SII-SWORD/CoKE huggingface dataset:
Pfam PF10221: Cell cycle and development regulator Mat89Bb (family)
This is entry represents the cell cycle regulator Mat89b (also known as protein asunder), which plays an evolutionarily conserved role as a crucial regulator of both cell cycle and development. It is a component of INT (Integrator) complex, being involved in the 3'-end processing of the U7 snRNA, and also the spliceosomal snRNAs U1 and U5. Mat89Bb is also required for the correct dynein-dynactin perinuclear localization. Mat89Bb is a PNG kinase substrate, that is essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells.
Pfam PF14091: Domain of unknown function (DUF4269) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved KTE 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 PF14902: Domain of unknown function (DUF4494) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 172 amino acids in length. There are two conserved sequence motifs: VDA and EAE. There is a single completely conserved residue E that may be functionally important.
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 PF01920: Prefoldin subunit (coiled_coil)
This family includes prefoldin subunits that are not detected by [pfam:PF02996].
Pfam PF12147: Putative methyltransferase (family)
This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with [pfam:PF00561]. The family shows homology to methyltransferases.
Pfam PF09620: CRISPR-associated protein (Cas_csx3) (family)
This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3).
Pfam PF25150: Trm732, TPR repeats (repeat)
This region of predicted of tetratricopeptide-like repeats is found in tRNA (32-2'-O)-methyltransferase regulator trm732 from Schizosaccharomyces pombe, which together with methyltransferase trm7, methylates the 2'-O-ribose of nucleotides at position 32 of the anticodon loop of substrate tRNAs. This entry is often found associated with [pfam:PF10350].
Pfam PF01712: Deoxynucleoside kinase (domain)
This family consists of various deoxynucleoside kinases cytidine [ec:2.7.1.74], guanosine [ec:2.7.1.113], adenosine [ec:2.7.1.76]  and thymidine kinase [ec:2.7.1.21] (which also phosphorylates deoxyuridine  and deoxycytosine.) These enzymes catalyse the production of  deoxynucleotide 5'-monophosphate from a deoxynucleoside.  Using ATP and yielding ADP in the process.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF02559: CarD-like/TRCF RID domain (domain)
This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription.
Pfam PF19484: Family of unknown function (DUF6020) (family)
This family of integral membrane proteins is functionally uncharacterised. This family of proteins is found in Firmicutes and Actinobacteria. Proteins in this family are typically between 587 and 710 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 PF20929: Programmed cell death protein 10, dimerisation domain (domain)
Programmed cell death 10 protein (PDCD10/CCM3) is part of the CCM complex and is required for neuronal migration. Outside of this complex, it is crucial in vascularization and in angiogenesis as it functions in vessel permeability and stability. This protein plays an essential role in early embryonic angiogenesis and cardiovascular development. PDCD10/CCM3 interacts with a variety of proteins, including paxillin, membrane receptor vascular epidermal growth factor receptor 2, CCM complex component CCM2 and germinal center kinase III proteins (GCKIII). It consists of a N-terminal dimerisation domain and a C-terminal focal adhesion targeting-homology (FAT-H) domain ([pfam:PF06840]). This entry represents the N-terminal dimerisation domain, consisting of four alpha-helices. This domain is also found at the C-terminal of GCKIIIs (STK24/MST3, STK25, STK26/MST4), which adopts a closely related fold. GCKIIIs are involved in the regulation of apoptosis, cell proliferation, polarity, migration, and cytoskeleton remodelling. This domain mediates homo and heterodimerisation. PDCD10/CCM3 forms a heterodimer with GCKIIIs analogous to CCM3 homodimer.
Pfam PF07253: Gypsy protein (family)
This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species.  Gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers. This family contains many members with full-length matches; however, it also includes a number of very short sequences and short matches of sequences with other unrelated domains on them, which cannot be excluded. These matches may represent remnants of once-functional genes.
Pfam PF04075: F420H(2)-dependent quinone reductase (family)
This family of proteins is found in the genera Mycobacterium and Streptomyces. Member protein Rv3547 has been characterised as a deazaflavin-dependent nitroreductase. Rv1558 is an F420H(2)-dependent quinone reductase involved in oxidative stress protection.
Pfam PF25097: Cnot1 ARM repeat (repeat)
This ARM domain is found toward the C terminus of  human CCR4-NOT transcription complex subunit 1 (CNOT1) and similar sequences from animals. CNOT1 is a scaffolding component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation.
Pfam PF23307: Kinase D-interacting substrate of 220 kDa-like, SAM domain-like (domain)
This is the predicted Sterile alpha motif (SAM) domain of human Kinase D-interacting substrate of 220 kDa (KIDINS220) and similar animal proteins. KIDINS220 promotes a prolonged MAP -kinase signalling by neurotrophins and is involved in nerve growth factor (NGF)-induced recruitment of RAPGEF2 to late endosomes and neurite outgrowth. This protein is rich in ankyrin repeats, has a KAP family P-loop domain ([pfam:PF07693]) and a SAM domain (this entry) with a predicted all alpha-helical structure.
Pfam PF05261: TraM protein, DNA-binding (family)
The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational  analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be  required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM  protein creates a physical link between the relaxosomal nucleoprotein  complex and the membrane-bound DNA transfer apparatus.
Pfam PF02987: Late embryogenesis abundant protein (repeat)
Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos  and under conditions of dehydration stress.  The function of  these proteins is unknown.
Pfam PF20129: Family of unknown function (DUF6519) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 1105 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 PF17414: MatP C-terminal ribbon-helix-helix domain (domain)
This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the C-terminal ribbon-helix-helix domain.
Pfam PF10179: Neuron-derived neurotrophic factor, first Fn(III) domain (domain)
This domain is found towards the N-terminal of Neuron-derived neurotrophic factor (NDNF) which contains the first fibronectin type III domain and one of the predicted N-linked glycosylation sites. NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization.
Pfam PF02925: Bacteriophage scaffolding protein D (domain)
The assembly of a macromolecular structure proceeds via a specific pathway of ordered events and occurs by changing of protein conformations as they join the assembly. The assembly process is aided by scaffolding proteins, which act as chaperones. In bacteriophages, scaffolding proteins B and D are responsible for procapsid formation. Copies of protein D (240) form the external scaffold, while 60 copies of protein B form the internal scaffold .
Wikipedia: In molecular biology, bacteriophage scaffolding proteins are proteins involved in bacteriophage assembly.
Pfam PF15838: LLLL and CFNLAS motif-containing protein 1 (family)
LLCFC1 (also known as SOF1) and its homologues can be found in eukaryotes. They have two conserved sequence motifs: LLLL and CFNLAS. LLCFC1 is a sperm protein required for sperm-oocyte fusion in mice.
Pfam PF04219: Protein of unknown function, DUF (family)
This is a family of uncharacterised 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 PF12978: Domain of Unknown Function with PDB structure (DUF3862) (family)
PDB:3D4E shared structural similarity to beta-lactamase inhibitory proteins (BLIP) which already include 1XXM, 1S0W, 1JTG, 2G2U, 2G2W, 2B5R, and 3due. All of structures are involved in beta-lactamase inhibitor complex.  (REF http://www.topsan.org/Proteins/JCSG/3d4e)
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 PF16912: Glucose dehydrogenase C-terminus (family)
This entry represents the C-terminal domain of glucose dehydrogenase.
Glucose 1 dehydrogenase (1.1.1.47) belongs to the medium-chain alcohol dehydrogenase superfamily and requires zinc for catalysis . It catalyses the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate via gluconolactone. It is involved in the degradation of glucose through a modified version of the Entner-Doudoroff pathway in Halobacteria  and a non-phosphorylative variant of the Entner-Doudoroff pathway in other organisms.

This entry includes a group of glucose 1 dehydrogenases from archaea.
Pfam PF22069: Androglobin, domain IV (domain)
Androglobin is a protein with a key role in spermatogenesis. It is required for sperm flagellum formation and maturation of elongating spermatids, both essential for male fertility. Androglobin contains an N-terminal cysteine protease domain that lacks the catalytic cysteine, a tandem of three beta-sandwich domains (domains II,|V,V) and a circularly permuted globin-like domain (domain III) that is inserted between domain II and |V. This entry represents domain IV. This domain is predicted to adopt a jelly-roll topology that is observed in galactose-binding domains. It has a significant sequence similarity to domains found in ciliary protein FAP42 and to domain III in calpains.
Pfam PF03744: 6-carboxyhexanoate--CoA ligase (family)
This family contains the enzyme 6-carboxyhexanoate--CoA ligase [ec:6.2.1.14]. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA. The enzyme requires magnesium as a cofactor and forms a homodimer.
Pfam PF21577: PG_0320-like, C-terminal domain (domain)
This domain is found at the C-terminal end of [swissprot:Q7MX90] from Porphyromonas gingivalis (PG_0320) and similar bacterial sequences. This domain is usually found associated with [pfam:PF07610]. It is functionally uncharacterised.
Pfam PF19953: Effector Associated Constant Component 1 (family)
Effector Associated Constant Component 1 (EACC1) is a component of a membrane-associated two-gene conflict system, a class of NTP-dependent biological conflict systems. It is found either a standalone domain or fused to EAD1 or EAD2. It is comprised of a single conserved TM helix with short, N- and C-terminal extensions. Predicted to insert into the membrane and protrude beyond both the outer and inner layers of the bilayer.
Pfam PF10643: Photosystem P840 reaction-centre cytochrome c-551 (family)
A photosynthetic reaction-centre complex is found in certain green sulphur bacteria such as Chlorobium vibrioforme which are anaerobic photo-auto-trophic organisms. The primary electron donor is P840, a probable B-Chl a dimer, and the primary electron acceptor is a B-Chl monomer. Also on the donor side c-type cytochromes are known to function as electron donors to photo-oxidised P840. This family is thus the secondary endogenous donor of the photosynthetic reaction-centre complex and is a membrane-bound cytochrome containing a single haem group.
Pfam PF04628: Sedlin, N-terminal conserved region (family)
Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400). This family represents an N-terminal conserved region.
Pfam PF20410: X-Tfes, XVIPCD (domain)
This conserved domain is found in Xanthomonas VirD4 interacting proteins (XVIPs) and other type IV secretion system (T4SS) specialised in translocating effector proteins (toxic effector proteins, X-Tfes) into competing gram-negative species, leading to target cell death. This domain interacts with the central all-alpha domain of VirD4. Its structure shows two well ordered N-terminal antiparallel alpha-helices that pack against a carboxyl-terminal three-stranded antiparallel beta sheet.
Pfam PF05113: Protein of unknown function (DUF693) (family)
This family consists of several uncharacterised proteins from Borrelia  burgdorferi (Lyme disease spirochete).
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 PF21709: Emaravirus ABC_C protein (family)
This family corresponds to the ABC proteins of clade C of emaraviruses (plant-infecting bunyaviruses). They are involved in pathogenicity, and may act as silencing suppressors in some species. These proteins may adopt an all-alpha topology.
Pfam PF12516: Protein of unknown function (DUF3719) (family)
This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved HLR sequence motif. There are two completely conserved residues (W and H) that may be functionally important.
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 PF12425: Protein of unknown function (DUF3673) (family)
This domain family is found in eukaryotes, and is approximately 50 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 PF16904: Phosphoribosylformylglycinamidine synthase II C-terminus (domain)
This is the C-terminal domain of phosphoribosylformylglycinamidine synthase II in Thermatoga and related species.
Pfam PF22258: Family of unknown function (DUF6949) (family)
This is a family of uncharacterised bacterial proteins. These proteins are enriched with hydrophobic residues and it is quite likely to be associated with the membrane.
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 PF14767: Replication protein A interacting middle (family)
This family of proteins represents the middle domain of replication protein A (RPA) interacting protein.  RPA interacting protein is involved in the import of RPA into the nucleus. This domain is responsible for interaction with RPA [].
Pfam PF13782: Stage V sporulation protein AB (family)
This family of proteins is required for sporulation.
Pfam PF18952: Family of unknown function (DUF5696) (family)
This is a family of unknown function with some overlap with clan family members of CL0058.
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 PF10444: Nbl1 / Borealin N terminal (family)
Nbl1 is a subunit of the conserved CPC, the chromosomal passenger complex, which regulates mitotic chromosome segregation.  In Fungi and Animalia, this complex consists of the kinase Aurora B/AIR-2/Ipl1p, INCENP/ICP-1/Sli15p, and Survivin/BIR-1/Bir1p.  In Animalia, a fourth subunit (Borealin/Dasra/CSC-1) is required for targeting CPC to centromeres and central spindles.  Nbl1 has been shown in budding yeast to be essential for viability, and for CPC localisation, stability, integrity, and function.  The N terminus of Borealin is homologous to Nbl1.  This family contains both Nbl1, and the N terminal region of Borealin.
Pfam PF10037: Mitochondrial 28S ribosomal protein S27 (repeat)
Members of this family of small ribosomal proteins possess one of three conserved blocks of sequence found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins, leaving open the possibility that MRP-S27 might be a functional partner of GTP-binding ribosomal proteins.
Pfam PF17303: Family of unknown function (DUF5352) (family)
This is a family of unknown function found mostly in Eukaryota.
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.