SII-SWORD/CoKE huggingface dataset:
Pfam PF00203: Ribosomal protein S19 (domain)
This entry represents the small ribosomal subunit protein uS19 family.
The small subunit ribosomal proteins can be categorised as: primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S19 contains 88-144 amino acid residues. In Escherichia coli, S19 is known to form a complex with S13 that binds strongly to 16S ribosomal RNA. Experimental evidence  has revealed that S19 is moderately exposed on the ribosomal surface, and is designated a secondary rRNA binding protein. S19 belongs to a family of ribosomal proteins  that includes: eubacterial S19; algal and plant chloroplast S19; cyanelle S19; archaebacterial S19; plant mitochondrial S19; and eukaryotic S15 ('rig' protein).
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF10924: Protein of unknown function (DUF2711) (family)
Some members in this family of proteins are annotated as ywbB however currently there is no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF18909: dATP/dGTP diphosphohydrolase, N-terminal (family)
This entry represent the N-terminal region of SHab15497_00040, an Acinetobacter phage protein that catalyses the hydrolysis of dGTP into dGMP, which is needed among others for the first step of biosynthesis of dZTP (2-amino-2'-deoxyadenosine-5'- triphosphate).
Pfam PF02354: Latrophilin Cytoplasmic C-terminal region (family)
This family consists of the cytoplasmic C-terminal region in latrophilin.  Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein coupled receptors that are involved in secretion.  Latrophilin mRNA is present only in neuronal tissue.  Lactrophillin interacts with G-alpha O.
Wikipedia: Latrophilins are a group of highly conserved G-protein coupled receptors from the adhesion G protein-coupled receptor family. These receptors were originally identified based on their ability to bind to a component of black widow spider venom known as alpha-latrotoxin. This conserved family of membrane proteins has up to three homologues in chordate species, including humans.
Pfam PF10455: Bin/amphiphysin/Rvs domain for vesicular trafficking (family)
This Pfam entry includes proteins that are not matched by [pfam:PF03114].
Wikipedia: In molecular biology, BAR domains are highly conserved protein dimerisation domains that occur in many proteins involved in membrane dynamics in a cell. The BAR domain is banana-shaped and binds to membrane via its concave face. It is capable of sensing membrane curvature by binding preferentially to curved membranes. BAR domains are named after three proteins that they are found in: Bin, Amphiphysin and Rvs.
Pfam PF10939: Protein of unknown function (DUF2631) (family)
This is s bacterial family of proteins with unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05513: TraA (family)
Conjugative transfer of a bacteriocin plasmid, pPD1, of Enterococcus faecalis is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. TraA transduces the signal of cPD1 to the mating response.
Pfam PF19050: PhoD related phosphatase (domain)
This entry contains a domain that is presumed to be a phosphatase enzyme based on its similarity to [pfam:PF09423].
Pfam PF17422: Family of unknown function (DUF5410) (family)
This is a family of unknown function found in Rickettsia.
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 PF07980: SusD family (repeat)
This domain is found in bacterial cell surface proteins such SusD [swissprot:Q8A1G2] and SusD-like proteins [swissprot:A7LXT5] as as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganisms that utilize a diverse array of glycans.  Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain 15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with Bacteroides thetaiotaomicron SusD (i.e alpha-helices and TPR regions). Based on this structural similarity, functional studies suggest that, RagB binding of glycans occurs at pockets on the molecular surface that are distinct from those of SusD.
Pfam PF18580: SUN2 helix-turn-helix domain (domain)
LINC complexes are formed by coupling of KASH (Klarsicht, ANC-1, and Syne/Nesprin Homology) and SUN (Sad1 and UNC-84) proteins from the inner and outer nuclear membranes (INM and ONM, respectively). the formation of LINC complexes by KASH and SUN proteins at the nuclear envelope (NE) establishes the physical linkage between the cytoskeleton and nuclear lamina, which is instrumental for the mechanical force transmission from the cytoplasm to the nuclear interior, and is essential for cellular processes such as nuclear positioning and migration, centrosome-nucleus anchorage, and chromosome dynamics. This entry represents an HTH domain found in SUN2 that forms a three-helix bundle to lock the SUN domain in an inactive conformation acting as an inhibitory component.
Pfam PF05621: Bacterial TniB protein (domain)
This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition. This entry represents a P-loop domain.
Pfam PF16496: SWIRM-associated domain at the N-terminal (family)
Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions.  The function of the individual regions is not known.
Pfam PF23207: Prospore membrane adapter protein SPO71 PH domain (domain)
This domain is found in the yeast Prospore membrane adapter protein SPO71 and related proteins. SPO71 is involved in the recruitment of the lipid transfer protein VPS13 to the prospore membrane during sporulation. It plays an impostant role in the prospore membrane development. The domain represented by this entry has a weak sequence similarity to PH domains and it is predicted to adopt similar structure. SPO71 is predicted to contain tandem of three PH domains. This domain is the first in the tandem.
Pfam PF15661: C6orf222, uncharacterised family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 618 and 652 amino acids in length.
Pfam PF07457: Protein of unknown function (DUF1516) (family)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 120 residues 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 PF08097: Conotoxin T-superfamily (family)
This family consists of the T-superfamily of conotoxins.  Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species.
Pfam PF03379: CcmB protein (family)
CcmB is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. CcmB is required for the export of haem to the periplasm.
Pfam PF12723: Protein of unknown function (DUF3809) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Deinococci bacteria. Proteins in this family are typically between 117 and 157 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 PF24835: Family of unknown function (DUF7717) (family)
This entry represents a group of uncharacterised proteins mainly from tailed bacteriophages.
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 PF21704: DNApol eta/Rev1, HhH motif (conserved_site)
This entry represents the HhH motif from DNA polymerase eta and DNA repair protein REV1, members of the  type-Y family of DNA polymerases.
Pfam PF18547: Halobacterial output domain 2 (domain)
HalOD2 (Halobacterial output domain 2) is a protein domain that is found in haloarchaea in combination with the Response_reg [pfam:PF00072] domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems).
Pfam PF04061: ORMDL family (family)
Evidence form suggests that ORMDLs are involved in protein folding in the ER.  Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1).
Pfam PF01508: Paramecium surface antigen domain (domain)
This domain is a cysteine rich extracellular repeat found in surface antigens of Paramecium.  The domain contains 8 cysteine residues.
Pfam PF16066: Domain of unknown function (DUF4808) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 106 and 135 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 PF16295: Tetracyclin repressor-like, C-terminal domain (domain)
This domain belongs to the TetR family of transcription factors. It is found in FadR, a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. Structural and functional analysis indicate that B. subtilis FadR belongs to the TetR family of transcription factors, where it represses five fad operons involved in the fatty acid beta-oxidation cycle. FadR directly binds to upstream regions of the fadR, fadH, fadN, lcfB and fadF genes, and is deactivated by binding with long-chain acyl-CoAs in a similar manner as E. coli FadR.
Pfam PF13532: 2OG-Fe(II) oxygenase superfamily (domain)
This superfamily brings together catalytic domains found in Alpha-ketoglutarate-dependent dioxygenase AlkB-like DNA/RNA demethylases.

AlkB is a DNA repair enzyme that removes methyl adducts and some larger alkylation lesions from endocyclic positions on purine and pyrimidine bases. It is a dioxygenase that requires molecular oxygen, alpha-ketoglutarate and iron .

The catalytic core of AlkB is homologous to other Fe-2OG dioxygenases . Two discrete global conformations have been observed for AlkB, differing in accessibility of a putative oxygen-diffusion tunnel .
Pfam PF16039: Domain of unknown function (DUF4791) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 189 and 203 amino acids in length. There are two conserved sequence motifs: PLPL and LGN. There is a single completely conserved residue N 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 PF12087: Protein of unknown function (DUF3564) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE 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 PF17288: Terminase RNAseH like domain (domain)
Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit . This entry represents the C-terminal domain of the large subunit.

Proteins containing this domain include gp2 from Bacillus phage SPP1 .
Pfam PF23375: Family of unknown function (DUF7094) (domain)
This domain is found in a group of proteins from halobacteria. It shows several Y and Q conserved residues and is predicted to show an antiparallel beta-sheet and an alpha-helix.
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 PF11353: Protein of unknown function (DUF3153) (family)
This family of proteins with unknown function appear to be restricted to Cyanobacteria. 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 PF14805: Tetrahydrodipicolinate N-succinyltransferase N-terminal (domain)
This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase.
Pfam PF03940: Male specific sperm protein (family)
This family of drosophila proteins are typified by the repetitive motif C-G-P.
Pfam PF13142: Domain of unknown function (DUF3960) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 72 and 89 amino acids in length.
Pfam PF04286: Protein of unknown function (DUF445) (family)
Predicted to be a membrane protein.
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 PF06271: RDD family (domain)
This family of proteins contain three highly conserved amino acids: one arginine and two aspartates, hence the name of RDD family.  This region contains two predicted transmembrane regions. The arginine occurs at the N terminus of the first helix and the first aspartate occurs in the middle of this helix. The molecular function of this region is unknown. However this region may be involved in transport of an as yet unknown set of ligands (Bateman A pers. obs.).
Pfam PF07146: Protein of unknown function (DUF1389) (family)
This family consists of several hypothetical bacterial proteins which seem to be specific to Chlamydia pneumoniae. Members of this family are typically around 400 residues in length. The function of this family is unknown.
Pfam PF05511: Mitochondrial ATP synthase coupling factor 6 (family)
Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments.
Wikipedia: ATP synthase-coupling factor 6, mitochondrial is an enzyme subunit that in humans is encoded by the ATP5PF gene.
Pfam PF21172: Periplasmic copper-binding protein CueP (family)
This protein family includes the periplasmic copper-binding protein CueP from Salmonella enterica and similar bacterial sequences. CueP is related to copper-resistance, copper-storage and is as an essential factor in the transfer of copper ions, playing a role in the suppression of oxidative stress. CueP, which adopts a dimeric assembly, consists of two domains: an N-terminal domain with two alpha-helices and three beta-strands organized into a beta-sheet and a larger C-terminal domain that comprises a four-stranded beta-sheet and a two-stranded beta-sheet that face each other.
Pfam PF03650: Mitochondrial pyruvate carriers (repeat)
This family includes mitochondrial pyruvate carrier proteins, such as Mpc 1/2 and their homologues. They mediate the uptake of pyruvate into mitochondria. In humans, Mpc1 and Mpc2 associate to form an ~150-kilodalton complex in the inner mitochondrial membrane. MPC1 contains two predicted transmembrane regions. MPC2 contains three predicted transmembrane regions. Several studies have demonstrated MPC involvement in the control of cell fate in cancer and gluconeogenesis in models of type 2 diabetes.