SII-SWORD/CoKE huggingface dataset:
Pfam PF05062: RICH domain (domain)
This presumed domain is about 85 residues in length and very rich in charged residues, hence the name RICH (Rich In CHarged residues). It is found in secreted proteins such as PspC [swissprot:Q9KK19], SpsA [swissprot:O33742] and IgA FC receptor [swissprot:P27951] from Streptococcus agalactiae. This domain could be involved in bacterial adherence or cell wall binding.
Pfam PF08512: Histone chaperone Rttp106-like, middle domain (domain)
This Pleckstrin homology (PH) domain is found in the middle region of Rttp106, a histone chaperone involved in heterochromatin-mediated silencing. It is also found in the final part of the middle domain of various FACT (facilitates chromatin transactions) complex subunits, such as Spt16 and either Pob3 (yeast) or the related SSRP1 (higher eukaryotes). This domain plays a role in DNA binding.
Pfam PF21059: BTB/POZ domain-containing protein 16, C-terminal domain (domain)
This is the C-terminal domain of BTB/POZ domain-containing protein 16 (BTBD16) which may adopt a beta-sandwich structure. The function of BTBD16 is not clear.
Pfam PF09122: Domain of unknown function (DUF1930) (domain)
Members of this family are found in 3-mercaptopyruvate sulfurtransferase, and have no known function. They adopt a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase.
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 PF01310: Adenovirus hexon associated protein, protein VIII (family)
See [pfam:PF01065]. This family represents Hexon.
Pfam PF12901: SUZ-C motif (domain)
The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.
Pfam PF14187: Domain of unknown function (DUF4310) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 231 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 PF10415: Fumarase C C-terminus (domain)
Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit. FumaraseC_C does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle.
Pfam PF10470: PKA-RI-RII subunit binding domain of A-kinase anchor protein (domain)
AKAP7_RIRII_bdg is the C-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP. The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction. The N-terminus, of family AKAP7_NLS, carries the nuclear localisation signal.
Pfam PF23819: Family of unknown function (DUF7189) (family)
This entry represents an uncharacterized protein of approximately 60-70 amino acids that is found in various phages, predominantly phages that infect members of the Enterobacteriaceae family such as Escherichia, Shigella, and Klebsiella.
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 PF21319: Zinc finger, FCS-type (domain)
This entry represents FCS-type zinc finger, named after the signature FCS residues associated with the third cysteine. It is present in several polycomb group proteins, and adopts a Zn-ribbon like fold. Molecular data suggest that this domain can bind RNA in non-specific manner.
Pfam PF00235: Profilin (domain)
This entry represents the profilin family, which are small eukaryotic proteins that have different functions. In plants, they are major allergens present in pollens .

The majority of the Profilin family members binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). They can also, in certain circumstances, promote actin polymerisation . However, some profilin family members, such as Profilin 4 from mammals, does not bind to actin and may have functions distinct from regulating actin dynamics . It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain . Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway .

This entry also includes Asgard archaeal profilins (Thor profilin, Loki profilin-1 and Loki profilin-2), which bind to actin and regulate the structure of the cytoskeleton. This indicates that Asgard archaea have a functional eukaryotic-like actin machinery .

Some profilins can also bind to polyphosphoinositides such as PIP2 . Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. The N-terminal region is thought to be involved in actin binding.
Wikipedia: Profilin is an actin-binding protein involved in the dynamic turnover and reconstruction of the actin cytoskeleton. It is found in most eukaryotic organisms. Profilin is important for spatially and temporally controlled growth of actin microfilaments, which is an essential process in cellular locomotion and cell shape changes. This restructuring of the actin cytoskeleton is essential for processes such as organ development, wound healing, and the hunting down of infectious intruders by cells of the immune system.
Pfam PF22503: Family of unknown function (DUF6992) (family)
This is a family of uncharacterised bacterial proteins. They are enriched with hydrophobic residues and are likely associated with the membrane. These proteins contain two conserved motifs GLDxxYxxxG and FLxxFD.
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 PF04439: Streptomycin adenylyltransferase (family)
Also known as Aminoglycoside 6- adenylyltransferase ([ec:2.7.7.-]), this protein confers resistance to aminoglycoside antibiotics.
Pfam PF08804: gp32 DNA binding protein like (domain)
gp32 is a single stranded (ss) DNA binding protein in bacteriophage T4 that is essential for DNA replication, recombination and repair. The ssDNA binding cleft of gp32 comprises regions from three structural subdomains.
Pfam PF16360: GTP-binding GTPase Middle Region (family)
This family locates between the N-terminal domain and MMR_HSR1 50S ribosome-binding GTPase of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This region is unknown for its function.
Pfam PF00545: ribonuclease (domain)
This enzyme hydrolyses RNA and oligoribonucleotides.
Wikipedia: Ribonuclease is a type of nuclease that catalyzes the degradation of RNA into smaller components. Ribonucleases can be divided into endoribonucleases and exoribonucleases, and comprise several sub-classes within the EC 2.7 and 3.1 classes of enzymes.
Pfam PF14216: Domain of unknown function (DUF4326) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) 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 PF14701: Glycogen debranching enzyme, glucanotransferase domain (domain)
This is a glucanotransferase catalytic domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDEs performs two functions: 4-alpha-D-glucanotransferase, [ec:2.4.1.25], and Amylo-alpha-1,6-glucosidase, [ec:3.2.1.33], performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzymes. The domain is a catalytic domain responsible for the glucanotransferase function. It belongs to the alpha-amylase clan and is predicted to have a structure of a 8-stranded alpha/beta barrel (TIM barrel) where strands are interrupted by long loops and additional mini-domains. In most other amylases, the catalytic domain is followed by a beta- barrel substrate binding domain, but presence of such a domain cannot be verified in the human (and other eukaryotic) GDE enzymes.
Pfam PF14098: Small, acid-soluble spore protein I (family)
This family of proteins is putatively assigned as a small, acid-soluble spore protein 1.  Proteins in this family are approximately 70 amino acids in length. There is a conserved LPGLGV sequence motif.
Pfam PF05705: Eukaryotic protein of unknown function (DUF829) (domain)
This family consists of several uncharacterised eukaryotic proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF22983: Mediator of RNA polymerase II transcription subunit 14, RM8 (repeat)
This entry represents an alpha/beta motif that is found tandemly repeated in the homologues of human Mediator of RNA polymerase II transcription subunit 14 (Med14). Med14 is a component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Med14 along with Med17 are scaffold subunits in nucleating Mediator. The major portion of Med14 exists in the Head-Shoulder module of the Mediator and consists of nine tandem repeats (RM1 to RM9), which are arranged in an atypical right-handed helix. This entry represents repeat RM8.
Pfam PF01927: Mut7-C RNAse domain (domain)
RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus.
Pfam PF07569: TUP1-like enhancer of split (repeat)
The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain [pfam:PF00400].
Pfam PF20416: U3 small nucleolar RNA-associated protein 20 domain (repeat)
This domain is found towards the C-terminal the U3 small nucleolar RNA-associated protein 20 (UTP20) from yeast and its human homologue, also known as DRIM (Down-Regulated In Metastasis). DRIM is differentially expressed in metastatic and non-metastatic human breast carcinoma cells. Proteins of this entry are involved in processing of non-coding RNA as components of the small-subunit (SSU) processome; SSU processome is involved in the biogenesis of the 18S rRNA. UTP20 is a huge alpha-solenoid that functions as a scaffold.
Pfam PF20374: Family of unknown function (DUF6669) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 161 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 PF08183: Stage V sporulation protein family (family)
This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber  of the sporangium during the process of sporulation in B. subtilis.  SpoVM forms an amphipathic alpha-helix and is recruited to the polar  septum shortly after the sporangium undergoes asymmetric division.  The function of SpoVM depends on proper subcellular localisation.
Pfam PF20519: Polycystin domain (domain)
This domain represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2, PKD2L and mucolipins. The polycystin domain display a sandwich-like shape with five beta-sheets in the tilted middle layer, three alpha-helices on one side and a large loop with two short antiparallel beta-sheets on the other.
Wikipedia: The Polycystin Cation Channel (PCC) Family consists of several transporters ranging in size from 500 to over 4000 amino acyl residues (aas) in length and exhibiting between 5 and 18 transmembrane segments (TMSs). This family is a constituent of the Voltage-Gated Ion Channel (VIC) Superfamily. These transporters generally catalyze the export of cations. A representative list of proteins belonging to the PCC family can be found in the Transporter Classification Database.
Pfam PF23801: Family of unknown function (DUF7177) (family)
The domain is around 80 amino acids in length. It occurs in phage that infect a variety of bacteria including Escherichia, Salmonella, Shigella, Klebsiella, Vibrio, Pantoea, Pectobacterium, Yersinia and Serratia.
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 PF14956: Domain of unknown function (DUF4505) (family)
This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 166 and 225 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 PF24161: Coiled-coil domain-containing protein 39 (family)
This entry represents the Coiled-coil domain-containing protein 39 (CCDC39) and related proteins. CCDC39 is an axonemal protein with coiled-coil domains required for assembly of inner dynein arms and the dynein regulatory complex, a key regulator of motor activity in cilia. Mutations in CCDC39 cause primary ciliary dyskinesia, a disorder caused by cilia and sperm dysmotility.
Pfam PF21395: Activity-regulated cytoskeleton-associated protein, capsid domain (domain)
This domain is found in Activity-regulated cytoskeleton-associated protein from humans (Arc), a master regulator of synaptic plasticity that promotes endocytosis of AMPA receptors and a postsynaptic mediator of activity-dependent synapse elimination in the developing cerebellum. This protein is associated with cognitive diseases. This Gag-like protein has the topology of a retroviral Gag protein, with a central capsid domain (this entry) with  two globular subdomains, the N-lobe and the C-lobe, consisting of four and five alpha-helices, connected by a short non-helical segment.
Pfam PF13137: Protein of unknown function (DUF3983) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 40 amino acids in length. There is a conserved AWRN sequence motif.
Pfam PF24139: Transportin-3/Importin-13 fourth TPR domain (repeat)
This entry represents the third TPR domain found in Transportin-3 (TNPO3) from animals, as well as orthologues like the uncharacterised protein YNR7 from yeast and MOS14 from plants. This entry also includes Importin-13 (IPO3) from animals. These proteins are involved in transport of target proteins into the nucleus. TNPO3 mediates the nuclear import of splicing factor serine/arginine (SR) proteins, such as RBM4, SFRS1 and SFRS2, by recognizing phosphorylated SR domains. This domain interacts with the RS region of the ASF protein for nuclear transport.
Pfam PF04770: ZF-HD protein dimerisation region (family)
This family of proteins has are plant transcription factors, and have been  named ZF-HD for zinc finger homeodomain proteins, on the basis of  similarity to proteins of known structure. This region is thought to  be involved in the formation of homo and heterodimers, and may form a zinc finger.
Pfam PF14727: PTHB1 N-terminal (repeat)
This entry represents the beta-propeller found at the N-terminal of PTHB1 protein (also known as Bardet-Biedl syndrome 9 protein, BBS9). This protein forms a part of the BBSome complex, which is required for ciliogenesis. PTHB1 is the major binding subunit of IFT38 C-terminal domain, which assists the BBSome in some of its roles. This beta-propeller, together with the N-terminal of ARL6, part of the platform of BBS2 and the beta-propeller of BBS7 defines a convex membrane-facing surface of the BBSome/ARL6 complex.
Pfam PF05846: Chordopoxvirus A15 protein (family)
This family consists of several Chordopoxvirus A15 like sequences.
Pfam PF07894: Scaffolding anchor of CK1 domain (family)
This entry represents the scaffolding anchor of CK1 domain (SACK1 domain) found in the FAM83 family, which includes FAM83A-H. This domain was formerly known as DUF1669 and it has been identified as a CK1 binding domain, which allows the correct subcellular localisation of both FAM83 proteins and the CK1 binding partners and their function. These proteins are involved in diverse biological processes, depending on their subcellular localisation and binding partners. FAM83A-H interact with the alpha and alpha-like isoforms of CK1, while FAM83A, B, E, and H also interact with the delta and epsilon isoforms of CK1. FAM83 members have  function as intermediaries in EGFR/RAS signalling. FAM83D has been reported to localise to the mitotic spindle and interact with the chromokinesin kinesin family member 22 (KIF22, also called Kid). FAM83G, also known as PAWS1 interacts with the transcription factor SMAD1 and promotes the transcription of non-canonical bone morphogenetic protein (BMP) target genes. FAM83H mutations have been associated with amelogenesis imperfecta.
Pfam PF25021: Teneurin NHL domain (repeat)
Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. This entry represents the NHL six-bladed beta-propeller domain which packs against the TTR, FN and shell domains with the bottom face and it is held in place by the FN domain which acts as a wedge to position the NHL at an angle perpendicular to the YD-shell domain. The top face of the NHL propeller contains extended loops, stabilised by five disulphide bonds, which are highly conserved among vertebrates members.
Pfam PF19593: Family of unknown function (DUF6098) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000847) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes  a member from the thienamycin biosynthetic gene cluster from  Streptomyces cattleya and it appears to be predominantly found in  actinobacteria.
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 PF11190: Protein of unknown function (DUF2976) (family)
This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed.
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 PF08003: Protein of unknown function (DUF1698) (family)
This family contains many hypothetical proteins.  It also includes two  putative methyltransferase proteins, [swissprot:Q8EEE6] and [swissprot:Q88MX8].
Pfam PF06624: Ribosome associated membrane protein RAMP4 (family)
This family consists of several ribosome associated membrane protein RAMP4 (or SERP1) sequences. Stabilisation of membrane proteins in response to stress involves the concerted action of a rescue unit in the ER membrane comprised of SERP1/RAMP4, other components of the translocon, and molecular chaperones in the ER.