SII-SWORD/CoKE huggingface dataset:
Antitoxin MqsA/HigA-2 (MqsA/HigA-2)
Type: Family

This is a family of prokaryotic proteins that are the antitoxin components of the toxin-antitoxin (TA) modules. Proteins in this entry include MqsA from Escherichia coli and HigA-2 from Vibrio cholerae serotype O1. MqsA acts as antidote to the mRNA interferase MqsR , while HigA-2 counteracts the effect of the HigB-2 toxin .
Bacterial toxin 5 (Ntox5)
Type: Family

A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Bacterial toxin 6 (Ntox6)
Type: Family

A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an α+β fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system .
Plasmodium falciparum erythrocyte membrane protein 1, N-terminal (PfEMP1_N)
Type: Domain

This entry represents a domain found in the most variable part of the variant surface antigen family member from Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) . PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors.
Putative polysaccharide deacetylase (Polysacc_deac_3)
Type: Family

This entry represents a group of putative polysaccharide deacetylases from bacteria, mainly from Bacteroidales.
Resistance to inhibitors of cholinesterase protein 3, N-terminal (RIC3_N)
Type: Domain

This entry represents the N-terminal domain of RIC3, a protein associated with nicotinic acetylcholine receptors (nAChRs), neurotransmitter-gated ion channels expressed at the neuromuscular junction and within the central and peripheral nervous systems . It can enhance functional expression of multiple nAChR subtypes . RIC3 promotes functional expression of homomeric alpha-7 and alpha-8 nicotinic acetylcholine receptors at the cell surface .
Tankyrase 1-binding protein, C-terminal (Tankyrase-bd_C)
Type: Domain

This protein domain is found at the C-terminal end of the Tankyrase binding protein in eukaryotes. The precise function of this protein is still unknown. However, it is known that interacts with the enzyme tankyrase, a telomeric poly(ADP-ribose) polymerase, by binding to it. Tankyrin catalyses poly(ADP-ribose) chain formation onto proteins. More specifically, it binds to the ankyrin domain in tankyrase . The protein domain is approximately 170 amino acids in length and contains two conserved sequence motifs: FPG and LKA.
Testis expressed sequence 15 domain (TEX15_dom)
Type: Domain

This entry represents a domain found in TEX15, a protein required for chromosomal synapsis and meiotic recombination. TEX15 regulates the loading of DNA repair proteins onto sites of double-stranded-breaks and, thus, its absence causes a failure in meiotic recombination . Two polymorphisms in the TEX15 gene could be considered the genetic risk factors for spermatogenic failure in the Chinese Han population .
Fission yeast Sec3, C-terminal (Sec3_C_2)
Type: Domain

This small Sec3 C-terminal domain is based around the fission yeast protein, and is rather shorter than the budding yeast/vertebrate domain Sec3_C (

). In fact it is only this coiled-coil region that they carry in common. The full length fission yeast (

) protein Sec3 is redundant with Exo70 for viability and for the localisation of other exocyst subunits, suggesting that these components act as exocyst tethers at the plasma membrane. Sec3, Exo70 and Sec5 are transported by the myosin V Myo52 along actin cables. The exocyst holo-complex, including Sec3 and Exo70, is present on exocytic vesicles, which can reach cell poles by either myosin-driven transport or random walk .
Ascaris metallocarboxypeptidase inhibitor (ACI44)
Type: Family

This entry represents a metallo-carboxypeptidase inhibitor, which protects roundworms of the genus Ascaris, common parasites of the human gastrointestinal tract, from host enzymes and the immune system .
G2 and S phase-expressed protein 1, N-terminal (GTSE1_N)
Type: Domain

This entry represents the N terminus of GTSE1 proteins. GTSE-1 (G2 and S phase-expressed-1) protein is specifically expressed during S and G2 phases of the cell cycle. It is mainly localised to the microtubules and when overexpressed delays the G2 to M transition. the full protein negatively regulates p53 transactivation function, protein levels, and p53-dependent apoptosis . This domain is found in eukaryotes, and is approximately 140 amino acids in length. There is a conserved FDFD sequence motif.
Nck-associated protein 5, C-terminal (NCKAP5_C)
Type: Domain

This entry represents the C-terminal domain of the Nck-associated protein 5 (NCKAP5), also known as the Peripheral clock protein. NCKAP5 interacts with the SH3-containing region of the adaptor protein Nck. Nck is a protein that interacts with receptor tyrosine kinases and guanine nucleotide exchange factor Sos. The role of Nck can be thought of as similar to Grb2. The role of NCKAP5 is to assist Nck with its adaptor protein role .
Domain of unknown function DUF4537 (DUF4537)
Type: Domain

The function of this domain is unknown. It is found in eukaryotes, and is typically between 119 and 141 amino acids in length. In humans, it is found in the uncharacterised protein C11orf16 and at the C-terminal of von Willebrand factor A domain-containing protein 3B (VWA3B). Mutations in VWA3B have been identified to cause cerebellar ataxia .
Protein of unknown function DUF4527 (DUF4527)
Type: Family

This family of proteins is functionally uncharacterised. This family of proteins is found in vertebrates.
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal (PGA_deacetylase_PgaB_C)
Type: Domain

This entry represents the C-terminal domain of PgaB, a polysaccharide de-N-acetylase involved in biofilm formation. PgaB contains an N-terminal domain that has deacetylase activity .
Protein MGARP, N-terminal (MGARP_N)
Type: Domain

This entry represents the N-terminal domain of the protein MGARP (also known as HUMMR) . HUMMR interacts with Miro, an mitochondrial membrane protein. It biases mitochondrial movement in the anterograde direction in response to hypoxia .
WG containing repeat (WG_beta_rep)
Type: Repeat

This repeat contains an N-terminal WG repeat motif. The extent of the repeat is poorly defined. This repeat may form a β-solenoid structure (Bateman A pers. obs.).
CECR6/TMEM121 family (CECR6/TMEM121)
Type: Family

This family includes Cat eye syndrome critical region protein 6 (also known as TMEM121B), a protein which has been identified in a screen for candidate genes for the developmental disorder Cat Eye Syndrome (CES) . It also includes the TMEM121 transmembrane proteins. The function of this family is unknown.
Domain of unknown function DUF4515 (DUF4515)
Type: Domain

This domain contains two completely conserved L residues that may be functionally important. Proteins with this domain include basal body-orientation factor 1 (bbof1), and coiled-coil domain-containing protein 166 and 121. Bbof1 is required to maintain cilia orientation .
Growth factor receptor domain 4 (GF_recep_IV)
Type: Domain

This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain (

) regulates the binding of ligands to the receptor L domains (

) .
Flagellar motor switch protein FliG, middle domain (FliG_M)
Type: Domain

This is the middle domain of the flagellar rotor protein FliG .
DNA polymerase III subunit delta, C-terminal (DNA_pol3_delt_C)
Type: Domain

This domain lies at the C terminus of the DNA polymerase III subunit delta. Within the clamp loader gamma complex of the DNA polymerase III, several C-terminal domains, of gamma, delta and delta' form a helical scaffold, on which the rest of the subunits are hung. The gamma complex, an AAA+ ATPase, is the bacterial homologue of the eukaryotic replication factor C that loads the sliding clamp (beta, homologous to PCNA) onto DNA .
ABC-transporter extension domain (ABC_tran_Xtn)
Type: Domain

In E.coli four ABC-F proteins have been characterised: EttA, YbiT, YheS, and Uup. EttA was shown to interact with the ribosome (

). YbiT, YheS, and Uup have also been shown to bind to the ribosome .

This domain is an extension of some members of

and other ABC-transporter families. It is not responsible for ribosome binding, but it is used by proteins which bind to the ribosome to stabilise the interaction.
RNA-binding protein KhpB, N-terminal (KhpB_N)
Type: Domain

This entry includes the RNA-binding protein KhpB, also known as RNA-binding protein Jag/EloR, a RNA chaperone that forms a complex with KhpA and binds to cellular RNA, controlling its expression. It plays a role in peptidoglycan (PG) homeostasis and cell length regulation, cell division and maintenance of cell shape . Bacillus subtilis KhpB/Jag is associated with SpoIIIJ, a gene necessary for the third stage of sporulation . This domain is found at the N terminus of the KhpB/Jag proteins, whose function is unknown.
AraC-type transcription regulator, ligand-binding domain (AraC_lig)
Type: Domain

This domain is found in members of the AraC family of transcription factors, where it represents the ligand binding domain.
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain (THDPS_M)
Type: Domain

This is the middle domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase .
Replicase polyprotein 1ab, peptidase C33-associated domain (Pdase_C33_assoc)
Type: Domain

The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. The function of this particular domain is not known. It is found downstream the peptidase C33 domain (

).
Nsp2, transmembrane domain (NSP2_TM_arteriviridae)
Type: Domain

This entry represents a domain found in NSP2 of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2 .
Prokaryotic E2 family D (Prok-E2_D)
Type: Family

This family is part of the E2/UBC superfamily of proteins found in several bacteria. Members of this family lack the conserved histidine of the classical E2-fold. However, they have an absolutely conserved histidine carboxyl-terminal to the conserved cysteine . Members of this family are usually present in a conserved gene neighbourhood with genes encoding members of the Ub modification pathway such as the E1, Ub and JAB proteins. These neighbourhoods also contain a gene encoding a rapidly diverging α-helical protein .
Glycogen debranching enzyme, central domain (AGL_central)
Type: Domain

This entry represents the central domain of the glycogen debranching enzyme AGL. AGL is a multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4-alpha-D-glucan 4-alpha-D-glycosyltransferase and amylo-1,6-glucosidase in glycogen degradation . This central domain follows the glucanotransferase domain and precedes the glucosidase domain. By analogy with baterial GDEs (glycogen debranching enzymes), this domain may be involved in substrate binding either for the N-terminal glucanotransferase and/or the C-terminal glucosidase (or both).
Pilus formation protein, N-terminal (T2SS-T3SS_pil_N)
Type: Domain

This domain is found N-terminal in putative pilus formation proteins of the type II/III secretion system.
Glycogen debranching enzyme, C-terminal (GDE_C)
Type: Domain

This entry represents the C-terminal domain of the glycogen debranching enzyme AGL. AGL is a multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4-alpha-D-glucan 4-alpha-D-glycosyltransferase and amylo-1,6-glucosidase in glycogen degradation . This is a glucosidase domain. Mutations in this region disrupt the glucosidase activity .
Uncharacterised protein YhfZ, C-terminal domain (YhfZ_C)
Type: Domain

This domain is found in YhfZ proteins from Escherichia coli and Shigella flexneri. The crystal structure of this proteins is known (

). This domain is often found in association with a helix-turn-helix domain.
Glycogen debranching enzyme, glucanotransferase domain (AGL_glucanoTrfase)
Type: Domain

This is a glucanotransferase catalytic domain of the glycogen debranching enzyme AGL. AGL is a multifunctional enzyme acting as 1,4-alpha-D-glucan:1,4-alpha-D-glucan 4-alpha-D-glycosyltransferase and amylo-1,6-glucosidase in glycogen degradation . This glucanotransferase domain is predicted to have a structure of a 8 stranded α/β barrel (TIM barrel) where strands are interrupted by long loops and additional mini-domains.
Type II restriction endonuclease EcoO109IR (RE_EcoO109IR)
Type: Domain

This domain is found in type II restriction endonuclease EcoO109IR .
Protein Lines, N-terminal (LINES_N)
Type: Domain

This entry represents the N terminus of protein lines . In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator .
DUF3741-associated sequence motif (DUF3741-assoc)
Type: Domain

This short domain is found frequently at the N terminus of domain DUF3741 (

). It contains the sequence motif VARLMGL.
Polysulfide reductase (NrfD_2)
Type: Family

Members of this family are thought to be part of the bacterial polysulfide reductase integral membrane protein complex.

Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compounds composed of chains of sulfur atoms, which in their simplest form are present as an anion with general formula Sn(2-). In nature, polysulfides are found in particularly high concentrations in extreme volcanic or geothermically active environments. Here, the reduction and oxidation of polysulfides are vital processes for many bacteria and are essential steps in the global sulfur cycle. In particular, the reduction of polysulfide to hydrogen sulfide in these environments is usually linked to energy-generating respiratory processes, supporting growth of many microorganisms, particularly hyperthermophiles .
Gamma-Tubulin ring complex non-core subunit mod21, N-terminal (Mod21_N)
Type: Domain

This entry represents the N-terminal domain of Mod21 from fission yeast, which interacts with Mozart1 (Mzt1) which modules gamma-tubulin ring complex (gamma-TRC) assembly and targeting, allowing gamma-TRC to be to be recruited to different microtubule-organising centres .

Mod21 is a non-core subunit of the larger gamma-tubulin ring complex that effects microtubule nucleation from both centrosomal and non-centrosomal sites. This subunit, unlike GCP2 and GCP3, is not essential for viability in the fission yeast, and may not be expressed in very high concentrations. Fission yeast can form a large gamma-Tubulin complex C similar to that found in higher eukaryotes, and this complex is important for maintaining normal levels of microtubule nucleation in vivo .
Endoglucanase Z, cellulose-binding domain (CBM_5_12_2)
Type: Domain

This C-terminal domain belongs to the CAZy family of carbohydrate-binding domains that are associated with glycosyl-hydrolases. It is suggested to bind cellulose. Proteins containing this domain include endoglucanase Z from Erwinia chrysanthemi .
Xylanase inhibitor, C-terminal (TAXi_C)
Type: Domain

This entry represents a domain found C-terminal in some aspartic proteinases and in xylanase inhibitors. The activity of these proteins is vital for plant-survival as xylanase produced by phytopathogens destroys plant
cells. In TAXI-type inhibitors, this domain is important for the differences in xylanase specificity .
ML-like domain (TRP_N)
Type: Domain

This domain is distantly similar to MD-2-related lipid-recognition domain (

) and conserves its pattern of conserved cysteines. This suggests that this domain may be involved in lipid binding. Proteins containing this domain include flavin carrier protein 1/2 from budding yeasts and TRP-like ion channel pkd2 from fission yeasts .
Peroxiredoxin-like 2A/B/C (PXL2A/B/C)
Type: Family

This family consists of proteins from the peroxiredoxin-like family, including PRXL2A, PXL2B (also known as prostamide/prostaglandin F synthase) and PXL2C (also known as AAED1). PRXL2A is a secreted redox regulatory protein with potent anti-inflammatory properties . PXL2C regulates proliferation and glycolysis in gastric cancer .
PLD-like domain (PLDc_3)
Type: Domain

This domain is found in a subset of the phospholipase D family members, including 5'-3' exonuclease PLD3/4 from animals and viral phospholipases such as envelope phospholipase F13 (also known as OPG057) and homologues .

Human PLD3 is a 5'->3' DNA exonuclease which digests single-stranded DNA and may regulate inflammatory cytokine responses via the degradation of nucleic acids. PLD3 was initially thought to have phospholipase D activity due to its HKD motifs. The second HKD motif contains Glu instead of the canonical Asp and, therefore, its catalytic phospholipase D activity is still controversial . PLD4, its closest homologue, does not posses phospholipase activity.

Envelope phospholipase F13 from Vaccinia virus is the major envelope protein that plays a role in the biogenesis of the viral double membrane and in egress of virus from the host cell that produces the wrapped form of virus that is required for cell-to-cell spread . It has been shown to have broad-specificity lipase activity .
Wax synthase domain (Wax_synthase_dom)
Type: Domain

This domain is found in membrane bound O-acyltransferases, including long-chain-alcohol O-fatty-acyltransferase (wax synthases) from plants and fungi and acyl-CoA sterol acyl transferase 1 from Arabidopsis .
H repeat-associated protein, N-terminal (YbfD_N)
Type: Domain

This entry represents the N-terminal domain of the H repeat-associated protein YbfD from E. coli. This domain is frequently found N-terminal to a transposase domain (

).
Tyrosine-protein kinase, G-rich domain (GNVR)
Type: Domain

This domain is found in a group of tyrosine-protein kinases and some exopolysaccharide transport proteins. There is a highly conserved GNVR sequence motif which characterises this domain. The function is not known.
DoxX family (DoxX)
Type: Family

This is a family of integral membrane proteins known as DoxX, mostly from bacteria, archaea and animals. In M. tuberculosis, DoxX forms a membrane-associated oxidoreductase complex (MRC) together with the superoxide-detoxifying enzyme (SodA) and a predicted thiol-oxidoreductase (SseA) . This complex physically links radical detoxification with cytosolic thiol homeostasis. All members of the MRC are required for the correct function as its impairments are correlated with defective recycling of mycothiol and accumulation of cellular oxidative damage .

This entry includes TMEM35A/B from animals. TMEM35A, also known as NACHO, acts as a acetylcholine receptor chaperone that mediates the proper assembly and functional expression of the nicotinic acetylcholine receptors (nAChRs) throughout the brain .
Putative HupE/UreJ protein (Put_HupE_UreJ)
Type: Family

This entry represents a group of putative HupE/UreJ proteins mostly from bacteria. These proteins contain many conserved histidines that may be involved in nickel binding.
CCA-adding enzyme, C-terminal (CCA-adding_enz_C)
Type: Domain

This entry represents the C-terminal domain of the CCA-adding enzymes. It is a putative tRNA nucleotidyltransferase domain. CCA-adding enzymes are responsible for the synthesis and repair of the 3' terminal CCA sequence of tRNA molecules. They are encoded by essential genes in almost all organisms and add the three ribonucleotides C, C, and A to the 3' end of tRNAs in sequential order .
Putative conjugal transfer protein TraF-related (Put_conjugal_transfer)
Type: Family

Proteins in this family are putative bacterial conjugal transfer proteins.
SbsA, Ig-like domain (SbsA_Ig)
Type: Domain

This Ig-like domain is found in surface-layer (S-layer) protein (SbsA) , among other proteins.
Putative Na+/H+ antiporter, N-terminal (Na_H_antiport_N)
Type: Domain

This entry represents the N-terminal domain of a group of integral membrane proteins, some of which are NA+/H+ antiporters .
Peptidase S8, pro-domain (S8_pro-domain)
Type: Domain

This domain is the pro-domain of several peptidases belonging to family S8 .
VTT domain (VTT_dom)
Type: Domain

This entry represents a domain found in Golgi apparatus membrane protein TVP38 from Saccharomyces cerevisiae, in human Vacuole membrane protein 1 (VMP1) and Transmembrane protein 41B (TMEM41B). TVP38 localises with the t-SNARE Tlg2 and is involved in vesicular trafficking and spindle migration . VMP1 and TMEM41B are phospholipid scramblases involved in lipid homeostasis and membrane dynamics processes .

The VTT (VMP1, TMEM41, and TVP38) domain was previously called the SNARE-associated domain. As there is no evidence that this domain associates with SNARE proteins, it was renamed .

This domain covers most of the protein length of some sequences of the DedA family, including Inner membrane protein YghB from Escherichia coli, which may be a membrane transporter required for proton motive force (PMF)-dependent drug efflux and may play a role in determining membrane lipid composition .
Mon2, C-terminal (Mon2_C)
Type: Domain

Mon2 proteins are found from fungi to plants, to human and is a scaffold protein involved in multiple aspects of endo membrane trafficking . The C-terminal region is essential for Mon2 activity .
DedA-like (DedA-like)
Type: Family

This entry represents the DedA family of proteins which includes the inner membrane proteins YghB, YqjA, and DedA. DedA may be involved in undecaprenyl phosphate (UndP) transport and recycling . It is involved in biosynthesis of LPS lipid A and in the maintenance of membrane potential and plays a role in virulence, probably by allowing bacteria to resist the host immune response YghB may be a membrane transporter required for proton motive force (PMF)-dependent drug efflux. It required, with YqjA, for the proper export of certain periplasmic amidases and, possibly, other Tat substrates. It may play a role in determining membrane lipid composition .
tRNA pseudouridylate synthase B, C-terminal (TruB_C)
Type: Domain

This C-terminal region is found on a subset of the tRNA pseudouridine synthase II TruB family. It is found from bacteria and archaea to fungi, plants and human.
Putative F0F1-ATPase subunit, Ca2+/Mg2+ transporter (ATPase_put)
Type: Family

This entry represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme. It carries two transmembrane helices and is a magnesium or calcium uniporter. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI .
Polyketide synthase, C-terminal extension (PKS_assoc)
Type: Domain

This entry represents the very C terminus of a group of polyketide synthases. Polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations . Proteins containing this domain can be found in proteins ranging from bacteria to human.
Branched-chain amino acid ATP-binding cassette transporter, C-terminal (BCA_ABC_TP_C)
Type: Domain

This domain is found C-terminal in branched-chain amino acid transporter LivG and LptB . It is approximately 30 amino acids in length and contains a conserved AYLG sequence motif. Structure and biochemical studies in LptB showed that this domain is essential for LPS transport .