SII-SWORD/CoKE huggingface dataset:
Pfam PF00996: GDP dissociation inhibitor (family)
Rab proteins constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic ; C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1 . REP-1 presents newly- synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction.

The mechanism of REP-1-mediated membrane association of Rab5 is similar to that mediated by Rab GDP dissociation inhibitor (GDI). REP-1 and Rab GDI also share other functional properties, including the ability to inhibit the release of GDP and to remove Rab proteins from membranes.

The crystal structure of the bovine alpha-isoform of Rab GDI has been determined to a resolution of 1.81A . The protein is composed of two main structural units: a large complex multi-sheet domain I, and a smaller Î±-helical domain II.

The structural organisation of domain I is closely related to FAD-containing monooxygenases and oxidases . Conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the domain . The two most conserved regions form a compact structure at the apex of the molecule; site-directed mutagenesis has shown these regions to play a critical role in the binding of Rab proteins .
Wikipedia: In molecular biology, the Guanosine dissociation inhibitors (GDIs) constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic. GDIs bind to the GDP-bound form of Rho and Rab small GTPases and not only prevent exchange, but also prevent the small GTPase from localizing at the membrane, which is their place of action. This inhibition can be removed by the action of a GDI displacement factor. GDIs also inhibit cdc42 by binding to its tail and preventing its insertion into membranes; hence it cannot trigger WASPs and cannot lead to nucleation of F-actin.
Pfam PF15913: Furin-like repeat, cysteine-rich (domain)
The furin-like cysteine rich region has been found in a variety of proteins from eukaryotes that are involved in the mechanism of signal transduction by receptor tyrosine kinases, which involves receptor aggregation.
Pfam PF23944: Profilin-like domain of unknown function (DUF7278) (domain)
This entry represents a domain found various uncharacterised bacterial proteins that according to ECOD adopts a profilin-like 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 PF22744: ToastRack found in some PspC (repeat)
This entry represents the ToastRack domain found fused to some PspC.
Pfam PF20995: Type VI lipase adapter protein Tla3, C-terminal (domain)
This entry represents the the C-terminal domain of Type VI lipase adapter protein Tla3, an adapter protein that targets and loads the Tle3 toxin onto the H2 type VI secretion system (H2-T6SS) machinery through an interaction with the TTR domain of VgrG2b and it seems to be specific for Tle3. This domain and its N-terminal ([pfam:PF11394]) are both required for the interaction with the toxin.
Pfam PF04631: Per os infectivity factor 2 (family)
This family includes several hypothetical baculoviral proteins, with predicted molecular weights of approximately 44 kD. Family members include per os infectivity factor 2 (PIF2). PIF2 forms a stable complex with PIF1, PIF3, PIF4 which is essential for oral infectivity of Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) in insect larvae, and P74 is also associated with this complex.
Pfam PF14595: Thioredoxin (family)
Wikipedia: The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.
Pfam PF03480: Bacterial extracellular solute-binding protein, family 7 (family)
This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes [swissprot:P37735], a C4-dicarboxylate-binding protein and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins.     Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component.
Wikipedia: Tripartite ATP-independent periplasmic transporters are a large family of solute transporters found in bacteria and archaea, but not in eukaryotes, that appear to be specific for the uptake of organic acids or related molecules containing a carboxylate or sulfonate group. They are unique in that they utilize a substrate binding protein (SBP) in combination with a secondary transporter.
Pfam PF10135: Rod binding protein (family)
Members of this family are involved in the assembly of the prokaryotic flagellar rod.
Pfam PF24985: Domain of unknown function (DUF7775) (domain)
This domain is found in uncharacterised insect proteins mainly from clade Diptera. It is predicted to fold into a four helical bundle which shares detectable similarity to Marvel-like domains. Some proteins contain two copies of this domain. It is likely to be associated with membrane.
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 PF12213: DNA polymerases epsilon N terminal (domain)
This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with [pfam:PF04042]. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains.
Pfam PF17801: Alpha galactosidase C-terminal beta sandwich domain (domain)
This domain is found at the C-terminus of alpha galactosidase enzymes.
Pfam PF19678: Family of unknown function (DUF6180) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042.
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 PF09609: CRISPR-associated protein, GSU0054 family (Cas_GSU0054) (family)
This entry represents a rare CRISPR-associated protein. So far, members are found in Geobacter sulfurreducens and in two unpublished genomes: Gemmata obscuriglobus and Actinomyces naeslundii. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins.
Pfam PF16518: T3SS negative regulator,GrlR (domain)
GrlR is a family of protobacterial type III secretion system negative regulators. Structurally, GrlR consists of a typical beta-barrel fold with eight beta-strands containing an internal hydrophobic cavity and a plug-like loop on one side of the barrel. Strong hydrophobic interactions between the two beta-barrels maintain its dimeric architecture. A unique surface-exposed EDED (Glu-Asp-Glu-Asp) motif is identified to be critical for GrlA-GrlR interaction and for the repressive activity of GrlR.  The locus of enterocyte effacement (LEE) is essential for virulence of enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). It encodes some 20 genes including an overall regulator ler and two others, GrlR and GrlA, that form the type three secretion system for infection. GrlR comlexes with GrlA to repress expression of ler. GrlA is found in family [pfam:PF00462].
Pfam PF04281: Mitochondrial import receptor subunit Tom22 (family)
The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins.  This family represents the Tom22 proteins.  The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face.
Wikipedia: The translocase of the outer membrane (TOM) is a complex of proteins found in the outer mitochondrial membrane of the mitochondria. It allows movement of proteins through this barrier and into the intermembrane space of the mitochondrion. Most of the proteins needed for mitochondrial function are encoded by the nucleus of the cell. The outer membrane of the mitochondrion is impermeable to large molecules greater than 5000 daltons. The TOM works in conjunction with the translocase of the inner membrane (TIM) to translocate proteins into the mitochondrion. Many of the proteins in the TOM complex, such as TOMM22, were first identified in Neurospora crassa and Saccharomyces cerevisiae. Many of the genes encoding these proteins are designated as TOMM (translocase of the outer mitochondrial membrane) complex genes.
Pfam PF08740: BCS1 N terminal (domain)
This domain is found at the N terminal of the mitochondrial ATPase BSC1.  It encodes the import and intramitochondrial sorting for the protein.
Wikipedia: Mitochondrial chaperone BCS1 (BCS1L), also known as BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone (h-BCS1), is a protein that in humans is encoded by the BCS1L gene. BCS1L is a chaperone protein involved in the assembly of Ubiquinol Cytochrome c Reductase, which is located in the inner mitochondrial membrane and is part of the electron transport chain. Mutations in this gene are associated with mitochondrial complex III deficiency, GRACILE syndrome, and Bjoernstad syndrome.
Pfam PF04801: RPC5 protein (family)
This family represents the RPC5 protein which is part of the RNA polymerase III complex.
Pfam PF17575: Family of unknown function (DUF5479) (family)
This is a family of unknown function found in Kappa-papillomavirus.
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 PF22027: NS3 RNA helicase, C-terminal helical domain (domain)
This entry represents the C-terminal all-alpha helical domain (referred to as domain 3) of hepatitis C virus RNA helicase (NS3). NS3 helicase consists of three domains, separated by a series of clefts. Bound ssDNA lies in a channel that separates domain 3 from domains 1 and 2. The 5' end of the oligonucleotide resides at the interface of domains 2 and 3 and its 3' end is positioned at the interface of domains 1. This domain is associated with domain 2 by a pair of antiparallel beta-strands.
Pfam PF22002: Mitoregulin (family)
This family represents human Mitoregulin (MTLN) and similar proteins predominantly found in vertebrates. MTLN has a regulatory role in adipocyte metabolism. This microprotein interacts directly with the beta subunit of the mitochondrial trifunctional protein, an enzyme critical in the beta-oxidation of long-chain fatty acids. It also increases mitochondrial membrane potential while decreasing mitochondrial reactive oxygen species.
Pfam PF21103: SSRP1 PH domain (domain)
SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. This entry represents the first of two PH-like domains in these proteins.
Pfam PF22402: Coat protein, P (projecting) domain (domain)
This entry represents the P (projecting) domain found at the C-terminal of ssRNA positive-strand viruses coat protein, such as that in tomato bushy stunt virus.
Pfam PF11497: NADH-quinone oxidoreductase chain 15 (family)
This protein, Nqo15, is a part of respiratory complex 1 which is a complex that plays a central role in cellular energy production in both bacteria and mitochondria. Nqo15 has a similar fold to Frataxin, the mitochondrial iron chaperone. This protein may have a role in iron-sulphur cluster regeneration in the complex. This domain represents more than half the molecular mass of the entire complex.
Pfam PF15015: Spermatogenesis-associated, N-terminal (family)
NYD-SP12, also known as SPATA16, is a germ-cell specific participant in the Golgi apparatus, and its expression is confined to spermatogenic epithelium, not being found in interstitial cells.  Computer analysis of the protein-sequence showed that NYD-SP12 contains a cluster of phosphorylation sites for protein kinase C as well as for cyclic nucleotide-dependent protein kinases. It is postulated that since the mutation of some Golgi apparatus' proteins are responsible for male infertility that NYD-SP12 might play a role in modification and sorting of acrosomal enzymes. OMIM:102530.
Pfam PF22031: Major capsid protein V20 C-terminal domain (domain)
This is the C-terminal domain of major capsid protein V20. This domain folds into a beta-sandwich with a jelly-roll topology.
Pfam PF22638: Flagellar hook-associated protein FlgK helical domain (domain)
This entry represents a mainly helical domain found in flagellar hook-associated protein FlgK and related proteins. FlgK is one of three hook associated proteins that form the hook-filament junction. This domain adopts a broken antiparallel helical bundle comprising six helical segments.
Pfam PF03822: NAF domain (domain)
The NAF domain is a 24 amino acid domain that is found in a plant-specific subgroup of serine-threonine protein kinases (CIPKs), that interact with calcineurin B-like calcium sensor proteins (CBLs). Whereas the N-terminal part of CIPKs comprises a conserved catalytic domain typical of Ser-Thr kinases, the much less conserved C-terminal domain appears to be unique to this subgroup of kinases. The only exception is the NAF domain that forms an 'island of conservation' in this otherwise variable region. The NAF domain has been named after the prominent conserved amino acids Asn-Ala-Phe. It represents a minimum protein interaction module that is both necessary and sufficient to mediate the interaction with the CBL calcium sensor proteins .

The secondary structure of the NAF domain is currently not known, but secondary structure computation of the C-terminal region of Arabidopsis thaliana CBL-interacting protein kinase 1 revealed a long helical structure .
Pfam PF24101: GTF3C1, extended winged-helix domain (domain)
This is the extended winged-helix domain (eWH) of human General transcription factor 3C polypeptide 1 (GTF3C1), a component of TFIIIC that initiates transcription complex assembly on tRNA and is required for transcription of 5S rRNA and other stable nuclear and cytoplasmic RNAs.
Pfam PF09294: Interferon-alpha/beta receptor, fibronectin type III (domain)
Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha.
Wikipedia: Type II cytokine receptors, also commonly known as class II cytokine receptors, are transmembrane proteins that are expressed on the surface of certain cells. They bind and respond to a select group of cytokines including interferon type I, interferon type II, interferon type III. and members of the interleukin-10 family These receptors are characterized by the lack of a WSXWS motif which differentiates them from type I cytokine receptors.
Pfam PF03062: MBOAT, membrane-bound O-acyltransferase family (family)
The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue.
Wikipedia: The MBOAT family of membrane proteins is a family of various acyltransferase enzymes. All family members contain multiple transmembrane domains and most carry two conserved residues, a conserved histidine (His) embedded in a hydrophobic stretch of residues and an asparagine (Asn) or histidine within a more hydrophilic region some 30-50 residues upstream.
Pfam PF23492: Bacterial PH domain (domain)
This entry represents a bacterial PH domain found in a group of proteins containing a Peptidase M48 domain.
Pfam PF20149: Domain of unknown function (DUF6532) (domain)
This entry represents a large family of uncharacterised fungal 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 PF03996: Hemagglutinin esterase (domain)
Haemagglutinin-esterase fusion glycoprotein (HEF) is a multi-functional protein embedded in the viral envelope of several viruses, including influenza C virus, coronaviruses and toroviruses . HEF is required for infectivity, and functions to recognise the host cell surface receptor, to fuse the viral and host cell membranes, and to destroy the receptor upon host cell infection. The haemagglutinin region of HEF is responsible for receptor recognition and membrane fusion, and bears a strong resemblance to the sialic acid-binding haemagglutinin found in influenza A and B viruses, except that it binds 9-O-acetylsialic acid. The esterase region of HEF is responsible for the destruction of the receptor, an action that is carried out by neuraminidase in influenza A and B viruses. The esterase domain is similar in structure to Streptomyces scabies esterase, and to acetylhydrolase, thioesterase I and rhamnogalacturonan acetylesterase.

The haemagglutinin-esterase glycoprotein HEF must be cleaved by the host's trypsin-like proteases to produce two peptides (HEF1 and HEF2) in order for the virus to be infectious. Once HEF is cleaved, the newly exposed N-terminal of the HEF2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the virus to infect the host cell.

The haemagglutinin-esterase glycoprotein is a trimer, where each monomer is composed of three domains: an elongated stem active in membrane fusion, an esterase domain, and a receptor-binding domain, where the stem and receptor-binding domains together resemble influenza A virus haemagglutinin. Two of these domains are composed of non-contiguous sequence: the receptor-binding haemagglutinin domain is inserted into a surface loop of the esterase domain, and the esterase domain is inserted into a surface loop of the haemagglutinin stem.
Pfam PF13368: Topoisomerase C-terminal repeat (domain)
This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif.
Pfam PF18985: Family of unknown function (DUF5718) (family)
This is a family of unknown function, mostly found in bacteria.
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 PF01466: Skp1 family, dimerisation domain (domain)
SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex . It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex  and is also involved in the ubiquitin pathway . In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 .
This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins , as well as in subunit D of the centromere DNA-binding protein complex Cbf3 . This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.
Pfam PF09299: Mu transposase, C-terminal (domain)
Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology.
Pfam PF22616: HMD N-terminal domain (domain)
This entry represents the N-terminal domain of 5,10-methenyltetrahydromethanopterin hydrogenase (HMD) and related proteins, an enzyme of the methanogenic energy metabolism. HMD is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron. This domain has a Rossmann fold-like structure that contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor.
Pfam PF06876: Plant self-incompatibility response (SCRL) protein (domain)
This family consists of several Plant self-incompatibility response (SCRL) proteins. The male component of the self-incompatibility response in Brassica has been shown to be encoded by the S locus cysteine-rich gene (SCR). SCR is related, at the sequence level, to the pollen coat protein (PCP) gene family whose members encode small, cysteine-rich proteins located in the proteo-lipidic surface layer (tryphine) of Brassica pollen grains.