SII-SWORD/CoKE huggingface dataset:
Pfam PF05100: Phage minor tail protein L (family)
This entry represents Tail tip protein (L) from Bacteriophage lambda and similar proteins found in tailed bacteriophages (Caudovirales) and prophages mostly from Proteobacteria. L is part of the distal tail tip complex which plays a role in DNA ejection during entry, and in tail assembly initiation during exit. The tail tip complex is assembled successively with three tail tip proteins J, one tail tip protein I, one tail tip protein L and one tail tip protein K. The tail tip complex interacts with tail measure protein to initiate tail tube assembly. The formation of the tail tip complex is completed by the addition of tail tip protein M, which is followed by tail tube polymerisation .
Pfam PF21943: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of DesT from Pseudomonas aeruginosa and similar bacterial transcriptional regulators. DesT is involved in the control of the unsaturated:saturated fatty acid ratio available for membrane lipid synthesis. This region folds into six helices that create the ligand-binding domain. It is normally found associated with [pfam:PF00440].
Pfam PF19323: BTB/POZ domain-containing protein KCTD4 C-terminus (family)
This entry represents the C-terminal region of BTB/POZ domain-containing protein KCTD4. This domain is highly variable among the BTB domain-containing KCTD proteins and it has been proposed that it could play a role in binding or recruiting diverse protein targets involved in different cellular processes, such us ubiquitination, cell proliferation or control of G-protein coupled receptors, among others.
Pfam PF05338: Protein of unknown function (DUF717) (family)
This family consists of several herpesvirus proteins of 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 PF23689: YldA-like (family)
This protein family includes Protein YldA from Escherichia coli, a 29-residues long sequence predicted to adopt an alpha-helical configuration.
Pfam PF06012: Domain of Unknown Function (DUF908) (family)
This is a domain of unknown function found at the N terminus of a family of E3 ubiquitin protein ligases, including yeast TOM1, many of which appear to play a role in mRNA transcription and processing. This domain is found in association with and immediately N-terminal to another domain of unknown function: IPR010314.
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 PF23544: AtuA ferredoxin-like domain (domain)
This ferredoxin-like fold is often found at the C-terminus of AtuA proteins. Although it is sometimes found as a separate protein in the same operon as AtuA. The precise function of this domain is now known.
Pfam PF12498: Basic leucine-zipper C terminal (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 174 and 411 amino acids in length. The family is found in association with [pfam:PF00170]. There is a conserved KVK sequence motif. There is a single completely conserved residue K that may be functionally important. Various bZIP proteins have been found and shown to play a role in seed-specific gene expression. bZIP binds to the alpha-globulin gene promoter, but not to promoters of other major storage genes such as glutelin, prolamin and albumin.
Pfam PF12042: Tubuliform egg casing silk strands structural domain (domain)
Spiders use fibroins to make silk strands. This family includes tubuliform silk fibroins which are used to protect egg cases. This domain is a structural domain which is found in repeats of up to 20 in many individuals (although this is not necessarily the case). RP1 makes up structural domains in the N terminal while RP2 makes up structural domains in the C terminal.
Wikipedia: Spidroins are the main proteins in spider silk. Different types of spider silk contain different spidroins, all of which are members of a single protein family. The most-researched type of spidroins are the major ampullate silk proteins (MaSp) used in the construction of dragline silk, the strongest type of spider silk. Dragline silk fiber was originally thought to be made up of two types of spidroins, spidroin-1 (MaSp1) and spidroin-2 (MaSp2) however recent transcriptomic analysis of over 1000 spider species has revealed multiple spidroins are expressed making it much more complex.
Pfam PF17598: Family of unknown function (DUF5494) (family)
This is a family of unknown function found in viruses.
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 PF00122: E1-E2 ATPase (family)
Wikipedia: The P-type plasma membrane H+-ATPase is found in plants and fungi. For the gastric H+/K+ ATPase, see Hydrogen potassium ATPase.
Pfam PF04692: Platelet-derived growth factor, N terminal region (family)
This family consists of the amino terminal regions of platelet-derived  growth factor (PDGF, [pfam:PF00341]) A and B chains.
Wikipedia: Platelet-derived growth factor receptors (PDGF-R) are cell surface tyrosine kinase receptors for members of the platelet-derived growth factor (PDGF) family. PDGF subunits -A and -B are important factors regulating cell proliferation, cellular differentiation, cell growth, development and many diseases including cancer. There are two forms of the PDGF-R, alpha and beta each encoded by a different gene. Depending on which growth factor is bound, PDGF-R homo- or heterodimerizes.
Pfam PF16273: Nuclear distribution C domain (domain)
This domain, approximately 40-50 residues in length, is  mainly found in nuclear migration proteins in various Mammalia species. It may play a role not only in mitosis and cytokinesis, but also in interkinetic nuclear migration and neuronal migration during neocortical development.
Pfam PF17869: Anosmin cysteine rich domain (domain)
This is the Cys-box (cysteine-rich) domain found on the N-terminal of anosmin-1 proteins. It is suggested that the Cys-box domain may resemble the cysteine-rich region of the insulin-like growth factor receptor. Family members are found in chordates.
Pfam PF12157: Protein of unknown function (DUF3591) (family)
This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins.
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 PF03765: CRAL/TRIO, N-terminal domain (domain)
This all-alpha domain is found to the N-terminus of [pfam:PF00650].
Pfam PF03548: Outer membrane lipoprotein carrier protein LolA (domain)
In Escherichia coli, lipoproteins are anchored to the periplasmic side of either the inner or outer membrane through N-terminal lipids, depending on the lipoprotein-sorting signal present at position 2 . Five Lol proteins are involved in the sorting and outer membrane localization of lipoproteins. LolCDE, an ATP binding cassette (ABC) transporter, in the inner membrane releases outer membrane-directed lipoproteins from the inner membrane in an ATP-dependent manner, leading to the formation of a water-soluble complex between the lipoprotein and the molecular chaperone, LolA. The LolA-lipoprotein complex crosses the periplasm and then interacts with outer membrane receptor LolB, which is essential for the anchoring of lipoproteins to the outer membrane .

E. coli lipoproteins are anchored to the inner or outer membrane depending on the residue at position 2. Aspartate at this position makes lipoproteins specific to the inner membrane, whereas other residues cause the release of lipoproteins from the inner membrane .
Pfam PF24366: Family of unknown function (DUF7522) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt an alpha-beta structure.
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 PF16646: Axin-1 tankyrase binding domain (disordered)
This is the N-terminal domain tankyrase binding domain of Axin-1.
Wikipedia: Axin-1 is a protein that in humans is encoded by the AXIN1 gene.
Pfam PF08960: STIV B116-like (domain)
The sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. It has 37 ORFs including B116, whose function is unknown. The structure of B116 reveals a fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel.
Pfam PF16702: Domain of unknown function (DUF5063) (family)
The function of DUF5063 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 PF17029: Domain of unknown function (DUF5100) (family)
This is a family of microsporidia-specific sequences of 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 PF23684: ORF20A (family)
This protein family includes ORF20A from Fowl aviadenovirus 4 and similar short viral sequences.
Pfam PF13992: YecR-like lipoprotein (family)
The YecR-like family of lipoproteins includes the YecR protein from E. coli [swissprot:P76308]. This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 110 amino acids in length.
Pfam PF18695: Cytosolic phospholipases A2 C2-domain (domain)
Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. In humans, the cPLA2 family contains six isoforms. Structural information of full length cPLA2alpha apo form, shows that it is composed of two domains; an N-terminal Ca2 + binding C2 domain and a C-terminal alpha/beta hydrolase core. This entry describes the N-terminal Ca2+ binding C2 domain which is composed of an eight-stranded antiparallel beta-sandwich consisting of two four-stranded beta-sheets. C2 domains are present in many lipid-binding proteins including Copines, CAPRI and Rabphilin-3A all of which are involved in membrane trafficking.
Pfam PF09114: Transcription factor MotA, activation domain (domain)
Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2.
Pfam PF01616: Orbivirus NS3 (family)
The function of this Orbivirus non structural protein is uncertain.   However it may play a role on release of the virus from infected cells.
Pfam PF10621: F420H2 dehydrogenase subunit FpoO (family)
This is the FpoO subunit of F420H2 dehydrogenase, an enzyme which oxidises reduced coenzyme F420.  Reduced coenzyme F420 is a universal electron carrier in methanogens.
Pfam PF19742: Family of unknown function (DUF6231) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000387) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the mangotoxin biosynthetic gene cluster  from Pseudomonas syringae pv. syringae. This family appears to  be predominantly found in 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 PF00942: Cellulose binding domain (domain)
Carbohydrate-binding modules (CBM) have been classified into more than 40 families according to sequence homology. Several cellulolytic enzymes share a conserved region of about 150 amino acid residues, the CBM3 domain . It has been classified in three different subtypes, termed family IIIa, IIIb and IIIc. The family IIIa (scaffoldin) and IIIb (mainly free enzymes) are closely similar in their primary structures and both types bind strongly to crystalline cellulose . Members of the family IIIc, fail to bind crystalline cellulose, but serve in a 'helper' capacity by feeding a single incoming cellulose chain into the active site of the neighbouring catalytic module pending hydrolysis .

The CBM3 domain is mainly found C-terminal to the catalytic domain, which correspond to a wide range of bacterial glycosyl hydrolases like family 9, family 5 and family 10.

The crystal structure of CBM3 has been solved . It consists of nine Î²-strands which form a compact domain that has an overall prismatic shape. It is arranged in two antiparallel Î²-sheets that stack face-to-face to form a Î² sandwich with jelly roll topology. Two defined surfaces, located on opposite sides of the molecule, contain conserved polar and aromatic residues which are probably involved in the binding of the CBM to cellulose . The first one forms a planar strip whereas the second one forms a shallow groove.

Some proteins known to contain a CBM3 domain are listed below:


 * Clostridial cellulosomal scaffolding proteins cipA, cipC and cbpA. They promote the binding of cellulose to the catalytic domains of the cellulolytic enzymes.
 * Bacterial cellulases A, B, F, G, I, N, Y, Z (Endo-1,4-beta-glucanase, 3.2.1.4).


This entry represents the CBM3 domain, which is also known as cellulose-binding domain family III (CBD III).
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF02509: Rotavirus non-structural protein 35, C-terminal (domain)
Rotavirus non-structural protein 35 (NS35, also known as NSP2) is a basic protein which possesses RNA-binding and helix-destabilising activities in addition to nucleoside and 5' RNA triphosphatase (NTPase/RTPase) and nucleoside-diphosphate (NDP) kinase-like  activities. NS35 forms a functional octamer which is essential for genome replication and formation of viroplasms. This is the C-terminal domain, which has nucleotide triphosphatase (NTPase) and nucleoside diphosphate kinase (NDP kinase) activities, required for dsRNA synthesis. Additionally, basic residues in a C-terminal helix of this domain contributes to sequence-independent RNA binding of NSP2.
Wikipedia: NSP2 (NS35), is one of five to six nonstructural proteins expressed by rotaviruses. The octameric NSP2 performs several key functions in the assembly of rotavirus particles. This nonstructural RNA-binding protein accumulates in cytoplasmic inclusions (viroplasms) and is required for genome replication. NSP2 is closely associated in vivo with the viral replicase. The non-structural protein NSP5 plays a role in the structure of viroplasms mediated by its interaction with NSP2.
Pfam PF07460: NUMOD3 motif (conserved_site)
NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG ([pfam:PF01541]) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease ([swissprot:P13299]).
Pfam PF09306: Bacteriophage, scaffolding protein (domain)
Members of this family of scaffolding proteins are produced by various bacteriophages.
Pfam PF07754: Small zinc finger protein HVO_2753-like, Zn-binding pocket (domain)
This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes.
Pfam PF12771: Starch-binding associating with outer membrane (repeat)
SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane.
Pfam PF06380: Protein of unknown function (DUF1072) (family)
This family consists of several Barley yellow dwarf virus proteins of 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 PF14152: YfhE-like protein (family)
The YfhE-like protein family includes the B. subtilis YfhE protein [swissprot:O31573], which is functionally uncharacterised. Its expression may be regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved QEV sequence motif.
Pfam PF15892: BNR repeat-containing family member (repeat)
BNR_4 is a family which carries the unique sequence motif SxDxGxTW which is so characteristic of the repeats of the BNR family, [pfam:PF02012]. It is unclear whether or not this unit is repeated throughout the sequences of this family, but if it is then the family is likely to be bacterial neuraminidase.
Wikipedia: Bacterial neuraminidase is type of neuraminidase and a virulence factor for many bacteria including Bacteroides fragilis and Pseudomonas aeruginosa.
Its function is to cleave a sialic acid residue off ganglioside-GM1 turning it into asialo-GM1 to which type 4 pili bind preferentially.
Pfam PF08336: Prolyl 4-Hydroxylase alpha-subunit, N-terminal region (family)
The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme ([ec:1.14.11.2]) is important in the post-translational modification of collagen, as it catalyses the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known.
Pfam PF16146: Domain of unknown function (DUF4854) (family)
This family consists of uncharacterized proteins found in firmicutes and high GC Gram+ bacteria associated with human and animal guts. The function of this family is unknown.
Pfam PF18869: RnaseLS-like HEPN (family)
RnaseLS-like HEPN.
Pfam PF24934: Domain of unknown function (DUF7752) (domain)
This domain is found in a group of uncharacterised animal proteins that also contain [pfam:PF05183]. This domain is predicted to adopt a mainly alpha helical structure. Its specific function 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 PF05311: Baculovirus 33KDa late protein (PP31) (family)
Autographa californica nuclear polyhedrosis virus (AcMNPV) pp31 is a  nuclear phosphoprotein that accumulates in the virogenic stroma, which is the viral replication centre in the infected-cell nucleus, binds to DNA, and serves as a late expression factor.
Pfam PF24878: Putative mannosyltransferase YkcB-like, C-terminal (domain)
This domain is found at the C-terminal end of the putative mannosyltransferase YkcB from Bacillus subtilis and similar sequences. This domain is predicted to adopt an alpha-beta configuration. It is usually found associated with [pfam:PF13231].
Pfam PF04867: Protein of unknown function (DUF643) (family)
Protein of unknown function found in Borrelia burgdorferi, the Lyme disease spirochete.
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.