SII-SWORD/CoKE huggingface dataset:
Pfam PF23609: EIPR1 beta-propeller (repeat)
This entry represents the beta-propeller found in eukaryotic EARP and GARP complex-interacting protein 1 (EIPR1). EIPR1 is a component of the endosomal retrieval machinery, binding to both the Endosome- Associated Recycling Protein (EARP) and Golgi-Associated Retrograde Protein (GARP) tethering complexes. GARP and EARP participate in SNARE -dependent fusion of endosome-derived carriers with the trans-Golgi network and recycling endosomes, respectively. EIPR1 is required for the stability of the EARP complex subunits and for the  localization of EARP and its association with membranes, but does not affect localization or function of the related GARP complex. WD repeat-containing protein (DWA2) from Arabidopsis thaliana is also a member of this family. DWA2 is a component of an E3 ubiquitin-protein ligase complex that acts as negative regulator in abscisic acid signaling.
Pfam PF18609: Exuperantia SAM-like domain (domain)
Exuperantia (Exu) is associated with localization of bicoid (bcd) mRNA and required for its localization at the anterior pole of the oocyte. Crystal structure of Exu reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The SAM-like domain interacts with its target RNA as a homodimer and is required for RNA binding activity.
Pfam PF18988: Family of unknown function (DUF5721) (family)
This is a family of unknown function, mostly found in Firmicutes.
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 PF04665: Poxvirus A32 protein (domain)
The A32 protein is thought to be involved in viral DNA packaging.
Pfam PF04559: Herpesvirus UL17 protein (family)
UL17 protein is required for DNA cleavage and packaging in herpes viruses. It has been shown to associate with immature B-type capsids, and is required for the the localisation of capsids and capsid proteins to the intranuclear sites where viral DNA is cleaved and packaged. In the virion, UL17 is a component of the tegument, which is a protein layer surrounding the viral capsid.
Pfam PF19962: Effector-associated domain 9 (domain)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements.
Pfam PF14102: Capsule biosynthesis CapC (family)
This family of proteins play a role in capsule biosynthesis. They are essential for gamma-polyglutamic acid (PGA) production.
Pfam PF18039: UBA-like domain (domain)
This entry represents a UBA-like domain found at the N-terminus of ribonuclease ZC3 proteins.
Pfam PF05814: Orf76 (Ac76) (family)
This family consists mainly of baculovirus proteins. Family members include Autographa californica multiple nucleopolyhedrovirus (AcMNPV), protein AC76. Ac76 has been shown to be involved in intranuclear microvesicle formation. Functional studies suggest that ac76 is essential for both BV (budded virus) and ODV (occlusion-derived virus) development but is not required for viral DNA synthesis.
Pfam PF00320: GATA zinc finger (domain)
This domain uses four cysteine residues to coordinate a zinc ion. This domain binds to DNA. Two GATA zinc fingers are found in the GATA transcription factors.  However there are several proteins which only contain a single copy of the domain.
Wikipedia: In molecular biology, GATA zinc fingers are zinc-containing domains found in a number of transcription factors. Some members of this class of zinc fingers specifically bind the DNA sequence (A/T)GATA(A/G) in the regulatory regions of genes., giving rise to the name of the domain. In these domains, a single zinc ion is coordinated by 4 cysteine residues. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed. Two GATA zinc fingers are found in GATA-family transcription factors. However, there are several proteins that only contain a single copy of the domain.
It is also worth noting that many GATA-type Znfs have not been experimentally demonstrated to be DNA-binding domains. Furthermore, several GATA-type Znfs have been demonstrated to act as protein-recognition domains. For example, the N-terminal Znf of GATA1 binds specifically to a zinc finger from the transcriptional coregulator FOG1 (ZFPM1).
Pfam PF24217: Family of unknown function (DUF7436) (domain)
This domain is found at the C-terminal end of a group of archaeal sequences that contain [pfam:PF01978] at the N-terminal. It is predicted to adopt an alpha-beta configuration.
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 PF00018: SH3 domain (domain)
SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase [swissprot:P12931]. The structure is a partly opened beta barrel.
Wikipedia: The SRC Homology 3 Domain is a small protein domain of about 60 amino acid residues. Initially, SH3 was described as a conserved sequence in the viral adaptor protein v-Crk. This domain is also present in the molecules of phospholipase and several cytoplasmic tyrosine kinases such as Abl and Src. It has also been identified in several other protein families such as: PI3 Kinase, Ras GTPase-activating protein, CDC24 and cdc25. SH3 domains are found in proteins of signaling pathways regulating the cytoskeleton, the Ras protein, and the Src kinase and many others. The SH3 proteins interact with adaptor proteins and tyrosine kinases. Interacting with tyrosine kinases, SH3 proteins usually bind far away from the active site. Approximately 300 SH3 domains are found in proteins encoded in the human genome. In addition to that, the SH3 domain was responsible for controlling protein-protein interactions in the signal transduction pathways and regulating the interactions of proteins involved in the cytoplasmic signaling.
Pfam PF23122: ITFG1, C2 domain (domain)
This entry represents the C2 domain present in integrin alpha FG-GAP repeat-containing 1 (ITFG1) proteins. ITFG1 promotes the adhesion between neighbouring cells through its extracellular domain and regulates microtubule dynamics through its intracellular domain.
Wikipedia: A C2 domain is a protein structural domain involved in targeting proteins to cell membranes. The typical version (PKC-C2) has a beta-sandwich composed of 8 β-strands that co-ordinates two or three calcium ions, which bind in a cavity formed by the first and final loops of the domain, on the membrane binding face. Many other C2 domain families don't have calcium binding activity.
Pfam PF03868: Ribosomal protein L6, N-terminal domain (domain)
This entry represents the N-terminal domain of Large ribosomal subunit protein eL6 and similar eukaryotic proteins.
Large ribosomal subunit protein uL6 was previously known as L6. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites .
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF19285: Neuromedin-U receptor 2, C-terminal (domain)
This domain represents the C-terminal region of the Neuromedin-U receptor 2, a rhodopsin-like GPCR member. It contains two potential casein kinase II phosphorylation sites at threonines residues and one protein kinase C phosphorylation site at a serine residue, which are important to regulate the receptor functionality. This receptor is predominantly expressed in the central nervous system, particularly in the medulla oblongata, pontine reticular formation, spinal cord and thalamus, as its physiological roles are related to modulation of sensory function, neuroendocrine control, food intake as well as with circadian rhythm. However, peripheral expression of this receptor has been determined and includes kidney (medulla), lung and trachea.
Pfam PF04647: Accessory gene regulator B (family)
The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system.  AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing.  AgrB is a transmembrane protein.
Pfam PF15768: Coiled-coil domain-containing protein 190 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 234 and 297 amino acids in length.
Pfam PF04908: SH3-binding, glutamic acid-rich protein (family)
This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity .

Adapter SH3BGRL from mammals is also included in this entry. This protein may function as a ubiquitin ligase-substrate adapter that bridges proteins together or proteins with mRNAs .
Pfam PF24473: ATP-dependent RNA helicase HrpB, connector region (domain)
This domain is found in ATP-dependent RNA helicase HrpB from Escherichia coli and similar proteins mainly found in proteobacteria. It is a connector element (CON) found immediately C-terminal to [pfam:PF08482].
Pfam PF08846: Domain of unknown function (DUF1816) (domain)
[swissprot:Q4C9H3] is associated with the [pfam:PF01383] domain suggesting this presumed domain could have a role in phycobilisomes.
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 PF19038: Third Longin domain of FUZ, MON1 and HPS1 (domain)
This entry represents a longin-like domain found in Fuz and related proteins. This entry is specific to the third Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia.
Pfam PF14022: Protein of unknown function (DUF4238) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 274 and 374 amino acids in length.
Pfam PF01443: Viral (Superfamily 1) RNA helicase (family)
Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.
Pfam PF03673: Uncharacterised protein family (UPF0128) (family)
The members of this family are about 240 amino acids in length. The proteins are as yet uncharacterised.
Pfam PF08192: Peptidase family S64 (family)
This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1.  The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced.  The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment.  This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad.
Pfam PF16694: Cytochrome P460 (domain)
This entry includes cytochrome P460 from Nitrosomonas europea. It is a monoheme c-type cytochrome. Its structure has been revealed .
Pfam PF05479: Photosystem I reaction centre subunit N (PSAN or PSI-N) (family)
This family contains several Photosystem I reaction centre subunit N (PSI-N) proteins. The protein has no known function although it is localised in the thylakoid lumen. PSI-N is a small extrinsic subunit at the lumen side and is very likely involved in the docking of plastocyanin.
Pfam PF02180: Bcl-2 homology region 4 (family)
Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans . In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.
Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes . At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases.

Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 . Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily . Full-length Bcl-2 proteins feature all four BH domains, seven Î±-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope.
Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) . Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon.
Wikipedia: The Bcl-2 family consists of a number of evolutionarily-conserved proteins that share Bcl-2 homology (BH) domains. The Bcl-2 family is most notable for their regulation of apoptosis, a form of programmed cell death, at the mitochondrion. The Bcl-2 family proteins consists of members that either promote or inhibit apoptosis, and control apoptosis by governing mitochondrial outer membrane permeabilization (MOMP), which is a key step in the intrinsic pathway of apoptosis. A total of 25 genes in the Bcl-2 family were identified by 2008.
Pfam PF00779: BTK motif (conserved_site)
Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains. The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Wikipedia: In molecular biology, the Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain and the Src homology 3 (SH3) domain. The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger, while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins. The TH domain may be of functional importance in various signalling pathways in different species. A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain.
Pfam PF17716: RAB7A-interacting MON1-CCZ1 complex subunit 1 (family)
RAB7A-interacting MON1-CCZ1 complex subunit 1 (RIMC1, previously known as UPF0600 protein C5orf51) plays an important role in the removal of damaged mitochondria via mitophagy by controlling the stability and localization of RAB7A. It is required for the recruitment of RAB7A and ATG9A vesicles to damaged mitochondria and promotes the stability of RAB7A by inhibiting its proteasomal degradation during mitophagy.
Pfam PF06644: ATP11 protein (family)
This family consists of several eukaryotic ATP11 proteins. In Saccharomyces cerevisiae, expression of functional F1-ATPase requires two proteins encoded by the ATP11 and ATP12 genes. Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic unit of the ATP synthase.
Pfam PF02129: X-Pro dipeptidyl-peptidase (S15 family) (family)
This entry represents a domain found in Xaa-Pro dipeptidyl-peptidases, which belong to MEROPS peptidase family S15 . It is also found in hydrolases from the CocE/NonD family. Cocaine esterase (CocE) hydrolyses cocaine endowing the bacteria with the ability to utilise cocaine as a sole source of carbon and energy .
Pfam PF24944: Domain of unknown function (DUF7758) (repeat)
This domain is found in uncharacterised proteins mainly from nematodes. It is composed of repetitive alpha-helical hairpins and has detectable similarity to 14-3-3 proteins.
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 PF12116: Stage III sporulation protein D (family)
This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.