SII-SWORD/CoKE huggingface dataset:
Adhesin, Dr family, signal peptide (Adhesin_Dr_signal_peptide)
Type: PTM

The Afa/Dr family of adhesins bind to the Dr blood group antigen component of decay-accelerating factor. These proteins contain both fimbriated and afimbriated adherence structures and mediate adherence of uropathogenic Escherichia coli to the urinary tract, leading to urinary tract infections (UTIs) and pregnancy complications . They also confer the mannose-resistant hemagglutination (MHRA) phenotype, which can be inhibited by chloramphenicol. The N-terminal portion of the mature protein is thought to be responsible for chloramphenicol sensitivity . These proteins remain attached to host cells or collagen once bound even in the presence of elevated shear stress or of chloramphenicol, a competitive inhibitor of binding .

This entry represents the signal peptide region necessary for protein secretion to the cell surface.
Fibronectin-binding repeat, SSURE (Fibronectin-binding_SSURE)
Type: Repeat

Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins . The proteins are further characterised by having an N-terminal motif resembling [YF]SIRKxxxGxxS[VIA]

and a C-terminal LPXTG motif-containing region which is a characteristic of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall.
Human herpes virus-8, Protein K1, cytoplasmic domain (HHSV-8_K1_cytoplasmic_dom)
Type: Domain

This entry represents a domain thought to to be at the cytoplasmic region of the Protein K1 from Human herpesvirus 8. This protein promotes host cell survival pathways and may contribute to pathogenesis by preventing infected cells from undergoing apoptosis. It is a highly glycosylated cytoplasmic and membrane protein similar to the immunoglobulin receptor family that is expressed as an inducible early-lytic-cycle gene product in primary effusion lymphoma cell-lines .
Envelope glycoprotein UL132 (UL132)
Type: Family

Envelope glycoprotein UL132 is a low-abundance structural component of Human Cytomegalovirus . UL132 has an important function for viral replication in tissue culture . It is essential for the formation of the viral assembly compartment (AC), hence, critical for the efficient production of infectious particles .
Fanconi Anaemia group E protein, C-terminal (Fanconi_anaemia_gr_E_prot_C)
Type: Domain

Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins.

The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex . This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any β-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus.
Filamentous haemagglutinin family outer membrane protein, domain of unknown function DUF3739 (Filamn_hemagglutn_DUF3739)
Type: Domain

This entry represents a conserved sequence domain found in a number of bacterial filamentous haemagglutinins, usually in association with

.
Transposase, putative, helix-turn-helix domain (Transposase_put_HTH)
Type: Domain

This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases , such as A625R from Paramecium bursaria Chlorella virus 1 and in RNA-guided DNA endonucleases, including TnpB from Deinococcus radiodurans, an RNA-guided dsDNA endonuclease that cleaves DNA downstream of the 5'-TTGAT-3' transposon-associated motif (TAM) guided by RNA derived from the right-end element of its insertion sequence element . This domain is usually associated with

and

.
Homotrimeric ring hydroxylase, catalytic domain (Homotrim_ring_OHase_catalytic)
Type: Domain

This entry represents the catalytic domain from a family of homotrimeric enzymes that hydroxylate aromatic compounds, including carbazole 1,9a-dioxygenase from Janthinobacterium. The catalytic domain is found C-termnial to the iron-sulphur-binding Rieske domain and is composed of antiparallel β sheets and α helices . It is part of a much larger superfamily of lipid binding domains which form a common fold that works as a versatile scaffold for binding bulky ligands .
DNA polymerase III, tau subunit, domain V (DNA_pol_III_tau_dom-5)
Type: Domain

This domain family is found in bacteria, and is approximately 140 amino acids in length. It is found in association with

. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme .
Protein of unknown function DUF3731 (DUF3731)
Type: Family

Proteins in this family are bacterial proteins of approximately 250 amino acids in length. There are two conserved sequence motifs: RPG and WRR. The proteins in this family are frequently annotated as DNA-K related proteins however there is little accompanying literature to confirm this.
Hyphally-regulated cell wall protein, N-terminal (Hyphal-reg_cell_wall_N)
Type: Domain

This entry represents a conserved domain found at the N terminus of a number of fungal proteins. These proteins are largely annotated as being hyphally-regulated cell wall proteins that are induced in response to hyphal development. Proteins containing this domain include Hpf1 from budding yeasts and Hyr1 from Candida albicans. Hpf1 can reduce haziness in white wine . Hyr1 is a GPI-anchored hyphal cell wall protein required for hyphal growth and virulence. It is involved in innate immune cell evasion through confering resistance to neutrophil killing .
Duffy-antigen binding, N-terminal (Duffy-antigen-binding_N)
Type: Domain

This entry represents the N terminus of the Duffy-antigen binding protein and is thought to bind to the human erythrocytes Duffy blood group determinant. These domains are found in eukaryotic proteins and are approximately 70 amino acids in length .
Extracellular fibrinogen binding protein, C-terminal (Extracellular_fibrinogen-bd_C)
Type: Domain

This entry represents the C-terminal region of bacterial extracellular fibrinogen binding proteins which is approximately 70 amino acids in length and contains a conserved VLK sequence motif. It also contains a helical motif involved in complement regulation . This motif binds to complement proteins and changes its conformation to a form which cannot activate downstream components of the complement cascade.
Tip attachment protein J, C-terminal receptor binding domain (GpJ_C)
Type: Domain

This entry represents the C-terminal receptor binding domain of Tip attachment protein J from Escherichia phage lambda (GpJ) and similar bacterial and viral proteins. This domain, which determines the host specificity of the phage, shows an immunoglobulin-like fold . It is often found in association with

and

. There are two completely conserved G residues that may be functionally important. Many of the proteins in this entry are annotated as fibronectin type III. This domain was previously known as DUF3672.

The Tip attachment protein J (GpJ) from Escherichia phage lambda is a crucial tail fibre protein responsible for recognising and binding the host cell's LamB receptor, thereby initiating infection. Structurally, GpJ forms the central tail fibre at the phage tip and undergoes conformational changes upon receptor engagement, which are essential for triggering DNA injection into the host . It interacts with other tail proteins during assembly, serving as a scaffold for tail tube formation and coordinating with the tape measure protein to regulate genome delivery . Mutations in GpJ can alter host specificity and affect phage stability, while its exposed position makes it a target for neutralising antibodies .
Glycoprotein 60, Cryptosporidium spp (Glycop-60_Cryptosporidium)
Type: Domain

This entry represents proteins that are highly conserved in Cryptosporidium spp. Many members are annotated as being a 60kDa glycoprotein.
Small ribosomal subunit protein mS45 (Ribosomal_mS45)
Type: Family

This entry represents the small ribosomal subunit protein mS45, also known as Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms .
Stomoxyn (Stomoxyn)
Type: Family

Stomoxyn is an insect antimicrobial peptide localised in the gut epithelium, which functions in killing a range of microorganisms, parasites and some viruses. In water, stomoxyn has a flexible random coil in structure, while in trifluoroethanol it adopts a stable helical structure. Structural similarities to the antimicrobial peptide cecropin A from Hyalophora cecropia suggest that it may function in a similar manner by disrupting the bacterial membrane .
Herpesvirus UL130, cytomegalovirus (Herpes_UL130_cytomegalovirus)
Type: Family

This entry represents UL130 from Human cytomegalovirus, a glycoprotein secreted from infected cells that is incorporated into the virion envelope as a Golgi-matured form. The protein promotes endothelial cell infection through a producer cell modification of the virion .
Iron-sulphur binding protein LdpA, C-terminal (Fe-S-bd_prot_LdpA_C)
Type: Domain

This entry represents the C-terminal region of the iron-sulphur protein LdpA (Light dependent period), which is found in phototropic organisms. LdpA was originally identified in cyanobacteria where it is involved in light-dependent modulation of the circadian clock. The presence of iron-sulphur clusters on LdpA suggests that it may modulate the circadian clock as an indirect function of light intensity by sensing changes in cellular physiology .
LRRC8, pannexin-like TM region (LRRC8_Pannexin-like)
Type: Domain

This entry represents the four transmembrane domains of metazoan leucine-rich-repeat-containing 8 proteins. These four TMs associate into hexamers resulting in homo- or heteromeric channels that connect the cytosol to the extracellular space .
Major surface glycoprotein 2, C-terminal (Maj_surf_glycoprot_2_C)
Type: Domain

Pneumocystis can cause potentially fatal pneumonia infections in immunosuppressed people. The most abundant protein on the surface of Pneumocystis is the major surface glycoprotein (Msg), which is encoded by a multi-copy gene family. Variation in the expressed Msg is thought to help this organism evade the host immune response. The Msg sequences segregate into two distinct branches, with recombination further increasing the diversity of the Msg sequences . This entry represents a conserved domain found towards the C terminus of Msg2, and is usually found in association with

.
Herpesvirus UL139, cytomegalovirus (Herpes_UL139_cytomegalovirus)
Type: Family

This entry represents eukaryotic and viral proteins of approximately 140 amino acids in length. The UL139 product shares sequence homology with human CD24, a signal transducer modulating B-cell activation responses, and the sequences in the G1c variant of UL139 contained a specific attachment site of prokaryotic membrane lipoprotein lipid .
MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding (NIFK_FHA_Ki67-binding)
Type: Domain

This entry represents eukaryotic proteins that contain a domain of approximately 40 amino acids in length. These proteins are found in association with

. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation .
Herpesvirus Glycoprotein B, antigenic domain, N-terminal (Glycoprot_B_antigenic_N)
Type: Domain

Herpesviruses are enveloped by a lipid bilayer that contains at least a dozen glycoproteins. The virion surface glycoproteins mediate recognition of susceptible cells and promote fusion of the viral envelope with the cell membrane, leading to virus entry.

This domain is found in viruses, and is approximately 40 amino acids in length. The domain is found in association with

. There are two conserved sequence motifs: SVS and TSS. This entry represents the N-terminal antigenic domain of glycoprotein B of Human herpesvirus 5 .
Influenza A proapoptotic protein PB1-F2 (Flu_proapoptotic_PB1-F2)
Type: Family

PB1-F2 is a protein found in almost all known strains of Influenza A virus - a negative sense ssRNA Orthomyxovirus . It originates from translation of the viral polymerase gene in an alternative reading frame . PB1-F2 consists of two independent structural domains, two closely neighbouring short helices at the N terminus, and an extended C-terminal helix . Although the protein has originally been described to induce apoptosis, it has now been shown that PB1-F2 more likely acts as an apoptosis promoter in concert with other apoptosis-inducing agents . PB1-F2 promotes apoptosis by localising to the mitochondria where it destabilises the membrane. This will cause release of cytochrome C which activates the caspase cascade of apoptosis through the endogenous pathway . In this way it acts like the Bcl-2 protein family which are physiological apoptotic regulators in cells .
Cold-shock protein, DEAD box A, C-terminal (Cold-shock_DEAD_Abox_C)
Type: Domain

This domain is found at the C terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination . This region contains several repeats which contain an ERRE sequence motif.
Mannosyltransferase 1, CMT1 (Mannosyltransferase_CMT1)
Type: Family

The capsule of pathogenic fungi is a complex polysaccharide whose formation is determined by a number of enzymes including, most importantly, alpha-1,3-mannosyltransferase 1 . It is responsible for addition of mannose residues in an alpha-1,3 linkage to a polymannosly precursor.
Intracellular growth locus C protein (Intracellular_growth_locus_C)
Type: Family

IglC protein is involved in the escape of Francisella tularensis live vaccine strain . It has been shown that the expression of IglC is essential for F. tularensis to induce macrophage apoptosis . IglC adopts a β-sandwich conformation that has no similarity to any known protein structure .
Bacteriophage T4, Gp40, head assembly (Phage_T4_Gp40)
Type: Family

This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex .
Cytochrome c oxidase subunit IV, actinobacteria (Cyt_c_oxidase_su4_actinobac)
Type: Family

This family of proteins is found in Gram-negative bacteria, mainly Actinobacteria, and represent the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex .
Herpes simplex virus, Tegument protein VP16, C-terminal (HSV_VP16_C)
Type: Domain

This domain is found in the C-terminal region of the HSV virion protein 16 (VP16 or Alpha-TIF) from Herpes Simplex virus. It appears in association with

and is about 30 amino acids in length. It is the carboxyl subdomain of the acidic transcriptional activation domain.

VP16 is a transcription promoter, an essential activator of viral immediate early (IE) promoters (alpha genes) during the lytic phase of viral infection. The protein associates with cellular transcription factors and DNA binding proteins to to enhance transcription rates. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc. The C-terminal residues of the protein are responsible for transcriptional activation. Within the C-terminal region there are two activation regions that can independently and cooperatively activate transcription .
Holliday junction recognition protein, HJURP, central domain (HJURP_central_dom)
Type: Domain

This entry represents a central, conserved region found in Holliday junction recognition protein from humans (HJURP) and similar proteins from vertebrates. This domain is not present in Holliday junction recognition proteins from fungi. However, both the N-terminal domain and a repeated domain that appears further downstream, also of unknown function, appear in all both vertebral and fungal Holliday junction recognition proteins.
Dispersed gene family protein 1, C-terminal (Dispersed_gene_fam_prot1_C)
Type: Domain

Dispersed gene family protein 1 (DGF-1) of Trypanosoma cruzi is one of the most abundant proteins in T. cruzi genome . It seems to have a preferential expression in amastigotes (intracellular replicative forms that develop in the mammalian host) . The function of this protein is not yet clear, however, it is likely to play a role in cell-to-cell interactions or signal transduction . This entry represents the C-terminal domain on this protein.
Cell wall mannoprotein 1 (Cell_wall_mannoprotein_1)
Type: Family

Hydrophobic surface binding proteins are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation .
Type-IV b secretion system, inner-membrane complex component (T4BSS_IcmL/DotI)
Type: Family

This is a family of DotI/IcmL proteins of type IVb secretion systems, that reside in the inner-membrane. It carries a single transmembrane helix in the N-terminal conserved region, has an extra-periplasmic domain, and is conserved in all T4BSSs including I-type conjugation systems (TraM). DotI/IcmL (and DotJ) may form an inner membrane complex that associates with the core complex .
Mitochondrial import inner membrane translocase subunit Tim54 (Mt_import_IM_translocase_Tim54)
Type: Family

Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targeting information, into the inner membrane .
Trypanosome invariant surface glycoprotein (Trypano_invariant_glycop)
Type: Family

This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75, that are found in the mammalian stage of the parasitic protozoan. The sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane α-helices and short cytoplasmic domains. They are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite .
Porin OmpL1 (Porin_OmpL1)
Type: Family

OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira. Specifically, it is a porin .
DnaJ-related protein, N-terminal (DnaJ-related_N)
Type: Domain

This domain family is approximately 130 amino acids in length and contains a conserved YYLD sequence motif. The proteins have a C-terminal DNA-J domain

and most of the sequences are annotated as DNA-J related proteins, other annotations include: DnaJ-class molecular chaperon and formate dehydrogenase; but there is currently no publications to support these annotations.
Mitochondrial division protein 1 (Mt_division_protein_1)
Type: Family

This entry represents mitochondrial division protein 1 (Mdv1), which is a component of the mitochondrial fission machinery in Saccharomyces cerevisiae. The protein is also involved in peroxisome proliferation . Mdv1 along with Fis1 is also involved in controlling Dnm-1 dependent devision, a GTPase involved in the mediation of mitochondrial division. In this role, Mdv1 is the linker between Fis1 and Dnm1. Mdv1 plays a key role in the regulation of Dnm1 self-assembly .

Mdv1 has a partially redundant function to CAF4 in acting as an adapter protein, binding to FIS1 on the mitochondrial outer membrane and recruiting the dynamin-like GTPase DNM1 to form mitochondrial fission complexes. Formation of these complexes is required to promote constriction and fission of the mitochondrial compartment at a late step in mitochondrial division . Mdv1 interacts with CAF4, DNM1 and FIS1, components of the mitochondrial fission machinery. It interacts via its N-terminal, coiled-coil extension (NTE) with FIS1, and via its WD repeats with DNM1. Mdv1 is uniformly distributed on the cytoplasmic face of the mitochondrial outer membrane. This localisation is dependent on FIS1. It reorganises to punctate structures on mitochondria, corresponding to mitochondrial constriction sites, at a late step in mitochondrial division. This relocalisation is dependent on DNM1.
Putative aromatic acid exporter, C-terminal (ArAE_1_C)
Type: Domain

This region is a presumed intracellular domain found in a set of bacterial presumed transporter proteins. The region is about 160 amino acids in length.
NF-kappa-B essential modulator NEMO, N-terminal (NEMO_N)
Type: Domain

This entry represents a conserved domain found at the N-terminal of NF-kappa-B essential modulator (NEMO) and optineurin proteins. NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation . NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini. The core domain of NEMO is a dimer which binds to two fragments of IKK .