non-ATPase regulatory subunit Rpn12 (26S_Psome_Rpn12)
Type: Family

Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes . This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides.

The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle (RP) and the 20S core particle (CP) . The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) . Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation .

This entry represents Rpn12 (also often annotated as 26S proteasome non-ATPase regulatory subunit 8). This protein has been shown to be important for the transition from metaphase to anaphase and the activation of Cdc28p kinase in yeast .
Protein of unknown function DUF599 (DUF599)
Type: Family

This family includes several uncharacterised proteins.
Aminoglycoside/hydroxyurea antibiotic resistance kinase (NH2Glyco/OHUrea_AB-resist_kin)
Type: Family

The aminoglycosides are a large group of biologically active bacterial secondary metabolites, best known for their antibiotic properties . Aminoglycoside phosphotransferases achieve inactivation of these enzymes by phosphorylation, utilising ATP. Likewise, hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety.
Pox virus E6 protein (Pox_E6)
Type: Family

This family contains fowlpox virus protein E6 and its homologues, including Protein OPG068 from Vaccinia virus. OPG068 plays an essential role for maintaining proper localization of the seven-protein complex and the viroplasm during assembly .
Putative inner membrane exporter, YdcZ (YdcZ)
Type: Family

DMT_YdcZ is a family of putative inner membrane exporters from both Gram-positive and Gram-negative bacteria.
TAFII55 protein, conserved region (TAFII55_prot_cons_reg)
Type: Domain

The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminal of the protein .
Archaeal flagella protein FlaD/E domain (Arch_fla_DE)
Type: Domain

Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species has always suggested that archaeal flagellar biogenesis is likely mediated by novel components. FlaD and FlaE, are present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site.

This entry represents a domain found in the N-teminal region of flaE but towards the C-terminal region of flaD .
Nanovirus coat protein (Nanovirus_coat)
Type: Family

This is a family of conserved coat proteins from the single stranded DNA Nanoviruses .
Poxvirus I3 ssDNA-binding (Poxvirus_I3_ssDNA-bd)
Type: Family

The 34kDa protein encoded by the I3 gene of vaccinia virus, named Protein OPG079, is expressed at early and intermediate times post-infection and is phosphorylated on serine residues. I3 protein demonstrates a striking affinity for single-stranded, but not for double-stranded, DNA. Electrophoretic mobility shift assays indicate that numerous I3 molecules can bind to a template, reflecting the stoichiometric interaction of I3 with DNA. Sequence analysis reveals that a pattern of aromatic and charged amino acids common to many replicative single-stranded DNA binding proteins (SSBs) is conserved in I3 . This protein plays an essential role in viral DNA replication .
Suppressor of silencing P0 (Virus_P0)
Type: Family

P0 is a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. It targets ARGONAUTE proteins for degradation . It may prevent RNA-induced silencing complex (RISC) assembly by interacting with one of its protein components, thus inhibiting formation of siRNA/miRNA-RISC, and ultimately leading to ARGONAUTE 1 (AGO1) degradation .
Phenol hydroxylase (Phenol_hydroxylase)
Type: Family

Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme, such as Phenol 2-monooxygenase, oxygenase component DmpO from Pseudomonas sp. , the other is a single-component monooxygenase. This signature is found in both types of enzymes .
Opioid growth factor receptor (OGFr) conserved domain (OGF_rcpt)
Type: Domain

Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The opioid growth factor receptor is an integral membrane protein associated with the nucleus. This conserved domain is situated at the N terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminal .
Poxvirus A32 (A32L)
Type: Family

The A32 protein from Vaccinia virus, also known as DNA packaging protein OPG160, is thought to be involved in viral DNA packaging .
Glycosyl transferase family 54 (Glyco_transf_54)
Type: Family

The complex-type of oligosaccharides are synthesised through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains.
Endosulphine (Endosulphine)
Type: Family

This endosulphine family includes cAMP-regulated phosphoprotein 19 (ARPP-19), alpha endosulphine and protein Igo1.
Tsg (Tsg)
Type: Family

Twisted gastrulation (Tsg) was identified in Drosophila melanogaster as being required to specify the dorsal-most structures in the embryo, for example, the amnioserosa. Biochemical experiments have revealed three key properties of Tsg:

It can synergistically inhibit Dpp/BMP action in both D. melanogaster and vertebrates by forming a tripartite complex between itself, SOG/chordin and a BMP ligand;

Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilisation;

Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling .
Gtr1/RagA G protein (Gtr1_RagA)
Type: Family

GTR1 was first identified in Saccharomyces cerevisiae (Baker's yeast) as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus.

Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily .
Antigen 332 repeat (Ag332)
Type: Repeat

To date many different Plasmodium antigens recognised by the hyperimmune system human sera have been cloned, sequenced and characterised. The majority contain tandemly repeated amino acid sequences which make up a considerable portion of the protein sequence. It has been suggested that these repeat-containing antigens may provide an immunological smokescreen to the parasite in order to evade the human immune system. This repeat is found in the Plasmodium falciparum Ag332 protein and occupies most of its length .
S-adenosyl-L-methionine dependent methyltransferase, SAV2177 type (SAM_dep_MeTrfase_SAV2177_type)
Type: Family

This family contains a SAM (S-adenosyl methyltransferase) domain, with a central β sheet with 3 α-helices on both sides. Crystal packing analysis of the structure of

suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met22. The UNL is likely to be a phenylalanine or phenylalanine-like molecule.
Polyketide synthesis cyclase (Polyketide_synth_cyclase)
Type: Family

Aromatic polyketides are assembled by a type II (iterative) polyketide synthases (PKSs) in bacteria. Type II PKS complexes consist of several monofunctional or bifunctional proteins which produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclization pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits .
Protein EXORDIUM-like (EXORDIUM-like)
Type: Family

This entry includes the EXORDIUM protein and related proteins. The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth . It mediates cell expansion in Arabidopsis leaves . This entry also includes PHI-1, a phosphate-induced protein of unknown function from Nicotiana tabacum .
Cwf19-like protein, C-terminal domain-2 (Cwf19-like_C_dom-2)
Type: Domain

This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (

) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing . CWF19-like protein DRN1 from Saccharomyces cerevisiae (

) is involved branched RNA metabolism, modulating the turnover of lariat-intron pre-mRNAs by the lariat-debranching enzyme DBR1 (

) . This domain is found in association with

, which is generally N-terminal and adjacent to this domain, and contain evolutionarily conserved cysteine and histidine residues in an arrangement similar to the CCCH-class of zinc fingers .