SII-SWORD/CoKE huggingface dataset:
Pfam PF03152: Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 (domain)
Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. UFD1 is a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated  with these conditions are thought to be due to defective neural crest cell differentiation. UFD1 is composed of an N-terminal conserved region (UT3) and a  C-terminal disordered region (UT6) which contains the binding sites for both Npl4 and Cdc48. UFD1 N-terminal domain contains the binding site for ubiquitin and has a similar structure to p97. It is made of two subdomains. This entry corresponds to the first subdomain of UFD1 UT3 which forms a double-psi beta barrel fold.
Pfam PF02115: RHO protein GDP dissociation inhibitor (domain)
The GDP dissociation inhibitor for rho proteins, rho GDI, regulates GDP/GTP exchange by inhibiting the dissociation of GDP from them. The protein contains 204 amino acids, with a calculated Mr value of 23,421. Hydropathy analysis shows it to be largely hydrophilic, with a single hydrophobic region. The protein plays an important role in the activation of the superoxide (O2-)-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21rac1 and rho GDI . The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI . Dissociation of these proteins might be mediated by the release of lipids (e.g., arachidonate and phosphatidate) from membranes through the action of phospholipases . The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.

Two homologues of rho GDP-dissociation inhibitors have been identified in Dicytostelium: GDI1 and GDI2. They are cytosolic proteins. GDI1 has been found to play a central role in cytokinesis through the regulation of Rho family GTPases Rac1s and/or RacE .

Rho GDI in yeast has been shown to have similar properties as mammalian rho GDI .
Wikipedia: RHO protein GDP dissociation inhibitor  of Rho proteins regulates GDP/GTP exchange. The protein plays an important role in the activation of the oxygen superoxide-generating NADPH oxidase of phagocytes. This process requires the interaction of membrane-associated cytochrome b559 with 3 cytosolic components: p47-phox, p67-phox and a heterodimer of the small G-protein p21Rac1 and rho GDI. The association of p21rac and GDI inhibits dissociation of GDP from p21rac, thereby maintaining it in an inactive form. The proteins are attached via a lipid tail on p21rac that binds to the hydrophobic region of GDI. Dissociation of these proteins might be mediated by the release of lipids from membranes through the action of phospholipases. The lipids may then compete with the lipid tail on p21rac for the hydrophobic pocket on GDI.
Pfam PF11557: Solitary outer membrane autotransporter beta-barrel domain (family)
Omp_AT is a family of Gram-negative Gamma-proteobacteria outer membrane autotransporter beta-barrel proteins. Secondary structure prediction indicates a beta-barrel domain of 12 beta-strands. with an N terminal helix running along the central barrel axis perpendicular to the 12 antiparallel strands that form the barrel. Autotransporter translocation units defined by a beta-barrel of 12 to 14 antiparallel strands with an N terminal helix perpendicular to the barrel.
Pfam PF07310: PAS domain (domain)
This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. This region is is distantly similar to other PAS domains.
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 PF11178: Protein of unknown function (DUF2963) (repeat)
This family of proteins with unknown function appears to be restricted to Mollicutes.
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 PF12621: Extracellular tail, of 10TM putative phosphate transporter (family)
This PHM7_ext family is found in plants and fungi. It represents the C-terminal extracellular domain of the putative phosphate transporter, PHM7. The three N-terminal TMS are found in family RSN1_TM, [pfam:PF02714]; the cytoplssmic domain is [pfam:PF14703], and the remaining 7TM region is in [pfam:PF02714].
Pfam PF19271: Nis1 family (domain)
Necrosis-inducing secreted protein 1 (Nis1) is a fungal secreted effector that induces necrotic lesions in plants it infects (2). This protein interacts with the host receptor-like kinases and inhibits their kinase activity.
Pfam PF12136: RNA polymerase Rpo13 subunit HTH domain (domain)
This domain is found in archaea, and is about 40 amino acids in length. It has a single completely conserved residue E that may be functionally important. It is found in the archaeal DNA dependent RNA polymerase. The domain is a 'helix-turn-helix' (HTH) domain in the Rpo13 subunit of the RNA polymerase. This domain is involved in downstream DNA binding, and the entire subunit has also been implicated in contacting transcription factor II B.
Pfam PF13207: AAA domain (domain)
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 PF20892: SidC, lipid-binding domain (domain)
SidC is one of the effectors delivered by Legionella pneumophila into the host cell. Like its paralogue SdcA, SidC anchor on the Legionella-containing vacuole (LCV) through binding to phosphatidylinositol-4-phosphate (PI(4)P) to facilitate the recruitment of endoplasmic reticulum (ER) proteins. SidC is organised into four domains that are packed into an arch-like shape: the N- terminal SNL domain ([pfam:PF18219]), the INS domain (which is inserted within the SNL domain), the PI(4)P binding domain or P4C domain (this entry), and a C-terminal domain ([pfam:PF20875]). The lipid binding domain shows a four alpha-helix bundle with one end sealed by a C-terminal short beta hairpin and a highly positively charged pocket at the other end formed by two loops connecting the alpha-helices. This pocket is thought to be the binding site, responsible for the stimulation of the E3 ligase activity of the SNL domain.
Pfam PF21946: LppM domain (domain)
This domain is found in LppM, a bacterial effector implicated in the early steps of Mycobacterium tuberculosis infection. LppM is anchored to the mycobacterial cell wall by a C-terminal membrane domain. An isoform that lacks the latter is secreted. This domain has unusual fold consisting of a beta-sandwich in which one of the sheets is extended with three strands packed with a helix. LppM is capable of binding phosphatidylinositol mannosides (PIM) derivatives.
Pfam PF15765: Domain of unknown function (DUF4694) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 154 and 217 amino acids in length. There is a conserved SSGY 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 PF10243: Microtubule-binding protein MIP-T3 CH-like domain (domain)
This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3.  The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved.
Pfam PF02384: N-6 DNA Methylase (family)
Restriction-modification (R-M) systems protect a bacterial  cell against invasion of foreign DNA by endonucleolytic  cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S ([pfam:PF01420]), and R. This family consists of N-6 adenine-specific DNA methylase [ec:2.1.1.72] from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes.
Wikipedia: In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Pfam PF20225: Family of unknown function (DUF6584) (repeat)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Actinobacteria and Firmicutes.  Many members are thought to contain TPR regions There are two conserved motifs, AxRL and LxxY.
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 PF03873: Anti sigma-E protein RseA, C-terminal domain (domain)
Sigma-E is important for the induction of proteins  involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and  preventing transcription from heat-shock promoters. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress.
Pfam PF10682: Glycoprotein of human cytomegalovirus HHV-5 (family)
This is glycoprotein UL40 from human cytomegalovirus or herpesvirus 5. The signal sequence of the UL40 polypeptide contains an HLA-E ligand identical with HLA-Cw*0304. The first 37 residues of UL40, including this ligand, are predicted to encode a signal peptide.  The virus thus prevents the lysis by NK (natural killer) cells of the cell it has invaded.
Pfam PF22945: LEM-3-like GIY-YIG domain (domain)
This domain is found in the metazoan homologues of LEM-3 DNA nuclease. LEM-3 processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates, or the perturbance of chromosome structure. It localizes to the midbody and this localization depends on factors needed for midbody assembly. LEM-3 is composed of two domains: a LEM domain and a GIY-YIG nuclease domain represented by this entry.
Pfam PF09514: SSXRD motif (conserved_site)
SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localise to this region.
Pfam PF07238: PilZ domain (domain)
PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix.
Wikipedia: The PilZ protein family is named after the type IV pilus control protein first identified in Pseudomonas aeruginosa, expressed as part of the pil operon. It has a cytoplasmic location and is essential for type IV fimbrial, or pilus, biogenesis. PilZ is a c-di-GMP binding domain and PilZ domain-containing proteins represent the best studied class of c-di-GMP effectors. C-di-GMP, cyclic diguanosine monophosphate, the second messenger in cells, is widespread in and unique to the bacterial kingdom. Elevated intracellular levels of c-di-GMP generally cause bacteria to change from a motile single-cell state to a sessile, adhesive surface-attached multicellular state called biofilm.
Pfam PF03249: Type specific antigen (family)
There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation. TSA56 is found in Orientia tsutsugamushi (O. tsutsugamushi), the causative agent of scrub typhus, an obligate intracellular pathogen. TSA56 is one of the three major outer membrane proteins of O. tsutsugamushi. It is required for adhesion. Furthermore, it has been demonstrated that O. tsutsugamushi, can bind to fibronectin (Fn) via the antigenic membrane protein, TSA56. There are 3 extracellular antigen domains (ADs), where ADIII and adjacent C-terminal region of TSA56 waswere shown to be sufficient for Fn interaction and prohibiting Fn-enhanced invasion.
Pfam PF06496: Protein of unknown function (DUF1097) (family)
This family consists of several bacterial putative membrane 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 PF13489: Methyltransferase domain (domain)
This family appears to be a methyltransferase domain.
Pfam PF16379: Domain of unknown function (DUF4989) (family)
This family around 300 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Alistipes species. The function of this family remains unknown. This entry contains a duplication of a DUF1735-like domain.
Pfam PF04855: SNF5 / SMARCB1 / INI1 (family)
SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes  characterised so far.  This family consists of the conserved region of SNF5, including a direct repeat motif.  SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF  complex. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs).
Pfam PF19954: Effector-associated domain 10 (domain)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements.
Pfam PF09880: Predicted membrane protein (DUF2107) (family)
This domain, found in various hypothetical archaeal 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 PF15238: Omega loop, TEAD interating region 3 (domain)
This entry represents the third TEAD interacting region (omega loop) present in YAP/TAZ, FAM181, and PERCC1 families. This conserved region is remotely related to the omega loop found in the Vestigial family (VGLL2 and VGLL3).
Pfam PF05393: Human adenovirus early E3A glycoprotein (family)
This family consists of several early glycoproteins from human adenoviruses.
Pfam PF05851: Lentivirus virion infectivity factor (VIF) (family)
This family consists of several feline specific Lentivirus virion infectivity factor (VIF) proteins. VIF is essential for productive FIV infection of host target cells in vitro.
Pfam PF05853: beta-keto acid cleavage enzyme (domain)
BKACE, beta-keto acid cleavage enzyme plays, a role in lysine degradation. In certain instances it catalyses the conversion of 3-keto-5-aminohexanoate and acetyl-CoA into acetoacetate and 3-aminobutyryl-CoA. The family is found to have at least 14 slightly different potential new enzymatic activities, all of which can therefore be designated as beta-keto acid cleavage enzymes.
Pfam PF06464: DMAP1-binding Domain (domain)
This domain binds DMAP1, a transcriptional co-repressor.
Pfam PF03348: Serine incorporator (Serinc) (family)
This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid.  Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis. SERINC3 (also known as TDE1) and SERINC5 are restriction factors required to restrict infectivity of lentiviruses, such as HIV-1; they act by inhibiting an early step of viral infection and they impair the penetration of the viral particle into the cytoplasm. SERINC3/5 are non-specific lipid transporters for phosphatidylserine, phosphatidylcholine, and phosphatidylethanolamine that functions as a scramblase that flips lipids in both directions across the membrane.
Pfam PF07401: Bovine Lentivirus VIF protein (family)
This family consists of several Lentivirus viral infectivity factor (VIF) proteins. VIF is known to be essential for ability of cell-free virus preparation to infect cells. Members of this family are specific to  Bovine immunodeficiency virus (BIV) and Jembrana disease virus which also infects cattle.
Pfam PF13817: IS66 C-terminal element (family)
This entry represents the C-terminal region of the insertion element IS66 transposase .
Pfam PF00757: Furin-like cysteine rich region (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 PF01586: Myogenic Basic domain (family)
This basic domain is found in the MyoD family of muscle specific proteins  that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding. With 12 residues of the basic domain involved in DNA binding. The basic domain forms an extended alpha helix in the structure.
Wikipedia: In molecular biology, the myogenic determination factor 5 proteins are a family of proteins found in eukaryotes. This family includes the Myf5 protein, which is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage.
Pfam PF18733: LA2681-like HEPN (domain)
LA2681-like HEPN nuclease.
Pfam PF06713: Bacterial PH domain (domain)
This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown. Members of this family have a PH domain like structure.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF09997: Predicted membrane protein (DUF2238) (family)
This domain, found in various hypothetical bacterial 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 PF08742: C8 domain (domain)
This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin.  It is often found on proteins containing [pfam:PF00094] and [pfam:PF01826].