SII-SWORD/CoKE huggingface dataset:
Pfam PF07154: Protein of unknown function (DUF1392) (family)
This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family 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 PF14163: Super-infection exclusion protein B (family)
This family includes superinfection exclusion proteins. These proteins prevent the growth of superinfecting phage which are insensitive to repression. It aborts lytic development of superinfecting phage.
Pfam PF15780: Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin (domain)
The ASH domain or N-terminal domain of abnormal spindle-like microcephaly-associated protein are found in proteins associated with cilia, flagella, the centrosome and the Golgi complex. The domain is also found in Hydin and OCRL whose deficiencies are associated with hydrocephalus and Lowe oculocerebrorenal syndrome (OCRL), respectively. The fact that Human ASPM protein carries an ASH domain indicates possible roles for ASPM in sperm flagellar or in ependymal cells' cilia. The presence of ASH in centrosomal and ciliary proteins indicates that ASPM may possess roles not only in mitotic spindle regulation, but also in ciliary and flagellar function.
Pfam PF16572: Long alpha hairpin domain of cation efflux system protein, CusB (domain)
HlyD_D4 is the long alpha-hairpin domain in the centre of CusB or HlyD proteins. CusB and HlyD proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons. HlyD_D4 is thought to interact with the alpha-helical tunnels of the corresponding outer-membrane channels, ie the periplasmic domain of CusC.
Pfam PF14173: ComG operon protein 7 (family)
This family is required for DNA-binding during transformation of competent bacterial cells.
Pfam PF04371: Porphyromonas-type peptidyl-arginine deiminase (family)
Peptidyl-arginine deiminase (PAD) enzymes catalyse the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia.  PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD ([pfam:PF03068]), which is a metalloenzyme.  PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologues). The predicted catalytic residues in PPAD ([swissprot:Q9RQJ2]) are Asp130, Asp187, His236, Asp238 and Cys351. These are absolutely conserved with the exception of Asp187 which is absent in two family members.  PPAD is also able to catalyse the deimination of free L-arginine, but has primarily peptidyl-arginine specificity.  It may have a FMN cofactor.
Pfam PF13937: Domain of unknown function (DUF4212) (family)
This family includes several putative integral membrane proteins which have been predicted as the putative subunit of transporters for D-alanine or lactate (See Supplementary note 5 in).
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 PF11280: Protein of unknown function (DUF3081) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF23185: CFAP43 N-terminal domain (repeat)
This entry represents a beta-propeller domain found at N-terminal region of CFAP43 from Trypanosoma sp, and similar sequences from lower eukaryotes, according to structural prediction. These proteins are essential for flagellar function and, consequently, cell proliferation in T. brucei.
Wikipedia: In structural biology, a beta-propeller (β-propeller) is a type of all-β protein architecture characterized by 4 to 8 highly symmetrical blade-shaped beta sheets arranged toroidally around a central axis. Together the beta-sheets form a funnel-like active site.
Pfam PF21809: Bacterial GH84, post-catalytic domain (domain)
This is a helical domain found after the catalytic domain of enzymes from the Glycoside hydrolase family 84 from Bacteroides spp. and certain pathogenic Clostridia spp.
Pfam PF08168: Nucleolar protein 11 N-terminal domain (repeat)
This entry represents the N-terminal beta propeller domain found in nucleolar protein 11 and its homologues. This entry was formerly the NUC205 domain which has been significantly extended based on AlphaFold models.
Pfam PF22147: Anti-CRISPR protein AcrIC5 (family)
AcrIC5 is one of the earliest discovered AcrIC families that inhibit type I-C CRISPR-Cas systems. AcrIC5 adopts an alpha/beta structure consisting of a beta-hairpin and three alpha-helices. The presence of a highly acidic surface patch suggests that AcrIC5 might inhibit the type I-C CRISPR-Cas system by directly binding to the DNA target binding site in the system by mimicking DNA.
Pfam PF02660: Glycerol-3-phosphate acyltransferase (family)
This family of enzymes catalyses the transfer of an acyl group from acyl-ACP to glycerol-3-phosphate to form lysophosphatidic acid].
Pfam PF16930: Putative porin (family)
This entry includes a group of putative bacterial porins. Their function is not clear.
Pfam PF04015: Domain of unknown function (DUF362) (domain)
Domain that is sometimes present in iron-sulphur 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 PF02067: Metallothionein family 5 (domain)
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds  species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units. This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Consequently, all class I and class I MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences.

Diptera (Drosophila, family 5) MTs are 40-43 residue proteins that contain 10 conserved cysteines arranged in five Cys-X-Cys groups. In particular, the consensus pattern C-G-x(2)-C-x-C-x(2)-Q-x(5)-C-x-C-x(2)-D-C-x-C has been found to be diagnostic of family 5 MTs. The protein is found primarily in the alimentary canal, and its induction is stimulated by ingestion of cadmium or copper . Mercury, silver and zinc induce the protein to a lesser extent. Family 5 includes subfamilies: d1, d2. Only one d2 is known until now. Subfamilies hit the same entry.
Pfam PF16872: Putative phage abortive infection protein (family)
Several members are annotated as putative phage abortive infection proteins.
Pfam PF08359: YsiA-like protein, C-terminal region (domain)
The members of this family are thought to be TetR-type transcriptional regulators that bear particular similarity to YsiA ([swissprot:P94548]), a hypothetical protein expressed by B. subtilis.
Pfam PF01335: Death effector domain (domain)
The death effector domain (DED) is a homotypic protein interaction module composed of a bundle of six Î±-helices. DED is related in sequence and structure to the death domain (DD, see IPR000488) and the caspase recruitment domain (CARD, see IPR001315), which work in similar pathways and show similar interaction properties . The dimerisation of DED domains is mediated primarily by electrostatic interactions. DED domains can be found in isolation, or in combination with other domains. Domains associated with DED include: caspase catalytic domains (in caspase-8, -10), death domains (in FADD), nuclear localisation sequences (in DEDD), transmembrane domains (in Bap31 and Bar), nucleotide-binding domains (in Dap3), coiled-coil domains (in Hip and Hippi), SAM domains (in Bar), and E2-binding RING domains (in Bar) .

Several DED-containing proteins are involved in the regulation of apoptosis through their interactions with DED-containing caspases, such as caspases 8 and 10 in humans, both of which contain tandem pairs of DEDs. There are many DED-containing modulators of apoptosis, which can either enhance or inhibit caspase activation .
Wikipedia: The death-effector domain (DED) is a protein interaction domain found only in eukaryotes that regulates a variety of cellular signalling pathways. The DED domain is found in inactive procaspases and proteins that regulate caspase activation in the apoptosis cascade such as FAS-associating death domain-containing protein (FADD). FADD recruits procaspase 8 and procaspase 10 into a death induced signaling complex (DISC). This recruitment is mediated by a homotypic interaction between the procaspase DED and a second DED that is death effector domain in an adaptor protein that is directly associated with activated TNF receptors. Complex formation allows proteolytic activation of procaspase into the active caspase form which results in the initiation of apoptosis. Structurally the DED domain are a subclass of protein motif known as the death fold and contains 6 alpha helices, that closely resemble the structure of the Death domain (DD).
Pfam PF09928: Predicted small integral membrane protein (DUF2160) (family)
The members of this family of hypothetical prokaryotic proteins have no known function. It is thought that they are transmembrane proteins, but their function has not been inferred yet.
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 PF07538: Clostridial hydrophobic W (repeat)
A novel extracellular macromolecular system has been proposed based on the proteins containing ChW repeats. ChW stands for Clostridial hydrophobic with conserved W (tryptophan). This repeat was originally described in Clostridium acetobutylicum but is also found in other Gram-positive bacteria including Enterococcus faecalis, Streptococcus agalactiae and Streptomyces coelicolor.
Pfam PF23188: Piezo1-like, transmembrane helical unit (domain)
This domain is found in Piezo-type mechanosensitive ion channel component 1 from mouse (Piezo1), a pore-forming subunit of a mechanosensitive non-specific cation channel that plays key roles in cell adhesion, blood vessel formation and vascular structure in both development and adult physiology. Piezo1 is a membrane protein with nine repetitive units consisting of four transmembrane helices each, named transmembrane helical units (THUs) that form a highly curved blade-like structure.. This entry represents one of the THUs of Piezo1.
Pfam PF00915: Calicivirus coat protein (domain)
Rabbit hemorrhagic disease virus (RHDV) which causes a highly contagious disease of wild and domestic rabbits belongs to the family Caliciviridae. The capsid protein self assembles to form  an icosahedral capsid with a T=3 symmetry. It is about 38nm in  diameter and consists of 180 capsid proteins. The capsid  encapsulates the genomic RNA and VP2 proteins and attaches the  virion to target cells by binding histo-blood group antigens present  on gastroduodenal epithelial cells. The Shell domain (S domain)  contains elements essential for the formation of the icosahedron.  The Protruding domain (P domain) is divided into sub-domains P1 and  P2. An hypervariable region in P2 is thought to play an important  role in receptor binding and immune reactivity.
Pfam PF08806: Sep15/SelM redox domain (domain)
Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif.  This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum. Structurally it resembles the thioredoxin-fold.
Wikipedia: 15 kDa selenoprotein is a protein that in humans is encoded by the SEP15 gene. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.
Pfam PF02765: Telomeric single stranded DNA binding POT1/CDC13 (domain)
This domain binds single stranded telomeric DNA and adopts an OB fold.  It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping.  POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms.
Pfam PF06989: BAALC N-terminus (family)
This family represents the N-terminal region of the mammalian BAALC proteins.     BAALC (brain and acute leukaemia, cytoplasmic), that is highly conserved among mammals but evidently absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms.  Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions.
Pfam PF14806: Coatomer beta subunit appendage platform (domain)
This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). It is a platform domain on the appendage that carries a highly conserved tryptophan.
Pfam PF02124: Marek's disease glycoprotein A (domain)
This is the Ig-like domain found from Envelope glycoprotein C and glycoprotein A (GA) from Herpesvirus. GA is thought to play an immunoevasive role in the pathogenesis of Marek's disease. It is a candidate for causing the early-stage immunosuppression that occurs after MDHV infection.
Pfam PF13166: AAA domain (domain)
This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.
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 PF06923: Glucitol operon activator protein (GutM) (family)
This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes.
Pfam PF13419: Haloacid dehalogenase-like hydrolase (family)
The haloacid dehalogenase (HAD) superfamily includes a diverse range of enzymes that use an asp carboxylate as a nucleophile .
Pfam PF11504: Colicin Ia (family)
Colicins are toxic molecules secreted to kill other bacteria in times of stress. Colicin Ia kills susceptible E.coli cells by binding to the colicin I receptor leading to the formation of a voltage-dependant ion channel. The protein can be divided into three domains, a translocation domain, a receptor binding domain and a channel forming domain.
Pfam PF20698: PIN domain associated with the TPR-GreAB-C-PIN system (domain)
This is a divergent PIN domain present in the TPR-GreAB-C-PIN type conflict system. These proteins have a constant module comprising of TPR-repeats, the GreA/B-C-terminal domain and the PIN domain. The N-terminal domain is variable and usually contains effector domains or EADs. The PIN domain is predicted to cleave emerging nascent transcripts.
Pfam PF17209: Hfq protein (domain)
This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria . It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA . It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage . Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor . The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the Î²4 strand in one molecule dimerises with the Î²5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure .

The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands .
Wikipedia: The Hfq protein encoded by the hfq gene was discovered in 1968 as an Escherichia coli host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles that are usually mediated by interacting with Hfq binding sRNA.
Pfam PF02912: Aminoacyl tRNA synthetase class II, N-terminal domain (domain)
Phenylalanine-tRNA ligase (also known as phenylalanyl-tRNA synthetase) from Thermus thermophilus has an Î±2/Î²2 type quaternary structure and is one of the most complicated members of the ligase family. Identification of phenylalanine-tRNA ligase a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other ligases . This is the N-terminal domain of phenylalanine-tRNA ligase.
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction . These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel Î²-sheet fold flanked by Î±-helices , and are mostly dimeric or multimeric, containing at least three conserved regions . However, tRNA binding involves an Î±-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c .
Pfam PF05651: Putative sugar diacid recognition (family)
This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. [swissprot:P36047]). An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region.
Pfam PF17110: Subunit 11 of the general transcription factor TFIIH (family)
TFB6 is a family of fungal proteins that form the 11th subunit of the general transcription factor TFIIH. TFB6 facilitates the dissociation of Ssl2 helicase from TFIIH after the initiation of transcription.
Pfam PF01427: D-ala-D-ala dipeptidase (family)
This group of metallopeptidases belong to MEROPS peptidase family M15 (clan MD), subfamily M15D (vanX D-Ala-D-Ala dipeptidase).

The D-alanyl-D-alanine dipeptidase enzyme from Enterococcus faecalis is also known as the vancomycin resistance protein VanX, and hydrolyses D-ala-D-ala. It has a 250-fold differential in catalytic efficiency for hydrolysis of D-ala-D-ala versus D-ala-D-lactate. The latter therefore remains intact for subsequent incorporation into peptidoglycan precursors that terminate in the dipeptide D-ala-D-lactate rather than the dipeptide D-ala-D-ala, thereby preventing vancomycin from binding. The enzyme requires a metal cofactor, and is induced by vancomycin through regulation by VanS and VanR.