SII-SWORD/CoKE huggingface dataset:
Late blight resistance protein R1A-like, N-terminal (R1A-like_N)
Type: Domain

R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain . This entry represents the LRR domain, found at the N-terminal and associated with the NB-ARC domain (

).
Heparan sulphate-N-deacetylase, deacetylase domain (Heparan_SO4_deacetylase_dom)
Type: Domain

This domain is found in heparan sulphate N-deacetylase enzymes. It is often found associated with

.

This entry represents the deacetylase domain which has a fold closely related to the CE domain of Agd3 from A. fumigatus .
MYND-type zinc finger-containing chromatin reader ZMYND8 (ZMYND8)
Type: Family

This family represents protein kinase C-binding protein 1 (PRKCBP1, also known as ZMYND8) from vertebrates, a chromatin reader that recognises dual histone modifications such as histone H3.1 dimethylated at 'Lys-36' and histone H4 acetylated at 'Lys-16' (H3.1K36me2-H4K16ac) and histone H3 methylated at 'Lys-4' and histone H4 acetylated at 'Lys-14' (H3K4me1-H3K14ac) . It acts as a transcriptional corepressor for KDM5D and EZH2 . ZMYND8 recognizes acetylated histone H4 and recruits the NuRD chromatin remodeling complex to damaged chromatin for transcriptional repression and double-strand break repair by homologous recombination . ZMYND8 also plays a role in neuronal development . This protein suppresses breast cancer, and prostate cancer cell invasion and metastasis. It has been proposed as a suitable epigenetic tool that can re-sensitize the chemo-refractory breast carcinoma .
Protein of unknown function DUF3545 (DUF3545)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important.
SERRATE/Ars2, N-terminal (SERRATE/Ars2_N)
Type: Domain

This domain can be found in the N terminus of the SERRATE (SE) from plants and its homologue, Ars2, from animals. They play a role in nuclear RNA metabolism. They interact with the nuclear cap-binding complex (CBC) and mediates interactions with diverse RNA processing and transport machineries in a transcript-dependent manner. Interestingly, the plant SERRATE does not have the RNA recognition motif (RRM) domain found in metazoans and S. pombe .
Sox, C-terminal (Sox_C)
Type: Domain

The Sox transcription factors are members of the Sry-related protein family that play multiple roles, mainly during development. Sox18, together with Sox7 and -17, constitutes the subgroup F within this family. Sox18 contains three major domains:the N-terminal HMG box, the central TAD domain and the C-terminal domain that contains a 9aaTAD motif . This entry represents the C-terminal domain.
Small G protein signalling modulator 1/2, Rab-binding domain (SGSM1/2_RBD)
Type: Domain

This domain adopts a PH-like fold. It has been called the Rab-binding domain (RBD) .

Small G-protein signalling modulator 1/2 (also known as RUTBC2/1) bind to Rab9A via their Pleckstrin homology (PH) domain . RUTBC1 stimulates GTP hydrolysis by Rab32 and Rab33B , while RUTBC2 appears to be a GAP for Rab36, Rab9A and associated proteins controling the recycling of mannose-6-phosphate receptors from late endosomes to the trans-Golgi .
Protein of unknown function DUF3549 (DUF3549)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif.
Protein of unknown function DUF3551 (DUF3551)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 79 to 104 amino acids in length. This protein has a single completely conserved residue C that may be functionally important.
Protein of unknown function DUF3553 (DUF3553)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Kank N-terminal motif (KN_motif)
Type: Conserved_site

This small motif is found at the N terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with

. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerisation and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors .
Very-long-chain aldehyde decarbonylase CER1-like, C-terminal (CER1-like_C)
Type: Domain

Very-long-chain aldehyde decarbonylase CER1 is an aldehyde decarbonylase involved in the conversion of aldehydes to alkanes. It is the core component of a very-long-chain alkane synthesis complex and it is involved in epicuticular wax biosynthesis and pollen fertility. CER1 is also linked to responses to biotic and abiotic stresses .

This is the C-terminal domain of CER1 from Arabidopsis and GL1 1-7 from rice. This domain has a conserved LEGW sequence motif. It is about 170 amino acids in length. This domain is found associated with

. It shares similarity to short chain dehydrogenases .
Protein of unknown function DUF3556, transmembrane (DUF3556_TM)
Type: Family

This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length.
Protein of unknown function DUF3557 (DUF3557)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length.
Protein of unknown function DUF3560 (DUF3560)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif.
Protein of unknown function DUF3562 (DUF3562)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Protein of unknown function DUF3563 (DUF3563)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 50 amino acids in length. This protein has conserved AYL and DLE sequence motifs.
Protein of unknown function DUF3564 (DUF3564)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE sequence motif.
Protein of unknown function DUF3565 (DUF3565)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH.
Domain of unknown function DUF3566. transmembrane (DUF3566_TM)
Type: Domain

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 136 to 304 amino acids in length. This region represents a transmembrane region found at the C terminus of the proteins.
Transcription factor Spt20 (Spt20)
Type: Family

This entry represents the Spt20 transcription factors in eukaryote organisms. The Spt20 protein is a subunit of the SAGA (Spt-Ada-Gcn5-acetyltransferase) complex, a large multiprotein complex involved in transcriptional regulation. In yeast, Spt20 plays a crucial role in maintaining the structural integrity of the SAGA complex, as no intact SAGA complex could be purified in Spt20 deletion strains. It is involved in chromatin organisation, histone acetylation, and IRE1-mediated unfolded protein response . The human homologue of Spt20 (hSPT20) has been identified as a bona fide subunit of the human SAGA complex and is required for its integrity . Functionally, Spt20 has been shown to participate in the regulation of specific genes. In yeast, it is required for the transcriptional elongation of PDR5 and the activation of seripauperin genes upon hypoxic stress exposure . In human cells, hSPT20 and other hSAGA subunits are specifically recruited to genes induced by endoplasmic reticulum (ER) stress .
Protein of unknown function DUF3567 (DUF3567)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif.
Lipoprotein Flpp3-like (Flpp3-like)
Type: Family

This entry represents a family of bacterial proteins, including the outer membrane lipoprotein Flpp3 from Francisella tularensis (

). This protein family was previously known as DUF3568. Flpp3, a virulence determinant of tularemia, shows a six stranded β-sheet supported with two crossing α-helices. It has a hydrophobic internal cavity that has been suggested to bind a small organic molecule. However, its specific function is still unknown .
Protein of unknown function DUF3570 (DUF3570)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 396 to 444 amino acids in length. Members in this family contain the conserved [S/T]GA[S/T] motif and are flavinylation substrates for ApbE, which suggests that they may be involved in extra cytosolic redox activities .
Protein CHLORORESPIRATORY REDUCTION 7 (CRR7)
Type: Family

This entry includes protein from cyanobacteria, blue-green algae and plants, including CRR7 (Chlororespiratory reduction 7) protein from Arabidopsis. CRR7 is part of the chloroplastic NAD(P)H dehydrogenase complex (NDH Complex) involved in respiration, photosystem I (PSI) cyclic electron transport and CO2 uptake . It is likely to be involved in the final step of the formation of the NDH Complex, in which its intermediate is inserted into thylakoids .
Protein of unknown function DUF3572 (DUF3572)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are about 100 amino acids in length and are found in bacteria.
Protein of unknown function DUF3573 (DUF3573)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 372 to 530 amino acids in length.
Protein of unknown function DUF3574 (DUF3574)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif.
Protein of unknown function DUF3575 (DUF3575)
Type: Family

This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 187 to 236 amino acids in length.
Protein of unknown function DUF3576 (DUF3576)
Type: Family

This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Protein of unknown function DUF3577 (DUF3577)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.

Members of this family regularly are found near a TopB family topoisomerase, in mobile elements such as certain pathogenicity islands, in regions of those islands thought to be involved in replication. The founding member of the family is STY4534 in Salmonella pathogenicity island 7 (SPI-7), a core protein shared by members of SPI-7's subclass of integrative and conjugative element (ICE) .
Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain (McrB_DNA-bd)
Type: Domain

This entry represents the DNA-binding domain found at the N-terminal of Type IV methyl-directed restriction enzyme EcoKMcrB subunit (mcrB, also known as 5-methylcytosine-specific restriction enzyme B McrB) from E. coli . McrB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and acts against 5-methylcytosine (5mC) preceded by a purine residue .
Surface lipoprotein of Spirochaetales order (Lipl32)
Type: Domain

Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria.
T cell CD4 receptor C-terminal region (Tcell_CD4_Cterm)
Type: Domain

This domain is the C-terminal domain of the CD4 T cell receptor. The C-terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalisation. This domain is involved in binding to the N-terminal of Lck co-receptor in a Zn2+ clasp structure.
Colicin E5 ribonuclease domain (Colicin_E5_C)
Type: Domain

Colicin is a protein produced by bacteria with Col plasmids. Its function is to attack Escherichia coli through actions on its inner membrane ion channels or through ribonuclease or deoxyribonuclease actions. The C-terminal domain is the ribonuclease domain. Colicin E5 specifically cleaves tRNA anticodons which recognise codons in the form NAY (N:any nucleotide, A:adenosine, Y:pyrimidine) which corresponds to tyrosine, histidine, asparagine and aspartic acid .
Plasminogen ligand, VEK-30 (Plasminogen_ligand_VEK-30)
Type: Domain

Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C-terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere' .
Splicing factor SF3a60 binding domain (SF3a60_bindingd)
Type: Domain

This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription.
Nuclear pore complex protein NUP96, C-terminal domain (Nup98_C)
Type: Domain

This entry represents the Nuclear pore complex protein Nup96 from animals its homologues from yeast and plants.

Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport in eukaryotic cells, playing essential roles in cellular homeostasis. The NPC is a modular structure composed of multiple copies of ~30 proteins (nucleoporins, Nups) arranged into distinct subcomplexes . A number of these peptides are synthesised as precursors and undergo self-catalysed cleavage. The largest NPC sub-complex is the heptameric Y-shaped mammalian Nup107-Nup160 complex (called Nup84 complex in budding yeast), an essential scaffolding component of the NPC .

Nup98 and Nup96 are encoded by the same gene that produces a 190 kDa polyprotein with autoproteolytic activity which generates the N-terminal NUP98 and C-terminal NUP96 proteins, part of the Nup107-Nup160 subcomplex . The yeast homologue Nup145 undergoes the similar proteolytic event to produce Nup145N and Nup145C, which are part of the Nup84 complex. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96, which is predicted to be an α helical solenoid, complexes with Sec13 in the middle of the heptamer. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex .
Polyribonucleotide phosphorylase C-terminal (PNPase_C)
Type: Domain

PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C-terminal protomer domain of the PNPase core. The function of the C-terminal protomer is to catalyse phosphorolysis through its two active sites .
Protein of unknown function DUF3579 (DUF3579)
Type: Family

This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif.
Sequence-variable mosaic (SVM), signal sequence (SVM_signal)
Type: Domain

This domain is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins . It is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length.
Salivary protein 15 (Salp15)
Type: Family

This is a family of 15kDa salivary proteins (Salp15) from Acari Arachnids that is induced on feeding and assists the parasite to remain attached to its arthropod host. By repressing calcium fluxes triggered by TCR engagement, Salp15 inhibits CD4+ T cell activation and interleukin (IL)-2 production . It downregulates host immune system by binding to both dendritic cells, and CD4+ T cells . Salp15 shows weak similarity to Inhibin A, a member of the TGF-beta superfamily that inhibits the production of cytokines and the proliferation of T cells.
Parvovirus non-structural protein 1, C-terminal (Parvovirus_NS1_C)
Type: Domain

Parvoviruses are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. Parvoviruses have been described that infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contain two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons .

NS1 protein is essential for viral life cycle stages, including DNA replication, trans-regulation of the two viral promoters, and modulation of heterologous promoters. It exhibits DNA binding, endonuclease and helicase activities and is a major contributor to the toxic effect on host cells . This is the transactivation domain of the parvovirus NS1 protein, located immediately C-terminal to the helicase .
SprA-related family (SprA-related)
Type: Family

This family of bacterial proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold . Proteins in this family are typically between 234 to 465 amino acids in length. Most members are annotated as being SprA-related.
Protein of unknown function DUF3581 (DUF3581)
Type: Family

This family consists of uncharacterised bacterial proteins.
Rifampin ADP-ribosyltransferase (Rifampin_Arr)
Type: Domain

Arr enzymes catalyze ADP-ribosylation of rifamycins, thus rendering rifamycin antibiotics ineffective. The opportunistic pathogen Mycobacterium smegmatis possesses a chromosomally encoded rifampin ADP-ribosyltransferase (Arr-ms). An homologue of Arr, Arr-2, is present in several transposons and integrons found in Gram-negative pathogenic bacteria. The structure of Arr-ms reveals similarity to protein ADP-ribosyltransferases, despite a lack of amino acid sequence similarity .
N-acetylmuramoyl-l-alanine amidase, C-terminal domain (Amidase_C)
Type: Domain

This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code

. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
D domain of beta-TrCP (Beta-TrCP_D)
Type: Domain

This entry represents the D domain of beta-TrCP, which is a member of the WD40 class of F box proteins, and functions as a ubiquitin ligase. The D domain of these F box proteins is involved in mediating dimerisation of the protein . Dimerisation is necessary to polyubiquitinate substrates, so this D domain is vital in directing substrates towards the proteasome for degradation.
PML-like, coiled-coil (PML-like_CC)
Type: Domain

PML, also known as TRIM19, acts in association with PML-nuclear bodies (PML-NBs) in a wide range of important cellular processes, such as tumor suppression, transcriptional regulation, apoptosis, senescence, DNA damage response, and viral defense mechanisms. It acts as the scaffold of PML-NBs allowing other proteins to shuttle in and out, a process which is regulated by SUMO-mediated modifications and interactions. PML exhibits antiviral activity as it stimulates the SUMOylation of a viral protein which is supposed to serve as a cellular mechanism to compromise specific functions of the viral effector IE1p72 . PML is defined by the TRIM/RBCC motif which consists of an N-terminal RING zinc finger (

), two BBox type zinc fingers (

), followed by a coiled-coil region , which is represented in this entry, and it is thought to mediate interactions with cytomegalovirus IE1 protein and/or other partners.

This entry also includes RNF207, which has a similar domain organisation as PML.
Protein of unknown function DUF3584 (DUF3584)
Type: Family

This family consist of uncharacterised bacterial and archaeal proteins.
PHTF1/2, N-terminal (PHTF1/2_N)
Type: Domain

This domain is found in a group of homeodomain containing proteins from animals, including PHTF1/2, and is typically between 101 and 140 amino acids in length. PHTF proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies . PHTF1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of PHTF1 .
Domain of unknown function DUF3586 (DUF3586)
Type: Domain

This domain is found in eukaryotes. This domain is about 80 amino acids in length and is found associated with

, and

.
Repeat element protein, Ichnovirus (REEP_Ichnovirus)
Type: Family

This entry includes repeat element protein from Ichnovirus. Its function is not clear.