SII-SWORD/CoKE huggingface dataset:
Pfam PF00318: Ribosomal protein S2 (family)
This entry represents the family of ribosomal uS2 proteins. They are required for the assembly of different ribosomal subunits and are widely distributed among all living organisms .

Ribosomal uS2 family in humans includes three members:


 * Small ribosomal subunits uS2 (also known as RPSA).
 * Small ribosomal subunits uS2B (also known as RPSA2).
 * Small ribosomal subunits uS2m in mitochondria (also known as MRPS2).


Ribosomal protein SA (RPSA), previously named 37 kDa laminin receptor precursor/67 kDa laminin receptor (LRP/LR), has been characterised as a multifunctional protein that plays multiple roles in different pathological processes .
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 PF17679: gp37/Dip protein (family)
This protein is found in the giant phage phi KZ. This protein has been shown to bind to RNAse E of the host P. aeruginosa and to inhibit the RNA degradation machinery of the bacterium.
Pfam PF13624: SurA-like N-terminal domain (domain)
This domain is found at the N-terminus of the chaperone SurA and related proteins such as PpiD and foldase PrsA. It is a helical domain that together with the C-terminal, forms a domain containing substrate-binding sites. The C-terminal of the SurA protein folds back and forms part of this domain also but is not included in the current alignment.
Pfam PF20270: CASPASE and TPR Repeat-Associated C-terminal domain (domain)
One of two constant domains forming the CATRA module which is in turn C-terminally fused to a diverse range of conflict effector domains. This gene, along with a gene encoding the CATASP domain and a gene encoding a TPR repeat region fused to a CASPASE domain, forms the three gene island making up the CATRA conflict systems. This all alpha-helical domain is predicted to be involved in recognition of invasive molecules or in the transmitting of a signal through conformational change, enabling CASPASE-mediated proteolysis to free the fused effector domains.
Pfam PF06609: Fungal trichothecene efflux pump (TRI12) (family)
This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes.
Pfam PF17784: Sulfotransferase domain (domain)
This family of proteins are distantly related to sulfotransferase enzymes. This protein in S. mansonii has been shown to be involved in resistance to oxamniquine and to have sulfotransferase activity.
Pfam PF23563: TRIP13 N-terminal domain (domain)
This domain is found N-terminal in the Pachytene checkpoint protein 2 homolog (also known as TRIP13) and related proteins. The AAA+ ATPase TRIP13 plays a key role in chromosomerecombination and chromosome structure development during meiosis. TRIP13 regulates both MAD2 and meiotic HORMADs by disassembling the HORMA domain-closure motif complexes. The domain represented in this entry is involved in the p31 recognition and binding. TRIP13 is also involved in the remodeling of Shieldin to regulate DNA repair pathway choice. This domain binds to the Mitotic spindle assembly checkpoint protein MAD2B (also known as REV7) and helps to reduce the flexibility of SHLD2.3-REV7 upon TRIP13 binding.
Pfam PF19459: Family of unknown function (DUF5996) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This  family includes a protein from the SW-163C biosynthetic gene  cluster from Streptomyces sp. SNA15896.
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 PF09848: Schlafen group 3, DNA/RNA helicase domain (domain)
This domain is found in at the C terminus of group 3 Schlafen proteins from mammals, and represents the DNA/RNA helicase domain. Schlafen proteins are involved in the control of cell proliferation, induction of immune responses, and in the regulation of viral replication. These proteins inhibit DNA replication and promote cell death in response to DNA damage. They play a role in genome surveillance to kill cells with defective replication. This domain is also found in various uncharacterised prokaryotic proteins fused to a DNA helicase, GIY-YIG or PD-(D/E)XK catalytic domain or HsdR-N(terminal) domain, which are similar to AAA DNA helicase, Type III restriction enzyme ATPase, RecD and RuvB helicase.
Pfam PF13936: Helix-turn-helix domain (domain)
This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF15034: KRTAP type 7 family (family)
This family of keratin associated proteins are found in vertebrate.
Pfam PF13907: Chromodomain-helicase-DNA-binding protein 1-like, C-terminal (domain)
This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins, including Chromodomain-helicase-DNA-binding protein 1 from humans (CHD1), an ATP-dependent chromatin-remodeling factor which acts as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. This helical domain consists of five alpha-helices organised in a variant helical bundle topology. Its surface is positively charged and can bind dsDNA and nucleosomes, but its specific function remains unknown.
Pfam PF20323: Family of unknown function (DUF6618) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 116 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 PF23860: Ribophorin II third domain (domain)
This entry represents the third domain of eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesised polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them.
Pfam PF12204: Domain of unknown function (DUF3598), N-terminal (domain)
This domain is predominantly found at the N-terminal end of proteins from cyanobacteria and plants, including Biogenesis factor required for ATP synthase 1 (BFA1, [swissprot:F4J1U2]) from Arabidopsis thaliana. BFA1 promotes the assembly of the CF1 subcomplex of the chloroplast ATP synthase by specifically interacting with the gamma and beta subunits. This domain consists of nine beta-sheets and two alpha- helices forming an atypical beta-barrel, which locates perpendicularly to the typical beta-barrel formed by the C-terminal domain.
Pfam PF04637: Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25) (family)
This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown.
Pfam PF17480: AlphaC N-terminal domain 2 (domain)
This is the second domain on the N-terminal region found on the alpha C protein (ACP). ACP is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. ACP consists of an N-terminal domain (NtACP; 170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. The NtACP, contains two structural domains, D1 and D2.  D1, the more distal (amino-terminal) portion [pfam:PF08829] and consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). This entry, D2 (connects distally to Domain 1 and proximally to the repeat region) consists of three antiparallel alpha helix coils. It is suggested that the GAG-binding region of ACP may extend from Domain 2 into the repeat region.
Pfam PF13683: Integrase core domain (domain)
The retroviral integrase is the enzyme responsible for the insertion of a DNA copy of the viral genome into host DNA, an essential step in the replication cycle of viruses . Integrases comprise three functional and structural domains: the central core domain, which contains the catalytic residues, an N-terminal zinc finger and a C-terminal DNA binding domain .

The integrase catalytic domain catalyses a series of reactions to integrate the viral genome into a host chromosome. In the first step, it removes two 3' end nucleotides from each strand of the linear viral DNA, leaving overhanging CA-OH ends. In the second step, the processed 3' ends are covalently joined to the 5' ends of the target DNA. In the third step, which probably involves additional cellular enzymes, unpaired nucleotides at the viral 5' ends are removed and the ends are joined to the target site 3' ends, generating an integrated provirus flanked by five base-pair direct repeats of the target site DNA .

The crystal structure of the catalytic domain shows a dimeric structure, with each monomer containing a five-stranded Î²-sheet and six Î±-helices . This fold is characteristic of the polynucleotidyltransferase superfamily whose members include RNase H, the bacteriophage Mu transposase, and the E. coli Holliday junction resolving enzyme, RuvC . The catalytic domain of integrase contains the DD35E triad motif. As in other DNA-binding proteins containing this motif, these acidic residues coordinate a divalent Mg2+ in the resting enzyme. Substituting any one of these residues abolishes both processing and integration activities of integrase.

The integrase catalytic domain is also found in various transposase proteins.
Pfam PF14921: Adenomatosis polyposis coli down-regulated 1 (domain)
The domain is duplicated in most members of this family. APCDD is directly regulated by the beta-catenin/Tcf complex, and its elevated expression promotes proliferation of colonic epithelial cells in vitro and in vivo. APCDD1 has an N-terminal signal-peptide and a C-terminal transmembrane region.  The domain is rich in cysteines, there being up to 12 such residues, a structural motif important for interaction between Wnt ligands and their receptors. APCDD1 is expressed in a broad repertoire of cell types, indicating that it may regulate a diverse range of biological processes controlled by Wnt signalling.
Pfam PF24128: Phage zinc binding protein (family)
This entry represents a small family of uncharacterised phage proteins. The alignment contains a small zinc binding motif at the C-terminus composed of a CXXC and CXXH motif. The N-terminus is composed of a two helical bundle. Structure prediction suggests that the two helices might mediate a homodimerisation interaction to form a four helical bundle structure.
Pfam PF03782: AMOP domain (domain)
This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges.
Pfam PF19041: Nuclear cap binding complex subunit CBP30 (family)
This entry represents the CBP30 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP30 is part of the complex that recognises this cap.
Pfam PF17256: Anaphase-promoting complex, subunit 16 (family)
The Anaphase-promoting complex/cyclosome (APC/C) is a 1.5 megaDaltons assembly ubiquitin ligase complex comprising 19 subunits. This multifunctional ubiquitin-protein ligase targets different substrates for ubiquitylation and therefore regulates a variety of cellular processes such as cell division, differentiation, genome stability, energy metabolism, cell death, autophagy as well as carcinogenesis. The APC/C complex contains two sub-complexes,the Platform and the Arc Lamp. The Arc Lamp, which mediates transient association with regulators and ubiquitination substrates, contains the small subunits APC16, CDC26, APC13, and tetratricopeptide repeat (TPR) proteins. APC16 is a conserved subunit of the APC/C. APC16 was found in association with tandem-affinity-purified mitotic checkpoint complex protein complexes. APC16 is a bona fide subunit of human APC/C. It is present in APC/C complexes throughout the cell cycle. The phenotype of APC16-depleted cells copies depletion of other APC/C subunits, and APC16 is important for APC/C activity towards mitotic substrates. APC16 sequence homologues can be identified in metazoans, but not fungi, by four conserved primary sequence stretches.
Wikipedia: Anaphase-promoting complex is an E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome. The APC/C is a large complex of 11–13 subunit proteins, including a cullin (Apc2) and RING (Apc11) subunit much like SCF. Other parts of the APC/C have unknown functions but are highly conserved.
Pfam PF03566: Peptidase family A21 (family)
The asparagine endopeptidases are all autocatalytic endopeptidases utilizing Asn at position P1. Cleavage occurs as a consequence of cyclization of the Asn residue .
This group of peptidases belongs to the MEROPS family N2 (clan NA). In the Nudaurelia capensis omega virus capsid protein the residues that form the catalytic dyad in the active site are Glu103 and Asn570. The cleavage mediated by the enzyme is an autolytic one, and the catalytic Asn is also the P1 residue in the cleavage site, Asn570-|-Phe571 releasing a 74-residue fragment from the C terminus of the coat protein. This cleavage occurs during the late stages of virion assembly. Heterologous expression of the coat protein gene of tetravirus in a baculovirus system results in the spontaneous assembly of virus-like particles (VLPs) that remain uncleaved when purified at neutral pH .
Pfam PF03772: Competence protein (family)
Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site.
Pfam PF00747: ssDNA binding protein (family)
This protein is found in herpesviruses and is needed for replication.
Wikipedia: Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans.
Pfam PF09622: Putative integral membrane protein (DUF2391) (family)
This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times.
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 PF05402: Coenzyme PQQ synthesis protein D (PqqD) (family)
This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.
Pfam PF10225: NEMP family (family)
This entry includes a group of nuclear envelope integral membrane proteins from animals and plants, including  NEMP1 from Xenopus laevis. NEMP1 is a RanGTP-binding  protein and is involved in eye development.
Pfam PF01292: Prokaryotic cytochrome b561 (domain)
This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit.  Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently.  This is a prokaryotic family.  Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188.
Wikipedia: Cytochrome b561 is an integral membrane protein responsible for electron transport, binding two heme groups non-covalently. It is a family of ascorbate-dependent oxidoreductase enzymes.
Pfam PF05597: Poly(hydroxyalcanoate) granule associated protein (phasin) (family)
Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Pfam PF07725: Leucine Rich Repeat (repeat)
This Pfam entry includes some LRRs that fail to be detected by the [pfam:PF00560] model.
Pfam PF24247: Repeat of unknown function (DUF7450) (repeat)
This entry represents a group of uncharacterised proteins from bacteria that, according to structure predictions (SwissProt:A0A7C3HQW7 or SwissProt:A0A5C6D6K5), they may contain novel repeats that fold into twisted long beta-hairpins different from typical beta-barrel hairpins and they do not exhibit homology to any beta-barrel.
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 PF00039: Fibronectin type I domain (domain)
Fibronectin type I repeats are one of the three repeats found in the fibronectin protein. Fibronectin is a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. Type I domain (FN1) is approximately 40 residues in length. Four conserved cysteines are involved in disulphide bonds. The 3D structure of the FN1 domain has been determined . It consists of two antiparallel Î²-sheets, first a double-stranded one, that is linked by a disulphide bond to a triple-stranded Î²-sheet. The second conserved disulphide bridge links the C-terminal adjacent strands of the domain.

In human tissue plasminogen activator chain A the FN1 domain together with the following epidermal growth factor (EGF)-like domain are involved in fibrin-binding . It has been suggested that these two modules form a single structural and functional unit . The two domains keep their specific tertiary structure, but interact intimately to bury a hydrophobic core; the inter-module linker makes up the third strand of the EGF-module's major Î²-sheet.
Wikipedia: Fibronectin, type I repeats are one of the three repeats found in the fibronectin protein. Fibronectin is a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin. Type I domain (FN1) is approximately 40 residues in length. Four conserved cysteines are involved in disulfide bonds. The 3D structure of the FN1 domain has been determined. It consists of two antiparallel beta-sheets, first a double-stranded one, that is linked by a disulfide bond to a triple-stranded beta-sheet. The second conserved disulfide bridge links the C-terminal adjacent strands of the domain.
Pfam PF15886: Carbohydrate binding domain (family 32) (domain)
This domain is found at the N-terminus of beta-1,3-glucan-binding proteins involved in recognition of invading micro-organisms. It often co-occurs with [pfam:PF00722] (Glycosyl hydrolases family 16). It recognises and binds to a triple-helical beta-1,3-glucan structure.
Pfam PF20688: GREB1, second domain (domain)
GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an estrogen-regulated gene expressed in breast cancer. Its exact function is not known but its expression is regulated by the coordinated binding of estrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene.  It acts as a regulator of hormone-dependent cancer growth in breast, ovarian and prostate cancers. This is a presumed domain found adjacent the N-terminal domain of GREB1 and GREB1-like proteins. Structure predictions suggest that it may adopt an alpha/beta fold.