SII-SWORD/CoKE huggingface dataset:
Pfam PF03812: 2-keto-3-deoxygluconate permease (family)
This family includes the characterised 2-Keto-3-Deoxygluconate transporters from Bacillus subtilis and Erwinia chrysanthemi. There are homologues of this protein found in both Gram-positive and Gram-negative bacteria.

In E. chrysanthemi, a phytopathogenic bacterium, degraded pectin products from plant cell walls are transported by 2-keto-3-deoxygluconate permease into the bacterial cell to provide a carbon and energy source . 2-keto-3-deoxygluconate permease can mediate the uptake of glucuronate with a low affinity .
Pfam PF24911: YfjL-like C-terminal domain (domain)
This entry represents the C-terminal domain of proteins related to B. subtilis YfjL protein.
Pfam PF15417: Domain of unknown function (DUF4624) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 150 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 PF01840: TCL1/MTCP1 family (family)
Two related oncogenes, TCL-1 [swissprot:P56279] and MTCP-1 [swissprot:P56278], are overexpressed in T cell prolymphocytic leukaemias as a result of chromosomal rearrangements that involve the translocation of one T cell receptor gene to either chromosome 14q32 or Xq28. This family contains two repeated motifs that form a single globular domain.
Wikipedia: In molecular biology, TCL-1/MTCP-1 is a protein domain found in proteins encoded for by two related protooncogenes, other words by genes that help promote cancer. They are, T-cell leukemia/lymphoma protein 1A TCL1A encoded by oncogene TCL-1 SWISSPROT and Protein p13 MTCP-1 encoded by MTCP-1 SWISSPROT.
Pfam PF09675: Chlamydia-phage Chp2 scaffold (Chlamy_scaf) (family)
Members of this entry are encoded by genes in chlamydia-phage such as Chp2. These viruses have around eight genes and obligately infect intracellular bacterial pathogens of the genus Chlamydia. This protein is annotated as VP3 or structural protein (as if a protein of mature viral particles), however, it is displaced from procapsids as DNA is packaged, and therefore is more correctly described as a scaffolding protein.
Pfam PF20743: Family of unknown function (DUF5580) C-terminal domain (domain)
This is a family of unknown function found in metazoa. This entry represents the C-terminal domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF01031: Dynamin central region (family)
This is the stalk region which lies between the GTPase domain, see [pfam:PF00350], and the pleckstrin  homology (PH) domain, see [pfam:PF00169]. This region dimerises in a cross-like fashion forming a dynamin dimer in which the two G-domains are oriented in opposite directions.
Wikipedia: Dynamin is a GTPase protein responsible for endocytosis in the eukaryotic cell. Dynamin is part of the "dynamin superfamily", which includes classical dynamins, dynamin-like proteins, Mx proteins, OPA1, mitofusins, and GBPs. Members of the dynamin family are principally involved in the scission of newly formed vesicles from the membrane of one cellular compartment and their targeting to, and fusion with, another compartment, both at the cell surface as well as at the Golgi apparatus. Dynamin family members also play a role in many processes including division of organelles, cytokinesis and microbial pathogen resistance.
Pfam PF21212: Dimerisation2-like domain (domain)
This domain is found at the N-terminal end of a group of bacterial methyltransferases, including SAM-dependent methyltransferase from Phocaeicola vulgatus (BVU_1015). It has a winged-helix structure and is usually found associated with [pfam:PF00891] and [pfam:PF13489].
Pfam PF20872: MalF, N-terminal region, transmembrane helices (domain)
MalF is a component of the maltose uptake system found in Proteobacteria, an ATP-binding cassette (ABC) transporter. This protein is composed of eight transmembrane (TM) helices and folds in a way its concave surface faces the similar assembly of MalG to enclose the maltose. This entry represents the first TM helices of this structure, which are located N-terminal to the large periplasmic loop (P2, [pfam:PF14785]).
Pfam PF15996: Arginine/serine-rich protein PNISR (family)
Pinin (PNN) has been identified as central in the establishment and maintenance of corneal epithelial cell-cell adhesion. Three SR-rich proteins have been identified that interact with the C terminus of PNN; one of them is this 130kDa nuclear protein, SRrp130, also known as PNISR . SRrp130 is a protein of 805 amino acid residues with multiple arginine-serine (RS) repeats but had no RNA recognition motif . Its function is unknown.
Wikipedia: Splicing factor, arginine/serine-rich 18 is a protein that in humans is encoded by the SFRS18 gene.
Pfam PF19970: vWA-MoxR associated protein middle region (VMAP-M) 9 (family)
Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities.
Pfam PF01713: Smr domain (domain)
This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 [swissprot:P23909] protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2 [swissprot:P94545]. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity. The full-length [swissprot:Q86UW6] also has the polynucleotide kinase activity.
Pfam PF21895: MTHFR, SAM-binding regulatory domain (domain)
This is the C-terminal SAM-binding regulatory domain of 5,10-methylenetetrahydrofolate reductase (MTHFR) that follows the catalytic domain and is unique to eukaryotes. This domain provides the required interface for MTHFR homo-dimerization, thus positioning the N-terminal serine-rich phosphorylation region near the SAM-binding site. The core of this domain comprises two mixed beta-sheets, one of which flanked with helices. This regulatory domain represents distinct architecture from the classical SAM-dependent methyltransferases and non-methyltransferases.
Pfam PF12950: TaqI-like C-terminal specificity domain (domain)
This domain is found at the C-terminus of the TaqI protein and is involved in DNA-binding and substrate recognition.
Pfam PF23351: BBS2 C-terminal helix bundle (domain)
This entry represents the C-terminal helix bundle domain of BBS2. BBS2 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. BBSome complex is required for ciliogenesis and the assembly and movement of intraflagellar transport proteins along the ciliary membrane.
Pfam PF00721: Virus coat protein (TMV like) (domain)
This family contains coat proteins from tobamoviruses, hordeiviruses, Tobraviruses, Furoviruses and Potyviruses.
Wikipedia: Tobamovirus is a genus of positive-strand RNA viruses in the family Virgaviridae. Many plants, including tobacco, potato, tomato, and squash, serve as natural hosts. Diseases associated with this genus include: necrotic lesions on leaves. The name Tobamovirus comes from the host and symptoms of the first virus discovered.
Pfam PF10531: SLBB domain (domain)
The soluble ligand-binding Î²-grasp domain (SLBB) contains a Î²-grasp fold. They are found in a diverse set of proteins that include the animal vitamin B12 uptake proteins; transcobalamin, intrinsic factor and the bacterial polysaccharide export proteins . Some proteins may be part of a membrane complex involved in electron transport, others are probably involved in the export of the extracellular polysaccharide colanic acid from the cell to medium.
Pfam PF00266: Aminotransferase class-V (domain)
This domain is found in amino transferases, and other enzymes including cysteine desulphurase [ec:4.4.1.-].
Wikipedia: Aminotransferase class-V  is an evolutionary conserved protein domain. This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.
Pfam PF05247: Flagellar transcriptional activator (FlhD) (family)
This family consists of several bacterial flagellar transcriptional activator (FlhD) proteins. FlhD combines with FlhC to form a regulatory complex in E. coli, this complex has been shown to be a global regulator  involved in many cellular processes as well as a flagellar transcriptional activator.
Pfam PF18085: Maltokinase N-terminal cap domain (domain)
Glycogen is a central energy storage molecule in bacteria and the metabolic pathways associated with its biosynthesis and degradation are crucial for maintaining cellular energy homeostasis. In mycobacteria, the GlgE pathway involves the combined action of trehalose synthase (TreS), maltokinase (Mak) and maltosyltransferase (GlgE). The N-terminal lobe can be divided into two subdomains: a cap N-terminal subdomain comprising the first 88 amino acid residues. This entry is for the cap N-terminal domain found in mycobacterial maltokinase (Mak), ([ec:2.7.1.175]). The N-terminal cap subdomain and the C-terminal lobe are predominantly acidic, the intermediate subdomain is enriched in positively charged residues. A structural search with only the first 88 amino acid residues of Mak, corresponding to the N-terminal cap subdomain of maltokinases, unveiled a resemblance with proteins displaying the cystatin fold and a remote similarity with the N-terminal domain of the serine/threonine protein kinase GCN2. Conservation of the cap subdomain in maltokinases (including the bifunctional TreS-Mak enzymes), in particular of the residues in the proximity of the P-loop, together with the potential flexibility of this region, are compatible with regulatory functions for this subdomain. Hence it is hypothesised that the N-terminal cap subdomain plays a central role in modulation of Mak enzymatic activity.
Pfam PF09392: Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF (family)
Type III secretion systems are essential virulence determinants for many gram-negative bacterial pathogens.  MxiH is an extracellular alpha helical needle that is required for translocation of effector proteins into host cells.  Once inside, the effector proteins subvert normal cell function to aid infection. The needle protein F, polymerises to form a shaft.
Pfam PF22561: Histidine Kinase domain observed in conflict contexts (domain)
This Histidine Kinase domain is predicted to function in signal transduction during effector activation in at least a subset of (TOTE TPR, OB, TBP, Effector) biological conflict systems.
Pfam PF07157: DNA circularisation protein N-terminus (family)
This family represents the N-terminus (approximately 100 residues) of a number of phage DNA circularisation proteins.
Pfam PF25118: Elongation factor-like GTPase 1-like domain (domain)
This domain is found in human Elongation factor-like GTPase 1 (EFL1) and similar eukaryotic proteins. EFL1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes
Pfam PF06145: Coronavirus nonstructural protein NS1 (family)
Bovine coronavirus NS1 encodes a 4.9 kDa protein.
Pfam PF09807: Elongation complex protein 6 (family)
ELP6 is a subunit of the RNA polymerase II elongator complex. The Elongator complex promotes RNA-polymerase II transcript elongation through histone acetylation in the nucleus and tRNA modification in the cytoplasm. ELP5 and ELP6 play a major role in the migration, invasion and tumorigenicity of melanoma cells, as integral subunits of Elongator
Pfam PF21042: Stu2, C-terminal segment (domain)
This is the C-terminal segment of Stu2, which binds the four-way junction of the Ndc80 complex (Ndc80c). This interaction is crucial for association of Stu2 with kinetochores, that when it is compromised, there is impairment in cell viability, biorientation defects and delay in cell cycle progression.
Pfam PF06546: Vertebrate heat shock transcription factor (family)
This family represents the C-terminal region of vertebrate heat shock transcription factors. Heat shock transcription factors regulate the expression of heat shock proteins - a set of proteins that protect the cell from damage caused by stress and aid the cell's recovery after the removal of stress. This C-terminal region is found with the N-terminal [pfam:PF00447], and may contain a three-stranded coiled-coil trimerisation domain and a CE2 regulatory region, the latter of which is  involved in sustained heat shock response.
Wikipedia: In molecular biology, heat shock factors (HSF), are the transcription factors that regulate the expression of the heat shock proteins. A typical example is the heat shock factor of Drosophila melanogaster.
Pfam PF15472: Domain of unknown function (DUF4638) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 240 and 272 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 PF04120: Low affinity iron permease (family)
Although originally identified as a low-affinity iron(II) permease , Fet4 has since been shown to import several other transition metal ions, including copper  and zinc . Copper, cobalt, and cadmium inhibit Fet4 . Fet4 is an integral protein of the plasma membrane . FET4 is not essential, not even in fet3 fet4 double mutants . Over expression of FET4 improves growth under alkaline conditions .
Pfam PF04127: DNA / pantothenate metabolism flavoprotein C-terminal (domain)
The DNA/pantothenate metabolism flavoprotein ([ec:4.1.1.36]) affects synthesis of DNA, and pantothenate metabolism. This entry represents the C-terminal domain.
Pfam PF24307: Family of unknown function (DUF7486) (repeat)
This entry represents a group of uncharacterised sequences that, according to structure predictions. they may consist on a novel repeat fold which comprise beta-hairpin-beta units organised in four and five units, forming two domains.
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 PF00602: Influenza RNA-dependent RNA polymerase subunit PB1 (family)
Two GTP binding sites exist in this protein.
Pfam PF13492: GAF domain (domain)
The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes . The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain . Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally stable states that are reversibly inter-convertible by light, the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region .

The GAF domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator required for activation of most Nif operons, which are directly involved in nitrogen fixation. NifA interacts with sigma-54 .
Wikipedia: The GAF domain is a type of protein domain that is found in a wide range of proteins from all species. The GAF domain is named after some of the proteins it is found in: cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. The first structure of a GAF domain solved by Ho and colleagues showed that this domain shared a similar fold with the PAS domain. In mammals, GAF domains are found in five members of the cyclic nucleotide phosphodiesterase superfamily: PDE2, PDE5, and PDE6 which bind cGMP to the GAF domain, PDE10 which binds cAMP, and PDE11 which binds both cGMP and cAMP.
Pfam PF21558: Bacteroidetes, Peptidase, S41 family, N-terminal domain (domain)
This domain is found at the N-terminal end of Peptidase, S41 family Bacteroides uniformis and similar proteins from bacteroidetes. It is found associated with [pfam:PF03572] and shows an alpha-beta configuration.
Pfam PF07889: Protein of unknown function (DUF1664) (coiled_coil)
The members of this family are hypothetical plant proteins of unknown function. The region  featured in this family is approximately 100  amino acids long.
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 PF01784: Duf34/NIF3 (NGG1p interacting factor 3) (family)
This family includes the DUF34/metal-binding protein/NIF3 proteins, which are widely distributed across superkingdoms. They were previously annotated as GTP cyclohydrolase 1 type 2 and, recently, through a comprehensive literature review and integrative bioinformatic analyses  it was revealed that annotations for these members were misleading  as they were based on a single set of in vitro results examining the NIF3 homolog of Helicobacter pylori. Actually, they have varied phenotypes with the unifying functional role as metal-binding proteins. This entry contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown.
Pfam PF17495: Vpr-like OrfA (family)
Family members include OrfA protein, a multifunctional accessory protein found in Feline immunodeficiency virus (FIV), a lentivirus that causes AIDS in domestic cats. Multiple potential functions have been ascribed to OrfA, including transactivation of viral protein expression, effects on virion formation and infectivity, host cell cycle arrest and downregulation of cell surface expression of the primary FIV receptor, CD134.
Pfam PF15517: TBP-interacting protein N-terminus (domain)
This is the N-terminal restriction endonuclease-like domain found in several archaeal TATA-binding protein (TBP)-interacting proteins.
Pfam PF15002: ERK and JNK pathways, inhibitor (family)
This coiled-coiled domain, CCDC134, is a secretory protein that inhibits Mitogen activated protein kinase (MAPK) pathways such as Raf-1/MEK/ERK and JNK/SAPK but not p38.  CCDC134 is widely expressed in normal adult tissues, tumour tissues and cell lines, which shows its importance in cell signal transduction pathways, transcription regulation and therefore cell survival. Additionally, CCDC134 is known to bind to a transcription adaptor, hADA2a, which forms part of the general control nonderepressible 5 (GCN5) histone acetyltransferase complex. Acetylation usually 'switches genes on' for transcription. Moreover, knocking out CCDC134 suppressed hADA2a-induced cell apoptosis activity and G1/S cell cycle arrest suggesting its importance in cell survival. This family of proteins is found in eukaryotes. Proteins in this family are typically between 188 and 257 amino acids in length. This family is a coiled-coil domain containing protein 134 (CCDC134) whereby the coiled-coiled domain is a ubiquitous motif involved in oligomerisation.
Pfam PF08880: QLQ (domain)
The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions.   This domain has thus been postulated to be involved in mediating  protein interactions.
Pfam PF17884: Domain of unknown function (DUF5591) (domain)
This is a domain of unknown function found in archaeal tRNA-guanine transglycosylase ([ec:2.4.2.48]) and in archaeosine synthase ([ec:2.6.1.97]) 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 PF06218: Nitrogen permease regulator 2 (family)
This family of regulators are involved in post-translational control  of  nitrogen permease.
Pfam PF05078: Protein of unknown function (DUF679) (family)
This family includes members such as plant proteins AtDMPs 1-10 (Arabidopsis thaliana DUF679 domain membrane proteins 1 -10). The AtDMP proteins are predicted to have four transmembrane spans, with cytosolic amino- and carboxy-termini. DMP1 is a membrane protein that may be involved in membrane fission during breakdown of the ER and the tonoplast during leaf senescence and in membrane fusion during vacuole biogenesis in roots. Several DMP proteins are expressed in senescing organs (DMP1, -3, -4) or tissues that will stall later in development (DMP1, -2, -4, -7). These expression patterns strongly suggest involvement of several DMPs in various programmed cell death processes, e.g. senescence, dehiscence and abscission. AtDMP8 and AtDMP9 however, have been shown to facilitate gamete fusion during double fertilisation in flowering plants.