SII-SWORD/CoKE huggingface dataset:
Pfam PF02888: Calmodulin binding domain (family)
Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.
Wikipedia: In molecular biology, calmodulin binding domain (CaMBD) is a protein domain found in small-conductance calcium-activated potassium channels (SK channels). These channels are independent of voltage and gated solely by intracellular Ca2+. They are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through the CaMBD, which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.
Pfam PF06598: Chlorovirus glycoprotein repeat (repeat)
This family consists of s number of repeats found in Chlorovirus glycoproteins. The function of this family is unknown.
Pfam PF16795: Archaeal phage integrase (domain)
Catalyses cleavage and ligation of DNA.
Pfam PF14443: DBC1 (domain)
DBC1 and it homologs from diverse eukaryotes are a catalytically inactive version of the Nudix hydrolase (MutT) domain. DBC1 is predicted to bind NAD metabolites and regulate the activity of SIRT1 or related deacetylases by sensing the soluble products or substrates of the NAD-dependent deacetylation reaction.
Pfam PF21153: NOL1/NOP2/Sun domain family member 5, N-terminal domain (domain)
NSUN5 (and the homologue from yeast RCM1) is a SAM-dependent methyltransferase that specifically methylates the C(5) position of cytosine 3782 in 28S rRNA. This is the N-terminal globular domain of NSUN5 which is required for targeting to nucleoli.
Pfam PF16367: RNA recognition motif (domain)
Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs . The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence . RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) . The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition . The motif also appears in a few single stranded DNA binding proteins.

The typical RRM consists of four anti-parallel Î²-strands and two Î±-helices arranged in a Î²-Î±-Î²-Î²-Î±-Î² fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases . The RRM is reviewed in a number of publications .

This entry also includes some bacterial putative RNA-binding proteins.
Pfam PF07347: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) (family)
This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) ([ec:1.6.5.3]). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane. The main function of the complex is the transport of electrons from NADH to ubiquinone, accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF02229: Transcriptional Coactivator p15 (PC4) (domain)
This domain is found at the C-terminal end of Activated RNA polymerase II transcriptional coactivator p15 from humans, YdbC from Lactococcus lactis, and other PC4 family members. p15 has a bipartite structure composed of an N-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. Activity is controlled by protein kinases that target the regulatory domain.
Pfam PF25054: PHD-type zinc finger (domain)
This presumed PHD-type zinc finger domain is found in a group of uncharacterised plant proteins.
Pfam PF11416: Syntaxin-5 N-terminal, Sly1p-binding domain (family)
Syntaxin-5_N is the Sed5 N-terminal and the N-terminus of Syntaxin-5-like proteins.  It is the region of Syntaxin that interacts with Sly1p, a positive regulator of intracellular membrane fusion, allowing SM (cytosolic Sec1/munc18-like) proteins to stay associated with the assembling fusion machinery. This allows the SM proteins to participate in late fusion steps.
Pfam PF06862: Utp25, C-terminal domain (domain)
UTP25 is a family of eukaryotic proteins. The family displays limited sequence similarity to DEAD-box RNA helicases, having alternative residues at the Walker A and DEAD-box sites, but conservation of structural and other key residues. The domain is required and sufficient for the interaction of Utp25 with Utp3. UTP25 interacts with nucleolar protein Nop19 in S. cerevisiae, and Nop19p is essential for the incorporation of Utp25p into pre-ribosomes. Proteins in this entry consist of two domains of which the C-terminal one is represented in this model.
Pfam PF18636: Mitochondrial morphogenesis protein SLD7 N-terminal domain (domain)
The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomes. Yeast Sld3 and its metazoan counterpart treslin are the hub proteins mediating protein associations critical for formation of the helicase. The Sld7 protein interacts with Sld3, and the complex formed is thought to regulate the function of Sld3. Although Sld7 is a non-essential DNA replication protein that is found in only a limited range of yeasts, its depletion slowed the growth of cells and caused a delay in the S phase. Structure analysis indicates that the N-terminal domain of Sld7 binds to the N-terminal region of Sld3.
Pfam PF14983: Sperm-associated microtubule inner protein 10 (family)
This family (previously DUF4513) represents homologs of Sperm-associated microtubule inner protein 10 (SPMIP10). SPMIP10 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs). It plays a role in the stabilisation of the interacting protomers of TEKTL1 - a tektin-like molecule that forms a filament in the cleft between protofilaments A11 and A12 . In the EM structure of sperm DMTs, SPMIP10 cradles the inter-TEKTL1 interface while interacting with protofilaments A11 and A12.
Pfam PF17625: Family of unknown function (DUF5509) (family)
This is a family of unknown function found in Baculoviridae.
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 PF12860: PAS fold (domain)
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.
Wikipedia: A Per-Arnt-Sim (PAS) domain is a protein domain found in all kingdoms of life. Generally, the PAS domain acts as a molecular sensor, whereby small molecules and other proteins associate via binding of the PAS domain. Due to this sensing capability, the PAS domain has been shown as the key structural motif involved in protein-protein interactions of the circadian clock, and it is also a common motif found in signaling proteins, where it functions as a signaling sensor.
Pfam PF17780: OCRE domain (domain)
The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands.
Pfam PF21927: Methyl-accepting chemotaxis protein McpB, second HAMP domain (domain)
This domain is found in Methyl-accepting chemotaxis protein McpB from Pseudomonas aeruginosa and similar sequences from proteobacteria. McpB, also known as Aerotaxis transducer Aer2, is a chemoreceptor that plays a critical role in the virulence and pathogenesis of the bacteria. This entry represents the second HAMP domain, which folds into a unique four-helix bundle that comparatively differs from the first and third HAMP domains of the same protein.
Pfam PF19544: Family of unknown function (DUF6068) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001902) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the bengamide  biosynthetic gene cluster from Myxococcus virescens and appears  to be predominantly found in cystobacterineae.
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 PF10233: Uncharacterized conserved protein CG6151-P (domain)
This is a family of small, less than 200 residue long, proteins which are named as CG6151-P proteins that are conserved from fungi to humans. The function is unknown.  The fungal members have a characteristic ICP sequence motif. Some members are annotated as putative clathrin-coated vesicle protein but this could not be defined.
Pfam PF09736: Pre-mRNA-splicing factor of RES complex (family)
This entry is characterised by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function.
Pfam PF03031: NLI interacting factor-like phosphatase (family)
This family contains a number of NLI interacting factor isoforms (eg. [swissprot:Q9PTJ8]) and also an N-terminal regions of RNA polymerase II CTC phosphatase ([swissprot:Q9Y5BO]) and FCP1 serine phosphatase ([swissprot:Q9PT70]). This region has been identified as the minimal phosphatase domain.
Pfam PF17493: Family of unknown function (DUF5428) (family)
This is a family of unknown function found in Betanecrovirus.
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 PF09375: Imelysin (family)
The imelysin peptidase was first identified in Pseudomonas aeruginosa. The active site residues have not been identified. However, His201 and Glu204 are completely conserved in the family and occur in an HXXE motif that is also found in family M14.
Pfam PF00601: Influenza non-structural protein (NS2) (family)
NS2 may play a role in promoting normal replication of the genomic RNAs by preventing the replication of short-length RNA species.
Pfam PF18209: Embryo surrounding factor 1 (domain)
This domain is Embryo surrounding factor 1 (ESF1) protein present in Arabidopsis thaliana. Maternally contributed central cell ESF1 peptides play an important role in suspensor formation and pro-embryo development. The biological activity of ESF1 depends on structural topology, which is stabilized by disulfide bonds.
Pfam PF07463: NUMOD4 motif (conserved_site)
NUMOD4 is a putative DNA-binding motif found in homing endonucleases and related proteins.
Pfam PF01910: Thiamine-binding protein (domain)
The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers.  Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions possibly regulated by the binding of small-molecule ligands. Solution of the structure of the hyperthermophilic anaerobic Thermotoga maritima sequence, UniProtKB:Q9WYV6, shows that this has a beta-alpha-beta-beta-alpha-beta ferredoxin-like fold and assembles as a homotetramer. It was possible to identify a pocket in each monmer that bound an unidentified ligand.  It was also found that it bound charged thiamine though not hydroxymethyl pyrimidine.  It is proposed that it is transporting charged thiamine around the cytoplasm. Under oxidative conditions this bacterium is under stress, and the transcriiptional unit within which this protein is expressed is up-regulated in these conditions, suggesting that the chelation of cytoplasmic thaimine is part of the response mechanism to such oxidatvie stress, which is mediated by this family.
Pfam PF00387: Phosphatidylinositol-specific phospholipase C, Y domain (family)
This associates with [pfam:PF00388] to form a single structural unit.
Wikipedia: Phosphoinositide phospholipase C is a family of eukaryotic intracellular enzymes that play an important role in signal transduction processes. These enzymes belong to a larger superfamily of Phospholipase C. Other families of phospholipase C enzymes have been identified in bacteria and trypanosomes. Phospholipases C are phosphodiesterases.
Pfam PF08516: ADAM cysteine-rich (family)
ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour.  It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity.
Wikipedia: ADAMs are a family of single-pass transmembrane and secreted metalloendopeptidases. All ADAMs are characterized by a particular domain organization featuring a pro-domain, a metalloprotease, a disintegrin, a cysteine-rich, an epidermal-growth factor like and a transmembrane domain, as well as a C-terminal cytoplasmic tail. Nonetheless, not all human ADAMs have a functional protease domain, which indicates that their biological function mainly depends on protein–protein interactions. Those ADAMs which are active proteases are classified as sheddases because they cut off or shed extracellular portions of transmembrane proteins. For example, ADAM10 can cut off part of the HER2 receptor, thereby activating it. ADAM genes are found in animals, choanoflagellates, fungi and some groups of green algae. Most green algae and all land plants likely lost ADAM proteins.
Pfam PF10383: Transcription-silencing protein Clr2 (family)
Clr2 is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Pfam PF24715: YxiF protein (domain)
This entry represents the uncharacterised YxiF protein from B. subtilis [swissprot:P42298].
Pfam PF10696: Protein of unknown function (DUF2501) (family)
Members of this family are all Proteobacteria. Several are annotated as being YjjA or YjjA-like, but this protein is uncharacterised.
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 PF19129: Family of unknown function (DUF5812) (family)
This is a family of unknown function predominantly found in Halobacteria.
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 PF05085: Protein of unknown function (DUF685) (family)
This family consists of several uncharacterised proteins from Borrelia burgdorferi (Lyme disease spirochete). There is some evidence to suggest that the proteins may be outer surface 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 PF09704: CRISPR-associated protein (Cas_Cas5) (family)
CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum.
Pfam PF22259: GPR128, GAIN subdomain A (domain)
GRP128, also known as Adhesion G-protein coupled receptor G7 (AGRG7), is an orphan receptor of the adhesion family (subclass B2) that belongs to class B GPCRs. Expression of GPR128 was detected in the mouse intestinal mucosa and is thought to be involved in energy balance. It consists of an N-terminal HormR-like domain, followed by the GAIN domain which consists of a stalk (comprising subdomains A and B) and a GPS motif. This entry represents the GAIN subdomain A of the stalk from GPR128 GAIN domain, which is all alpha-helical.
Pfam PF02931: Neurotransmitter-gated ion-channel ligand binding domain (family)
This family is the extracellular ligand binding domain of these ion channels.  This domain forms a pentameric arrangement in the known structure.
Wikipedia: Ligand-gated ion channels (LICs, LGIC), also commonly referred to as ionotropic receptors, are a group of transmembrane ion-channel proteins which open to allow ions such as Na+, K+, Ca2+, and/or Cl− to pass through the membrane in response to the binding of a chemical messenger (i.e. a ligand), such as a neurotransmitter.
Pfam PF22233: Response regulator PhyR, sigma-like domain (domain)
PhyR is a signal transduction response regulator found in Alphaproteobacteria with a C-terminal receiver domain ([pfam:PF00072]) and extracytoplasmic function (ECF) sigma factor-like domain at the N-terminal which is represented in this entry. PhyR is the regulator of the two-component signal transduction system which controls transcription in response to general stress.
Pfam PF18831: Leucine-rich repeat (repeat)
This Pfam entry includes some LRRs that fail to be detected with the [pfam:PF00560] model. This entry represents one repeat unit.
Pfam PF07324: DiGeorge syndrome critical region 6 (DGCR6) protein (family)
This family contains DiGeorge syndrome critical region 6 (DGCR6) proteins (approximately 200 residues long) of a number of vertebrates. DGCR6 is a candidate for involvement in the DiGeorge syndrome pathology by playing a role in neural crest cell migration into the third and fourth pharyngeal pouches, the structures from which derive the organs affected in DiGeorge syndrome. Also found in this family is the Drosophila melanogaster gonadal protein gdl.
Pfam PF05137: Fimbrial assembly protein (PilN) (family)
PilN forms a stable heterodimer with PilO through interaction of their periplasmic domains, being essential for the assembly of a functional complex. PilN requires PilO for a proper folding and they depend on each other for their stability . PilN also interacts with PilM causing conformational changes that allow PilM monomerisation.

This entry also includes Type II secretion system protein L. Type II secretion (T2S) and type IV pilus systems share evolutionary origins, being structurally and functionally related . DNA utilization protein HofN from E.coli is also included in this entry. It is involved in DNA uptake and DNA utilisation as a carbon and energy source, conferring competitive advantage. This protein is encoded by a gene homologue to com genes in Haemophilus influenzae, involved in pilus biogenesis, protein secretion, competence-transformation, and twitching motility .
Bacterial type IV pili are surface filaments critical for diverse biological processes including surface and host cell adhesion, colonisation, biofilm formation, twitching motility, DNA uptake during natural transformation and virulence . The proteins necessary to form the type IV pili inner-membrane complex, are included in the pilMNOPQ operon which encodes the cytoplasmic actin-like protein PilM, PilN, PilO, the periplasmic lipoprotein PilP and the outer-membrane secretin PilQ. The inner-membrane PilM/N/O/P complex is required for the optimal function of the outer-membrane secretin PilQ. This cluster is highly conserved across the type IV pilus-producing bacterial species, and all of these proteins have been shown to be essential for twitching motility .
Pfam PF16394: Domain of unknown function (DUF5003) (family)
This small family of proteins is functionally uncharacterised. This family is found in bacteroides. Proteins in this family are typically between 500 and 650 amino acids in length.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.