SII-SWORD/CoKE huggingface dataset:
Pfam PF03179: Vacuolar (H+)-ATPase G subunit (coiled_coil)
This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialised cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation.
Wikipedia: Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pumps protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
Pfam PF06227: Poxvirus Bcl-2-like proteins (family)
This family represents a group of Poxvirus Bcl-2-like proteins that function as immunomodulators to evade the host innate immune response through the inhibition of apoptosis or blocking the activation of pro-inflammatory transcription factors, such as interferon (IFN) regulatory factor-3 (IRF-3) and nuclear factor-kappaB (NF-kappaB). These proteins have low sequence identity but high structural similarity to the eukaryotic Bcl-2 protein family. They have a Bcl-2 fold which comprises a central hydrophobic alpha-helix that is surrounded by an additional layer of 6-7 amphipathic alpha-helices. Included in this family are proteins B14, A52, A46, C6, K7, N1, and N2. Protein N1 has the unusual dual ability of modulating apoptosis and inflammatory signalling. Protein K7, in addition to its anti-inflammatory activity, forms a complex with RNA helicase DDX3 and antagonises interferon-beta promoter induction.
Pfam PF08940: Domain of unknown function (DUF1918) (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 PF18829: Importin repeat 6 (repeat)
The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam  entry represents two consecutive repeat units and includes sequences  captured by [pfam:PF18808].
Pfam PF24094: SH3BP4, DEATH domain-like (domain)
This domain is found towards the C-terminal end of human SH3 domain-binding protein 4 (SH3BP4) and similar proteins mainly found in animals. SH3BP4 may function in transferrin receptor internalisation at the plasma membrane through a cargo-specific control of clathrin-mediated endocytosis. This domain, which is often found N-terminal to [pfam:PF23637], is predicted to show a DEATH domain-like all-alpha structure.
Pfam PF07103: Protein of unknown function (DUF1365) (family)
This family consists of several bacterial and plant proteins of around 250 residues in length. The function of this family is unknown.
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 PF23536: TraK C-terminal domain (domain)
This entry represents the C-terminal domain from TraK proteins. The TraK C-terminal domain is a structural motif identified within bacterial type IV secretion systems (T4SSs), which are key players in the dissemination of multi-drug resistance. This domain contributes to the formation of the outer-membrane core complex (OMCCF) of T4SS encoded by conjugative F plasmids. The structure of the TraK C-terminal domain shows a compact fold consisting of 4 beta-strands and one alpha helix. This domain interacts with other components of the OMCCF, including TraV and other TraK C-terminal domains. Within the structural unit of the OMCCF, TraK C-terminal domains assemble as dimers, with each domain flipped 180 degrees relative to the other. The TraK C-terminal dimer sits laterally on top of the TraK N-terminal dimer, contributing to the overall stability of the complex. An electrostatic interaction between specific residues within TraK subunits likely participates in the stabilization of the TraK C-terminal dimer.
Pfam PF18349: PAZ domain (domain)
This is a Paz domain found in Argonaute proteins from Aquifex aeolicus bacteria. The PAZ core fold in Aquifex aeolicus bacteria Ago (Aa-Ago) proteins is closely related to the human hAgo1 PAZ domain. Structural and functional studies of Aa-Ago indicate that conformational rearrangement of the PAZ domain may be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex.
Pfam PF20588: Cyclin-D-binding Myb-like transcription factor 1 N-terminal (domain)
This domain is found at the N-terminal of Cyclin-D-binding Myb-like transcription factor 1 (DMTF1), which is rich in acidic residues, adjacent [pfam:PF00249]. DMTF1 is a tumour suppressor that interacts with and activates CDKN2A/ARF in response to Ras-Raf signalling, thus inducing p53-dependent cell cycle arrest.
Pfam PF16096: Fragile X-related 1 protein C-terminal region 2 (disordered)
FXR_C1 is a small highly conserved region of the C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with [pfam:PF05641], [pfam:PF00013]. This family is immediately C-terminal to the core C terminal region, PF12235, and contains at least one block of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs.
Pfam PF15093: Sperm-associated microtubule inner protein 4 (family)
This family (previously DUF4555) includes the homologs of human sperm-associated microtubule inner protein 4 (SPMIP4) that is found predominantly in testis. SPMIP4 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs). Members of this family adopt rather extended conformation and contain a single or multiple Mn motifs. Each Mn motif consists of a 5- to 6-residue helix flanked by a Tyr/Phe residue on one end and by a Ser/Thr on the other that binds the shoulder of the alpha-tubulin S9/S10 loop. Members of this family are likely to stabilise the microtubule structure in the sperm flagella.
Pfam PF00794: PI3-kinase family, ras-binding domain (domain)
Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly  significant similarity) to Ras-binding [pfam:PF00788] domains  (unpublished observation).
Pfam PF05890: Eukaryotic rRNA processing protein EBP2 (family)
This family consists of several Eukaryotic rRNA processing protein EBP2 sequences.  Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis.  This family also plays a role in chromosome segregation.
Pfam PF23874: Hfq-like protein (domain)
This entry represents a phage protein that contains a central Hfq-like domain. This suggests that this protein may have an RNA binding function. AlphaFold prediction suggests a confident homohexameric structure.  This entry represents a hypothetical protein found in several mycobacteriophages, including Bxz1, Mangeria, Derek, DrPhinkDaddy, Phusco and Jedediah. The proteins are typically around 155 amino acids in length.
Pfam PF14803: Nudix N-terminal (domain)
Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases.
Pfam PF22143: C5a peptidase, fibronectin type III domain (domain)
This domain is found at the C-terminal end of C5a peptidase from Streptococcus pyogenes (ScpA) and similar sequences from firmicutes. ScpA is a multidomain cell-envelope subtilase that cleaves complement component C5a. This protein consists of a catalytic domain ([pfam:PF00082]) with an inserted PA domain ([pfam:PF02225]) and and three tandemly arranged fibronectin type III domains (Fn1-Fn3). This entry represents the last FN domain.
Pfam PF10812: Protein of unknown function (DUF2561) (family)
This family of proteins with unknown function appears to be restricted to Mycobacterium spp.
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 PF21442: Polymerase basic protein 2 (PB2), '627' domain (domain)
PB2 is a subunit of the RNA-dependent RNA polymerase which is responsible for  replication and transcription of virus RNA segments. This entry represents the so-called '627 domain', named because it contains the host specificity residue 627 which is a lysine in human Influenza A virus and a glutamate in avian strains. It contains a large positively charged region, consistent with its ability to bind RNA.
Pfam PF12691: Bacteriophage tail terminator protein (domain)
This entry represents a family of likely phage tail termination proteins which form a hexameric ring that connects the phage neck to the tail.
Pfam PF15001: AP-5 complex subunit sigma-1 (family)
This family of proteins are subunits of the adaptor protein complex AP-5.
Pfam PF03009: Glycerophosphoryl diester phosphodiesterase family (family)
E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has been noted. This family appears to have weak but not significant matches to mammalian phospholipase C [pfam:PF00388], which suggests that this family may adopt a TIM barrel fold.
Wikipedia: The enzyme glycerophosphodiester phosphodiesterase ({EC 3.1.4.46) catalyzes the reactiona glycerophosphodiester + H2O  an alcohol + sn-glycerol 3-phosphate
Pfam PF21429: Sliding-clamp-loader large subunit, C-terminal domain (domain)
This domain is found at the C-terminal end of Sliding-clamp-loader large subunit from Bacteriophage T4 (Gp44) and similar proteins predominantly found in tailed bacteriophages. Gp44 functions as an ATPase enzyme. It also contains an AAA module ([pfam:PF00004]).
Pfam PF22198: Glucokinase regulatory protein, second SIS domain (domain)
Glucokinase regulatory protein (GKRP) binds glucokinase (GK) mainly through hydrophobic interactions, functioning as an allosteric switch in blood glucose control by the liver. GKRP is trilobal in shape, consisting of two topologically identical sugar isomerase (SIS) domains capped by an alpha-helical lid domain ([pfam:PF20741]). This entry represents the second SIS domain from GKRP.
Pfam PF12426: RNA dependent RNA polymerase (family)
This domain family is found in viruses, and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) 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 PF24842: Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 (domain)
Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. UFD1 is a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated  with these conditions are thought to be due to defective neural crest cell differentiation. UFD1 is composed of an N-terminal conserved region (UT3) and a  C-terminal disordered region (UT6) which contains the binding sites for both Npl4 and Cdc48. UFD1 N-terminal domain contains the binding site for ubiquitin and has a similar structure to p97. It is made of two subdomains. This entry corresponds to the second subdomain of UFD1 UT3 which has a mixed alpha/beta roll structure.
Pfam PF20954: Phage tail base-plate attachment protein N0 domain (domain)
Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames. This entry represents the N0 domain.
Pfam PF22110: TFIIIA, beta-beta-alpha zinc finger (domain)
This entry represents a beta-beta-alpha zinc finger from TFIIIA, a transcription factor involved in ribosomal large subunit biogenesis. It binds the approximately 50 base pairs internal control region (ICR) of 5S ribosomal RNA genes. It is required for their RNA polymerase III-dependent transcription and may also maintain the transcription of other genes.
Pfam PF09467: Hypothetical protein Yopt (domain)
This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms homo-dimers, with each monomer consisting of one alpha helix and three beta strands.
Pfam PF06438: Heme-binding protein A (HasA) (domain)
Free iron is limited in vertebrate hosts, thus an alternative to siderophores has been developed by pathogenic bacteria to access host iron bound in protein complexes.  HasA is a secreted hemophore that has the ability to obtain iron from hemoglobin. Once bound to HasA, the heme is shuttled to the receptor HasR, which releases the heme into the bacterium.
Pfam PF01735: Lysophospholipase catalytic domain (family)
This family consists of Lysophospholipase / phospholipase B [ec:3.1.1.5] and cytosolic phospholipase A2 EC:3.1.4 which also has a C2 domain [pfam:PF00168].  Phospholipase B enzymes catalyse the release of fatty acids from lysophsopholipids and are capable in vitro of hydrolysing all  phospholipids extractable form yeast cells.  Cytosolic phospholipase A2 associates with natural membranes in response to physiological increases in Ca2+ and selectively hydrolyses arachidonyl phospholipids, the aligned region corresponds the the carboxy-terminal Ca2+-independent catalytic  domain of the protein as discussed in.
Wikipedia: The enzyme lysophospholipase (EC 3.1.1.5) catalyzes the reaction2-lysophosphatidylcholine + H2O  glycerophosphocholine + a carboxylate
Pfam PF06701: Mib_herc2 (domain)
Named "mib/herc2 domain" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect).
Pfam PF20618: Bacterial GPD, NAD-dependent C-terminal (domain)
This is the C-terminal domain of NAD-dependent glycerol-3-phosphate dehydrogenase (GPD) from bacteria and archaea. GPD catalyses the reversible reduction of dihydroxyacetone phosphate to glycerol-3-phosphate.
Pfam PF24518: B-cell receptor CD22-like, first Ig-like (domain)
This is the first immunoglobulin-like (Ig-like) domain found in human B-cell receptor CD22 and similar animal sequences. CD22 plays a role in various aspects of B-cell biology including differentiation, antigen presentation, and trafficking to bone marrow.
Pfam PF25071: Domain of unknown function (DUF7795) (domain)
This domain is fund in uncharacterised plant proteins. It is predicted to fold into alpha- helical bundle.
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 PF18370: Rhamnogalacturonan I lyases beta-sheet domain (domain)
This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW ([ec:4.2.2.23]) and YesX ([ec:4.2.2.24]), cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Other family members carrying this domain are hemagglutinin A, lysine gingipain (Kgp) and Chitinase C ([ec:3.2.1.14]).
Pfam PF11581: Antagonist of EGFR signalling, Argos (family)
Argos is a natural secreted antagonist of EGFR signalling which functions by binding growth factor ligands that activate EGFR by forming a clamp like structure using three disulphide-bonded beta-sheet domains.
Pfam PF04806: EspF protein repeat (repeat)
The enteropathogenic Escherichia coli EspF secreted protein induces host cell apoptosis. Its proline-rich structure suggests that it may act by binding to SH3 domains or EVH1 domains of host cell signalling proteins.
Pfam PF24647: Phage blade protein (family)
This entry represents a small family of short uncharacterised phage proteins. Structure prediction of A0A1J0MI44 suggests the protein adopts a four stranded sheet that can form homo-oligomers, with a homohexamer forming a beta propeller structure (iPTM=0.93). The function of these protein is unknown.
Pfam PF18618: HP0268 (domain)
HP0268 is a small, characterized protein that is conserved in H. pylori strains and consists of 80 amino acid residues with a molecular weight of approximately 9.5 kDa. HP0268 has nicking endonuclease and RNase activities, both of which are specific for a single-strand of nucleotides. It is structurally similar to small MutS-related (SMR) domains, that can be categorized roughly into three subfamilies according to their arrangement in the domain architecture.HP0268 falls into subfamily 3 that is found as stand-alone type proteins. It is proposed that HP0268 has become an evolutionary intermediate between RNases and nicking endonucleases during H. pylori adaptation to the extremely acidic environment of the stomach.
Pfam PF23054: N4BP1, C-terminal UBA domain (domain)
This domain is found in the N4BP1 family which includes the NEDD4-binding protein 1, KHNYN and other related proteins. This domain has a significant sequence and structural similarity to known UBA domains. It was shown that is responsible for binding ubiquitin-like protein NEDD8.
Pfam PF02484: Rhabdovirus Non-virion protein (family)
Infectious hematopoietic necrosis virus (IHNV) is a member of the family Rhabdoviridae. The non-virion protein (NV) is coded for by one of the six genes of the IHNV genome, but is absent in vesiculovirus -like rhabdovirus.
Pfam PF09889: Probable treble clef (family)
This domain, found in various hypothetical archaeal proteins, has no known function.  Structural modelling suggests this domain may bind nucleic acids.
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 PF04175: Protein of unknown function (DUF406) (family)
Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterised enzyme specific for gamma proteobacteria.
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 PF19734: Family of unknown function (DUF6224) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000084) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from  the laidlomycin biosynthetic gene cluster from Streptomyces sp.  CS684.
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 PF15963: Myb DNA-binding like (domain)
This entry represents the Myb domain found in transcription factor TFIIIB component B''.
Transcription by RNA polymerase III (pol III) is a complex molecular process orchestrated by the two main transcription factors, TFIIIB and TFIIIC. The TFIIIB complex can be recruited by TFIIIC to upstream DNA and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling . Saccharomyces cerevisiae TFIIIB is a complex of three subunits, the TATA box-binding protein TBP, the TFIIB-related factor BRF, and the beta'' protein.
The myb-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of approximately 55 amino acids, typically occurring in a tandem repeat in eukaryotic transcription factors. The domain is named after the retroviral oncogene v-myb, and its cellular counterpart c-myb, which encode nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G .