SII-SWORD/CoKE huggingface dataset:
Influenza B matrix protein 2 (Flu_B_M2)
Type: Family

BM2 is integral membrane protein that displays H(+) ion channel activity that plays critical roles in production of infectious virus. It is synthesised in the late phase of infection and incorporated into the virion. The cytoplasmic domain of the BM2 protein is required for firm association of the M1 protein with lipid membranes, vRNP complex incorporation into virions, and virion morphology .
FecR protein (FecR)
Type: Domain

This entry represents the homologs of Ferric citrate uptake sigma factor regulator FecR

. This protein is required for transcriptional activation of the fecABCDE operon by sigma factor FecI . It undergoes sequential cleavage to produce an N-terminal cytoplasmic fragment which is released from the membrane and binds to FecI, allowing it to activate transcription of the fecABCDE operon which mediates ferric citrate transport . In the absence of citrate, FecR inactivates FecI .

FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Hyaluronan/mRNA-binding protein (HABP4_PAIRBP1-bd)
Type: Domain

This entry represents a domain found in the HABP4 protein family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role
in vivo
. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan . PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability . However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function.

Hyaluronan/mRNA-binding protein may be involved in nuclear functions such as the remodeling of chromatin and the regulation of transcription .
Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (Thio_Ohase/aa_AcTrfase)
Type: Domain

This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) . This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism . For example, in peroxisomes, the hydrolase acts on bile-CoA esters .
LMP repeat (LMP_rpt)
Type: Repeat

This repeated sequence element is found in the LMP group of surface-located membrane proteins of Mycoplasma hominis. The the number of repeats in the protein affects the tendency of cells to spontaneously aggregate. Agglutination may be an important factor in colonization. Non-agglutinating microorganisms might easily be distributed whereas aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried .
Domain of unknown function DUF629 (DUF629)
Type: Domain

This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Domain of unknown function DUF627, N-terminal (DUF627_N)
Type: Domain

This domain represents the N-terminal region of several plant proteins of unknown function.
Domain of unknown function DUF632 (DUF632)
Type: Domain

This conserved region contains a leucine zipper-like domain. The proteins are found only in plants and their functions are unknown.
Domain of unknown function DUF630 (DUF630)
Type: Domain

This region is sometimes found at the N terminus of putative plant bZIP proteins

. The function of this conserved region is not known.
Domain of unknown function DUF547 (DUF547)
Type: Domain

This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans and Arabidopsis thaliana (Mouse-ear cress).
Rhabdovirus matrix protein M (Rhabdo_M)
Type: Family

Matrix (M) protein is an important structural component of rhabdovirus virions, and also plays a number of roles during the replication cycle of the virus . It is involved in condensing and targeting the ribonucleoprotein (RNP) coil to the plasma membrane. M interacts specifically with the transmembrane spike protein (G) and it is important for the incorporation of G protein into budding virions .
ssDNA-binding protein, baculovirus (ssDNA-bd_baculovirus)
Type: Family

This is a family of Baculovirus ssDNA-binding proteins.
Late protein H7, poxvirus (Poxvirus_H7)
Type: Family

This is a family of poxvirus late H7 proteins.
Protein of unknown function DUF620 (DUF620)
Type: Family

This is a family of uncharacterised proteins.
Protein of unknown function DUF621 (DUF621)
Type: Family

This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans, and is noted to have possible G-protein-coupled receptor-like activity.
Sarcoglycan complex subunit protein (Sarcoglycan)
Type: Family

The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma, delta and zeta members .
LMBR1-like membrane protein (LMBR1-like_membr_prot)
Type: Family

This group of proteins have a conserved C-terminal region which is found in LMBR1 and in the lipocalin-1 receptor. LMBR1 was thought to play a role in preaxial polydactyly, but recent evidence now suggests this not to be the case . Vertebrate members of this family may play a role in limb development . Lysosomal cobalamin transport escort protein LMBD1 is a lysosomal membrane chaperone required to export cobalamin from lysosome to the cytosol, allowing its conversion to cofactors . This protein showed homology to the lipocalin membrane receptor (LIMR) .
BRRF1, herpesviridae (Herpes_BBRF1)
Type: Family

Most proteins in this entry are uncharacterised viral proteins translated from gene 49. The UL6 locus of pseudorabies virus (PRV) has a gene cluster with homology to herpes simplex virus UL5, UL6, UL7 and UL8, Epstein-Barr virus BBRF1 and BBRF2, and Kaposi sarcoma-associated herpes virus ORF43 and ORF42 .
Carbohydrate deacetylase YdjC-like (YdjC-like)
Type: Family

This entry includes YdjC deacetylase-like proteins , including chitooligosaccharide deacetylase ChbG .
INO80 complex subunit B-like conserved region (INO80B_C)
Type: Domain

This is a group of proteins with a conserved C-terminal region which is found in INO80 complex subunit B (INO80B, Ies2 homologue, also known as PAPA-1). INO80B is a component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair .
Plasmid encoded RepA protein (RepA_C)
Type: Family

This is a family of plasmid encoded proteins involved in plasmid replication. The role of RepA in the replication process is not clearly understood .
Herpesvirus Orf11 (Herpes_Orf11)
Type: Family

This family of proteins are found in Herpesvirus. This family includes proteins called ORF10 and ORF11 amongst others.
Per os infectivity factor 4 (AcMNPV_PIF-4)
Type: Family

This family of viral proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) Orf96, which encodes a per os infectivity factor (PIF-4) . Baculoviruses encode per os infectivity factors (PIFs) on the envelope surface of occlusion-derived virus (ODV) to initiate the efficient primary infection in midgut.
Fzo/mitofusin HR2 domain (Fzo/mitofusin_HR2)
Type: Domain

This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis . This conserved region is also found in the human mitofusin protein .

This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion .
NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-like (NADH_UbQ_FeS_4_mit-like)
Type: Family

This entry includes NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 (NDUS4), an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), initially identified in Neurospora crassa as a 21kDa protein . It is believed that members of this family are not involved in catalysis. This entry also includes uncharacterised bacterial sequences.
DNA-directed RNA polymerase III subunit Rpc5 (RNA_pol_III_Rpc5)
Type: Family

DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses, being involved in innate immune response, as it induces type I interferon and NF-Kappa-B through the RIG-I pathway . DNA-directed RNA polymerase III subunit RPC5 is a specific peripheric component of RNA polymerase III complex. This subunit forms a subcomplex with RPC4 which is close to the active centre allowing the formation of the open promoter complex and facilitates termination and reinitiation. RPC5 mutations are associated with impaired type I INF and increased susceptibility to viral infections .
Serine/threonine-protein phosphatase 4 regulatory subunit 3-like, central domain (P4R3-like_central_dom)
Type: Domain

This entry represents a domain found in Serine/threonine-protein phosphatase 4 regulatory subunit 3A/B/C from humans (P4R3A/B/C, also known as SMEK homologue 1/2/3) and similar proteins from eukaryotes. P4R3B is a regulatory subunit of serine/threonine-protein phosphatase 4 (PP4) that form a complex with its catalytic subunit (PP4c) and regulate its activity. PP4c is involved in developmental progression, chemotaxis, expression of stress response genes and cell movement . The specific function of this domain is still unknown.
XLR/SYCP3/FAM9 domain (XLR/SYCP3/FAM9_dom)
Type: Domain

This entry represents a conserved region found in the members of the FAM9 and XLR/SYCP3 families.

SYCP3, also known as COR1, is a component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase .
Nonstructural protein NSM (Bunya_NSM)
Type: Family

This is a family of plant infecting tospovirus NSM proteins a number of which contain the phospholipase A2 histidine active site,

.
Sulphydryl oxidase, FAD-linked, ERV1/ALR-type (Sulphydryl_Oase_FAD-link_ERV1)
Type: Family

This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.
Type III secretion protein EspF (T3SS_EspF)
Type: Repeat

Enteropathogenic Escherichia coli O127:H6 attaches to the intestinal mucosa through actin pedestals that are created after it has injected the Type III secretion protein EspF (E. coli secreted protein F-like protein from prophage U) into the cells. EspF recruits the actin machinery by activating the WASP (Wiscott-Aldrich syndrome protein) family of actin nucleating factors . Subsequent cell-death (apoptosis) is caused by EspF being targeted to the mitochondria as a consequence of its mitochondrial targeting sequence. Import into mitochondria leads to a loss of membrane potential, leakage of cytochrome c and activation of the apoptotic caspase cascade. Mutation of leucine to glutamic at position 16 of EspF (L16E) resulted in the failure of EspF import into mitochondria; mitochondrial membrane potential was not affected and cell death abolished. This suggests that the targeting of EspF to mitochondria is essential for bacterial pathogenesis and apoptosis .
Geminivirus AC4/5, conserved domain 1 (Gemini_AC4_5_cons_dom_1)
Type: Domain

This entry represents a conserved domain found in Gemini virus AC4 and AC5 proteins .
Citrus tristeza virus P23 protein (CTV_P23)
Type: Family

This family of proteins contains p23 from the citrus tristeza virus, which is a member of the Closteroviridae. CTV produces more positive than negative RNA strands, and p23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains .
HupH hydrogenase expression protein, C-terminal (HupH_Hydgase_express_prot_C)
Type: Domain

This entry represents the C-terminal conserved domain found in bacterial hydrogenase expression proteins (HupH), which are necessary for hydrogenase synthesis. The precise function of HupH is unknown .
Zinc finger, Sec23/Sec24-type (Znf_Sec23_Sec24)
Type: Domain

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex . COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation .

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger, an α/β trunk domain (

), an all-helical region (

), and a C-terminal gelsolin-like domain (

). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the β-barrel at the periphery of the complex.
Sec23/Sec24, trunk domain (Sec23/24_trunk_dom)
Type: Domain

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex . COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation .

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (

), an α/β trunk domain, an all-helical region (

), and a C-terminal gelsolin-like domain (

). This entry describes the Sec23/24 α/β trunk domain, which is formed from a single, approximately 250-residue segment plugged into the β-barrel between strands β1 and β19. The trunk has an α/β fold with a vWA topology, and it forms the dimer interface, primarily involving strand β14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.
Hepatocyte nuclear factor 1, beta isoform, C-terminal (HNF1b_C)
Type: Domain

This domain consists of a region found within the alpha isoform and at the C terminus of the beta isoform of the homeobox-containing transcription factor of HNF-1. Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing. The C-terminal region of HNF-1 is responsible for the activation of transcription . Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) .
Hepatocyte nuclear factor 1, alpha isoform C-terminal (HNF1a_C)
Type: Domain

This domain consists of an alternative C terminus of homeobox-containing transcription factor HNF-1, found in the HNF-1A isoform. Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing. The C-terminal region of HNF-1 is responsible for the activation of transcription, and HNF-1A, which has this C-terminal extension, transactivates less well than the B and C isoforms . Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) .
Hepatocyte nuclear factor 1, N-terminal (HNF-1_N)
Type: Domain

This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) .
Sec23/Sec24, helical domain (Sec23/24_helical_dom)
Type: Domain

COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex . COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation .

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a β-barrel, a zinc-finger (

), an α/β trunk domain (

), an all-helical region, and a C-terminal gelsolin-like domain (

). This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.
tRNA methyltransferase TrmK (TrmK)
Type: Family

This family of proteins includes the tRNA methyltransferase TrmK, which catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 22 (m1A22) in tRNA .
Umbravirus long distance movement protein (Umbravirus_LDM)
Type: Family

The long distance movement protein of Umbraviruses mediates the movement of viral RNA through the phloem of infected plants .
Protein of unknown function DUF716 (DUF716)
Type: Family

These sequences are a family of uncharacterised hypothetical proteins restricted to eukaryotes (

) represents a sequence from Nicotiana tabacum (Common tobacco) which is up regulated in response to TMV infection.
Flavin-dependent halogenase (Flavin_halogenase)
Type: Family

This family consists of tryptophan halogenases from bacteria and related halogenases from eukaryotes such as fungi and Dictyostelium .

The bacterial flavin-dependent tryptophan halogenase PrnA catalyses the chlorination of tryptophan to form 7-chlorotryptophan . The halogenase PltM from the soil bacteria Pseudomonas protegens, catalyses the chlorination of the intermediate compound phloroglucinol to form PG-Cl and PG-Cl2 during antibiotics synthesis, toxic to other bacteria or fungi. These chlorinated compounds regulate the synthesis of a second antibiotic, pyoluteorin .

The halogenase gsfI of Penicillium aethiopicum is required for the biosynthesis of the antifungal griseofulvin, a drug used to treat dermatophyte infections. Halogenase gsfI chlorinates the intermediate compound griseophenone C to former another intermediate, griseophenone B . Sulochrin halogenase from Aspergillus terreus converts sulochrin to dihydrogeodin, a step in the biosynthesis of geodin .

The halogenase OtaD, also known as Ochratoxin biosynthesis cluster protein 5, is part of the gene cluster that mediates the biosynthesis of ochratoxin A (OTA), a mycotoxin demonstrated to have nephrotoxic, immunotoxic, genotoxic, neurotoxic, and teratogenic properties .
Timeless, N-terminal (Timeless_N)
Type: Domain

This entry represents the N-terminal domain of the Timeless protein.

The timeless gene in Drosophila melanogasteris involved in circadian rhythm control . Drosophila contains two paralogs, dTIM and dTIM2, acting in clock/photoreception and chromosome integrity/photoreception respectively. The mammalian TIMELESS (TIM) protein, originally identified based on its similarity to Drosophila dTIM, interacts with the clock proteins dCRY and dPER and is essential for circadian rhythm generation and photo-entrainment in the fly . However, phylogenetic sequence analysis has demonstrated that dTIM2 is likely to be the orthologue of mammalian TIM and other widely conserved TIM-like proteins in eukaryotes . These proteins include Saccharomyces cerevisiae Tof1, Schizosaccharomyces pombe Swi1, and Caenorhabditis elegans TIM. These proteins are not involved in the core clock mechanism, but instead play important roles in chromosome integrity, efficient cell growth and/or development , with the exception of dTIM-2, that has an additional function in retinal photoreception .

Saccharomyces cerevisiae Tof1 is a subunit of a replication-pausing checkpoint complex (Tof1-Mrc1-Csm3) that acts at the stalled replication fork to promote sister chromatid cohesion after DNA damage, facilitating gap repair of damaged DNA . Schizosaccharomyces pombe Swi1 and Swi3 form the fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks .
Disks large homolog 5, N-terminal (DLG5_N)
Type: Domain

This entry represents a domain found at the N-terminal of disks large homologue 5 (DLG5) from humans and similar proteins mainly found in chordates. It is is named takusan after a Japanese word meaning 'many'. Members of this group regulate synaptic activity . DLG5 acts as a regulator of the Hippo signaling pathway .
Herpesvirus UL49 tegument protein (Herpes_UL49)
Type: Family

This is a family of herpesvirus UL49 tegument proteins. It was shown that interactions between herpesvirus envelope and tegument proteins may play a role in secondary envelopment during herpesvirus virion maturation.
Rad21/Rec8-like protein, C-terminal, eukaryotic (Rad21/Rec8_C_eu)
Type: Domain

This domain represents a conserved C-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Rad21/Rec8 like proteins mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex . Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation .
Rad21/Rec8-like protein, N-terminal (Rad21_Rec8_N)
Type: Domain

This domain represents a conserved N-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Rad21/Rec8 like proteins mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex . Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation .