SII-SWORD/CoKE huggingface dataset:
Pfam PF06602: Myotubularin-like phosphatase domain (domain)
This family represents the phosphatase domain within eukaryotic myotubularin-related proteins. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
Wikipedia: Myotubularin domain represents a region within eukaryotic myotubularin-related proteins that is sometimes found with the GRAM domain. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease.
Pfam PF22301: Aldos-2-ulose dehydratase, beta-propeller domain (repeat)
This domain is found in Aldos-2-ulose dehydratase from Phanerodontia chrysosporium (AUDH) and similar sequences from invertebrates and fungi. AUDH is a bifunctional enzyme which catalyses the dehydration of anhydrofructose into ascopyrone M, and the isomerisation of ascopyrone M into microthecin. It is organised into three domains: an N-terminal domain with a beta-propeller fold (this entry), a middle domain containing two cupin folds ([pfam:PF18637]) and a C-terminal lectin domain. This domain folds into a seven-bladed beta-propeller, where each blade is made up of a four-stranded, antiparallel beta-sheet.
Pfam PF09485: CRISPR-associated protein Cse2 (CRISPR_cse2) (family)
Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family of proteins, represented by CT1973 from Chlorobaculum tepidum, is encoded by genes found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse2.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF09428: Fungal protein of unknown function (DUF2011) (family)
This is a family of fungal proteins whose function is unknown. They might be distantly related to CUSTOS proteins from animals.
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 PF21027: Cellulose-binding protein Sde0182, C-terminal domain (domain)
This domain is found at the C-terminal end of Cellulose-binding protein Sde0182 from Saccharophagus degradans ([swissprot:Q21PD3]), which seems to have capacity to bind plant carbohydrates. This region shows a beta-sandwich fold that consists of two beta-sheets with seven beta-strands in total. It has structural similarity to a polycystic kidney domain (PKD, [pfam:PF00801]) and lacks the solvent exposed aromatic residues typically associated with an ability to bind carbohydrates. This domain is also found in other uncharacterised bacterial and fungal proteins.
Pfam PF03277: Herpesvirus UL4 family (family)
This is a family of Herpes virus UL4 proteins, which are related to Human herpesvirus 1 (HHV-1), Human herpesvirus 2 (HHV-2), Equid herpesvirus 1 (Equine herpesvirus 1, EHV-1) 58, and Human herpesvirus 3 VZV-32 56 proteins.
Pfam PF10824: Excreted virulence factor EspC, type VII ESX diderm (domain)
T7SS_ESX-EspC is a family of exported virulence proteins from largely Acinetobacteria and a few Fimicutes, Gram-positive bacteria. It is exported in conjunction with EspA as an interacting pair.ED   F8ADQ6.1/227-313; F8ADQ6.1/227-313;
Pfam PF06488: Phage tail tube protein (domain)
This is a family of Siphoviridae phage tail tube proteins including several from Lactococcus lactis.
Pfam PF18680: Plasmodium host cell traversal SPECT1 (domain)
This domain is found in SPECT1 (sporozoite microneme protein essential for cell traversal). It is formed of a four alpha-helix bundle with a 'hook'-like feature at one end. These helices in parallel or antiparallel alignment.
Pfam PF23845: Non-contractile tail sheath protein TIM barrel (domain)
This entry represents the TIM barrel domain found in the non-contractile tail sheath protein of Bacteriophage N4 (BPN4). This protein is essential for BPN4 infectivity and it is hypothesized that it mediates binding with target cell receptors. The function of this domain is unknown. This entry also includes sequences from bacteria, predominantly from Sphingobium spp.
Pfam PF02275: Linear amide C-N hydrolases, choloylglycine hydrolase family (domain)
This family includes several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides.  These include choloylglycine hydrolase (conjugated bile acid hydrolase, CBAH) [ec:3.5.1.24], penicillin acylase [ec:3.5.1.11] and acid ceramidase [ec:3.5.1.23]. This domain forms the alpha-subunit for members from vertebral species, see family NAAA-beta, [pfam:PF15508].
Wikipedia: In enzymology, a choloylglycine hydrolase (EC 3.5.1.24) is an enzyme that catalyzes the chemical reaction3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oylglycine + H2O  3alpha,7alpha,12alpha-trihydroxy-5beta-cholanate + glycine
Pfam PF19388: Family of unknown function (DUF5963) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001171) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF20445: Retrotransposon hot spot proteins N-terminal (domain)
Members of this entry are retrotransposon hot spot (RHS) proteins. They are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a conserved box 1 with a P-loop motif and a retrotransposon insertion site at the C-terminal ([pfam:PF07999]). This domain represents the N-terminal region of the conserved box 1 from RHSPs.
Pfam PF16544: Homodimerisation region of STAR domain protein (domain)
This family is the homodimerisation domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. Dimerisation is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerisation domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerisation domain, and the KH plus Qua2 is the RNA-binding region.
Pfam PF11078: Optomotor-blind protein N-terminal region (family)
This family is conserved in Drosophila spp. Optomotor-blind is one of the essential toolkit proteins for coordinating development in diverse animal taxa, and in Drosophila it plays a key role in establishing the abdominal pigmentation pattern, in development of the central nervous system and leg and wing imaginal disc-formation of Drosophila melanogaster. This is the N-terminal region of the protein and does not include the T-box-containing transcription factor that plays a part in DNA-binding.
Pfam PF02933: Cell division protein 48 (CDC48), domain 2 (domain)
This domain has a double psi-beta barrel fold and includes VCP-like  ATPase and N-ethylmaleimide sensitive fusion protein N-terminal  domains.  Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases [pfam:PF00004] is a substrate  185-residue recognition domain.
Wikipedia: In molecular biology, the CDC48 N-terminal domain is a protein domain found in AAA ATPases including cell division protein 48 (CDC48), VCP-like ATPase and N-ethylmaleimide sensitive fusion protein. It is a substrate recognition domain which binds polypeptides, prevents protein aggregation, and catalyses refolding of permissive substrates. It is composed of two equally sized subdomains. The amino-terminal subdomain (CDC48_N) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain (CDC48_2) forms a novel six-stranded beta-clam fold. Together these subdomains form a kidney-shaped structure, in close agreement with results from electron microscopy. CDC48_N is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases.
Pfam PF01085: Hedgehog amino-terminal signalling domain (domain)
For the carboxyl Hint module, see [pfam:PF01079]. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation.
Wikipedia: The Hedgehog signaling pathway is a signaling pathway that transmits information to embryonic cells required for proper cell differentiation. Different parts of the embryo have different concentrations of hedgehog signaling proteins. The pathway also has roles in the adult. Diseases associated with the malfunction of this pathway include cancer.
Pfam PF19748: Family of unknown function (DUF6235) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. This family 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 PF00366: Ribosomal protein S17 (domain)
This family includes small ribosomal subunit protein uS17 (formerly known as 30S ribosomal protein S17 and 40S ribosomal protein S11) .
The ribosomal proteins catalyse ribosome assembly and stabilise the rRNA, tuning the structure of the ribosome for optimal function. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . 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 uS17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli (primary rRNA binding protein), and is thought to be involved in the recognition of termination codons. Experimental evidence  has revealed that uS17 has virtually no groups exposed on the ribosomal surface.
Pfam PF16691: Domain of unknown function (DUF5062) (domain)
This family is found in Vibrio spp. 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 PF16827: zinc-finger (domain)
This is a family of putative zinc-fingers from Actinobacteriales.
Pfam PF18106: Rolling Circle replication initiation protein N-terminal domain (domain)
This is the N-terminal domain of the Rolling Circle Replication Initiator Protein (Rep) from Geobacillus stearothermophilus. This protein acts on plasmids from family pT181 to initiate replication, recruit a helicase to the site of initiation and terminate replication after DNA synthesis. These proteins possess a unique active site and a catalytically essential metal ion is bound in a distinct manner from other rolling circle Reps.
Pfam PF22864: ArgL-like (family)
This protein family includes the putative translational regulatory protein ArgL from Escherichia coli, the product of a small open reading frame (smORF), which may serve a regulatory role in the expression of its downstream gene.
Pfam PF02544: 3-oxo-5-alpha-steroid 4-dehydrogenase (family)
This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, [ec:1.3.99.5] Also known as Steroid 5-alpha-reductase, the reaction catalysed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor  3-oxo-delta(4)-steroid + reduced acceptor.  The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development.  In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is [swissprot:Q38944] (DET2) a steroid reductase from Arabidopsis.  Mutations in this enzyme cause defects in light-regulated development.
Pfam PF06608: Cilia- and flagella-associated protein 68 (family)
This family represents the homologues of Cilia- and flagella-associated protein 68 (CFAP68). This protein is a microtubule inner protein (MIP) part of the doublet microtubules (DMTs). CFAP68 belongs to the axoneme core-MIPs and binds to the protofilament A09 of the sperm DMTs.
Pfam PF14760: Rnk N-terminus (domain)
This domain occurs at the N-terminus of Rnk, an RNA polymerase-interacting protein of the GreA/GreB family ([pfam:PF01272]). It has a coiled coil structure.
Pfam PF12422: Condensin II non structural maintenance of chromosomes subunit (family)
This domain family is found in eukaryotes, and is approximately 150 amino acids in length. This family is part of a non-SMC subunit of condensin II which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II.
Pfam PF20763: Phage phi29, UDG inhibitor P56 (family)
Protein p56 from Bacillus subtilis phage phi29 inhibits the host uracil-DNA glycosylase (UDG) activity, preventing its binding to DNA and therefore viral replication from being compromised. p56 adopts a dimeric fold, with three anti-parallel beta sheets and a helical region linked by three short loops in each polypeptide chain. The highly anionic region of the protein plays a key role in the inhibition, which occurs by mimicking the DNA substrate. This domain family is mainly found in tailed bacteriophages.
Pfam PF23686: YkiC-like (family)
This protein family includes Protein YkiC from Escherichia coli, a 39-residue long sequence predicted to adopt an alpha -helical configuration.
Pfam PF11099: Apoptosis regulator M11L like (family)
Apoptosis regulators function to modulate the apoptotic cascades and thereby favour productive viral replication. M11L inhibits mitochondrial-dependant apoptosis by mimicking and competing with host proteins for the binding and blocking of Bak and Bax, two executioner proteins.
Pfam PF10168: Nuclear pore component (repeat)
Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.
Pfam PF05372: Delta lysin family (family)
Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin  forms an amphipathic helix upon binding to lipid bilayers. The precise mode of action of delta-lysis is unclear.
Pfam PF01618: MotA/TolQ/ExbB proton channel family (family)
This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels.  MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller. ExbB is part of the TonB-dependent transduction complex.  The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane.
Pfam PF01986: Domain of unknown function DUF123 (family)
This archaebacterial domain has no known function. It is attached to an endonuclease domain in [swissprot:Q58030]. The domain contains several conserved cysteines and histidines.  This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.).
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 PF14962: Mitochondria Localisation Sequence (family)
This family contains a protein found in eukaryotes. Proteins in this family are typically between 240 and 613 amino acids in length. The family is found in association with [pfam:PF07992]. This protein family is an N-terminal domain for the mitochondrial localisation sequence for an apoptosis-inducing factor. The protein is also known as Corneal endothelium-specific protein 1 or as Ovary-specific acidic protein. It is thought to be important for membrane function and is expressed in the ovary and corneal endothelium.
Pfam PF18383: Intraflagellar transport 81 calponin homology domain (domain)
This is the N-terminal domain found in IFT81 proteins. Crystal structure analysis revealed that IFT81-N adopts the fold of a calponin homology (CH) domain with structural similarity to the kinetochore complex component NDC80 with microtubule (MT)-binding properties. Functional analysis show that IFT74 and IFT81 form a tubulin-binding module required for ciliogenesis. It is suggested that IFT81-N binds the globular domain of tubulin to provide specificity, and IFT74-N recognizes the beta-tubulin tail to increase affinity.
Wikipedia: Calponin homology domain (or CH domain) is a family of actin binding domains found in both cytoskeletal proteins and signal transduction proteins. The domain is about 100 amino acids in length and is composed of four alpha helices. It comprises the following groups of actin-binding domains:Actinin-type (including spectrin, fimbrin, ABP-280)
Calponin-type
Pfam PF13291: ACT domain (domain)
ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein.
Pfam PF21524: SAM domain-containing protein 1, WH domain (domain)
SAM domain-containing protein 1 (SAMD1, also known as Atherin) is an unmethylated CpG island (CGI)-binding protein that acts as a repressive chromatin regulator. It consists of a C-terminal SAM domain ([pfam:PF00536]), a central unstructured region and an atypical winged-helix N-terminal domain that directly recognizes unmethylated CpG-containing DNA. This domain has also been found in the transcriptional regulators KAT6A, KAT6B, and ZMYND11 which were grouped together as a novel class of WH domains. This entry represents this novel group of WH domains.
Pfam PF02044: Bombesin-like peptide (family)
Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies ; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known , gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide that regulates exocrine and endocrine secretions, smooth muscle contraction, saciety, blood pressure, blood glucose, body temperature, and it is thought to play a role in reproduction and in different behavioral responses like stress or fear . Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.
Wikipedia: Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells.
Pfam PF19057: PH domain (domain)
This entry contains a PH domain found in RhoGEF proteins such as [swissprot:O15013].
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.