SII-SWORD/CoKE huggingface dataset:
Pfam PF00660: Seripauperin and TIP1 family (family)
It has recently been shown  that three yeast proteins, two of which are known to be induced by various stress conditions, are structurally related and are probably part of a larger family. These proteins include cold-shock inducible protein TIR1 (also known as serine-rich protein 1, SRP1), which is induced by glucose  and cold shock ; temperature-shock inducible protein 1 (SRP2) ; seripauperins, which are closely related protein of about 13kDa (120 to 124 residues) and are generally encoded at the extremity of yeast chromosomes (eg. PAU1, PAU2, PAU3, PAU4, PAU5, PAU6, YBR301w, YGL261c, YGR294w, YHL046c, YIL176c, YIR041w and YKL224c) ; and hypothetical proteins YIL011w, YJR150c and YJR151c. These proteins all seem to start with a putative signal sequence followed by a conserved domain of about 90 residues. In TIR1, TIR2, TIP1, YIL011w, YJR150c and YJR151c, this domain is followed by a repetitive serine and alanine rich region absent in the other members of this family.
Pfam PF02312: Core binding factor beta subunit (family)
Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has been show to have a structure related to the OB fold.
Pfam PF24293: Edg1, TPR repeats (repeat)
This entry represents a region of tetratricopeptide-like repeats found in a group of animal proteins, including protein edg-1 from Caenorhabditis elegans, which plays a role in regulating deps-1 cluster formation in the germline.
Pfam PF02821: Staphylokinase/Streptokinase family (domain)
This entry represents staphylokinases.

Staphylokinase (also known as SAK) from Staphylococcus aureus is a virulence factor due to its interaction with plasminogen and alpha-defensins in the hosts. The binding of staphylokinase to plasminogen results in the formation of active plasmin, a proteolytic enzyme facilitating bacterial penetration into the surrounding tissues . However, once the host tissues are infected, the interaction between staphylokinase and plasminogen decreases disease severity . The three-dimensional structure of streptokinase  is believed to contain two independently folded domains, each with a ubiquitin-like fold.
Wikipedia: Streptokinase is a thrombolytic medication activating plasminogen by nonenzymatic mechanism. As a medication it is used to break down clots in some cases of myocardial infarction, pulmonary embolism, and arterial thromboembolism. The type of heart attack it is used in is an ST elevation myocardial infarction (STEMI). It is given by injection into a vein.
Pfam PF06775: Putative adipose-regulatory protein (Seipin) (family)
Seipin is a protein of approximately 400 residues, in humans, which is the product of a gene homologous to the murine guanine nucleotide-binding protein (G protein) gamma-3 linked gene. This gene is implicated in the regulation of body fat distribution and insulin resistance and particularly in the auto-immune disease Berardinelli-Seip congenital lipodystrophy type 2. Seipin has no similarity with other known proteins or consensus motifs that might predict its function, but it is predicted to contain two transmembrane domains at residues 28-49 and 237-258, in human, and a third transmembrane domain might be present at residues 155-173. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V.
Wikipedia: Seipin is a homo-oligomeric integral membrane protein in the endoplasmic reticulum (ER) that concentrates at junctions with cytoplasmic lipid droplets (LDs). Alternatively, seipin can be referred to as Berardinelli–Seip congenital lipodystrophy type 2 protein (BSCL2), and it is encoded by the corresponding gene of the same name, i.e. BSCL2. At protein level, seipin is expressed in cortical neurons in the frontal lobes, as well as motor neurons in the spinal cord. It is highly expressed in areas like the brain, testis and adipose tissue. Seipin's function is still unclear but it has been localized close to lipid droplets, and cells knocked out in seipin have anomalous droplets. Hence, recent evidence suggests that seipin plays a crucial role in lipid droplet biogenesis.
Pfam PF15033: Kinocilin protein (family)
This family of kinocilin proteins is found in vertebrate. In mouse it has been shown that this protein is expressed primarily in the kinocilium of sensory cells in the inner ear.
Pfam PF04157: EAP30/Vps36 family (family)
This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking.  EAP30 is a subunit of the ELL complex.  The ELL is an 80-kDa RNA polymerase II transcription factor.  ELL interacts with three other proteins to form the complex known as ELL complex.  The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity.
Pfam PF23844: Non-contractile tail sheath N-terminal domain (domain)
This entry represents the N-terminal domain found in the non-contractile tail sheath protein from Bacteriophage N4 (BPN4). This protein is essential for BPN4 infectivity and it is hypothesized that it mediates binding with target cell receptors. The function of this domain is unknown. This entry also includes sequences from bacteria, predominantly from Sphingobium spp.
Pfam PF18517: Leucine zipper with capping helix domain (domain)
This domain is found at the C-terminal region of Hop2 and Mnd1 proteins.  In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation.  The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament.
Pfam PF13969: Pab87 octamerisation domain (domain)
This domain was first characterised as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi. The domain is reported to play a crucial role in Pab87 octamerisation and active site compartmentalisation. Its up-and-down 8-stranded beta-barrel 3D structure is reminiscent of the one found in lipocalins.
Pfam PF07853: Domain of unknown function (DUF1648) (domain)
This domain is found in proteins expressed by bacterial or archaeal species. Some of these are annotated as being transmembrane  proteins, and in fact many of these sequences contain a high proportion of hydrophobic residues. One protein containing this domain is immunity protein SdpI (swiss:O32241) from Bacillus subtilis, which provides protection for the cell against the toxic effects of its own SdpC killing factor, and also functions as a receptor/signal transduction protein.
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 PF00727: Interleukin 4 (domain)
Cytokines are protein messengers that carry information from cell to cell . Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE ; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4), which this entry represents, has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds . One half of the structure is dominated by a 4 Î±-helix bundle with a left-handed twist . The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel Î²-sheet .
Wikipedia: The interleukin 4 is a cytokine that induces differentiation of naive helper T cells (Th0 cells) to Th2 cells. Upon activation by IL-4, Th2 cells subsequently produce additional IL-4 in a positive feedback loop. IL-4 is produced primarily by mast cells, Th2 cells, eosinophils and basophils. It is closely related and has functions similar to IL-13.
Pfam PF17788: HypF Kae1-like domain (domain)
This domain is found in the HypF protein. In the structure it is one of the two subdomains of the Kae1 domain.
Pfam PF07469: Nuclear receptor coactivator, DUF1518 (domain)
This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors.
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 PF05754: Domain of unknown function (DUF834) (domain)
This short presumed domain is found in a large number of hypothetical plant proteins. The domain is quite rich in conserved glycine residues.      It occurs in some putative transposons but currently 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 PF23742: C3G9 VBS-like domain (domain)
This domain is found in the yeast uncharacterized protein C3G9.05 and related proteins. It is predicted to adopt a four-helical up-and-down bundle with significant similarity to VBS-like domains.
Pfam PF22780: HI0933-like protein barrel and H2TH domain (family)
This entry represents two structural domains that are found inserted within a Rossmann domain.
Pfam PF17917: RNase H-like domain found in reverse transcriptase (domain)
DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain.
Pfam PF04557: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 (family)
This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function.
Pfam PF15907: Integrin-alpha FG-GAP repeat-containing protein 2 (repeat)
Members of this family are annotated as being integrin-alpha FG-GAP repeat-containing protein 2.
Pfam PF11517: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2) (family)
Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1.The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA. An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1.
Pfam PF23294: TopBP1/SLF1, BRCT domain (domain)
This entry represents a BRCT domain found in TopBP1 (also known as DNA topoisomerase II-beta-binding protein 1) and SLF1 (SMC5-SMC6 complex localization factor protein 1). TopBP1 functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. SLF1 plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance. This entry corresponds to the eight BRCT domain of TopBP1 and the second one in SLF1.
Pfam PF08847: Chlororespiratory reduction 6 (domain)
Chlororespiratory reduction 6 (Crr6) is a factor required for the assembly or stabilisation of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis.
Pfam PF10667: Protein of unknown function (DUF2486) (family)
This family is made up of members from various Burkholderia spp. The function is unknown.
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 PF19307: Type 2A encapsulin shell protein SrpI-like (domain)
This entry includes type 2A encapsulin shell protein SrpI from Synechococcus elongatus and its homologues from Mycobacteria, such as [Swissprot:P46841] from Mycobacterium leprae, which forms a large 950 kDa complex with itself. It has been described as the most antigenic protein in human leprosy patients, being useful for serodiagnosis of leprosy. Some members of this family contain an N-terminal cyclic nucleotide binding domain [pfam:PF00027]. This family includes proteins annotated as phage capsid proteins, such as UniProt:A0A1X9IAH4 suggesting that in bacteria this protein is a co-opted phage protein. There is a clear evolutionary relationship between the bacterial encapsulins and Caudovirales bacteriophages as they share the HK97 fold of the capsid proteins.
Pfam PF21535: Uncharacterized motility-related protein HVO_2248 (family)
This family represents a group of uncharacterised proteins from archaea, including the Uncharacterized motility-related protein HVO_2248 from Haloferax, which is related to hypermotility and predicted as a cytoplasmic protein. Homologues of HVO_2248 are only found in Halobacteria.
Pfam PF18757: Nucleotide modification associated domain 5 (domain)
An alpha+beta fold domain associated with DNA base modifying genes in prokaryotes, and likely to be involved in modified DNA base biosynthesis.
Pfam PF05251: Oligosaccharyltransferase subunit 5 (family)
Eukaryotic N-glycosylation is catalysed in the ER lumen, where the enzyme oligosaccharyltransferase (OTase) transfers donor glycans from a dolichol pyrophosphate (DolP) carrier (Lipid-linked oligosaccharide; LLO) to polypeptides. The yeast OTase is a hetero-oligomeric complex composed of essential (Ost1, Ost2, Wbp1, Stt3, and Swp1) and nonessential (Ost3, Ost4, Ost5, and Ost6) subunits. This domain family is found in Ost5, [swissprot:Q92316]. The precise function of this subunit is not known, however Ost5 appears to form a sub-complex with Ost1, and this sub-complex associates with the catalytic Stt3 subunit of OTase. Down regulation of Ost5 resulted in a limited effect on glycosylation and no effect on the stability of Ost1 or Stt3 subunits.
Pfam PF01866: Putative diphthamide synthesis protein (family)
Diphthamide_syn, diphthamide synthase, catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. [swissprot:Q16439] is a candidate tumour suppressor gene. DPH2 from yeast [swissprot:P32461], which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a post-translationally modified histidine residue present in EF2. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2).
Pfam PF08166: PELP1, middle domain (repeat)
This domain is found in middle of PELP1 (Proline-, glutamic acid- and leucine-rich protein 1, also known as modulator of nongenomic activity of estrogen receptor) which consists of HEAT repeats. PELP1 is a coactivator of estrogen receptor-mediated transcription and a corepressor of other nuclear hormone receptors and sequence-specific transcription factors. It forms the Five Friends of Methylated Chtop (5FMC) nuclear complex, together with the Sumo-specific protease Senp3, Wdr18, Tex10, and Las1L, in which it constitutes the core of 5FMC. This complex is recruited by Chromatin target of Prmt1 (Chtop, a vertebrate-specific chromatin-bound protein that plays an important role in transcriptional regulation) when the latter is arginine-methylated by Prmt1.
Pfam PF25052: Defensin-like family (domain)
This entry represents defensin-like proteins from Arabidopsis thaliana and related plant proteins.
Pfam PF05774: Herpesvirus helicase-primase complex component (family)
This family consists of several helicase-primase complex components from the Gammaherpesviruses.
Pfam PF17030: Putative beta-lactamase-like family (family)
This is a family derived from microsporidia-specific proteins. There is homology to the beta-lactamase domain.
Pfam PF05947: Type VI secretion system, TssF (family)
This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS) , including TssF. TssF is homologues to phage tail proteins and is required for proper assembly of the Hcp tube (the T6SS inner tube) in bacteria. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. T6SSs contain 13 conserved components (TssA-TssM) which are thought to form the core apparatus and to enable effector proteins to be injected into target cells in a single cell-contact-dependent step.  TssF one of the core components of T6SSs machinery, has been shown to be recruited by TssK into the membrane-associated T6SS complex, contributing to the dynamic mechanism of the system. Furthermore, it has been reported to interact with TssG proteins stabilizing each other while making contact with TssE, TssK and VgrG as well as with tube and sheath components. Bioinformatic analysis suggest that TssF and TssG share similarities with the J and I proteins of the bacteriophage P2 baseplate respectively. Further experimental studies show that functional TssF and TssK proteins assemble into static foci near the cell envelope. Moreover, biochemical and cytological approaches provide support to the role of TssE, TssF, TssG, TssK and VgrG as T6SS baseplate components and to a sequential recruitment hierarchy (membrane complex, baseplate, tail tube/sheath) during T6SS biogenesis.
Pfam PF12975: Domain of unknown function (DUF3859) (domain)
This short domain is functionally uncharacterised.
Pfam PF11374: Protein of unknown function (DUF3176) (family)
This eukaryotic family of 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 PF10018: Vitamin-D-receptor interacting Mediator subunit 4 (family)
Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter.
Wikipedia: Mediator of RNA polymerase II transcription subunit 4 also known as mediator complex subunit 4 (MED4), a component of Mediator or vitamin D3 receptor-interacting protein complex 36 kDa component (DRIP36) is a protein that in humans is encoded by the MED4 gene.
Pfam PF15352: Susceptibility to monomelic amyotrophy (family)
This family of proteins is associated with a susceptibility to monomelic amyotrophy.
Pfam PF06440: DNA polymerase III, theta subunit (domain)
DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit.   The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered.   The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5'  exonucleolytic proofreading activity of epsilon.
Wikipedia: In E. coli and other bacteria, holE is a gene that encodes the theta subunit of DNA polymerase III.
Pfam PF00979: Reovirus outer capsid protein, Sigma 3 (family)
Sigma 3 is the major outer capsid protein of reovirus. Sigma 3 is encoded by genome segment 4.  Sigma 3 binds to  double stranded RNA and associates with polypeptide u1 and  its cleavage product u1C to form the outer shell of the virion. The Sigma 3 protein possesses a zinc-finger motif and an RNA-binding domain in the N and C termini respectively. This protein is also thought to play a role in pathogenesis.
Pfam PF22189: RickCE N-terminal (domain)
This is a presumed domain found at the N-terminal of rickCE ubiquitin-like proteases, such as [swissprot:Q1RK35], which may have a Rossmann-like fold similar to that in glycosyltransferases (Foldseek structural comparison).
Pfam PF14229: Domain of unknown function (DUF4332) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 134 and 356 amino acids in length. This domain contains helix-hairpin-helix motifs.
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.