SII-SWORD/CoKE huggingface dataset:
Pfam PF02225: PA domain (domain)
The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor [swissprot:O22925] and members of the RZF family [swissprot:O43567]. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors.
Wikipedia: The PA clan is the largest group of proteases with common ancestry as identified by structural homology. Members have a chymotrypsin-like fold and similar proteolysis mechanisms but can have identity of &lt;10%. The clan contains both cysteine and serine proteases. PA clan proteases can be found in plants, animals, fungi, eubacteria, archaea and viruses.
Pfam PF08447: PAS fold (domain)
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF15120: Sperm acrosome-associated protein 9 (family)
This family of proteins found in eukaryotes represents sperm acrosome-associated protein 9 (SPACA9, previously known as C9orf9 or MAST). Sperm acrosome-associated protein 9 has been suggested to form a complex with calcium-binding proteins calreticulin and caldendrin localised to the acrosome. Despite this, no known protein  interaction motifs have been identified in MAST/SPACA9.
Pfam PF24410: wHTH-Hsp90_Na associated (domain)
This is a wHTH domain commonly observed in tandem repeats with 5 or more modules and located at the C-terminal of HSP90 proteins engaged in antiviral immunity. These proteins often additionally feature an inactive HD-CE domain ([pfam:PF24401]) at the N-terminal. Structural modelling suggests that the wHTH repeats form a ring-shaped module for recognising nucleic acids.
Pfam PF04489: Protein of unknown function (DUF570) (family)
Protein of unknown function, found in herpesvirus and cytomegalovirus.
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 PF23047: Domain of unknown function (DUF7038) (domain)
This entry represents a domain found in a family of uncharacterized proteins in nematodes. In some proteins, this domain appears internally duplicated.
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 PF15256: SPATIAL (family)
SPATIAL (stromal protein associated with thymii and lymph node) proteins may be involved in spermatid differentiation.
Pfam PF18406: Ferredoxin-like domain in Api92-like protein (domain)
This domain has a ferredoxin like fold.  It is often found to the C terminus of [pfam:PF06924].
Pfam PF07869: Protein of unknown function (DUF1656) (family)
This entry represents a putative component of efflux pumps that comprise MFP and FUSC proteins. Several members are in an operon with and have similar mutants phenotypes as an RND efflux pump and a fusaric acid resistance-like protein. This system is involved in transporting diverse substrates including 4-hydroxybenzoate and octanoate.
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 PF22844: CATSPERE beta-propeller domain (repeat)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. This entry includes CATSPERE, the auxiliary subunit epsilon of the CatSper complex. This is a multi-domain protein which has a similar domain organisation as the other auxiliary subunits, beta, gamma and delta. The epsilon subunit has an additional N-terminal domain (NTD2) which is followed by a beta-propeller domain, represented in this entry.
Pfam PF24090: Family of unknown function (DUF7375) (family)
This family represents a small family of uncharacterised proteins from pseudomonas phage. These proteins range in length from 114 and 130 amino acids. Structure prediction suggests the proteins adopt an open set of alpha helical segments as a monomer. However, homodimer prediction shows a confident interaction (iPTM 0.79). The dimer shows distinct charge distribution with a linear positively charged surface.
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 PF04528: Adenovirus early E4 34 kDa protein conserved region (family)
Conserved region found in the Adenovirus E4 34 kDa protein.
Pfam PF02783: Methyl-coenzyme M reductase beta subunit, N-terminal domain (domain)
Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha ([pfam:PF02249]), 2 beta (this family), and 2 gamma ([pfam:PF02240]) subunits with two identical nickel porphinoid active sites. The N-terminal domain has an alpha/beta ferredoxin-like fold.
Pfam PF02594: Uncharacterised ACR, YggU family COG1872 (domain)
This entry describes a group of proteins of unknown function found in all cellular organisms. Structures for two of these proteins, YggU from Escherichia coli and MTH637 from the archaea Methanobacterium thermoautotrophicum, have been determined; they have a core 2-layer Î±/Î² structure consisting of Î²(2)-loop-Î±-Î²(2)-Î± structural elements .
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 PF02239: Cytochrome D1 heme domain (repeat)
Cytochrome cd1 (nitrite reductase) catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side  chains ligate the d1 heme iron of the active site in the oxidised  state.
Pfam PF16720: Albumin I chain a (domain)
The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43 kDa receptor. This domain represents the a chain.
Pfam PF09951: Immunity protein Imm33 domain (domain)
This domain has been identified as a putative family of immunity proteins found in bacterial toxin/antitoxin systems. This domain was previously called DUF2185.
Pfam PF11169: Protein of unknown function (DUF2956) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14699: N-terminal domain from the human glycogen debranching enzyme (family)
This domain is found on the very N-terminal of eukaryotic variants of the glycogen debranching enzyme (GDE), where it is immediately followed by the aldolase-like domain. The eukaryotic GDE 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 enzyme.  The domain is involved in the glucosyltransferase activity, probably as a substrate-binding module (by analogy with other glucosyltransferases).
Pfam PF08713: DNA alkylation repair enzyme (repeat)
Proteins in this family are predicted to be DNA alkylation repair enzymes.  The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure.
Pfam PF12263: Protein of unknown function (DUF3611) (family)
This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) 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 PF10792: Protein of unknown function (DUF2605) (family)
This family is conserved in Cyanobacteria. The function is not known.
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 PF00683: TB domain (family)
This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin.
Pfam PF13181: Tetratricopeptide repeat (repeat)
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins . It mediates protein-protein interactions and the assembly of multiprotein complexes . The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel Î±-helices . The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B.
Wikipedia: The tetratricopeptide repeat (TPR) is a structural motif. It consists of a degenerate 34 amino acid tandem repeat identified in a wide variety of proteins. It is found in tandem arrays of 3–16 motifs, which form scaffolds to mediate protein–protein interactions and often the assembly of multiprotein complexes. These alpha-helix pair repeats usually fold together to produce a single, linear solenoid domain called a TPR domain. Proteins with such domains include the anaphase-promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67-phox, hsp90-binding immunophilins, transcription factors, the protein kinase R (PKR), the major receptor for peroxisomal matrix protein import PEX5, protein arginine methyltransferase 9 (PRMT9), and mitochondrial import proteins.
Pfam PF16082: Bacteriophage holin family, superfamily II-like (family)
Phage_holin_2_4 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion.
Pfam PF14661: HAUS augmin-like complex subunit 6 N-terminus (family)
This family includes the N-terminus of HAUS augmin-like complex subunit 6. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis.
Pfam PF16765: Pesticin immunity protein (family)
Pim is the immunity protein produced by Yersinia pestis and other Gammaproteobacteria to protect themselves against the bacteriostatic activity of the toxin pesticin, [pfam:PF16754].
Pfam PF19674: Family of unknown function (DUF6177) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000360) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the GE81112 biosynthetic gene cluster from  Streptomyces sp. L-49973 and 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 PF03142: Chitin synthase (family)
Members of this family are fungal chitin synthase [ec:2.4.1.16] enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N)  UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).
Wikipedia: In enzymology, a chitin synthase is an enzyme that catalyzes the chemical reactionUDP-N-acetyl-D-glucosamine + [1,4-(N-acetyl-beta-D-glucosaminyl)]n  UDP + [1,4-(N-acetyl-beta-D-glucosaminyl)]n+1
Pfam PF23110: KCTD8/12/16 H1 domain (domain)
This entry represents the H1 domain found in the Potassium channel tetramerization domain-containing protein 8/12/16 (KCTD8/12/16), which consists of a five-stranded antiparallel beta-sheet interrupted by two alpha-helices, according to the structure described in. The H1 domain found at the C-terminal of these proteins, engages in interactions with G-protein beta-gamma subunits and has been described to be responsible for desensitization in KCTD12.
Pfam PF18087: Rubisco Assembly chaperone C-terminal domain (domain)
This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1).  Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate ribulose-1,5-bisphosphate. The beta domains primary function is dimerization, which is critical for Raf1 to achieve the necessary avidity for complex formation with RbcL (the large complex sub-unbit of Rubsico) assembly intermediates. The beta domain is also involved, to a small extent, in binding to RbcL with use of the lustiness near the beta domain's conserved top surface.
Pfam PF16131: Torus domain (domain)
This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger.
Pfam PF15367: Calcium-binding and spermatid-specific protein 1 (family)
CABS1 is a family of proteins found in eukaryotes. It is also known as NYD-SP26. It binds calcium and is specifically expressed in the elongate spermatids and then localised into the principal piece of flagella of matured spermatozoa.
Pfam PF03501: Plectin/S10 domain (domain)
This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.
Pfam PF24456: RETREG1-3/ARL6IP-like, N-terminal reticulon-homology domain (domain)
This entry represents the N-terminal reticulon-homology domain (RHD) of Reticulophagy regulator 1-3 (RETREG1-3), ARL-6 -interacting protein 1 (ARL6IP) and similar animal sequences. These proteins are regulators involved in endoplasmic reticulum tubulation that have been associated with diverse neurological diseases.
Pfam PF10035: Uncharacterized protein conserved in bacteria (DUF2179) (domain)
This domain, found in various hypothetical bacterial proteins, has 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 PF09034: TRADD, N-terminal domain (domain)
The N terminal domain of 'Tumour necrosis factor receptor type 1 associated death domain protein' (TRADD) folds into an alpha-beta sandwich with a four-stranded beta sheet and six alpha helices, each forming one layer of the structure. The domain allows docking of TRADD onto 'tumour necrosis factor receptor-associated factor' (TRAF): the binding is at the beta-sandwich domain, away from the coiled-coil domain. Binding ensures the recruitment of cIAPs to the signaling complex, which may be important for direct caspase-8 inhibition and the immediate suppression of apoptosis at the apical point of the cascade. This domain is structurally related to the small-molecule-binding ACT domain (RRM-like fold).
Pfam PF10321: Serpentine type 7TM GPCR chemoreceptor Srt (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srt is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF21024: Peptidase A3B (domain)
This entry includes the aspartic peptidase domain from the P3 polyprotein of Pararetroviruses (such as rice tungro bacilliform virus), a member of the family Caulimoviridae. P3 contains a putative movement protein (MP), the capsid protein (CP), the aspartate protease (PR) and the reverse transcriptase (RT) with a ribonuclease H activity. PR proteolytically processes P3. The sequence DSGS is believed to be the RTBV protease active site. The RTBV PR domain forms peptidase family A3 subfamily B.
Pfam PF22122: Internalin K domain D2 (domain)
This domain is found at the elbow of internalin surface proteins InlK-like, used by the bacteria to invade mammalian cells. This domain has a beta-sandwich-like fold.
Pfam PF02361: Cobalt transport protein (family)
This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons.  In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF10162: G8 domain (repeat)
This domain is found in disease proteins PKHD1 and CEMIP2 (also known as KIAA1199) and is named G8 after its 8 conserved glycines. It contains 10-beta strands and an alpha-helix. CEMIP2 is an inactive cell surface hyaluronidase that, unlike its mouse orthologue, has no catalytic hyaluronic acid-degrading activity, but acts as a regulator of hyaluronan (HA) metabolism through regulation of expression of CEMIP and HAS2.
Pfam PF14890: Intein splicing domain (family)
Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain.  This domain represents the splicing domain.
Pfam PF14798: Calcium homeostasis modulator (family)
This family of proteins control cytosolic calcium concentration. They are transmembrane proteins which may be pore-forming ion channels.
Pfam PF01619: Proline dehydrogenase (family)
The proline oxidase/dehydrogenase 1.5.99.8 is responsible for the first step in the conversion of proline to glutamate for use as a carbon and nitrogen source. The enzyme requires FAD as a cofactor, and is induced by proline.
Pfam PF14415: Domain of unknown function (DUF4424) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 310 and 361 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.