SII-SWORD/CoKE huggingface dataset:
Neural chondroitin sulphate proteoglycan cytoplasmic (Neural_ProG_Cyt)
Type: Domain

This entry represents the C-terminal cytoplasmic domain of vertebrate neural chondroitin sulphate proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis . This domain contains a number of potential sites of phosphorylation by protein kinase C .
YjiS/Atu8161/CcaF1-like domain (YjiS/Atu8161/CcaF1-like_dom)
Type: Domain

This arginine rich domain is found at the C-terminal end of YjiS from Salmonella Typhimurium (

), YjiS from Escherichia coli and similar short sequences from proteobacteria. In S.Typhimurium, this inner membrane-associated small protein acts as a suppressor of flagella production, leading to pathogen escape from infected host cells . In E.coli, yjiA and yjiS are widely shared genes flanking the variable Immigration Control Region (ICR) restriction-modification cassettes of enterobacterial genomes. The yjiS gene defines the left border of the Immigration Control Region (ICR), and yjiA defines the right border .

In the plant pathogen Agrobacterium tumefaciens (also known as Agrobacterium fabrum), some small proteins that contain this domain, such as Atu8161 (

) are involved in nutrient acquisition and central carbon metabolism ,

The 71 amino acid protein CcaF1 from Rhodobacter sphaeroides (RSP_6037,

) is an RNA binding protein that has a role in the oxidative stress defence . This microprotein also promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins .

In some uncharacterised proteins, this domain, previously known as DUF1127, covers the whole sequence.
Protein of unknown function UPF0435 (UPF0435)
Type: Family

This family consists of several short, hypothetical bacterial proteins of unknown function.
Transcription activator, Churchill (Transcrpt_activator_Churchill)
Type: Family

This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors .
Protein of unknown function DUF1132 (DUF1132)
Type: Family

This family consists of several hypothetical proteins from Neisseria species. The function of this family is unknown.
Type III secretion system, secretion protein K (T3SS_K)
Type: Family

This family consists of secretion proteins like Yersinia YscK. The function of this protein is unknown but it belongs to an operon involved in the secretion of Yop proteins across bacterial membranes .
Mad1/Cdc20-bound-Mad2 binding protein (MAD1/Cdc20-bound-Mad2-bd)
Type: Family

This entry represents Mad1 and Cdc20-bound-Mad2 binding proteins that are involved in the cell-cycle surveillance mechanism called the spindle checkpoint . This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, which exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerisation and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex .
PerB (PerB)
Type: Family

This family consists of several PerB or BfpV proteins found specifically in Escherichia coli. PerB is thought to play a role in regulating the expression of BfpA .
Nucleoid disruption protein (Phage_Ndd)
Type: Family

This family consists of several nuclear disruption (Ndd) proteins from T4-like phages. Early in a Bacteriophage T4 infection, the phage ndd gene causes the rapid destruction of the structure of the Escherichia coli nucleoid. The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid .
Protein of unknown function DUF1138 (DUF1138)
Type: Family

This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Raspberry bushy dwarf virus coat (RBDV_coat)
Type: Family

This family consists of several Raspberry bushy dwarf virus (RBDV) coat proteins.
Borna disease virus P24 (BDV_P24)
Type: Family

Borna disease virus (BDV) is a non-cytolytic, neurotropic RNA virus that has a broad host range in warm-blooded animals. BDV is an enveloped virus, non-segmented, negative-stranded RNA genome and has an organisation characteristic of a member of Bornaviridae in the order of Mononegavirale. This family consists of several BDV P24 (phosphoprotein 24) proteins. They are essential components of the RNA polymerase transcription and replication complex.
Photosystem II PsbX (PSII_PsbX)
Type: Family

The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII , and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site .

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 .
Fiji disease virus, Vp7-2 (FDV_Vp7-2)
Type: Family

This family consists of several hypothetical Fijivirus proteins of unknown function.
Protein of unknown function DUF1140 (DUF1140)
Type: Family

This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown.
Orthopoxvirus F6 (Orthopox_F6)
Type: Family

This family consists of several Orthopoxvirus F6L proteins the function of which is unknown. F6L is also known as Protein OPG050.
Nucleocapsid, Phlebovirus/Tenuivirus (Capsid_Phlebovir/Tenuivir)
Type: Family

This entry represents nucleocapsid proteins from the ssRNA viruses Tenuivirus and Phlebovirus . These are ssRNA viruses.

In crystal structures, the nucleocapsid protein from the Rift Valley fever virus (RVFV) displays a ring-shaped oligomeric assembly . Electron microscopy (EM) also demonstrates that, in complex with RNA, the nucleocapsid protein forms rings in solution .
Prokineticin (Prokineticin)
Type: Family

The prokineticin family includes prokinectin itself and related proteins such as BM8 and the AVIToxins. The suprachiasmatic nucleus (SCN) controls the circadian rhythm of physiological and behavioural processes in mammals. It has been shown that prokineticin 2 (PK2), a cysteine-rich secreted protein, functions as an output molecule from the SCN circadian clock. PK2 messenger RNA is rhythmically expressed in the SCN, and the phase of PK2 rhythm is responsive to light entrainment. Molecular and genetic studies have revealed that PK2 is a gene that is controlled by a circadian clock .
Cilia- and flagella-associated protein 68 (CFAP68)
Type: Family

This family consists of cilia- and flagella-associated protein 68 from animals, a microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating .
Protein of unknown function DUF1145 (DUF1145)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Protein of unknown function DUF1146 (DUF1146)
Type: Family

Members of this protein family are small, typically about 80 residues in length, and are highly hydrophobic. The gene is found so far only in a subset of the firmicutes in association with genes of the ATP synthase F1 complex or NADH-quinone oxidoreductase. This family includes YwzB from Bacillus subtilis.
Circovirus 2, Orf1 (Circovirus2_Orf1)
Type: Family

This family consists of Circovirus 2 ORF1 (also known as Protein NS0), which may be involved in host modulation .
BsuBI/PstI restriction endonuclease domain (Restrct_endonuc_II_BsuBI_C)
Type: Domain

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , as summarised below:

Type I enzymes (

) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (

) activities.

Type II enzymes (

) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.

Type III enzymes (

) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (

).

Type IV enzymes target methylated DNA.

Type II restriction endonucleases (

) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four β-strands and one α-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin . However, there is still considerable diversity amongst restriction endonucleases . The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone .

This entry represents the C terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (

). The enzymes of the BsuBI restriction/modification (R/M) system recognise the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system .
Maize streak virus, 13.1kDa (Maize_streak_virus_13.1kDa)
Type: Family

This family consists of several Maize streak virus proteins of unknown function.
Protein of unknown function DUF1149 (DUF1149)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
Protein of unknown function DUF1150 (DUF1150)
Type: Family

This entry consists of several hypothetical bacterial proteins of unknown function.
SepQ (SepQ)
Type: Family

This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear.
FAM107 (FAM107)
Type: Family

This entry includes FAM107A/B. FAM107A (also known as DRR1) is an actin-associated protein that plays important roles in tumor cell growth, neuron survival and spine formation . The function of FAM107B is not clear.
Protein of unknown function DUF1153 (DUF1153)
Type: Family

This family consists of several short, hypothetical bacterial proteins of unknown function.
Cucumber mosaic virus, OrfIIB (CucumberMosaicV_OrfIIB)
Type: Family

This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown.
Domain of unknown function DUF1156 (DUF1156)
Type: Domain

This entry represents a conserved region within hypothetical prokaryotic and archaeal proteins of unknown function.
Plasmalemma vesicle-associated protein (PV-1)
Type: Family

This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to vertebrates. PV-1 is a component of the endothelial fenestral and stomatal diaphragms . PV-1 is retained on the cell surface of enddotelial cells by structures capable of forming diaphragms, but undergoes rapid internalization and degradation in the absence of these structures .
Vang-like protein (VANGL)
Type: Family

VANGL proteins play important roles in the establishment of planar cell polarity (PCP) . Vangl2 is required for retinal axon guidance , kidney-branching morphogenesis and glomerular maturation . It also plays a role in the orientation of stereociliary bundles in the cochlea and is required for polarization and movement of myocardializing cells in the outflow tract and seems to act via RHOA signaling to regulate this process . It is required for cell surface localization of FZD3 and FZD6 in the inner ear .
Basal layer antifungal peptide (BAP)
Type: Family

This family consists of several basal layer antifungal peptide (BAP) sequences specific to Zea mays (Maize). The BAP2 peptide exhibits potent broad-range activity against a range of filamentous fungi, including several plant pathogens .
Signal peptidase complex subunit 1 (Spc1/SPCS1)
Type: Family

Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins .

This family represents the Signal peptidase complex subunit 1 (SPCS1) and its homologues, such as Spc1 from budding yeasts. The signal peptidase complex cleaves the signal sequence from proteins targeted to the endoplasmic reticulum (ER). Mammalian signal peptidase is as a complex of five different polypeptide chains , while the budding yeast SPC comprises four proteins . Budding yeast Spc1 has been shown to be a nonessential component of the signal peptidase complex . However, the Drosophila spase12 (yeast Spc1 homologue) null alleles are embryonic lethal .

Interestingly, human SPC12 has been linked to post-translational processing of proteins involved in virion assembly and secretion from flaviviruses .
Vacuolar protein sorting-associated protein 13, VPS13 adaptor binding domain (VPS13_VAB)
Type: Domain

This entry represents the VPS13 adaptor binding (VAB) domain, previously known as SHR-BD, found in VPS13 . This domain interacts with Ypt35 which recruits VPS13 to endosomal and vacuolar membranes, and with Mcp1 to target VPS13 at mitochondria . In plants, this domain is found to be the region which interacts with SHR or the SHORT-ROOT transcription factor, a regulator of root-growth and asymmetric cell division that separates ground tissue into endodermis and cortex. The plant protein containing the SHR-BD is named SHRUBBY or SHBY (

) . This domain interacts with Proline-X-Proline (Pro-X-Pro) motif present in receptor proteins at contact sites .

This domain comprises six repeated modules, each of them containing nine β-strands connected by loops and arranged into a β-sandwich .

VPS13 proteins have been implicated in processes including vesicle fusion, autophagy, and actin regulation. They bind phospholipids and act as channels that mediate the transfer of lipids between membranes at organelle contact sites . It has been proposed that members of this entry have the capacity to bind and likely transfer tens of glycerolipids at once. Yeast VPS13 acts at multiple cellular sites, namely the interface between mitochondria and the vacuole, on endosomes, on the nuclear-vacuole junction and the vacuole, depending on the carbon source and metabolic state. Most evidence showed that mammalian VPS13A, VPS13C and VPS13D localize at contacts between the ER and other organelles, i.e. VPS13A and VPS13D bridge the ER to mitochondria, VPS13C bridges the ER to late endosomes and lysosomes and VPS13B may localize to endosome-endosome contacts . Mutations in human VPS13 proteins (VPS13A-D) cause different diseases such as Chorea-acanthocytosis, Cohen syndrome, Parkinson's disease, and spastic ataxia, respectively which suggests they have different functions . Members of this entry belong to the repeating β-groove (RBG) superfamily. These proteins share a structure made of multiple repeating modules consisting of five β-sheets followed by a loop .
Protein of unknown function DUF1163 (DUF1163)
Type: Family

This entry represents a group of hypothetical Arabidopsis thaliana proteins of unknown function.
Tight junction protein, claudin-like (Claudin-like)
Type: Family

This is a family of probable membrane tight junction, claudin-like, proteins.
Tenuivirus PVC2 (Tenui_PVC2)
Type: Family

This family consists of several Tenuivirus PVC2 proteins from Rice grassy stunt virus, Maize stripe virus and Rice hoja blanca virus. The function of this family is unknown.
PRKR-interacting protein 1 (Prkrip1)
Type: Family

Prkrip1, also known as protein C114, is a double-stranded RNA-binding protein . It consists of a fully extended N-terminal loop (residues 51-75) and an 18-turn α helix (residues 76-142). It directly links the catalytic centre with the U2 snRNP at the periphery of the spliceosome .
VirE3 (VirE3)
Type: Family

This family represents a conserved region within Agrobacterium tumefaciens VirE3. Agrobacterium tumefaciens (a plant pathogen) has a tumour-inducing (Ti) plasmid of which part, the transfer (T)-region, is transferred to plant cells during the infection process. Vir proteins mediate the processing of the T-region and the transfer of a single-stranded (ss) DNA copy of this region, the T-strand, into the recipient cells. VirE3 is a translocated effector protein, but its specific role has not been established .
Protein wntless (Wntless)
Type: Family

Protein wntless (WLS) regulates Wnt proteins sorting and secretion in a feedback regulatory mechanism . This reciprocal interaction plays a key role in the regulation of expression, subcellular location, binding and organelle-specific association of Wnt proteins. It also plays also an important role in establishment of the anterior-posterior body axis formation during development . This protein is homologous to GPR180, TMEM145, and TMEM181, which have been described as GOST proteins (for GOLD domain seven-transmembrane helix proteins) together with TMEM87A/B, GPR107, and GPR108, as they share the same domain architecture consisting of a GOLD domain atop of a membrane-spanning seven-transmembrane helix domain .
Protein of unknown function DUF1173 (DUF1173)
Type: Family

This family contains a group of hypothetical bacterial proteins that contain three conserved cysteine residues towards the N-terminal. The function of these proteins is unknown.
Phage shock protein B (Phageshock_PspB)
Type: Family

This family consists of several bacterial phage shock protein B (PspB) sequences, also known as envelope stress response membrane protein PspB. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages . Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one . PspB is both a regulator and an effector protein of the phage shock response .
Microneme Etmic-2 (Microneme_Etmic-2)
Type: Family

This family consists of several Microneme protein Etmic-2 sequences from Eimeria tenella. Etmic-2 is a 50kDa acidic protein, which is found within the microneme organelles of E. tenella sporozoites and merozoites .
Repeat of unknown function DUF1174 (DUF1174)
Type: Repeat

This entry consists of a number of Caenorhabditis elegans specific repeats of around 36 residues in length which are found in two hypothetical proteins.
Protein of unknown function DUF1175 (DUF1175)
Type: Family

This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.
Lactococcus phage c2, major capsid protein (Lactococcus_phage_c2_MCP)
Type: Family

This family consists of several Lactococcus lactis bacteriophage major capsid proteins.
Protein of unknown function DUF1176 (DUF1176)
Type: Family

This family consists of several hypothetical bacterial proteins of around 340 residues in length. Members of this family contain six highly conserved cysteine residues. The function of this family is unknown.
Protein of unknown function DUF1177 (DUF1177)
Type: Family

This family consists of several hypothetical archaeal and bacterial proteins of around 300 residues in length. The function of this family is unknown.
Protein of unknown function DUF1178 (DUF1178)
Type: Family

This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Sjoegren syndrome/scleroderma autoantigen 1 (SSSCA1)
Type: Family

This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences, also known as ZNRD2. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis .
Protein of unknown function DUF1179 (DUF1179)
Type: Family

This family consists of several hypothetical Caenorhabditis elegans proteins of around 106 residues in length. The function of the family is unknown.
Membrane protein FAM174-like (FAM174-like)
Type: Family

This entry represents a group of animal membrane proteins, including human Membrane protein FAM174B, which is essential for Golgi structural integrity .