SII-SWORD/CoKE huggingface dataset:
Pfam PF00337: Galactoside-binding lectin (domain)
This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase ([swissprot:Q05315], [ec:3.1.1.5]).
Wikipedia: Galectins are a class of proteins that bind specifically to β-galactoside sugars, such as N-acetyllactosamine, which can be bound to proteins by either N-linked or O-linked glycosylation. They are also termed S-type lectins due to their dependency on disulphide bonds for stability and carbohydrate binding. There have been about 15 galectins discovered in mammals, encoded by the LGALS genes, which are numbered in a consecutive manner. Only galectin-1, -2, -3, -4, -7, -7B, -8, -9, -9B, 9C, -10, -12, -13, -14, and -16 have been identified in humans. Galectin-5 and -6 are found in rodents, whereas galectin-11 and -15 are uniquely found in sheep and goats. Members of the galectin family have also been discovered in other mammals, birds, amphibians, fish, nematodes, sponges, and some fungi. Unlike the majority of lectins they are not membrane bound, but soluble proteins with both intra- and extracellular functions. They have distinct but overlapping distributions but found primarily in the cytosol, nucleus, extracellular matrix or in circulation. Although many galectins must be secreted, they do not have a typical signal peptide required for classical secretion. The mechanism and reason for this non-classical secretion pathway is unknown.
Pfam PF14658: EF-hand domain (domain)
This entry represents the EF-hand-like domain found in protein KASH5. KASH5 is a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the connection between the nuclear lamina and the cytoskeleton . It interacts (via the last 22 AA) with SUN1; this interaction mediates telomere localisation .
Wikipedia: The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins.
Pfam PF04222: Protein of unknown function (DUF416) (family)
This is a bacterial protein family of unknown function. Proteins in this family adopt an alpha helical structure. Genome context analysis has suggested a high probability of a functional association with histidine kinases, which implicates proteins in this family to play a role in signalling (information from TOPSAN 2Q9R).
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 PF22118: Decaheme cytochrome c component MtrF-like domain III (domain)
This entry includes the decaheme cytochrome c component MtrF from the MtrFDE complex, an homologue of MtrC. In Shewanella oneidensis, these proteins are located at bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits and allow the utilization of extracellular mineral forms of iron and manganese as respiratory electron acceptors. Members of this entry consist of four domains: domain I and III containing seven antiparallel beta-strands in an extended Greek key topology; domains II and IV each bind five tightly packed hemes covalently attached to the Cys residues of the five CXXCH motifs in each domain and form the central core ([pfam:PF22113]), flanked by domains I and III. This entry represents domain III of MtrF and similar proteins.
Pfam PF23786: Phage baseplate wedge subunit (family)
This family represents a conserved phage baseplate wedge subunit found in phages infecting Enterobacteria. The baseplate is a complex phage structure that facilitates host cell attachment and injection of the phage DNA into the host cell. The wedge subunits form part of the baseplate structure. The family is part of the ViI-like phage group.
Pfam PF15733: Domain of unknown function (DUF4682) (family)
This domain family is found in eukaryotes, and is typically between 152 and 183 amino acids in length. The family is found in association with [pfam:PF00566]. There is a conserved NHLL 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 PF09751: Nuclear protein Es2 (family)
This entry is of a family of proteins of approximately 500 residues with alternating regions of low complexity and conservation where the domain similarities are strong.  Apart from a predicted coiled-coil domain, no other known functional domains have been characterised. The protein appears to be expressed in the nucleus and particularly highly in the pons sub-region of the brain. The protein is clearly necessary for normal development of the nervous system.
Pfam PF01170: RMKL-like, methyltransferase domain (domain)
This domain is the methyltransferase domain found in ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (RmlKL), tRNA (guanine(10)-N2)-dimethyltransferase from Methanocaldococcus jannaschii and similar proteins, which have a THUMP domain at the N-terminal.
Pfam PF16962: Putative ABC exporter (family)
This is a family of putative ABC_exporters from Firmicutes.
Pfam PF16078: 2-oxoglutarate dehydrogenase N-terminus (family)
This domain is found at the N-terminus of 2-oxoglutarate dehydrogenases.
Pfam PF11931: SF3a60/Prp9 C-terminal (family)
This domain corresponds to the C-terminal region of SF3a60 subunit (Prp9 in yeast counterpart) from the highly conserved heterotrimeric complex SF3a found in eukaryotes. It is essential for pre-mRNA splicing that functions in spliceosome assembly within the mature U2 snRNP (small ribonucleoprotein particle). This domain has two conserved sequence motifs: PIP and CEICG. It contains a zinc-finger domain of the C2H2-type which might be important for RNA binding and protein-protein interactions with components of the SF3b complex.
Pfam PF07199: Protein of unknown function (DUF1411) (domain)
This entry represents a domain approximately 150 residues long that is sometimes repeated within some Babesia bovis proteins of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF08926: Domain of unknown function (DUF1908) (domain)
This domain is found in a set of hypothetical/structural eukaryotic 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 PF18283: Carbohydrate binding module 77 (domain)
This domain is the non-catalytic carbohydrate binding module 77 (CBM77) present in Ruminococcus flavefaciens. CBMs fulfil a critical targeting function in plant cell wall depolymerisation. In CBM77, a cluster of conserved basic residues (Lys1092, Lys1107 and Lys1162) confer calcium-independent recognition of homogalacturonan.
Pfam PF24648: Domain of unknown function (DUF7641) (domain)
This entry includes uncharacterised sequences from Plasmodium sp. and similar sequences from Apicomplexa. This entry may represent transmembrane helices.
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 PF04452: RNA methyltransferase domain (domain)
RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner.  The Escherichia coli member is specific for U1498 methylation.
Pfam PF07219: HemY protein N-terminus (repeat)
This family represents the N-terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. This is a membrane protein involved in a late step of protoheme IX synthesis.
Pfam PF08620: RPAP1-like, C-terminal (family)
Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Pfam PF07558: Shugoshin N-terminal coiled-coil region (coiled_coil)
The Shugoshin protein is found to have this conserved N-terminal coiled-coil region and a highly conserved C-terminal basic region, family Shugoshin_C [pfam:PF07557]. Shugoshin is a crucial target of Bub1 kinase function at kinetochores, necessary for both meiotic and mitotic localisation of shugoshin to the kinetochore. Human shugoshin is diffusible and mediates kinetochore-driven formation of kinetochore-microtubules during bipolar spindle assembly. Further, the primary role of shugoshin is to ensure bipolar attachment of kinetochores, and its role in protecting cohesion has co-developed to facilitate this process.
Wikipedia: In molecular biology, the protein domain named the Shugoshin N-terminal coiled-coil region is a domain found on the N-terminal region of the Shugoshin protein in eukaryotes. It has a role in attaching to the kinetochores, structures on the chromatids where microtubules attach. Shugoshin has a conserved coiled-coil N-terminal domain and a highly conserved C-terminal region. Shugoshin is a crucial target of Bub1 kinase that plays a central role in the cohesion of chromosomes during cell division.
Pfam PF13933: Putative peptidase family (domain)
This family of putative peptidases are closely related to the M35 family [pfam:PF02102]. In this family the metal binding HEXXH motif is replaced with HRXXH. The exact function of these proteins is unknown. Members of this family are found to be fungal allergens.
Pfam PF18998: Divergent InlB B-repeat domain (domain)
This family of domains are found in bacterial cell surface proteins. They are often found in tandem array. This domain is closely related to [pfam:PF09479].
Pfam PF02886: LBP / BPI / CETP family, C-terminal domain (domain)
The N and C terminal domains of the LBP/BPI/CETP family are structurally similar.
Wikipedia: In molecular biology, the lipid-binding serum glycoproteins family, also known as the BPI/LBP/Plunc family or LBP/BPI/CETP family represents a family which includes mammalian lipid-binding serum glycoproteins and/or proteins containing a structural motif known as the BPI fold. Members of this family include:Bactericidal permeability-increasing protein (BPI)
Lipopolysaccharide-binding protein (LBP)
Cholesteryl ester transfer protein (CETP)
Phospholipid transfer protein (PLTP)
Palate, lung and nasal epithelium carcinoma-associated protein (PLUNC)
Pfam PF04393: Protein of unknown function (DUF535) (family)
Family member Shigella flexneri VirK ([swissprot:Q99QA5]) is a virulence protein required for the expression, or correct membrane localisation of IcsA  (VirG) on the bacterial cell surface,. This family also includes Pasteurella haemolytica lapB ([swissprot:P32181]),  which is thought to be membrane-associated.
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 PF11711: Inner membrane protein import complex subunit Tim54 (family)
Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targetting information, into the inner membrane.
Pfam PF01455: HupF/HypC family (family)
The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation and maturation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process . They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation .
Pfam PF12717: non-SMC mitotic condensation complex subunit 1 (repeat)
The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis.
Pfam PF07587: Protein of unknown function (DUF1553) (family)
A family of proteins found in Rhodopirellula baltica.
Pfam PF13795: HupE / UreJ protein (family)
These proteins contain many conserved histidines that may be involved in nickel binding.
Pfam PF12121: Dermaseptin (family)
This protein is found in eukaryotes. Proteins in this family are typically between 30 to 76 amino acids in length. This protein is found associated with [pfam:PF03032]. This domain is part of a dermaseptin protein which is used as an antimicrobial agent. The full protein is almost completely defined in an alpha helical domain. It creates high levels of disorder at the level of the phospholipid head group of bacterial membranes suggesting that it partitions into the bilayer where it severely disrupts membrane packing.
Wikipedia: Dermaseptins are a family of peptides isolated from skin of the frog genus Phyllomedusa. The sequence of the dermaseptins varies greatly but due to the presence of lysine residues all are cationic and most have the potential to form amphipathic helices in water or when integrated with the lipid bilayer of the bacterial membrane. Clear separation of two lobes of positive and negative intramolecular electrostatic potential is thought to be important in cytotoxic activity. Dermaseptins are typically 27-34 amino acid residues in length and were the first vertebrate peptides demonstrated as having a lethal effect on the filamentous fungi implicated in severe opportunistic infections accompanying immunodeficiency syndrome and immunosuppressive drug therapy.
Pfam PF14982: UPF0731 family (family)
The UPF0731 family of uncharacterised proteins is found in mammals.
Pfam PF07246: Phlebovirus nonstructural protein NS-M (family)
This family consists of several Phlebovirus nonstructural NS-M proteins which represent the N-terminal region of the M polyprotein precursor. The function of this family is unknown.
Pfam PF11932: Protein of unknown function (DUF3450) (coiled_coil)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 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 PF09777: Osteopetrosis-associated transmembrane protein 1 precursor (family)
Members of this family of proteins are required for osteoclast and melanocyte maturation and function. Mutations give rise to autosomal recessive osteopetrosis [MIM:259700]; also called autosomal recessive Albers-Schonberg disease.
Wikipedia: Osteopetrosis-associated transmembrane protein 1 is a protein that in humans is encoded by the OSTM1 gene. It is required for osteoclast and melanocyte maturation and function.
Pfam PF15831: Small integral membrane protein 5/18/22 (family)
This entry represents a small family of single-pass membrane proteins described as small integral membrane proteins, including SMIM5/18/22 which have been described as variants of the Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encode protein. CASIMO1 controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors. Loss of CASIMO1 disturbs the organisation of the actin cytoskeleton, leads to inhibitions of cell motility, and stalls the cell cycle in the G0/G1 phase.
Pfam PF21678: Csf1 N-terminal region (repeat)
This entry includes Csf1 protein from yeast, which is the orthologue of human BLTP1. Csf1 also known as Cold sensitive for fermentation protein 1 is a fungal membrane protein required for fermentation at low temperature. Csf1, similar to BLTP1, is a tube-forming lipid transport protein which provides phosphatidylethanolamine for glycosylphosphatidylinositol (GPI) anchor synthesis in the endoplasmic reticulum. These proteins belong to the repeating beta-groove (RBG) superfamily which are conserved lipid transfer proteins containing long hydrophobic grooves consisting of multiple repeating modules made of five beta-sheets followed by a loop.
Pfam PF15440: THRAP3/BCLAF1 family (family)
This family includes thyroid hormone receptor-associated protein 3 (THRAP3), which is a spliceosome component and a subunit of the TRAP complex which plays a role in pre-mRNA splicing and in mRNA decay. It also includes the transcriptional repressor Bcl-2-associated transcription factor 1 (BCLAF1).
Pfam PF13753: Putative flagellar system-associated repeat (domain)
This family appears to be a repeated unit that can occur up to 29 times in these outer membrane proteins. It is putatively associated with a novel flagellar system.
Pfam PF05269: Bacteriophage CII protein (family)
This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages.
Pfam PF01192: RNA polymerase Rpb6 (family)
Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit.  Rpb6 and omega are structurally conserved and both function in polymerase assembly.
Pfam PF11961: Domain of unknown function (DUF3475) (family)
This entry represents the N-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with [pfam:PF05003]. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana.  PSI proteins are plant-specific and promote growth.
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 PF19881: Family of unknown function (DUF6354) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001735) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular  the pentostatine biosynthetic gene cluster from Streptomyces  antibioticus.
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 PF21455: Pyrrolysine biosynthesis protein PylD, N-terminal domain (domain)
This domain is found at the N-terminal end of Pyrrolysine biosynthesis protein PylD from Methanosarcina acetivorans, a dehydrogenase that catalyses the final step in the biosynthesis of the amino acid pyrrolysine.
Pfam PF18220: Adhesin BspA variable domain (domain)
This domain is found in BspA protein present in Streptococcus agalactiae. BspA is an antigen I/II family polypeptide that confers adhesion linked to pathogenesis in group B Streptococcus. This domain is referred to as the variable domain (BspA-V). BspA-V is responsible for binding to scavenger receptor gp340. BspA-V adopts a fold that is distinct from those of other AgI/II family polypeptide variable domains.
Pfam PF08303: tRNA ligase kinase domain (domain)
This domain is found in fungal tRNA ligases and has kinase activity.  tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. This family contains a P-loop motif.
Pfam PF21602: GldM third domain (domain)
This immunoglobulin-like domain is found in bacteria in the GldM protein.  GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes.
Pfam PF00308: Bacterial DnaA ATPAse domain (domain)
This entry represents the ATPAse domain of DnaA and similar proteins.
Wikipedia: DnaA is a protein that activates initiation of DNA replication in bacteria. Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. It is a replication initiation factor which promotes the unwinding of DNA at oriC. The DnaA proteins found in all bacteria engage with the DnaA boxes to start chromosomal replication. The onset of the initiation phase of DNA replication is determined by the concentration of DnaA. DnaA accumulates during growth and then triggers the initiation of replication. Replication begins with active DnaA binding to 9-mer (9-bp) repeats upstream of oriC. Binding of DnaA leads to strand separation at the 13-mer repeats. This binding causes the DNA to loop in preparation for melting open by the helicase DnaB.