SII-SWORD/CoKE huggingface dataset:
Pfam PF05381: Tymovirus endopeptidase (family)
Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products.  The auto-peptidase activity has been mapped to the central part of this polyprotein.
Pfam PF11592: Central core of the bacterial effector protein AvrPto (family)
This family of proteins represents the bacterial effector protein AvrPto from Pseudomonas syringae. This is the central core region of the protein which consists of a three-helix bundle motif. AvrPto is part of a type III secretion system from P.syringae which is involved in the bacterial speck disease of tomato. In resistant plants, AvrPto interacts with the host Pto kinase, which elicits an antibacterial defense response. In plants lacking resistance, the Pto kinase is not present and AvrPto acts as a virulence factor, promoting bacterial growth.
Pfam PF19377: Family of unknown function (DUF5952) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000178) is described by MIBiG as an example of the following biosynthetic class, polyketide.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08373: RAP domain (domain)
This domain is found in various eukaryotic species, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain. The domain is involved in plant defence in response to bacterial infection.
Pfam PF09495: Protein of unknown function (DUF2462) (family)
This protein is highly conserved, but its function is unknown. It can be isolated from HeLa cell nucleoli and is found to be homologous with Leydig cell tumour protein whose function is unknown [1, supplementary Table I].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00741: Gas vesicle protein (family)
This family includes gas vesicle proteins such as GvpJ.
Wikipedia: GvpA is a gas vesicle structural protein found in different phyla of bacteria and archaea for example in Halobacterium salinarum or Haloferax mediterranei. Gas vesicles are small, hollow, gas filled protein structures found in several cyanobacterial and archaebacterial microorganisms. They allow the positioning of the bacteria at a favourable depth for growth.
Pfam PF17267: Family of unknown function (DUF5333) (family)
This family of uncharacterized proteins is mostly found in Alphaproteobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19574: Outer membrane lipoprotein carrier protein LolA-like (domain)
This family of proteins is related to the [pfam:PF03548] and found in proteobacteria.
Pfam PF07911: Protein of unknown function (DUF1677) (family)
The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01201: Ribosomal protein S8e (family)
This entry represents the small ribosomal subunit protein eS8 from archaea and eukaryotes , which consists of a number of proteins with either about 220 amino acids (in eukaryotes) or about 125 amino acids (in archaea).
This entry also contains proteins annotated as NSA2, which are though to be involved in ribosomal biogenesis of the 60S ribosomal subunit, having a role in the quality control of pre-60S particles. They are a component of the pre-66S ribosomal particle.
Pfam PF18899: Domain of unknown function (DUF5655) (domain)
This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 122 and 304 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08726: Ca2+ insensitive EF hand (domain)
EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes.  EF hands usually bind to Ca2+ ions which causes a major conformational change that allows the protein to interact with its designated targets.  This domain corresponds to an EF hand which has partially or entirely lost its calcium-binding properties.  The calcium insensitive EF hand is still able to mediate protein-protein recognition.
Pfam PF13477: Glycosyl transferase 4-like (domain)
MshA belongs to the GT-B structural family of glycosyltransferases whose members have a two-domain structure with both domains exhibiting a Rossman-type fold . This entry represents the N-terminal domain found in MshA and the subfamily 4 of glycosyltransferases family 1.
Pfam PF23133: Domain of unknown function (DUF7050) (domain)
This domain is found N-terminal in a group of uncharacterised proteins mainly from plants. It shares a significant sequence similarity with the N-terminal domain of bHLH-MYC and R2R3-MYB transcription factors ([pfam:PF14215]) and it is predicted to adopt similar structure.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23125: Antitoxin Xre/MbcA/ParS-like, middle domain (domain)
This entry represents a small domain found in the middle region of a group of bacterial sequences related to the antitoxin components of a type II toxin-antitoxin (TA) system Xre/MbcA/ParS. This domain may consist of four beta-sheets and two short alpha-helices, which is followed by a toxin-binding domain ([pfam:PF09722]).
Pfam PF07223: UBA-like domain (DUF1421) (domain)
This domain represents a conserved region that has a UBA like fold. It is found in a number of plant proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09966: Uncharacterized protein conserved in bacteria (DUF2200) (family)
This domain, found in various hypothetical bacterial proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01492: Geminivirus C4 protein (family)
This family consists of the N terminal region of geminivirus C4 or AC4 proteins.  In Tomato yellow leaf curl geminivirus (TYLCV) the C4 protein is necessary for efficient spreading of the virus in tomato plants.
Pfam PF11674: Protein of unknown function (DUF3270) (family)
This family of proteins with unknown function appears to be restricted to Streptococcus.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12870: Domain of unknown function (DUF4878) (domain)
This is a family of putative lipoproteins from bacteria. The family is probably related to the NTF2-like transpeptidase family.
Pfam PF04723: Glycine reductase complex selenoprotein A (family)
Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. A member of this family may also exist in Treponema denticola.
Pfam PF11786: Aft1 HRA domain (disordered)
This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses.  The HRA domain is involved in meiotic recombination.  It has been shown to be necessary and sufficient to activate recombination.
Pfam PF04237: YjbR (family)
YjbR has a CyaY-like fold.
Pfam PF05112: Baculovirus P47 protein (family)
This family consists of several Baculovirus P47 proteins which is one of the primary components of Baculovirus encoded RNA polymerase, which  initiates transcription from late and very late promoters.
Pfam PF08862: Domain of unknown function DUF1829 (domain)
This short domain is usually associated with [pfam:PF08861].
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00761: Polyomavirus coat protein (family)
This family includes the VP2 and VP3 internal coat proteins from Polyomaviruses, which are small dsDNA tumour viruses. Their capsids contain 360 copies of the VP1 proteins IPR000662 arranged in 72 pentamers. This capsid encloses the internal proteins VP2 and VP3, as well as the viral DNA. A single copy of VP2 or VP3 associates with each VP1 pentamer. A crystal structure shows that the C-terminal region of the VP2/VP3 protein interacts with the VP1 pentamer .
Wikipedia: Minor capsid protein VP2 and minor capsid protein VP3 are viral proteins that are components of the polyomavirus capsid. Polyomavirus capsids are composed of three proteins; the major component is major capsid protein VP1, which self-assembles into pentamers that in turn self-assemble into enclosed icosahedral structures. The minor components are VP2 and VP3, which bind in the interior of the capsid.
Pfam PF02149: Kinase associated domain 1 (domain)
Members of the KIN2/PAR-1/MARK kinase subfamily are conserved from yeast to human and share the same domain organisation: an N-terminal kinase domain (IPR000719) and a C-terminal kinase associated domain 1 (KA1). Some members of the KIN1/PAR-1/MARK family also contain an UBA domain (IPR015940). Members of this kinase subfamily are involved in various biological processes such as cell polarity, cell cycle control, intracellular signalling, microtubule stability and protein stability . The function of the KA1 domain is not yet known but several studies strongly suggest that it is involved in protein localisation. In addition, it has been reported that this C-terminal region acts as an autoinhibitory domain for the N-terminal kinase domain .

Some proteins known to contain a KA1 domain are listed below:


 * Mammalian MAP/microtubule affinity-regulating kinases (MARK 1,2,3). They regulate polarity in neuronal cell models and appear to function redundantly in phosphorylating MT-associated proteins and in regulating MT stability .
 * Mammalian maternal embryonic leucine zipper kinase (MELK). It phosphorylates ZNF622 and may contribute to its redirection to the nucleus. It may be involved in the inhibition of spliceosome assembly during mitosis.
 * Caenorhabditis elegans and drosophila PAR-1 protein. It is required for establishing polarity in embryos where it is asymmetrically distributed .
 * Fungal Kin1 and Kin2 protein kinases involved in regulation of exocytosis. They localise to the cytoplasmic face of the plasma membrane .


The KA1 domain comprises about 50 amino acid residues and end in the highly conserved Glu-Leu-Lys-Leu motif, termed the ELKL motif which forms a concave surface surrounded by positively charged residues, being important for the KA1 domain function. This domain adopts a compact Î±+Î² structure with a Î²-Î±-Î²-Î²-Î²-Î²-Î± topology .
Wikipedia: In molecular biology, members of the KIN2/PAR-1/MARK kinase family of proteins are kinases that are conserved from yeast to human and share the same domain organisation: an N-terminal kinase domain and a C-terminal kinase associated domain 1 (KA1). Some members of this family also contain an UBA domain. Members of this kinase family are involved in various biological processes such as cell polarity, cell cycle control, intracellular signalling, microtubule stability and protein stability. The function of the KA1 domain is not yet known.
Pfam PF01832: Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase (domain)
This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase [ec:3.2.1.96]. As well as the flageller protein J [swissprot:P75942] that has been shown to hydrolyse peptidoglycan.
Wikipedia: In molecular biology, glycoside hydrolase family 73 is a family of glycoside hydrolases.
Pfam PF02891: MIZ/SP-RING zinc finger (domain)
This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation.
Wikipedia: In molecular biology the MIZ-type zinc finger domain is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2. Other proteins containing this domain include the human pias family. The name MIZ is derived from Msx-interacting-zinc finger. The crystal structure of S. cerevisiae sumo e3 ligase siz1 containing this domain has been solved.
Pfam PF15158: Cation channel sperm-associated auxiliary subunit TMEM249 (family)
This family of proteins is found in eukaryotes and includes Cation channel sperm-associated auxiliary subunit TMEM249 from human (also known as C8orfK29). It is an auxiliary component of the CatSper complex, a complex involved in sperm cell hyperactivation. TMEM249 contributes to the assembly of the CatSpermasome.
Pfam PF04379: ApaG domain (family)
The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity.
Pfam PF09088: MIF4G like (repeat)
Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices.
Pfam PF08285: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3) (family)
This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation.  DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex.
Pfam PF23760: DDB1- and CUL4-associated factor 12 beta propeller (repeat)
This entry represents the beta-propeller domain found in DDB1- and CUL4-associated factor 12 proteins (DCAF12) as well as DCAF12-like proteins 1 and 2 (DCAF12L1 and DCAF12L2) from animals. DCAF proteins have been hypothesised to play important roles during spermatogenesis due to their high level of conservation in mammals and testis enrichment. Mutations in DCAF12L1 has only been associated to male infertility in humans but not in mice. In insects, mutations in the DCAF12 homolog impairs larval development. The function of this domain is unknown.
Pfam PF15400: Testis-expressed sequence 33 protein family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 147 and 280 amino acids in length. There are two conserved sequence motifs: NIRH and SYT. The function is not known.
Pfam PF21431: Colicin/Pyocin-S2, DNase domain (domain)
This entry represents the DNAse domain from colicin/pyocin bacteriocins, such as pyocin-S2 from Pseudomonas aeruginosa and colicin E7/E9 from E. coli. This domain has an alpha/beta fold containing a Zn2+ ion binding site.
Pfam PF17964: Bacterial Ig domain (domain)
This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.
Pfam PF03909: BSD domain (domain)
This domain contains a distinctive -FW- motif. It is found in a family  of eukaryotic transcription factors as well as a set of proteins of unknown function.
Wikipedia: In molecular biology, the BSD domain is an approximately 60-amino-acid-long protein domain named after the BTF2-like transcription factors, synapse-associated proteins and DOS2-like proteins in which it is found. It is also found in several hypothetical proteins. It occurs in one or two copies in a variety of species ranging from primal protozoan to human, and can be found associated with other domains such as the BTB domain or the U-box in multidomain proteins. Its function is as yet unknown.
Pfam PF17594: Phage Tail fiber assembly helper gene product 57 (family)
Gene product 57 (Gp57) is a chaperone protein for short tail fiberphage protein that acts as a molecular chaperone of gp12, increasing the folding efficacy and production efficiency.
Pfam PF02699: Preprotein translocase subunit (family)
See.
Pfam PF02685: Glucokinase (family)
This is a family of glucokinases or glucose kinases [ec:2.7.1.2]. These enzymes phosphorylate glucose using ATP as a donor to give glucose-6-phosphate and ADP.
Wikipedia: Glucokinase is an enzyme that facilitates phosphorylation of glucose to glucose-6-phosphate. Glucokinase occurs in cells in the liver and pancreas of humans and most other vertebrates. In each of these organs it plays an important role in the regulation of carbohydrate metabolism by acting as a glucose sensor, triggering shifts in metabolism or cell function in response to rising or falling levels of glucose, such as occur after a meal or when fasting. Mutations of the gene for this enzyme can cause unusual forms of diabetes or hypoglycemia.
Pfam PF14167: YfkD-like protein (family)
The YfkD-like protein family includes the B. subtilis YfkD protein [swissprot:O34579], which is functionally uncharacterised. Its expression is regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins, and by the forespore-specific sigma factor sigma-G. This family of proteins is found in bacteria. Proteins in this family are typically between 254 and 265 amino acids in length.
Pfam PF22741: DSP-PTPase phosphatase fused to NAD+ Kinase (domain)
While the land plant version of this DSP-PTPase domain is likely inactive as the catalytic cysteine is replaced by serine or threonine, the rest are predicted to be active. Keeping with the proposed sugar phosphatase activity in related members, these domains could potentially function as phosphatases converting NADP to NAD+.
Pfam PF11754: Velvet factor (family)
The velvet factor is conserved in many fungal species and is found to have gained different roles depending on the organism's need, expanding the conserved role in developmental programmes. The velvet factor orthologues can be adapted to the fungal-specific life cycle and may be involved in diverse functions such as sclerotia formation and toxin production, as in A. parasiticus, nutrition-dependent sporulation, as in A. fumigatus, or the microconidia-to-macroconidia ratio and cell wall formation, as in the heterothallic fungus Fusarium verticilloides [.
Pfam PF17981: Cysteine Rich ADD domain (domain)
This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in ATRX proteins. Chromatin-associated human protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental retardation called ATR-X syndrome. Mutations or knockdown of ATRX expression cause diverse effects, including altered patterns of DNA methylation, a telomere-dysfunction phenotype, aberrant chromosome segregation, premature sister chromatid separation and changes in gene expression. ATRX localizes predominantly to large, tandemly repeated regions (such as telomeres, centromeres and ribosomal DNA) associated with heterochromatin, and studies show that it directs H3.3 deposition to pericentric and telomeric heterochromatin. The ADD domain of ATRX, in which most syndrome-causing mutations occur, engages the N-terminal tail of histone H3 through two rigidly oriented binding pockets, one for unmodified Lys4 and the other for di- or trimethylated Lys9. Mutations in the ATRX ADD domain cause mislocalization of ATRX protein to heterochromatin, and this may contribute to understanding the underlying etiology of ATRX syndrome. Structure analysis of the ADD domain of ATRX revealed that it contains a PHD zinc-finger domain packed against a GATA-like zinc finger. Same structure is also found in the DNMT3 DNA methyltransferases and DNMT3L.
Wikipedia: The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain proteins HAT3.1 in Arabidopsis and maize ZmHox1a. 
The PHD zinc finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.