SII-SWORD/CoKE huggingface dataset:
Pfam PF00008: EGF-like domain (domain)
There is no clear separation between noise and signal. [pfam:PF00053] is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam).  The family is hard to model due to many similar but  different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.
Wikipedia: The EGF-like domain is an evolutionary conserved protein domain, which derives its name from the epidermal growth factor where it was first described. It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins. Most occurrences of the EGF-like domain are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted. An exception to this is the prostaglandin-endoperoxide synthase. The EGF-like domain includes 6 cysteine residues which in the epidermal growth factor have been shown to form 3 disulfide bonds. The structures of 4-disulfide EGF-domains have been solved from the laminin and integrin proteins. The main structure of EGF-like domains is a two-stranded β-sheet followed by a loop to a short C-terminal, two-stranded β-sheet. These two β-sheets are usually denoted as the major (N-terminal) and minor (C-terminal) sheets. EGF-like domains frequently occur in numerous tandem copies in proteins: these repeats typically fold together to form a single, linear solenoid domain block as a functional unit.
Pfam PF12212: PAZ domain (domain)
This entry corresponds to the PAZ domain found in some archaeal argonaute proteins. It is an siRNA binding domain.
Wikipedia: The Argonaute protein family, first discovered for its evolutionarily conserved stem cell function, plays a central role in RNA silencing processes as essential components of the RNA-induced silencing complex (RISC). RISC is responsible for the gene silencing phenomenon known as RNA interference (RNAi). Argonaute proteins bind different classes of small non-coding RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). Small RNAs guide Argonaute proteins to their specific targets through sequence complementarity, which then leads to mRNA cleavage, translation inhibition, and/or the initiation of mRNA decay.
Pfam PF10181: GPI-GlcNAc transferase complex, PIG-H component (family)
PIG-H is a family of conserved proteins that complexes with three other proteins to form the GPI-GnT (glycosylphosphatidylinositol anchor biosynthesis transferase) complex. It appears to be a peripheral membrane protein facing the cytoplasm involved in the first step in GPI anchor formation.
Pfam PF11550: Intracellular growth locus C protein (family)
IglC protein is involved in the escape of F.tularensis live vaccine strain. It has been shown that the expression of IglC is essential for F.tularensis to induce macrophage apoptosis. IglC adopts a beta-sandwich conformation that has no similarity to any known protein structure.
Pfam PF14337: Abortive infection alpha (family)
Enterococci such as Enterococcus faecalis and Enterococcus faecium are part of the normal human gut microbiota. However they can also be a source of nosocomial infections specially in immunocompromised patients. Virulent bacteriophages, i.e., viruses that infect and obligatorily lyse bacteria might provide alternative options for combating them. Yet, bacterial resistance to phage is taking place in similar fashion to antibiotic resistance. This might be, in part due to temperate phages that are stably associated with their host. They compete for their bacterial host, in addition to repressor-dependent immunity against similar phages, some phage express genes conferring resistance to infection by more or less unrelated phages. They can encode abortive infection (Abi) mechanisms that cause an interruption of invasive phage development and a premature death of the infected bacteria. For instance, E. faecalis V583 prophage 6 confers resistance to the virulent phage Idefix infection mainly due to Abia-alpha protein. This Pfam family corresponds to Abi-alpha protein sequences which is mostly found in prophages, arguing that it is essentially a temperate phage weapon to fight against other phages.
Pfam PF23615: MIT1 Chromo domain (domain)
This domain is found in the Chromatin remodeling factor mit1 (MIT1) from fission yeast and related proteins. MIT1 is required for proper positioning of the nucleosomes at heterochromatic loci and for transcriptional gene silencing function of the multienzyme effector complex SHREC. The domain represented by this entry is predicted to fold into a globular structure with significant similarity to Chromo domain.
Pfam PF22045: Chloramphenicol halogenase CmlS C-terminal domain (domain)
Chloramphenicol halogenase CmlS belongs to the large and diverse superfamily of flavin-dependent halogenases. CmlS is one of the few enzymes known to halogenate an alkyl group. This entry represents the C-terminal domain of CmlS that resembles an arch-like structure above a central alpha-helix. This domain creates a T-shaped tunnel leading to the halogenation active site and thus likely directs substrates into the active site to achieve the desired specificity.
Pfam PF07483: Tryptophan-rich Synechocystis species C-terminal domain (family)
This domain is found at the C-terminus, normally between 2-3 copies, of a range of Synechocystis membrane proteins. This domain is fairly tryptophan rich as well.
Pfam PF22603: RAE1/2 domain I, C-terminal region (domain)
This entry represents the C-terminal region of domain I from Rab escort proteins 1/2 (RAE1/2, also known as Rab proteins geranylgeranyltransferase component A 1/2) which are the substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex. These proteins bind unprenylated Rab proteins and presents the substrate peptide to the catalytic component B and remains bound to it after the geranylgeranyl transfer reaction.
Pfam PF07224: Chlorophyllase (family)
This family consists of several plant specific Chlorophyllase proteins ([ec:3.1.1.14]). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of ester bond to yield chlorophyllide and phytol.
Wikipedia: Chlorophyllase is an essential enzyme in chlorophyll metabolism. It is a membrane proteins commonly known as chlase (EC 3.1.1.14, CLH) with systematic name chlorophyll chlorophyllidohydrolase. It catalyzes the reactionchlorophyll + H2O = phytol + chlorophyllide
Pfam PF21567: Gp22 (family)
This protein family includes Gp22 from Bacillus phage SPP1 ([swissprot:O48465]), an protein that shows a significant structural similarity with the N-terminal shoulder domain ([pfam:PF20747]) of Receptor binding protein from Lactococcus phage p2 (RBP). It folds into two small three-stranded antiparallel beta-sheets and one large five-stranded mixed beta-sheet forming a pseudo-beta-sandwich.
Pfam PF24119: Domain of unknown function (DUF7393) (domain)
This small uncharacterised phage protein has a 5 stranded beta barrel 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 PF18708: MapZ extracellular C-terminal domain 2 (domain)
In the pneumococcus cell division, MapZ (Midcell Anchored Protein Z) locates at the division site before FtsZ and guides septum positioning. MapZ forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ-ring through direct protein-protein interactions. Structural analysis indicate that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. The extracellular C-terminal domain carries a conserved patch of amino acids which plays a crucial function in binding peptidoglycan and positioning MapZ at the cell equator.
Pfam PF19778: Endonuclease domain (domain)
This represents the C-terminal endonuclease domain found in a variety of class III restriction endonuclease 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 PF12555: SteA-like C-terminal domain (domain)
This domain family is found in bacteria, and is approximately 50 amino acids in length. This domain is found at the C-terminal of SteA proteins from Corynebacterium. SteA and SteB are conserved components of the cytokinetic ring among Corynebacterineae that may play a critical role in the final stages of cytokinesis as they probably form a complex to promote cell separation by RipC-FtsEX. They may coordinate peptidoglycan remodelling with the biogenesis of other envelope layers during cell division.
Pfam PF11570: Coiled-coil receptor-binding R-domain of colicin E2 (coiled_coil)
E2 is a DNase which utilises the outer membrane receptor BtuB to bind to and enter the cell. This family of proteins is E2R135 (residues 321-443) which is the part of E2 which is responsible for binding to BtuB in a coiled coil formation.
Pfam PF11874: Domain of unknown function (DUF3394) (family)
This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with [pfam:PF06808].
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 PF23810: Family of unknown function (DUF7182) (family)
This entry represents an uncharacterized protein found in various mycobacteriophages. The protein contains a predicted transmembrane helix and is typically around 60 amino acids in length. Its 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 PF09913: Predicted membrane protein (DUF2142) (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 PF03446: NAD binding domain of 6-phosphogluconate dehydrogenase (domain)
The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.
Pfam PF12048: Protein of unknown function (DUF3530) (domain)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes.
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 PF13671: AAA domain (domain)
This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF24404: Novel STAND NTPase 7 (domain)
This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems.
Pfam PF05914: RIB43A (family)
This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterised in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells.
Pfam PF24540: REST-like, C2H2-type zinc finger (domain)
This is a C2H2-type zinc finger found in human RE1-silencing transcription factor (REST) and similar sequences from vertebrates. REST is a transcriptional repressor which binds neuron-restrictive silencer element (NRSE) and represses neuronal gene transcription in non-neuronal cells.
Pfam PF22598: CdsD, periplasmic PD2 domain (domain)
This domain is found in CdsD from Chlamydia trachomatis ([swissprot:O84671]) and similar sequences from Chlamydiia. CdsD is a structural contact-dependent secretion (Cds) protein that form part of the basal body of the type III secretion system (T3SS) injectisome of the bacteria. The periplasmic part of this protein contains at least 3 domains: PD1, PD2 (this entry) and PD3 ([pfam:PF04972]), all of them sharing the same alpha-beta-beta-alpha-beta topology, known as the BON fold, in which the two antiparallel alpha-helices are on the same side of a three stranded beta-sheet.
Pfam PF21208: Selenocysteine-specific elongation factor, eukaryotes, 3rd domain (domain)
This domain is found in Selenocysteine-specific elongation factor from humans (SelB) and similar sequences from eukaryotes. SelB is a translation factor necessary for the incorporation of selenocysteine into proteins. This protein adopts a chalice-like structure composed of four domains. This entry represents the third domain, which folds into a barrel structure consisting of seven antiparallel beta-strands and a long alpha-helix. This domain has similarity to the third domain of EF-Tu.
Pfam PF01111: Cyclin-dependent kinase regulatory subunit (domain)
In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division . The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded Î²-barrel structure . Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs . Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation .
Wikipedia: In molecular biology, the cyclin-dependent kinase regulatory subunit family is a family of proteins consisting of the regulatory subunits of cyclin-dependent protein kinases.
Pfam PF24459: Domain of unknown function (DUF7574) (domain)
This entry represents a small family of uncharacterised phage 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 PF23433: Family of unknown function (DUF7119) (domain)
This domain is found in a group of uncharacterised proteins mainly from archaea. It is predicted to adopt an all-helical configuration.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16822: SGNH hydrolase-like domain, acetyltransferase AlgX (domain)
ALGX is a family found in bacteria. The domain demonstrates catalytic activity similar to that of the SGNH hydrolase-like domain, with the typical Ser-His-Asp triad found in this enzyme. Alginate is an exopolysaccharide that contributes to biofilm formation. ALGX is secreted into the biofilm and is responsible for the acetylation of biofilm polymers that help protect them from host destruction.
Pfam PF01803: LIM-domain binding protein (family)
The LIM-domain binding protein, binds to the LIM domain [pfam:PF00412] of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) [swissprot:P70662] is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development. The Drosophila protein Chip [swissprot:O18353] is required for segmentation and activity of a remote wing margin enhancer. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions.
Wikipedia: In molecular biology, the LIM domain-binding protein family is a family of proteins which binds to the LIM domain of LIM homeodomain proteins which are transcriptional regulators of development.
Pfam PF01691: Adenovirus E1B 19K protein / small t-antigen (family)
This family consists of adenovirus E1B 19K protein or small t-antigen. The E1B 19K protein inhibits E1A induced apoptosis and hence prolongs the viability of the host cell. It can also inhibit apoptosis mediated by tumour necrosis factor alpha and Fas antigen. E1B 19K blocks apoptosis by interacting with and inhibiting the p53-inducible and death- promoting Bax protein.  The E1B region of adenovirus encodes two proteins E1B 19K the small t-antigen as found in this family and E1B 55K the large t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis.
Pfam PF01325: Iron dependent repressor, N-terminal DNA binding domain (domain)
This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Wikipedia: In molecular biology, the iron dependent repressors are a family of bacterial and archaeal transcriptional repressors.
Pfam PF01150: GDA1/CD39 (nucleoside phosphatase) family (family)
A number of nucleoside diphosphate and triphosphate hydrolases as well as some yet uncharacterised proteins have been found to belong to the same family . The uncharacterised proteins all seem to be membrane-bound.
Pfam PF14254: Domain of unknown function (DUF4348) (family)
Two structures have been solved form this DUF, PDB:4mjf and PDB:3sbu. TOPSAN records that both proteins are the only structural representatives of Pfam PF14254, DUF4348. There are no other significant hits in FFAS. DUF4348 has ~200 proteins, all from Bacteroidetes, and all with a single domain architecture with just one DUF4348 domain. There appears to be a possible gene duplication in the protein as the N-terminal domain (approx residues 25-174) and C-terminal domain (approx residues 175-286) superimpose quite well with ~1.9A r.m.s.d. and ~30% sequence identity.
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 PF15233: Synaptonemal complex central element protein 1 (coiled_coil)
This family of proteins includes synaptonemal complex central element protein 1, a component of the synaptonemal complex involved in meiosis, and synaptonemal complex central element protein 1-like, which may be involved in meiosis.
Pfam PF19848: Family of unknown function (DUF6323) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001520) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  aurantinin B biosynthetic gene cluster from Bacillus subtilis. This family appears to be predominantly present in Firmicutes.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.