SII-SWORD/CoKE huggingface dataset:
Pfam PF04333: MlaA lipoprotein (family)
MlaA is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. MlaA is required for the intercellular spreading of Shigella flexneri. It is attached to the outer membrane by a lipid anchor.
Wikipedia: General bacterial porins are a family of porin proteins from the outer membranes of Gram-negative bacteria. The porins act as molecular filters for hydrophilic compounds. They are responsible for the 'molecular sieve' properties of the outer membrane. Porins form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Some porins form general diffusion channels that allow any solute up to a certain size to cross the membrane, while other porins are specific for one particular solute and contain a binding site for that solute inside the pores. As porins are the major outer membrane proteins, they also serve as receptor sites for the binding of phages and bacteriocins.
Pfam PF08220: DeoR-like helix-turn-helix domain (domain)
The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain ofvabout 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively.

DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping .

It is worth noting that the DeoR in this entry is represented by the protein, UniProt P0ACK5, from E. coli. Not the DeoR, UniProt P39140, from Bacillus subtilis. Despite sharing the same name, these two proteins do not share protein sequence similarity .
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 PF21004: mRNA capping enzyme catalytic subunit, GTase, NTPase domain (domain)
mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module ([pfam:PF03291]). The N-terminal module comprises a TPase domain ([pfam:PF10640]), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, this entry) and OB fold ([pfam:PF21005]) domains. The TPase and GTase modules stabilize their active conformations and their contacts also clamp the NTase and OB fold.
Pfam PF19075: Family of unknown function (DUF5771) (family)
This is a family of uncharacterised proteins of unknown function found in viruses which apparently has N-acetyltransferase activity.
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 PF13074: Protein of unknown function (DUF3938) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.
Pfam PF07694: 5TMR of 5TMR-LYT (domain)
This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type).
Pfam PF02840: Prp18 domain (family)
The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles.
Pfam PF02687: FtsX-like permease C-terminal (domain)
This entry represents the C-terminal helices found in members of the ABC type 3 transporter family of permeases, including Cell division protein FtsX from Gram-negative and Gram-positive bacteria, Permease protein MacB, Lipoprotein-releasing system transmembrane protein LolC ([swissprot:P57382]) which  has been shown to transport lipids targeted to the outer membrane across the inner membrane. This region contains three transmembrane helices.
Pfam PF24388: Permuted GreAB-C (domain)
This is a circular permuted GreAB-C-domain in antiviral immunity systems featuring TPR-repeats, a GreA/B-C-terminal domain and a PIN domain, with a variable N-terminal domain often harbouring effector domains.
Pfam PF14819: Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term (domain)
The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets.
Pfam PF07885: Ion channel (family)
This family includes the two membrane helix type ion channels found in bacteria.
Wikipedia: The transmembrane cation channel superfamily was defined in InterPro and Pfam as the family of tetrameric ion channels. These include the sodium, potassium, calcium, ryanodine receptor, HCN, CNG, CatSper, and TRP channels. This large group of ion channels apparently includes families 1.A.1, 1.A.2, 1.A.3, and 1.A.4 of the TCDB transporter classification.
Pfam PF17974: Galactose-binding domain-like (domain)
Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase, phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va, membrane-anchored ephrin for the Eph family of receptor tyrosine kinases, and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1. The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold.
Pfam PF17933: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in Rv1219c of Mycobacterium tuberculosis.  Structural studies indicate that the helix alpha 10 of the C-terminal end of Rv1219c forms a long arm feature, a feature which is unique in Rv1219c compared to some other members of the TetR family. Furthermore, it has been shown that substrate binding occurs in the C-terminal regulatory domain of Rv1219c.
Pfam PF22664: Trichothecene 3-O-acetyltransferase-like N-terminal domain (domain)
This entry represents the N-terminal domain of trichothecene 3-O-acetyltransferase from Fusarium graminearum and its homologues. These proteins consist of N- and C-terminal ([pfam:PF02458]) domains arranged in a doughnut-form. The active site lies in the doughnut-hole formed by the interface between these domains.
Pfam PF18044: CCCH-type zinc finger (domain)
This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases.
Pfam PF23407: Apc4 WD40 domain C-terminal half, fungal (repeat)
Apc4 is a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This complex acts by ubiquitination and degradation of target proteins. Apc4 consists of a beta-propeller that is split by a long alpha-helical domain ([pfam:PF12816]) which generate an L-shaped molecule. APC4 interacts with APC5; the N-terminal of APC1  serves to stabilise the union between APC4 and APC5, both of which lie towards the bottom-front of the APC. This entry represents the C-terminal half of the beta-propeller of Apc4 from S.pombe and related fungal sequences, that are not recognised in [pfam:PF23405].
Pfam PF17578: Family of unknown function (DUF5481) (family)
This is a family of unknown function found in Myoviridae.
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 PF05683: Fumarase C-terminus (family)
This family consists of the C terminal region of several bacterial fumarate hydratase proteins (FumA and FumB). Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth.
Pfam PF18250: Effector immunity protein Tgi2PP (domain)
This domain is Tgi2PP found in Pseudomonas protegens. Tgi2PP is part of the Tge2PP- Tgi2PP Effector-immunity pair secreted by the type VI secretion system (T6SS). Tgi2PP interacts predominantly by hydrogen bonding and hydrophobic interactions with Tge2PP via the insertion of the beta-sheet core of Tgi2PP into the substrate-binding groove of Tge2PP. Tgi2PP contains a similar topology to the periplasmic E. coli colicin M immunity protein.
Pfam PF01179: Copper amine oxidase, enzyme domain (domain)
Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyse the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme.
Wikipedia: Amine oxidase (copper-containing) (AOC) (EC 1.4.3.21 and EC 1.4.3.22; formerly EC 1.4.3.6) is a family of amine oxidase enzymes which includes both primary-amine oxidase and diamine oxidase; these enzymes catalyze the oxidation of a wide range of biogenic amines including many neurotransmitters, histamine and xenobiotic amines. They act as a disulphide-linked homodimer. They catalyse the oxidation of primary amines to aldehydes, with the subsequent release of ammonia and hydrogen peroxide, which requires one copper ion per subunit and topaquinone as cofactor:RCH2NH2 + H2O + O2  RCHO + NH3 + H2O2
Pfam PF01984: Double-stranded DNA-binding domain (family)
This domain is believed to bind double-stranded DNA of 20 bases length.
Pfam PF11817: Foie gras liver health family 1 (repeat)
Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first. The C-terminus of this region contains TPR repeats.
Pfam PF13841: Beta defensin (domain)
The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonisation.
Wikipedia: Beta defensins  are a family of vertebrate defensins. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization.
Pfam PF24086: Domain of unknown function (DUF7371) (domain)
This domain is found in uncharacterised proteins mainly from fungi. It is predicted to adopt a beta-sandwich with similarity to galactose-binding 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 PF09627: PrgU-like protein (domain)
PrgU is a protein of plasmid in origin expressed mainly in Enterococcus bacteria. It forms a six beta-strand barrel with three accompanying alpha helices and is probably a homo-dimer in the cell. PrgU probably acts as a RNA-binding regulator that mitigates toxicity accompanying overproduction of PrgB-like adhesins, which are involved in conjugative transfer.
Pfam PF21795: Protein jagged-1-like, atypical EGF2 (domain)
This domain is found in human Protein jagged-1 (JAG1) and similar sequences mainly found in animals. JAG1 is a ligand for multiple Notch receptors and involved in the mediation of Notch signalling. This protein shows a large extracellular region made of a poorly characterized N-terminal region ([pfam:PF07657]), a DSL (Delta/Serrate/Lag-2) domain ([pfam:PF01414]), a series of 16 epidermal growth factor (EGF) tandem repeats, and a cysteine-rich juxtamembrane region. This entry represents the second atypical EGF domain, which constitutes the receptor binding region of JAG1 together with the DSL domain and the first atypical EGF domain.
Pfam PF19745: Alpha-(1,6)-fucosyltransferase N- and catalytic domains (domain)
This entry represents the N-terminal coiled-coil and the catalytic domains of the Alpha-(1,6)-fucosyltransferase (FUT8), an enzyme that catalyses the transfer of a fucose residue in alpha 1-6 linkage to the N-Acetylglucosamine (GlcNAc) residue in N-glycans. The catalytic domain comprises two structures, an open sheet alpha/beta structure, which contains five helices and three beta- strands at the N-terminal, and a Rossmann fold that contains five helices and five beta-strands at the C-terminal. The latter is conserved among the alpha1,2-, alpha1,6-, and protein O-fucosyltransferases and is similar to GT-B group glycosyltransferases.
Pfam PF23733: GRXCR1, C-terminal (domain)
This domain is found at the C-terminal end of human Glutaredoxin domain-containing cysteine-rich protein 1 (GRXCR1) and similar eukaryotic sequences. GRXCR1 is thought to play a role in actin filament architecture in developing stereocilia of sensory cells. This domain is often found associated with [pfam:PF00462].
Pfam PF01357: Expansin C-terminal domain (domain)
This domain is found at the C-terminus of expansins, plant cell wall proteins involved in the non-enzymatic rearrangement of cell walls during cell growth. It contains the allergens lol PI, PII and PIII from Lolium perenne.
Pfam PF24976: Lipocalin domain (domain)
This entry represents a family of lipocalin domains usually found in nematode proteins.  Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel. In some proteins this domain is attached to Cullin-like domains suggesting a possible role in scaffolding E3 ligase complexes. This family appears to be most similar to [pfam:PF08212].
Wikipedia: The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron as well as heme. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.
Pfam PF05057: Putative serine esterase (DUF676) (family)
This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold.
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 PF14522: Cytochrome c7 and related cytochrome c (family)
This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated, while in c7-type the last haem is His-Met co-ordinated. Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity. This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA.
Pfam PF22064: Cep192 domain 2 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the second domain found in the metazoan Cep192 homologs.
Pfam PF19910: Domain of unknown function (DUF6383) (domain)
This presumed domain is functionally uncharacterised. This domain is mainly found at the C-terminal of uncharacterised proteins, predominantly from Bacteriodetes. It is about 74 amino acids in length and it contains the GQ and GxxV/IV conserved sequence motifs.  This domain has similarity to the Type IX secretion system targeting domain.
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 PF23202: ZNF598 PAH domain (repeat)
This PAH domain is found in human E3 ubiquitin-protein ligase ZNF598 and related eukaryotic proteins. ZNF598 plays a key role in the ribosome quality control (RQC), a pathway that takes place when the ribosome has stalled during translation, leading to degradation of nascent peptide chains. ZNF598 is activated when ribosomes are stalled following translation of prematurely polyadenylated mRNAs. Independently of its role in RQC, this protein may also act as a negative regulator of interferon-stimulated gene expression.
Pfam PF04475: Protein of unknown function (DUF555) (family)
Family of uncharacterised, hypothetical archaeal 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 PF05279: Aspartyl beta-hydroxylase N-terminal region (family)
This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyses the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins.
Pfam PF21093: Nucleoporin Nup188, N-terminal subdomain III (repeat)
Nup188 one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes. The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of the at least six that make up the NPC, and as such is symmetrically localised on both faces of the NPC at the nuclear end, being integrally bound to the C-terminus of Pom34p. This protein folds into an extended stack of helices where the N-terminal forms a closed ring (subdivided into subdomains I-III in) and the C-terminal forms a more regular, superhelical structure. This entry represents the helical segment of subdomain III described in, which consists of an array of HEAT and ARM repeats with an inserted SH3-like domain.
Pfam PF02538: Hydantoinase B/oxoprolinase (family)
This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase ([swissprot:P97608]) [ec:3.5.2.9] which catalyses the formation of L-glutamate from  5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to [pfam:PF01968].