SII-SWORD/CoKE huggingface dataset:
Pfam PF00677: Lumazine binding domain (domain)
This domain binds to derivatives of lumazine  in some proteins. Some proteins have lost the residues involved in binding lumazine.
Pfam PF14448: Nuclease N terminal (family)
This is a conserved short region that is found in many bacterial polymorphic toxin proteins. It is often located before C-terminal nuclease domains.
Pfam PF14868: Domain of unknown function (DUF4487) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif. There is a single completely conserved residue W 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 PF18890: FANCL UBC-like domain 2 (domain)
This entry represents the second of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2.
Pfam PF11388: Phagosome trafficking protein DotA (family)
DotA is essential for intracellular growth in Legionella. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake.
Pfam PF21881: A223 penton protein second domain (domain)
This Pfam entry represents the Sulfolobus turreted icosahedral virus (STIV) penton protein second jelly roll domain. STIV is a virus that infects the archaeon Sulfolobus solfataricus and was isolated in acidic hot springs. The virus has a unique architecture based on a pseudo T = 31d capsid symmetry with each icosahedral asymmetric unit consisting of 15 copies of the coat subunit (B345), one copy of the A223 penton base protein, one copy of the C381 turret protein, and one copy of the A55 membrane protein. The pentameric penton base protein is a crucial component of the virus as it forms the vertices of the capsid shell and decorates the penton base structure forming the first floor of the turret. The penton protein contains three different layers, with the N termini forming a 10-stranded beta-pore, the middle layer comprising a canonical viral jelly-roll forming a pentameric ring, and the C-terminal forming a second pentameric ring of jelly-rolls. The virus shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. The conservation of the A223 penton base jelly-roll fold, as well as the B345 double jelly-roll fold, strongly suggests an evolutionary connection for these protein modules among phages, archaeal viruses, and eukaryotic viruses.
Pfam PF12214: Cell cycle regulated microtubule associated protein (family)
This domain is found in eukaryotes. This domain is typically between 127 to 182 amino acids in length. This domain is found associated with [pfam:PF06886]. This domain is found in the protein TPX2 (a.k.a p100) which is involved in cell cycling. It is only expressed between the start of the S phase and completion of cytokinesis. The microtubule-associated protein TPX2 has been reported to be crucial for mitotic spindle formation. This domain is close to the C terminal of TPX2. The protein importin alpha regulates the activity of TPX2 by binding to the nuclear localisation signal in this domain.
Pfam PF17562: Styelin (family)
This is a family of antimicrobial peptides found in Stela clava (Sea squirt). Family members are alpha-helical phenylalanine-rich antimicrobial peptides effective against a panel of Gram-negative and Gram-positive bacteria. Styelin contains unusual amino acids such as dihydroxyarginine, dihydroxylysine, 6-bromotryptophan, and 3,4-dihydroxyphenylalanine which are important for the antimicrobial activity at high salt concentrations.
Pfam PF20215: Family of unknown function (DUF6575) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 403 amino acids in length. There some conserved motifs, Y/FL, WL and LP.
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 PF24420: Domain of unknown function (DUF7551) (domain)
This entry represents a domain found in a group of uncharacterised proteins from Halobacteria. This domain contains a pair 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 PF16411: Outer membrane protein SusF_SusE (family)
SusE and SusF are two outer membrane proteins composed of tandem starch specific carbohydrate binding modules (CBMs) with no enzymatic activity. They are are likely to play an important role in starch metabolism in Bacteroides. It has been speculated that they could compete for starch in the human intestinal tract by sequestering starch at the bacterial surface and away from competitors. SusE has higher affinity for starch compared to SusF.
Pfam PF23262: NFD4, C-terminal domain (domain)
This domain is found at the C-terminal end of Protein NUCLEAR FUSION DEFECTIVE 4 from Arabidopsis thaliana (NFD4) and similar sequences predominantly found in plants. NFD4 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. This protein is predicted to organise into two all -alpha domains, [pfam:PF06813] and this entry.
Pfam PF05408: Foot-and-mouth virus L-proteinase (family)
Corresponds to Merops family C28. Protein fold of the peptidase unit for members of this family resembles that of papain. The leader proteinase of foot and mouth disease virus (FMDV) cleaves itself from the growing polyprotein and also cleaves the host translation initiation factor 4GI (eIF4G), thus inhibiting 5'-cap dependent translation.
Pfam PF21195: Complement components C8A/B/C6, EGF-like domain (domain)
This domain is found in the alpha and beta chains of Complement component C8 (C8A/B), in Complement components C6 (C6) from humans, constituents of the membrane attack complex (MAC) that play a key role in the innate and adaptive immune response by forming pores in the plasma membrane of target cells. This entry represents the rigid, disulfide-rich epidermal growth factor (EGF) domain, which is included in the regulatory segment of these proteins. It is found C-terminal to the membrane attack complex perforin domain [pfam:PF01823] and N-terminal to the thrombospondin type 1 domain [pfam:PF00090].
Pfam PF11849: Domain of unknown function (DUF3369) (domain)
This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 170 amino acids in length. The domain appears to be related to the GAF domain.
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 PF08347: N-terminal CTNNB1 binding (family)
This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes ([pfam:PF00505]) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation.  Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation.
Pfam PF04139: Rad9 (family)
Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage.  It contains a Bcl-2 homology domain 3 (BH3).
Pfam PF19406: PKD-like domain (domain)
Presumed PKD-like domain found as tandem repeats in bacterial cell surface proteins, commonly associated with Bact_lectin adhesive domain.
Pfam PF07965: Integrin beta tail domain (domain)
This is the beta tail domain of the Integrin protein.  Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions.
Wikipedia: Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
Pfam PF24768: ARMC5 (repeat)
This entry represents the ARM-repeats domain of ARMC5 from animal, a protein involved in fetal development, T-cell function and adrenal gland growth homeostasis. It negatively regulates adrenal cells survival. It plays a role in steroidogenesis, modulates steroidogenic enzymes expression and cortisol production.
Pfam PF03006: Haemolysin-III related (family)
Members of this family are integral membrane proteins.  This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea. This family belongs to the CREST superfamily, which are distantly related to GPCRs.
Pfam PF06409: Nuclear pore complex interacting protein (NPIP) (domain)
This entry includes a series of primate specific nuclear pore complex interacting protein (NPIP) sequences. The function of this family is unknown but is well conserved from African apes to humans. This entry represents helical segments that in some members constitute almost the full length of the sequences, while in others are found at the N-terminal, associated with a beta-solenoid repeat at the C-terminal ([pfam:PF20885]).
Pfam PF11832: Protein of unknown function (DUF3352) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 538 to 575 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 PF16847: Avirulence AvrPtoB, BAK1-binding domain (domain)
AvrPtoB_bdg is a binding region on a family of bacterial plant pathogenic proteins. Type III effector proteins are injected into plants by bacteria when they are under attack, eg Pseudomonas syringae when attacking tomato. AvrPtoB is one such effector that suppresses the plants' PAMP-triggered innate immunity.  PAMPs are pathogen/microbe-associated molecular patterns that are detected as non-self by a host.  AvrPtoB suppresses this response by binding to BAK1, a kinase that acts with several pattern recognition receptors to activate defence signalling. AvrPtoB_bdg is the region of AvrPtoB that binds to BAK1 thereby preventing its kinase activity after the perception of flagellin.
Pfam PF19786: Family of unknown function (DUF6270) (family)
This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 258 and 528 amino acids in length. There is a conserved GSC sequence motif.
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 PF21283: EPCAM/Trop-2, C-terminal (domain)
EpCAM (epithelial cell adhesion molecule, also known as Trop-1) and Trop-2 (also known as tumor-associated calcium signal transducer 2, TACSTD2) are transmembrane glycoproteins that belong to the tumour-associated calcium signal transducer (TACSTD) family. They are evolutionarily related and both are implicated in signaling triggered by proteolytic cleavage within the ectodomain. They share an overall similar structure but differ in their dimers formation. They consist of an ectodomain with an N-terminal, thyroglobulin type-1 (TY, [pfam:PF00086]) and C-terminal domains. This entry represents the C-terminal domain of EpCAM and Trop-2, which has an alpha+beta fold.
Pfam PF09865: Predicted periplasmic protein (DUF2092) (domain)
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 PF20199: Replication initiator protein, pSAM2 (family)
This entry represents a family of protein that can be found in (and are an essential part of) actinomycete integrative and conjugative elements (AICEs).
Pfam PF06040: Adenovirus E3 protein (family)
This family consists of several Adenovirus E3 proteins. The E3 protein does not seem to be essential for virus replication in cultured cells suggesting that the protein may function in virus-host interactions.
Pfam PF22788: COP9 signalosome complex subunit 3, N-terminal helical repeats (repeat)
This entry represents the N-terminal helical repeat domain from COP9 signalosome complex subunit 3, a component of the eight-subunit COP9 signalosome complex (CSN), which inactivate Cullin-RING E3 ubiquitin ligases (CRLs) by removing their covalently attached activator, NEDD8. The CSN complex has two organisational centres, one consisting of an open ring formed by association of the WH subdomains from the PCI proteins (CSN1-4 and CSN7-8) and a bundle comprising the C-terminal alpha-helices from each subunit. The N-terminal helical repeat domains of the PCI proteins radiate from the PCI ring at the base of the complex.
Pfam PF24705: Domain of unknown function (DUF7668) (domain)
This entry represents a bacterial protein domain 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 PF24935: NUP210-like, Ig-like domain 6 (domain)
This domain is found in human Nuclear pore membrane glycoprotein 210 (NUP210), which is essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. NUP210 is composed of multiple immunoglobin-like (Ig-like) domains and forms a ring around the NPC within the NE lumen.
Pfam PF00524: E1 Protein, N terminal domain (family)
Papillomaviruses (PPV) are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication . It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins .

The E1 protein is a 70kDa polypeptide with a centrally-located DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase . In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel Î² sheet bordered by four loosely packed Î± helices on one side and two tightly packed helices on the other . Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity .

This entry represents the N-terminal region of E1, which contains the nuclear localisation signal.
Pfam PF22547: Swiss Army Knife, 2H phosphoesterase domain (domain)
The Swiss Army Knife class of proteins features a diverse domain repertoire acting to repair RNA damaged in the wake of RNase attacks. 2H-SAK is one such domain, a phosphatase of the rhodanese-phosphatase superfamily. It is predicted to 'clean' RNA ends by removing phosphate groups, preparing them for ligation by their associating RNA ligases.
Pfam PF13511: Domain of unknown function (DUF4124) (domain)
This presumed domain is found in a variety of bacterial proteins. It is found associated at the N-terminus associated with other domains such as the SLT domain and glutaredoxin domains in some proteins. The function of this domain is unknown, but it may have an Ig-like fold.
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 PF20722: Domain of unknown function (DUF6830) (domain)
This presumed domain is functionally uncharacterised. This domain family is predominantly found in Basidiomycetes. There are several highly conserved residues: P, W, Q and G.
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 PF16200: C-terminal region of band_7 (family)
This domain is found on a subset of proteins as a C-terminal extension of the Band_7 family, [pfam:PF01145].  It is found in proteins fro bacteria to fungi, plants and mammals.
Pfam PF23333: VWC2L-like, N-terminal domain (domain)
This domain is found at the N-terminal of human von Willebrand factor C domain-containing protein 2-like (VWC2L) and similar proteins predominantly found in vertebrates. VWC2L may play a role in neurogenesis, bone differentiation and matrix mineralisation. This domain is predicted to adopt an all-beta configuration.
Pfam PF02866: lactate/malate dehydrogenase, alpha/beta C-terminal domain (domain)
L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family.  Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.
Wikipedia: Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the conversion of pyruvate to lactate and back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.
Pfam PF08414: Respiratory burst NADPH oxidase (family)
This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism.  It tends to occur to the N-terminus of an EF-hand ([pfam:PF00036]), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants.
Pfam PF19979: Family of unknown function (DUF6415) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the  kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in Actinobacteria.
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 PF14090: Winged helix-turn-helix domain (domain)
This winged helix-turn-helix domain is often found in phage proteins and in bacteria and is likely to be involved in DNA-binding.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.