SII-SWORD/CoKE huggingface dataset:
Pfam PF01248: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (domain)
This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118.
Pfam PF16549: Type II secretion system (T2SS) pilotin, S protein (domain)
T2S_S is the S protein or pilotin of the bacterial Gram-negative secretion system in Vibrio and some E.coli and Shigella. It is given the suffix _2 to distinguish it from the PulS_OutS family of pilotins from Klebsiella and Dickeya, etc. AspS is functionally equivalent and yet structurally unrelated to the pilotins found in Klebsiella and other bacteria. AspS binds to a specific targeting sequence in the Vibrio-type secretins, enhancing the kinetics of secretin assembly; homologues of AspS are found in all species of Vibrio as well those few strains of Escherichia and Shigella that have acquired a Vibrio-type T2SS. PulS is the Kelbsiella pilotin, found in PulS_OutS, [pfam:PF09691]. Not all species with a type II secretion system have this pilotin or S protein.
Pfam PF06723: MreB/Mbl protein (family)
This family consists of bacterial MreB and Mbl proteins as well as two related archaeal sequences. MreB is known to be a rod shape-determining protein in bacteria and goes to make up the bacterial cytoskeleton. Genes coding for MreB/Mbl are only found in elongated bacteria, not in coccoid forms. It has been speculated that constituents of the eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today's bacterial proteins FtsZ and MreB/Mbl.
Wikipedia: MreB is a protein found in bacteria that has been identified as a homologue of actin, as indicated by similarities in tertiary structure and conservation of active site peptide sequence. The conservation of protein structure suggests the common ancestry of the cytoskeletal elements formed by actin, found in eukaryotes, and MreB, found in prokaryotes. Indeed, recent studies have found that MreB proteins polymerize to form filaments that are similar to actin microfilaments. It has been shown to form multilayer sheets comprising diagonally interwoven filaments in the presence of ATP or GTP.
Pfam PF13872: P-loop containing NTP hydrolase pore-1 (domain)
This entry represents the AAA domain found in Strawberry notch protein.
Strawberry notch proteins carry DExD/H-box groups and helicase C-terminal domains. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes . Strawberry notch was first identified in Drosophila where functions downstream of Notch and regulates gene expression during development .
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF18995: Proteolysis_6 C-terminal (domain)
This is the C-terminal domain mainly found in E3 ubiquitin ligases. Proteolysis 6 (PRT6) encodes a ubiquitin E3 ligase belonging to the N-end rule pathway of targeted protein degradation, which is a specialised subset of the ubiquitin proteasome system. In Arabidopsis, at least two N-recognins (E3 ubiquitin ligases) with different substrate specificities exist, namely PROTEOLYSIS1 (PRT1) and PRT6.
Pfam PF17282: Family of unknown function (DUF5347) (family)
This family of unknown function is found in Bacteria, mainly 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 PF02818: PPAK motif (conserved_site)
These motifs are found in the PEVK region of titin.
Pfam PF00344: SecY (family)
This family consists of the protein translocase subunit SecY and protein transport protein Sec61 subunit alpha (Sec61a).

Sec61a is part of the Sec61 complex, which plays a crucial role in the insertion of secretory and membrane polypeptides into the ER. It is required for assembly of membrane and secretory proteins.
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains . Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices.
Wikipedia: The SecY protein is the main transmembrane subunit of the bacterial Sec export pathway and of a protein-secreting ATPase complex, also known as a SecYEG translocon. Homologs of the SecYEG complex are found in eukaryotes and in archaea, where the subunit is known as Sec61α.
Pfam PF06106: S. aureus uracil DNA glycosylase inhibitor (domain)
Uracil-DNA glycosylase inhibitors, are DNA mimic proteins that prevent the DNA binding sites of UDGs (Uracil DNA glycosylase) from interacting with their DNA substrate. SSP0047 [swissprot:Q4A134] (or SAUGI; for Staphylococcus aureus uracil-DNA glycosylase inhibitor) acts as a uracil-DNA glycosylase inhibitor that breaks the uracil-removing activity of S. aureus uracil-DNA glycosylase (SAUDG) [pfam:PF03167]. The SAUGI/SAUDG complex has been determined, and shows that SAUGI binds to the SAUDG DNA binding region via several strong interactions, by using a hydrophobic pocket to hold SAUDG's protruding residue (i.e. SAUDG Leu184, E. coli UDG Leu191 and B. subtilis UDG Phe191). By binding to SAUDG in this way, SAUGI thus prevents SAUDG from binding to its DNA substrate and performing DNA repair activity.
Pfam PF08221: RNA polymerase III subunit RPC82 helix-turn-helix domain (domain)
This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix.
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 PF15793: Shieldin complex subunit 2, C-terminal (domain)
This entry represents the C-terminal OB fold domain found in Shieldin complex subunit 2 (SHLD2, formerly known as FAM35A). SHLD2 is a component of the shieldin complex, which plays an important role in repair of DNA double-stranded breaks (DSBs).
Pfam PF10903: Protein of unknown function (DUF2691) (family)
This bacterial 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 PF08736: FERM adjacent (FA) (family)
This region is found adjacent to Band 4.1 / FERM domains ([pfam:PF00373]) in a subset of FERM containing protein.  The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates.
Pfam PF22034: Uncharacterized protein B-129, C2H2 zinc finger (domain)
This entry represents a C2H2 zinc finger found at the C-terminal of of poorly characterised viral proteins,  including the uncharacterised protein B-129 from Sulfolobus spindle-shape virus 1 (SSV1).
Pfam PF21349: Rubrerythrin, rubredoxin-like domain (domain)
Rubrerythrin (RUBY) is a fusion protein containing an N-terminal diiron-binding domain ([pfam:PF02915]) and a C-terminal rubredoxin-like domain. RUBY may play a role in oxidative stress.  This entry represents the rubredoxin-like domain of RUBY and reverse rubrerythrin 1/2 from Clostridium acetobutylicum (RRBR1/2). RRBRs function as the terminal component of an NADH peroxidase when using NADH:rubredoxin oxidoreductase (NROR) as the electron transport intermediary from NADH to RRBRs and play an important role in the oxidative stress defense system of C. acetobutylicum.
Pfam PF18253: Hsp70-interacting protein N N-terminal domain (domain)
This is the N-terminal domain, known as HipN, found in Hsp70-interacting protein (Hip) present in Rattus norvegicus. Hip cooperates with the chaperone Hsp70 in protein folding and prevention of aggregation and may delay substrate release by slowing ADP dissociation from Hsp70. HipN is responsible for N-terminal homo-dimerization which is necessary so that the Hip dimer can interact with Hsp70 molecules.
Pfam PF01975: Survival protein SurE (domain)
E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase.  It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family [swissprot:P38254].  [swissprot:P30887] can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases.
Wikipedia: In molecular biology, the protein domain surE refers to survival protein E. It was originally found that cells that did not contain this protein, could not survive in the stationary phase, at above normal temperatures, and in high-salt media. Hence the name, survival protein E. It is a metal ion-dependent phosphatase that is found in bacteria, and eukaryotes. It is an important stress response protein. This domain is found in acid phosphatases, 5'-nucleotidases, 3'-nucleotidases and exopolyphosphatases.
Pfam PF23872: Domain of unknown function (DUF7227) (domain)
This domain of unknown function is found in various phage and bacterial proteins. The domain length ranges from approximately 200 to 260 amino 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 PF03341: Poxvirus mRNA capping enzyme, small subunit (family)
The small subunit of the poxvirus mRNA capping enzyme has been found to have a structure which suggests that it started life as an RNA cap 2-prime O-methyltransferase. It has subsequently evolved to a catalytically inactive form that has been retained in order to help stabilise the large subunit, D1, and to enhance its methyltransferase activity through an allosteric mechanism.
Pfam PF06574: FAD synthetase (family)
This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity.  They catalyse the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD.  This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity.
Wikipedia: The prokaryotic riboflavin biosynthesis protein is a bifunctional enzyme found in bacteria that catalyzes the phosphorylation of riboflavin into flavin mononucleotide (FMN) and the adenylylation of FMN into flavin adenine dinucleotide (FAD). It consists of a C-terminal riboflavin kinase and an N-terminal FMN-adenylyltransferase. This bacterial protein is functionally similar to the monofunctional riboflavin kinases and FMN-adenylyltransferases of eukaryotic organisms, but only the riboflavin kinases are structurally homologous.
Pfam PF14932: HAUS augmin-like complex subunit 3 (family)
This domain is subunit three of the augmin complex found from Drosophila to humans. The HAUS-augmin complex is made up of eight subunits.     The augmin complex interacts with gamma-TuRC, and attenuation of this interaction severely impairs spindle MT generation. Furthermore, we provide evidence that human augmin plays critical and non-redundant roles in the kinetochore-MT attachment and also central spindle formation during anaphase in human cells.The HAUS complex is required for mitotic spindle assembly and for maintenance of centrosome integrity.
Pfam PF19765: Family of unknown function (DUF6252) (family)
This family of proteins found in bacteria is functionally uncharacterised. Proteins in this family are typically between 166 and 277 amino acids in length. A conserved glycine residue and the conserved sequences GTF and GxF can be found at the C-terminal.
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 PF11994: Protein of unknown function (DUF3489) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W 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 PF16491: CAAX prenyl protease N-terminal, five membrane helices (domain)
The five N-terminal five transmembrane alpha-helices of peptidase_M48 family proteins including the CAAX prenyl proteases reside completely within the membrane of the endoplasmic reticulum.
Pfam PF12515: Ca2+-ATPase N terminal autoinhibitory domain (family)
This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with [pfam:PF00689], [pfam:PF00122], [pfam:PF00702], [pfam:PF00690]. There is a conserved RRFR sequence motif. There are two completely conserved residues (F and W) that may be functionally important. This family is the N terminal autoinhibitory domain of an endosomal Ca2+-ATPase.
Pfam PF06160: Septation ring formation regulator, EzrA (family)
During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site.  EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats.
Pfam PF16612: C-terminal unstructured region of RGS12 (disordered)
RGS12_usC is a region of Regulator of G-protein signalling 12 proteins that is natively unstructured and lies at the very C-terminus. It has a highly conserved central section. The function is not known.
Pfam PF21954: TUNAR (family)
This protein family includes the human protein TUNAR and similar sequences from vertebrates. TUNAR is a 48-amino-acid micropeptide with a single-pass transmembrane domain involved in the regulation of intracellular calcium levels in neurons and in the endoplasmic reticulum of pancreatic beta cells, where it also enhances glucose-stimulated insulin secretion.
Pfam PF12520: Protein of unknown function (DUF3723) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 374 and 1069 amino acids in length. There is a conserved LGF sequence 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 PF23444: Family of unknown function (DUF7127) (family)
This family represents a group of proteins from halobacteria. Members adopt a beta configuration with high similarity to the CS domain ([pfam:PF04969]).
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 PF19464: Family of unknown function (DUF6001) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000919) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family  includes a protein from the phaseolotoxin biosynthetic gene cluster  from Pseudomonas syringae.
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 PF19899: Family of unknown function (DUF6372) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis.
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 PF19415: Astrovirus transmembrane protein 1A (family)
This entry represents the transmembrane protein 1A from human astrovirus. This protein is part of the non-structural 1a polyprotein.
Pfam PF05058: ActA Protein (family)
The ActA family is found in Listeria and is associated with motility. ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerisation and propulsion of the bacterium through the cytoplasm of the host cell.
Pfam PF22267: Transcriptional regulator MlrA, C-terminal domain (domain)
The HTH transcription regulator MlrA belongs to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by re configuring the spacer between the -35 and -10 promoter elements. MlrA it is also known as YehV, and has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella yphimurium. MlrA is part of a signaling cascade that regulates curli biosynthesis. These proteins have dissimilar C-terminal domains bind specific coactivator molecules. This entry represents the C-terminal domain, which is structurally similar to a B12 binding domain ([pfam:PF02310]).
Pfam PF16363: GDP-mannose 4,6 dehydratase (domain)
This entry represents NAD- and NADP-binding domains with a core Rossmann-type fold, which consists of 3-layers Î±/Î²/Î±, where the six Î²-strands are parallel in the order 321456. Many different enzymes contain an NAD/NADP-binding domain, including:


 * C-terminal domain of alcohol dehydrogenases 
 * Tyrosine-dependent oxidoreductases (also known as short-chain dehydrogenases) 
 * N-terminal domain of glyceraldehyde-3-phosphate dehydrogenase 
 * NAD-binding domain of formate/glycerate dehydrogenases 
 * N-terminal domain of sirohaem synthase 
 * N-terminal domain of lactate dehydrogenase 
 * N-terminal domain of 6-phosphogluconate dehydrogenase (the Î²-sheet is extended to 8 strands) 
 * C-terminal domain of amino acid dehydrogenases (an extra N-terminal helix displaces the C-terminal helix 
 * NAD-binding domain of certain potassium channels 
 * C-terminal domain of the transcriptional repressor Rex 
 * Ornithine cyclodeaminase 
 * CoA-binding N-terminal domain of the alpha chain of succinyl-CoA synthetase
Pfam PF06856: Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17 (family)
This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17; it is a family of uncharacterised viral proteins.
Pfam PF15561: Immunity protein 15 (family)
A predicted immunity protein with an alpha+beta fold and several conserved polar and hydrophobic residues. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems.
Pfam PF07293: Protein of unknown function (DUF1450) (family)
This family consists of several hypothetical bacterial proteins of around 80 residues in length. Members of this family contain four highly conserved cysteine residues. 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 PF24604: PelB, C-terminal beta barrel domain (domain)
This transmembrane beta-barrel domain is found at the C-terminal end of PelB from Pseudomonas aeruginosa and similar proteins from proteobacteria. PelB plays a key role in biofilm formation in this organism.