SII-SWORD/CoKE huggingface dataset:
Pfam PF20281: C-terminal domain 5 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF14694: Lines N-terminus (family)
This family represents the N-terminus of protein lines. In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator.
Pfam PF21302: RlmA, N-terminal (domain)
This is the N-terminal zinc-binding domain of 23S rRNA (guanine(745)-N(1))-methyltransferase RlmA from E. coli and similar proteins, which is responsible for specific recognition and binding of its rRNA substrate.
Pfam PF15244: Spermatogenesis-associated protein 7, or HSD3 (family)
Spermatogenesis-associated protein HSD3 also goes by the name of spermatogenesis-associated protein 7 or SPAT7. The family carries a single transmembrane domain. It functions in several tissues, and is expressed in the developing and mature mouse retina; it is expressed in multiple retinal layers in the adult mouse retina. Mutations lead to LCA disease, or Leber congenital amaurosis, which results in a number of retinal dystrophies. The disease- phenotype is characterised by severe visual loss at birth, nystagmus, a variety of fundus changes, and minimal or absent recordable responses on the electroretinogram (ERG).
Pfam PF13480: Acetyltransferase (GNAT) domain (domain)
This family contains proteins with N-acetyltransferase functions.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF12174: RCD1-SRO-TAF4 (RST) plant domain (domain)
This domain is found in plant RCD1, SRO and TAF4 proteins, hence its name of RST. It is required for interaction with multiple plant transcription factors. Radical-Induced Cell Death1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana, as is its closest homologue, SRO1 - Similar To RCD-One1. TBP-Associated Factor 4 (TAF4) and TAF4-b are components of the transcription initiation factor complex TFIID.
Pfam PF14818: SOGA 1/2-like, coiled-coil (coiled_coil)
This entry represents a coiled-coil region found in microtubule cross-linking factors 1 and 2 (also known as SOGA1/2), which are members of the SOGA (suppressor of glucose by autophagy) family and in the uncharacterised human protein KIAA0408. SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin- and insulin-dependent manner. SOGA1/2 are required for faithful chromosome segregation during mitosis. These proteins contain long coiled-coils that dimerize and holds two N-terminal domains that bind to microtubules. This region is found in association with [pfam:PF11365].
Pfam PF04757: Pex2 / Pex12 amino terminal region (family)
This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger ([pfam:PF00097]) domain.
Pfam PF05285: SDA1, conserved domain (domain)
This entry includes SDA1 protein and its homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. This region is found after the HEAT repeats found at SDA1 N-terminal ([pfam:PF08158]). According to structure predictions, it consists of short alpha helices and disorder region.
Pfam PF02946: GTF2I-like repeat (family)
This region of sequence similarity is found up to six times in a variety of proteins including GTF2I.  It has been suggested that this may be a DNA binding domain.
Pfam PF17246: Cell division control protein 24, OB domain 1 (domain)
This family contains OB-fold domains that bind to nucleic acids. The family includes a domain found in Cell division control protein 24 (Cdc24). Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity. Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis.
Pfam PF23246: CDK5 regulatory subunit-associated protein 2-like, coiled coil (coiled_coil)
This domain is found in human CDK5 regulatory subunit-associated protein 2 (CDK5RAP2) and similar proteins mainly from vertebrates. CDK5RAP2 is a potential regulator of CDK5 activity that plays a role in the spindle checkpoint activation and regulates centrosomal maturation. This entry represents a centrally located region that forms an alpha-helical coiled-coil (CC).
Pfam PF06898: Putative stage IV sporulation protein YqfD (family)
This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis ([swissprot:P54469]) is known to be essential for efficient sporulation although its exact function is unknown.
Pfam PF21373: Zinc finger HIT domain-containing protein 3, C-terminal domain (domain)
This domain is found at the C-terminal end of Zinc finger HIT domain- containing protein 3 from humans (ZNHIT3), a cofactor of the RNA-binding nuclear protein NUFIP1. This domain shows five alpha- helices.
Pfam PF09347: Domain of unknown function (DUF1989) (domain)
This family of proteins are functionally uncharacterised.
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 PF22777: Vitamin K-dependent gamma-carboxylase, lumenal domain (domain)
Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl  carboxylase (VKGC) post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase. This entry represents the lumenal domain found in animals and bacteria. This domain is associated with [pfam:PF05090].
Pfam PF04610: TrbL/VirB6 plasmid conjugal transfer protein (family)
VirB proteins are suggested to act at the bacterial surface and there play an important role in directing t-DNA transfer to plant cells. VirB6 from Agrobacterium tumefaciens is an essential component of the type IV secretion machinery for T pilus formation and genetic transformation of plants. Absence of VirB6 leads to reduced cellular levels of VirB5 and VirB3, which were proposed to assist T pilus formation as minor component(s) or assembly factor(s), respectively .
Pfam PF13164: Diedel (family)
Diedel (die) was identified as an insect immune response protein. It is up-regulated after a septic injury and may act as a negative regulator of the JAK/STAT signalling pathway. Its homologues can be found in Drosophila and  Acyrtosiphon pisum. Interestingly, the orthologues of the die  gene are present in the genome of insect DNA viruses of the Baculoviridae and Ascoviridae families. The viral  homologues suppress the immune deficiency (IMD) pathway in Drosophila.
Pfam PF05244: Brucella outer membrane protein 2 (family)
This family consists of several outer membrane proteins (2a and 2b) from brucella bacteria. Brucellae are Gram-negative, facultative intracellular bacteria that can infect many species of animals and man.
Pfam PF06471: Coronavirus proofreading exoribonuclease (family)
This region of coronavirus polyproteins encodes the NSP14 protein. Its N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping. NSP14 forms the nsp14-nsp10 complex involved in RNA viral proofreading. This association stimulates its ExoN activity. There are not yet publicly available structures of SARS-CoV-2 NSP14, but computed homology model based on the structure of SARS-CoV-1 NSP14 (PDB:5C8S) revealed that they share ~95% sequence identity.
Pfam PF02744: Galactose-1-phosphate uridyl transferase, C-terminal domain (domain)
SCOP reports fold duplication with N-terminal domain.  Both involved in Zn and Fe binding.
Wikipedia: Galactose-1-phosphate uridyltransferase is an enzyme responsible for converting ingested galactose to glucose.
Pfam PF17207: MCM OB domain (domain)
This family contains an OB-fold found within MCM proteins.  This domain contains an insertion at the zinc binding motif.
Pfam PF22649: Cgl0159-like (domain)
This domain is found in the homologues of uncharacterised protein Cgl0159. It adopts classical (beta/alpha)8 barrel. Members of this family share significant similarity with Deoxyribose-phosphate aldolase.
Pfam PF04934: MED6 mediator sub complex component (family)
Component of RNA polymerase II holoenzyme and mediator sub complex.
Wikipedia: Mediator of RNA polymerase II transcription subunit 6 is one of the subunits of the Mediator complex. It is an enzyme that in humans is encoded by the MED6 gene.
Pfam PF24890: Allantoinase, composite domain (domain)
This entry represents the N-terminal region of the composite domain of Allantoinase (ALN), a protein that catalyses the conversion of allantoin (5-ureidohydantoin) to allantoate by hydrolytic cleavage of the five-member hydantoin ring. The composite domain of metal-dependent hydrolases has a pseudo-barrel fold that is interrupted by the catalytic beta/alpha domain.
Pfam PF22533: Protein P1-like, WIV domain (domain)
This domain is found in a group of proteins from arthropod -infecting viruses, including Protein P1 from Acyrthosiphon pisum virus. This region has been named 'Widespread, Intriguing, Versatile' (WIV) domain. This region is likely to play a role in viral infection of arthropods.
Pfam PF20133: Protein HHL1-like (family)
This entry represents a group of proteins from plants and Cyanobacteria, including HHL1 from Arabidopsis. HHL1 functions in protecting photosystem II against photodamage.
Pfam PF14785: Maltose transport system permease protein MalF P2 domain (family)
This is the second periplasmic domain (P2 domain) of the maltose transport system permease protein MalF.
Pfam PF04960: Glutaminase (domain)
This family of enzymes deaminates glutamine to glutamate [ec:3.5.1.2].
Wikipedia: Glutaminase is an amidohydrolase enzyme that generates glutamate from glutamine. Glutaminase has tissue-specific isoenzymes. Glutaminase has an important role in glial cells.
Pfam PF22813: TcaA protein second domain (domain)
This entry represents the second domain of the TcaA protein.
Pfam PF11629: C terminal SARAH domain of Mst1 (family)
This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process.
Pfam PF02170: PAZ domain (domain)
This domain is named PAZ after the proteins Piwi  Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
Pfam PF09937: Uncharacterized protein conserved in bacteria (DUF2169) (family)
This domain, found in various hypothetical prokaryotic 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 PF00027: Cyclic nucleotide-binding domain (domain)
This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Wikipedia: Proteins that bind cyclic nucleotides share a structural domain of about 120 residues. The best studied of these proteins is the prokaryotic catabolite gene activator where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the beta-barrel. cAMP- and cGMP-dependent protein kinases contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterized, one is found in rod cells where it plays a role in visual signal 
transduction.
Pfam PF06851: Protein of unknown function (DUF1247) (family)
This family contains a number of hypothetical viral proteins of unknown function approximately 200 residues long.
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 PF11474: Telomerase reverse transcriptase, TEN domain (domain)
This is the N-terminal domain of Telomerase reverse transcriptase from Tetrahymena thermophila (TERT), named TEN. The TEN domain is able to bind both RNA and telomeric DNA and contributes towards telomerase catalysis. This domain has a structure that consists of a core beta sheet surrounded by seven alpha helices and a short beta hairpin. Members of this group are found in eukaryotes.
Pfam PF15121: TMEM71 protein family (family)
The function of this family, TMEM71, is not known, however it is predicted to be a transmembrane protein. This family of proteins is found in eukaryotes and located in the cell membrane. Proteins in this family vary between 41 and 291 amino acids in length.
Pfam PF07011: Early Flowering 4 domain (domain)
This domain forms an alpha-helical homodimer in ELF4 proteins. Protein EARLY FLOWERING 4 (Elf4) is a component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles.
Pfam PF24516: KNTC1 second ARM-repeats domain (repeat)
This entry represents the second segment of ARM repeats present in KNTC1 (also known as ROD), following the beta-propeller domain. KNTC1 is a crucial component of the mitotic checkpoint, ensuring cells do not exit mitosis prematurely. KNTC1 is required for the assembly of essential complexes onto kinetochores, such as dynein-dynactin and MAD1-MAD2. KNTC1 is the major subunit of the RZZ (ROD-Zwilch-ZW10) complex, which plays a significant role in spindle assembly, kinetochore-microtubule attachment, and spindle pole separation.
Pfam PF10746: Phage holin T7 family, holin superfamily II (family)
Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.
Pfam PF19189: Mtf2 family (repeat)
This family appears to be distantly related to PPR repeats.
Pfam PF21673: CCDC93 protein N-terminal domain (domain)
This entry represents the N-terminal helical domain from the CCDC93 protein. This protein is part of the complex termed the CCC complex that is composed of CCDC22, CCDC93 and various COMMD proteins.
Pfam PF07938: Fungal fucose-specific lectin (repeat)
Lectins are involved in many recognition events at the molecular or cellular level. These fungal lectins, such as Aleuria aurantia lectin (AAL,  [swissprot:P18891]), specifically recognise fucosylated  glycans. AAL is a dimeric protein, with each monomer  being organised into a six-bladed beta-propeller fold and a small antiparallel two-stranded beta-sheet. The beta-propeller fold is important in fucose recognition; five binding pockets are found between the propeller blades. The small beta-sheet, on the other hand, is involved in the dimerisation process.
Wikipedia: In molecular biology, the fungal fucose-specific lectin family is a family of lectins. Lectins are proteins which are involved in many recognition events at the molecular or cellular level. These fungal lectins, such as Aleuria aurantia lectin AAL, specifically recognise fucosylated glycans. AAL is a dimeric protein, with each monomer being organised into a six-bladed beta-propeller fold and a small antiparallel two-stranded beta-sheet. The beta-propeller fold is important in fucose recognition; five binding pockets are found between the propeller blades. The small beta-sheet, on the other hand, is involved in the dimerisation process.
Pfam PF18471: Ribosomal L27 protein C-terminal domain (domain)
This is the C-terminal domain of 54S ribosomal protein L2 (also known as Mitochondrial large ribosomal subunit protein bL27m). bL27 C-terminal region interacts with an expansion segment of 21S rRNA to form part of the central protuberance.
Pfam PF24710: Family of unknown function (DUF7671) (domain)
This entry represents a family of uncharacterised bacterial proteins. The protein forms a single beta barrel domain which shows some structural similarity to the N-terminal domain of the PriA protein. However, structure prediction does not support this protein having a DNA-binding function like PriA.
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 PF11421: ATP synthase F1 beta subunit (family)
The NMR solution structure of the protein in SDS micelles was found to contain two helices, an N-terminal amphipathic alpha-helix and a C-terminal alpha-helix separated by a large unstructured internal domain. The N-terminal alpha-helix is the Tom20 receptor binding site whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site.
Pfam PF21306: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of bacterial transcriptional regulators, including RolR from Corynebacterium glutamicum ([swissprot:Q8NR95]), which is involved in aromatic catabolism. This signal-receiving domain shows an all-alpha-helical fold. It is found associated with [pfam:PF00440], responsible for DNA-binding.
Pfam PF24146: K1 capsule-specific polysaccharide lyase, C-terminal domain (domain)
This entry represents the C-terminal domain of K1 capsule-specific polysaccharide lyase and related proteins. K1-lyase functions as a receptor binding protein (RBP) and mediates the attachment to the host capsular exopolysaccharides. This enzyme possesses a lyase activity that specifically degrades the K1-type polysaccharides of Klebsiella pneumoniae capsule. This domain adopts a beta-sandwich fold.
Pfam PF16051: Domain of unknown function (DUF4797) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved SGLPT sequence motif. There are two completely conserved residues (P and G) that may be functionally important.
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 PF18814: phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5 (domain)
A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues.
Pfam PF12511: Protein of unknown function (DUF3716) (family)
This domain family is found in eukaryotes, and is approximately 60 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 PF02453: Reticulon (family)
Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologues.