SII-SWORD/CoKE huggingface dataset:
Filamentous haemagglutinin repeat (Filamentous_hemagglutn_rpt)
Type: Repeat

This highly divergent repeat occurs in number of filamentous haemagglutinin (FHA) proteins implicated in cell aggregation . Filamentous haemagglutinin from Bordetella pertussis, the infectious agent in childhood whooping cough, expresses filamentous haemagglutinin as a surface-exposed and secreted protein that acts as a major virulence attachment factor, functioning as both a primary adhesin and an immunomodulator to bind the bacterial to cells of the respiratory epithelium . The FHA molecule has a globular head that consists of two domains: a shaft and a flexible tail. Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short β-helical strands separated by β-turns .
Nitrogen fixation protein FixH (FixH)
Type: Family

This family consists of several Rhizobium FixH like proteins. It has been suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalysed by FixG .
Cbb3-type cytochrome oxidase component (Cbb3-typ_cyt_oxidase_comp)
Type: Family

This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon .

Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyses the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism . The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I . Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear centre. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases .
Flagellar protein FliT (FliT)
Type: Family

This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum . FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium .
G/X antigen (GAGE_fam)
Type: Family

This family consists of several GAGE, PAGE and XAGE proteins. These antigens have been implicated in human cancers .

PAGE4 from humans is an intrinsically disordered protein . It has been shown to protect prostate cancer cells from DNA damage and apoptosis under oxidative stress by modulating MAPK signalling pathway .
Mediator complex, subunit Med15, fungi (Mediator_Med15_fun)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role .
GETHR pentapeptide repeat (GETHR_repeat)
Type: Repeat

This pentapeptide repeat is found in Plasmodium species and other organisms. The most conserved amino acid at each position leads to its name GETHR. The function of this repeat is unknown.
Golgi phosphoprotein 3-like (GPP34-like)
Type: Family

This family consists of several eukaryotic GPP34 like proteins. GPP34 (also known as golgi phosphoprotein 3) localises to the Golgi complex and is conserved from Saccharomyces cerevisiae to humans. The cytosolic-ally exposed location of GPP34 predicts a role for a novel coat protein in Golgi trafficking . The budding yeast GPP34 homologue, also known as Vps74, is a phosphatidylinositol-4-phosphate-binding protein that links Golgi membranes to the cytoskeleton and may participate in the tensile force required for vesicle budding from the Golgi .

This family also includes uncharacterised proteins from bacteria.
GUN4-like (GUN4-like)
Type: Domain

GUN4 is a porphyrin-binding protein involved in chlorophyll biosynthesis regulation and intracellular signaling, found in aerobic photosynthetic organisms . It has been implicated in retrograde signalling between the chloroplast and nucleus . GUN4 can bind protoporphyrin IX (PIX) and magnesium protoporphyrin IX (MgPIX), substrate and product of the Mg-chelatase, as well as heme and cobalt protoporphyrin IX (CoPIX) . It may play a role in protecting plants from reactive oxygen species (ROS)-mediated damage .
Glycosyltransferase 34 (Glyco_trans_34)
Type: Family

This family represents a group of glycosyltransferases from plants and fungi, including Mnn10/Mnn11 from budding yeasts, Gma12/Gmh1-3 from fission yeasts and xyloglucan 6-xylosyltransferase 1/2 (XXT1/XXT2) from Arabidopsis.

Mnn10 and Mnn11 are subunits of a Golgi mannosyltransferase complex, which mediates elongation of the polysaccharide mannan backbone .
Glycogen synthase (Glycogen_synth)
Type: Family

This family consists of the eukaryotic glycogen synthase proteins GYS1 and GYS2. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P) .
Nematode fatty acid retinoid binding (Gp-FAR-1)
Type: Family

Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems .
Gas vesicle protein H (GvpH)
Type: Family

This family consists of prokaryotic GvpH proteins which may be involved in gas vesicle synthesis, including Gas vesicle protein H from Haloferax mediterranei .
Gas vesicle protein GvpO (Gas-vesicle_GvpO)
Type: Family

This family consists of prokaryotic GvpO proteins which are required for gas vesicle synthesis , including Gas vesicle protein O from Streptomyces sp.
Trimeric autotransporter adhesin YadA-like, stalk domain (Coiled_stalk_dom)
Type: Domain

This is the stalk domain of the trimeric autotransporter adhesin YadA. The coiled-coil neck region makes the transition from the globular head region to the narrower stalk domain . The stalk domain confers serum resistance .

The Yersinia adhesin A (YadA) is a trimeric autotransporter adhesin of enteric yersiniae. It consists of three major domains: a head mediating adherence to host cells, a stalk involved in serum resistance, and an anchor that forms a membrane pore and is responsible for the autotransport function .
Hook, C-terminal (Hook_C)
Type: Domain

The Hook family consists of several proteins from different eukaryotic organisms, first identified in Drosophila melanogaster in which play a role in endocytic cargo sorting . In Drosophila and fungi there is a single Hook gene, whereas mammals have three Hook genes, Hook1, Hook2 and Hook3. Endogenous Hook3 binds to Golgi membranes while both Hook1 and Hook2 are localised to discrete but unidentified cellular structures . In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubule structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head .

They are a widely expressed class of dynein-associated cargo adaptor proteins which include different domains. The N-terminal part of these proteins is sufficient to form a stable complex with dynein-dynactin and includes the most conserved region within the first 160 amino acids, termed the Hook domain. This domain is followed by three coiled-coil domains, important for dimerization and activation of dynein-dynactin complex motility, and then a C-terminal domain that binds a variety of proteins specific for each Hook isoform, involved in binding to specific organelles (organelle-binding domains). All mammalian Hook isoforms form a complex with Fused Toes and the Fused Toes- and Hook-interacting protein; fungal homologues of these proteins are important for dynein-mediated early endosome transport by linking Hook to the cargo .

This entry represents the central coiled-coiled region and the divergent C-terminal domain from Hook proteins.
HR-like lesion-inducer (HR_lesion)
Type: Family

This is a family of plant proteins that are associated with the hypersensitive response (HR) pathway of defence against plant pathogens.
This family belongs to the DoxD-like superfamily. Members of this family like other members of this superfamily are likely to form homodimers.
Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain (FhaB/CdiA-like_TPS)
Type: Domain

This entry represents a conserved TPS (two-partner secretion) transport domain found near the N terminus of a number of large, repetitive bacterial proteins, including tRNA nuclease CdiA from Escherichia coli, Filamentous hemagglutinin from Bordetella pertussis (FhaB) and Hemolysin from Proteus mirabilis (HpmA). CdiA is a toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighbouring target bacteria in a contact-dependent fashion . FhaB is one of the most efficiently secreted proteins in Gram-negative bacteria. It plays a role in host-cell binding and infection . HpmA is a exotoxin that attack blood cell membranes and cause cell rupture. This domain, essential for secretion, folds into a β-helix .
Gas vesicle protein GvpC, halobacteria (Gas-vesicle_GvpC_halobac)
Type: Family

This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes .
Trimeric autotransporter adhesin YadA-like, head domain (Adhesin_Head_dom)
Type: Domain

This entry represents the head domain of YadA. This domain is composed almost solely of β-sheets making a novel nine coiled left-handed parallel β-roll (LPBR), surrounded by a partly disordered (N)-terminal random coil and a C-terminal neck region, which consists of a random coil and a short helix at the start of the stalk domain .

The Yersinia adhesin A (YadA) is a trimeric autotransporter adhesin of enteric yersiniae. It consists of three major domains: a head mediating adherence to host cells, a stalk involved in serum resistance, and an anchor that forms a membrane pore and is responsible for the autotransport function .
Herpesvirus BLRF2 (Herpes_BLRF2)
Type: Family

This family consists of several herpes virus BLRF2 tegument proteins.
Human herpesvirus U15 (Herpes_U15)
Type: Family

U15 is an ORF present in human herpesvirus 6 (HHV-6) that was initially isolated from patients with the AIDS and lymphoproliferative disorders, but was subsequently shown to be responsible for the common childhood disease exanthema subitum (roseola). Several gene fragments of HHV-6 have been shown to activate the human immunodeficiency virus (HIV) type 1 long terminal repeat (LTR) . The ORF U15 encodes a protein of 110 amino acids, whose function in unknown.
Roseolovirus glycoprotein U47 (Roseolovirus_U47)
Type: Family

This is a family of U47 herpesvirus proteins . U47 protein is also known as 120kDa glycoprotein O (or 130kDa glycoprotein O from human herpesvirus 6A). U47 proteins are modified with N-linked oligosaccharides and co-immunoprecipitated with glycoprotein H. They may have a role in cell-cell fusion in virus infection .
Envelope glycoprotein N domain (GN_domain)
Type: Domain

Glycoprotein N (gN) is a Herpesvirus envelope glycoprotein necessary for proper maturation of glycoprotein M (gM) . This entry represents the C-terminal domain.
Herpesvirus ICP27-like (ICP27-like)
Type: Family

This entry includes a group of proteins from Herpesviridae, including ICP27 from Human herpesvirus 1. ICP27 is a multifunctional regulatory protein that plays an essential role in viral transcription, nuclear export of intronless RNAs, translation of viral transcripts, and virion host shutoff function . It interacts with the nuclear pore complex through Nup62 and may compete with some host cell transport receptors for binding, resulting in inhibition of those host transport pathways . It also regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner .
Herpesvirus UL82/UL83 (Herpes_UL82/UL83)
Type: Family

This family represents the N-terminal region of the UL82 and UL83 proteins from Betaherpesvirus sp., such as Human cytomegalovirus (HHV-5) (Human herpesvirus 5). As viruses are reliant upon their host cell to serve as proper environments for their replication, many have evolved mechanisms to alter intracellular conditions to suit their own needs. HHV-5 induces quiescent cells to enter the cell cycle and then arrests them in late G(1), before they enter the S phase, a cell cycle compartment that is presumably favourable for viral replication. The protein product of the HHV-5 UL82 gene, pp71, can accelerate the movement of cells through the G(1) phase of the cell cycle. This activity would help infected cells reach the late G(1) arrest point sooner and thus may stimulate the infectious cycle. pp71 also induces DNA synthesis in quiescent cells, but a pp71 mutant protein that is unable to induce quiescent cells to enter the cell cycle still retains the ability to accelerate the G(1) phase. Thus, the mechanism through which pp71 accelerates G(1) cell cycle progression appears to be distinct from the one that it employs to induce quiescent cells to exit G(0) and subsequently enter the S phase .
Herpesvirus, helicase-primase complex component (Helicase-primas_cplx_Herpesvir)
Type: Domain

This family consists of several helicase-primase complex components from the Gammaherpesviruses.
Uncharacterised protein family HicB (Uncharacterised_HicB)
Type: Family

This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches .
Adenovirus type 2, E3A glycoprotein (Adenovirus_Type-2_E3A)
Type: Family

This family consists of several early glycoproteins (E3A) and adenovirus death protein, from human adenovirus type 2.
Immediate early response (IER)
Type: Family

This family consists of eukaryotic immediate early response (IER) proteins 2 and 5. The role of IER5 is unclear, although it plays an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2, although it is thought to play a role in mediating cellular responses to a variety of extracellular signals .
Helicobacter pylori IceA2 (IceA2)
Type: Family

This family consists of several Helicobacter pylori specific IceA2 proteins. The function of this family is unknown.
Inositol-tetrakisphosphate 1-kinase (Inositol_tetrakis-P_1-kinase)
Type: Family

This entry represents inositol-tetrakisphosphate 1-kinase, which is also called inositol 1,3,4-trisphosphate 5/6-kinase.

Inositol-tetrakisphosphate 1-kinase can phosphorylate various inositol polyphosphates, such as Ins(3,4,5,6)P4 or Ins(1,3,4)P3. Phosphorylation of Ins(3,4,5,6)P4 at position 1 forms Ins(1,3,4,5,6)P5 which has regulatory importance, since Ins(3,4,5,6)P4 is an inhibitor of plasma membrane Ca(2+)-activated Cl(-) channels. Phosphorylation of Ins(1,3,4)P3 on O-5 and O-6 forms Ins(1,3,4,6)P4, an essential molecule in the hexakisphosphate (InsP6) pathway .
Jumping translocation breakpoint (JTB)
Type: Family

This family contains several jumping translocation breakpoint proteins or JTBs. Jumping translocation (JT) is an unbalanced translocation that comprises amplified chromosomal segments jumping to various telomeres. JTB, located at 1q21, has been found to fuse with the telomeric repeats of acceptor telomeres in a case of JT. hJTB (Homo sapiens JTB) encodes a transmembrane protein that is highly conserved among divergent eukaryotic species. JT results in a hJTB truncation, which potentially produces an hJTB product devoid of the transmembrane domain. hJTB is located in a gene-rich region at 1q21, called EDC (Epidermal Differentiation Complex) . JTB has also been implicated in prostatic carcinomas .
Kinesin-associated protein 3 (KAP3)
Type: Family

This family consists of kinesin-associated protein 3 (KAP3, also known as SMAP). In human and mouse, KAP3 is involved in tethering the chromosomes to the spindle pole and in chromosome movement. It binds to the tail domain of the KIF3A/KIF3B heterodimer to form a heterotrimeric KIF3 complex and may regulate the membrane binding of this complex .
Yeast cell wall synthesis Kre9/Knh1, C-terminal (Kre9/Knh1_C)
Type: Domain

This entry represents the C-terminal domain of the Knh1 protein, which is a glycoprotein that is involved in cell wall beta 1,6-glucan synthesis. Proteins containing this domain also include functional homologue of Knh1, Kre9. In Saccharomyces cerevisiae, a kre9 null mutation leads to severe growth defects, aberrant multi-budded morphology, and mating defects . Over-expression of Knh1 suppresses growth defects of a kre9 null mutant . Knh1 is required for propionic acid resistance .
Fibroin light chain (L-fibroin)
Type: Family

This family consists of several moth fibroin light chain (L-fibroin) proteins. Fibroin of Bombyx mori is secreted into the lumen of posterior silk gland (PSG) from the surrounding PSG cells as a molecular complex consisting of a heavy (H)-chain of approximately 350kDa, a light (L)-chain of 25kDa and a P25 of about 27kDa. The H- and L-chains are disulphide-linked but P25 is associated with the H-L complex by non-covalent force .
L6 membrane (L6_membrane)
Type: Family

This family consists of several eukaryotic L6 membrane proteins. L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily it has now been found that that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 family . Several members of this family have been implicated in Homo sapiens cancer .
Torsin-1A-interacting protein 1/2 (TOIP1/2)
Type: Family

This entry represents Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1), which are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane . These proteins interact with and activate Torsin A, an AAA+ ATPase localized to the endoplasmic reticulum (ER), through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity . A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease .
Leukocyte cell-derived chemotaxin 2 (LECT2)
Type: Family

This family consists of several leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown . It contains an M23 metalloendopeptidase fold, but was found to be catalytically inactive as a metalloendopeptidase .
LISCH7 (LISCH7)
Type: Domain

This domain consists of mammalian LISCH7 protein homologues. LISCH7 is a liver-specific BHLH-ZIP transcription factor.
LRV FeS4 cluster (LRV_FeS)
Type: Domain

This iron sulphur cluster is found at the N terminus of some proteins containing leucine-repeat variant (LRV) repeats (

). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cys residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats . Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.
Virion infectivity factor, Lentivirus (Vir_infectivity_fact_Lentivir)
Type: Family

This family consists of several feline-specific Lentivirus virion infectivity factor (VIF) proteins. VIF is essential for productive Feline immunodeficiency virus infection of host target cells
in vitro
.