SII-SWORD/CoKE huggingface dataset:
Pfam PF01225: Mur ligase family, catalytic domain (domain)
This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC ([swissprot:P17952]), MurD ([swissprot:P14900]), MurE ([swissprot:P22188]),  MurF ([swissprot:P11880]), Mpl ([swissprot:P37773]) and FolC ([swissprot:P08192]). MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan.  Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide.  The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine.  The peptide moiety is synthesised by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.
Wikipedia: The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria comprises a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step process comprising three main stages:formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc).
addition of a short polypeptide chain to the UDPMurNAc.
addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.
Pfam PF13862: BCCIP (family)
This family of proteins includes BRCA2 and CDKN1A-interacting protein (BCCIP) and BCP1. In fungi, BCP1 is involved in nuclear export, actin cytoskeleton organisation and vesicular transport. Its homologue in human and mouse, BCCIP, may promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A/p21 and may be required for repair of DNA damage by homologous recombination in conjunction with BRCA2.
Pfam PF25058: Tetratricopeptide repeat protein 21 ARM repeat (repeat)
This entry represents an ARM-repeats domain found in the middle region of Tetratricopeptide repeat protein 21 (TT21) from human and its homologues. TT21 is an intraflagellar transport (IFT)-associated protein required for spermatogenesis. It is involved in sperm flagellar formation and intraflagellar transport.
Pfam PF13168: Poxvirus B22R protein C-terminal (family)
This is the highly conserved C-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses.
Pfam PF11245: Protein of unknown function (DUF2544) (family)
This is a bacterial family of proteins with unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15435: UNC119-binding protein C5orf30 homologue (family)
UNC119_bdg is a family of eukaryotic proteins that probably plays a role in trafficking of proteins, via interaction with unc119 family cargo adapters. The family may play a role in ciliary membrane localisation.
Pfam PF13369: Transglutaminase-like superfamily (family)
This domain can be found in the N terminus of the bacterial SirB1 protein. It can also be found in the mammalian F-box only protein 21 (FBXO21).
Pfam PF19352: Tetracyclin repressor-like, C-terminal domain (domain)
This presumed domain belongs to the tetracycline repressor (TetR) C-terminal domain family of proteins, which are involved in a wide variety of gene regulations. This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found to the C-terminus of [pfam:PF00440].
Pfam PF21663: WipA-like, phosphatase domain (domain)
This entry represents the phosphatase domain of WipA protein from Legionella pneumophila. WipA is one of the effector proteins involved in pathogenesis and targets tyrosine-phosphorylated peptides.
Pfam PF16729: Domain of unknown function (DUF5067) (domain)
The function of DUF5067 is not clear.
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 PF11412: Thiol:disulfide interchange protein DsbD, N-terminal (domain)
This entry represents the N-terminal domain of DsbD, a transmembrane electron transporter. DsbD binds to a DsbC dimer and selectively activates it using electrons from the cytoplasm. The N-terminal domain of DsbD (DsbDN) is capable of forming disulfides with oxidized DsbC, DsbE, or DsbG as well as with reduced DsbD.
Pfam PF11363: Protein of unknown function (DUF3164) (family)
This family of 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 PF14700: DNA-directed RNA polymerase N-terminal (domain)
This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex.
Pfam PF10602: 26S proteasome subunit RPN7 (repeat)
RPN7 (known as the non ATPase regulatory subunit 6 in higher eukaryotes) is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity.  The 26S proteasome is is involved in the ATP-dependent degradation of ubiquitinated proteins.
Pfam PF18552: PheRS DNA binding domain 1 (domain)
This is a DNA-binding fold domain found in Phenylalanyl-tRNA Synthetase ([ec:6.1.1.20]) N-terminal region. This domain belongs to a superfamily of 'winged helix' DNA-biding domains. The topology of DBD-1 and DBD-3 closely resembles the topology of the Z-DNA-binding domain Zalpha of double-stranded RNA (dsRNA) adenosine deaminase and other domains from DNA-binding proteins. Mutational analysis indicate that DBD-1, 2 and 3 play critical roles in tRNA-Phe binding and recognition, i.e., from the drastic reduction of aminoacylation activity seen upon removal of the N-terminal domains.
Pfam PF23942: Domain of unknown function (DUF7277) (domain)
This entry represents the N-terminal domain from a large family of uncharacterised phage proteins that typically contain three domains.
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 PF17560: Aphid Megourins (family)
This family is fond in the vetch aphid Megoura viciae with members such as Megourin 1, 2 and 3. Megourins are antimicrobial peptides that act against Gram-positive bacteria and fungi.
Pfam PF16288: Domain of unknown function (DUF4934) (repeat)
This family consists of uncharacterised proteins around 400 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis and Bacteroides sp. The function of this family is unknown.
Pfam PF19076: Surface adhesin CshA repetitive domain (domain)
Repeat domain from surface fibrillar adhesin CshA. This domain forms  several tandem repeats with high sequence identity. CshA is found primarily in streptococci species, but also in other Gram+ bacteria.
Pfam PF18022: Ricin-type beta-trefoil lectin C-terminal domain (domain)
This is the C-terminal domain of the beta chain found in Polyporus squamosus lectin protein (PSL). PSL binds specifically to glycans terminating with the sequence: Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is not involved in the binding to the Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is characterized by a central five-stranded beta-sheet that is flanked by three alpha-helices and topped by a short strand. It shows high fold similarity to its closest relative, the Gal.alpha1-3Gal-binding agglutinin from the mushroom Marasmius oreades agglutinin (MOA).
Pfam PF05526: Rhodococcus equi virulence-associated protein (family)
This family consists of several virulence-associated proteins from Rhodococcus equi. Rhodococcus equi is an important pulmonary pathogen of foals and is increasingly isolated from pneumonic infections and other infections in human immunodeficiency virus (HIV)-infected patients. Isolates from foals possess a large virulence plasmid, varying in size from 80 to 90 kb. Isolates lacking the plasmid are avirulent to foals. Little is known about the function of the plasmid apart from its encoding a virulence associated surface proteins.
Pfam PF10988: Putative auto-transporter adhesin, head GIN domain (repeat)
This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8, it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two.  It seems likely that this family belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens.  In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).
Wikipedia: Bacterial adhesins are cell-surface components or appendages of bacteria that facilitate adhesion or adherence to other cells or to surfaces, usually in the host they are infecting or living in. Adhesins are a type of virulence factor.
Pfam PF00479: Glucose-6-phosphate dehydrogenase, NAD binding domain (domain)
Glucose-6-phosphate dehydrogenase (1.1.1.49) (G6PDH) is a ubiquitous protein, present in bacteria and all eukaryotic cell types . The enzyme catalyses the the first step in the pentose pathway, i.e. the conversion of glucose-6-phosphate to gluconolactone 6-phosphate in the presence of NADP, producing NADPH. The ubiquitous expression of the enzyme gives it a major role in the production of NADPH for the many NADPH-mediated reductive processes in all cells, and is critical for NADPH homeostasis and redox regulation . Deficiency of G6PDH is a common genetic abnormality affecting millions of people worldwide. Many sequence variants, most caused by single point mutations, are known, exhibiting a wide variety of phenotypes with the distinctive one being chronic and drug- or food-induced hemolytic anemia, attributed to the inability to produce NADPH and withstand harmful oxidants in erythrocyte cells .
This entry represents the NAD-binding domain of glucose-6-phosphate dehydrogenase.
Wikipedia: Glucose-6-phosphate dehydrogenase (G6PD or G6PDH) (EC 1.1.1.49) is a cytosolic enzyme that catalyzes the chemical reactionD-glucose 6-phosphate + NADP+ + H2O ⇌ 6-phospho-D-glucono-1,5-lactone + NADPH + H+
Pfam PF05632: Borrelia burgdorferi protein of unknown function (DUF792) (family)
This family consists of several hypothetical proteins from the Lyme disease spirochete Borrelia burgdorferi.
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 PF03590: Aspartate-ammonia ligase (domain)
Aspartate--ammonia ligase (asparagine synthetase) 6.3.1.1 catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. This family represents one of the two non-homologous forms of aspartate--ammonia ligase found in Escherichia coli. This type is also found in Haemophilus influenzae, Treponema pallidum and Lactobacillus delbrueckii, but appears to have a very limited distribution. The fact that the protein from the H. influenzae is more than 70% identical to that from the spirochete T. pallidum, but less than 65% identical to that from the closely related E. coli, strongly suggests lateral transfer.

AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB .
Pfam PF12571: Phage tail-collar fibre protein, N-terminal (domain)
This domain is found at the N-terminal of bacterial and viral sequences. There are two completely conserved residues (K and W) that may be functionally important. The members are annotated as being putative phage tail or tail-collar proteins.
Pfam PF01719: Plasmid replication protein, origin binding domain (family)
This entry includes of various bacterial plasmid replication (Rep)  proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence. They consist of a N-terminal origin binding domain (OBD) which is the DNA-binding/catalytic domain that belongs to the HUH endonuclease superfamily and a C-terminal oligomerisation domain (OD), an helical domain responsible for the hexameric state of the protein.
Pfam PF06696: Streptococcal surface antigen repeat (repeat)
This family consists of a number of ~25 residue long repeats found commonly in Streptococcal surface antigens although one copy is present in the HPSR2-heavy chain potential motor protein of Giardia lamblia ([swissprot:Q24984]). This family is often found in conjunction with [pfam:PF00746].
Pfam PF19891: Family of unknown function (DUF6364) (family)
This family of uncharacterised proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length and they seem to belong to the toxin-antitoxin system. They are likely to contain a ribbon-helix-helix DNA-binding motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16776: Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain (domain)
This entry represents the PH domain found in the N terminus of type II inositol 1,4,5-trisphosphate 5-phosphatase (INPP5B). The structure of this domain has been revealed . INPP5B hydrolyses phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signalling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signalling events .

INPP5B contains a PH domain, a 5-phosphatase domain, an ASH domain and a Rho-GAP domain. It shares ~45% sequence identity with OCRL1 (not included in this entry) and has the same domain organization. However, a loop in the Rho GAP domain contains a second clathrin box which is absent in INPP5B. INPP5B shares most interacting partners with OCRL, except for clathrin and the endocytic clathrin adaptor AP-2 .
Pfam PF12032: Regulatory CLIP domain of proteinases (domain)
CLIP is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively.
Pfam PF22518: Domain of unknown function (DUF6997) (domain)
This domain is found C-terminal in a group of uncharacterised proteins. It usually follows winged helix domain [pfam:PF22515]. This domain is related to PD-(D/E)XK nucleases and it is predicted to adopt the same structure with similar active site architecture.
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 PF20863: IcmR, middle region (domain)
IcmR plays a role in the Dot/Icm translocase from Legionella pneumophila. This Type IVb secretion system (T4bSS) is responsible for the delivery of protein effectors to the host cell cytoplasm. The middle region of IcmR (this entry) binds to the N-terminal domain of IcmQ, which is essential for IcmQ ([pfam:PF09475]) to function correctly. The interacting domains form helical hairpins within a four-helix bundle that is stabilized by hydrophobic packing.
Pfam PF20229: Protein ChrB, N-terminal (domain)
This is the N-terminal domain found in Chromate resistance protein ChrB, a protein involved in the reduction of chromate accumulation and are essential for chromate resistance. This domain may be involved in DNA binding and contains two highly conserved arginine residues important for its function.
Pfam PF00446: Gonadotropin-releasing hormone (family)
The gonadotropin-releasing hormones (GnRH) (gonadoliberin) are a family of peptides that play a pivotal role in reproduction. The main function of GnRH is to act on the pituitary to stimulate the synthesis and secretion of luteinizing and follicle-stimulating hormones, but GnRH also acts on the brain, retina, sympathetic nervous system, gonads and placenta in certain species. There seems to be at least three forms of GnRH . The second form is expressed in midbrain and seems to be widespread. The third form has only been found so far in fish. GnRH is a C-terminal amidated decapeptide processed from a larger precursor protein. Four of the ten residues are perfectly conserved in all species where GnRH has been sequenced.
Wikipedia: The gonadotropin-releasing hormones (GnRH) (gonadoliberin) are a family of peptides that play a pivotal role in reproduction. The main function of GnRH is to act on the pituitary to stimulate the synthesis and secretion of luteinizing and follicle-stimulating hormones, but GnRH also acts on the brain, retina, sympathetic nervous system, gonads, and placenta in certain species. There seems to be at least three forms of GnRH. The second form is expressed in midbrain and seems to be widespread. The third form has been found so far only in fish. GnRH is a C-terminal amidated decapeptide processed from a larger precursor protein. Four of the ten residues are perfectly conserved in all species where GnRH has been sequenced.
Pfam PF01671: African swine fever virus multigene family 360 protein (family)
The multigene family 360 protein are found within the African swine fever virus (ASF) genome which consist of dsDNA and has similar structural features to the poxyviruses. The biological function of this family is not known. Although [swissprot:Q65137] is a major structural protein.
Pfam PF23449: CFAP184 CBM-like domain (domain)
This entry represents a domain found in Cilia- and flagella-associated protein 184 (also known as CCDC96, SwissProt:I7M6D6) from Tetrahymena thermophila and similar sequences. CFAP184 forms a complex with CFAP263, and acts as a regulator of ciliary beating that connects radial spoke 3 (RS3) to the inner dynein arm (IDA) and the nexin-dynein regulatory complex (N-DRC). This domain may have a CBM-like (carbohydrate-binding module) fold according to structure predictions and comparison.
Pfam PF09006: Lung surfactant protein D coiled-coil trimerisation (coiled_coil)
This domain, predominantly found in lung surfactant protein D, forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein.
Wikipedia: In molecular biology, Pulmonary surfactant protein D (SP-D) is a protein domain predominantly found in lung surfactant. This protein plays a special role; its primary task is to act as a defence protein against any pathogens that may invade the lung. It also plays a role in lubricating the lung and preventing it from collapse. It has an interesting structure as it forms a triple-helical parallel coiled coil, helps the protein to fold into a trimer.
Pfam PF21100: MCM protein C-terminal winged helix-turn-helix domain (domain)
The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. This entry represents a C-terminal winged helix-turn-helix domain found at the C-terminus of MCM proteins.
Pfam PF19027: Family of unknown function (DUF5752) (family)
This family includes the OrfY protein from the hyperthermophilic archaeum Thermoproteus tenax. This protein co-occurs with the treS/P protein in an operon regulating the synthesis of trehalose. The structure of this protein shows it contains an internal duplication.
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 PF08685: GON domain (domain)
The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins.  It contains several conserved cysteine residues.