SII-SWORD/CoKE huggingface dataset:
Pfam PF20501: MBH, subunit E (domain)
Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to  be exposed to the cytoplasm and form the peripheral arm.  The remaining 10 subunits are predicted to be integral membrane  proteins forming the membrane arm, made of 44 transmembrane helices  (TMH).  MbhA, B, C and F form the Sodium translocation module.  MbhD, E, G and H form the Proton translocation module.  MbhI is the linker between the hydrogenase module and the  proton-translocating membrane module. It anchors the discontinuous  TMH7 of MbhH via its middle lateral helix and the C-terminal  of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I. MbhE has two transmembrane helices: TMH1 and TMH2.
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 PF12714: TILa domain (domain)
This cysteine rich domain occurs along side the TIL [pfam:PF01826] domain and is likely to be a distantly related relative.
Pfam PF11315: Mediator complex subunit 30 (domain)
Med30 is a metazoan-specific subunit of Mediator, having no homologues in yeasts.
Wikipedia: Mediator of RNA polymerase II transcription subunit 30 is an enzyme that in humans is encoded by the MED30 gene. It represents subunit Med30 of the Mediator complex and is metazoan-specific, having no homologues in yeasts.
Pfam PF07608: Protein of unknown function (DUF1571) (domain)
A family of paralogous proteins in Rhodopirellula baltica.
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 PF15841: Transmembrane protein 239 family (family)
This family of proteins is found in primates. Proteins in this family are typically between 152 and 198 amino acids in length.
Pfam PF13108: Protein of unknown function (DUF3969) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length.
Pfam PF08169: RBB1NT (NUC162) domain (domain)
This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family.
Pfam PF01602: Adaptin N terminal region (repeat)
This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles.
Pfam PF12068: Rab-binding domain (RBD) (domain)
This domain has been called the Rab-binding domain (RBD). The domain adopts a Ph-like fold.  This domain is found associated with [pfam:PF00566].
Pfam PF04447: dATP/dGTP pyrophosphohydrolase (domain)
This domain is found in phage proteins, such as A0A2H5BHG5 from Acinetobacter phage SH-Ab 15497, which are associated with PurZ, an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. This domain has dATP and dGTP pyrophosphohydrolase activity; it catalyses the hydrolysis of dATP/dGTP to pyrophosphate and dAMP/dGMP, respectively, with little or no activities for NTPs and pyrimidine dNTPs. It is suggested that enzymes containing this domain supply dGMP as the substrate for PurZ, elevating dZTP level to promote Z incorporation.
Pfam PF19200: 6-phospho-N-acetylmuramidase, N-terminal (domain)
This domain represents the N-terminal domain of 6-phospho-N-acetylmuramidase (MupG) from Staphylococcus aureus, also found in putative phospho sugar glycosidases from Gram-negative and -positive species, but mainly firmicutes. MupG, specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of the proteins containing this domain may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most of these proteins appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). This entry is the larger N-terminal domain that constitutes a TIM-barrel like structure and the C-terminal domain is similar to the cyclophilin family. It should be noted that some proteins lack the C-terminal domain.
Pfam PF21719: MIOS, alpha-solenoid (repeat)
GATOR complex protein MIOS, a component of the GATOR subcomplex GATOR2 which consists of MIOS, SEC13, SEH1L, WDR24 and WDR59, and it activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex. Sea4 is the counterpart from yeast, a component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis. This entry represents a region between the WD40 and the zinc ribbon-like domains, which may have an alpha-solenoid structure.
Pfam PF23218: AIR9 PH-like domain (domain)
This is a PH-like domain found at the C-terminal of AIR9 from Arabidopsis thaliana and similar proteins from plants. It may adopt a partly opened beta-barrel topology that is capped by an alpha-helix. Interaction between AIR9 and POK1 is important for division plane orientation and plant growth in Arabidopsis thaliana.
Pfam PF13258: Domain of unknown function (DUF4049) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 310 and 324 amino acids in length. According to structure prediction and comparison (DALI server) it is suggested that it  may adopt a metallo-dependent phosphatase 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 PF11698: V-ATPase subunit H (repeat)
The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer.  This domain corresponds to the C terminal domain of the H subunit of V-ATPase.  The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation.
Pfam PF20224: Family of unknown function (DUF6583) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly in Firmicutes. Proteins in this family are typically between 454 and 596 amino acids in length. There are two highly conserved residues, a Tyr and an Asp.
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 PF20292: ABC-three component (ABC-3C) system Middle Component 7 (family)
Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC7 is a MC unifiable with the HTH fold.
Pfam PF20267: GREB1 C-terminal region (domain)
GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an oestrogen-regulated gene expressed in breast cancer. Its exact function is not known but its expression is regulated by the coordinated binding of oestrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene. This entry represents the C-terminal domain, which may adopt a twisted alpha/beta structure comprising parallel beta-sheets connected by alpha-helices that surround the sheet, as revealed from structure predictions.
Pfam PF10593: Z1 domain (domain)
This uncharacterised domain was identified by Iyer and colleagues. It is found associated with a helicase domain of superfamily type II.
Pfam PF03787: RAMP superfamily (family)
The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs.
Pfam PF24023: Family of unknown function (DUF7335) (family)
This entry represents a small family of uncharacterised phage 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 PF06535: Repulsive guidance molecule (RGM) N-terminus (family)
This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but [swissprot:Q8JG54] from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum.
Pfam PF20350: Family of unknown function (DUF6645) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF03629], [pfam:PF08410].
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 PF14864: Alkyl sulfatase C-terminal (domain)
This domain is found at the C-terminus of alkyl sulfatases. Together with the N-terminal catalytic domain, this domain forms a hydrophobic chute and may recruit hydrophobic substrates.
Pfam PF16686: ssDNA-binding domain of telomere protection protein (domain)
POT1PC is the ssDNA-binding domain on a family of fungal telomere protection protein 1 proteins.  POT1PC is able to accommodate heterogeneous ssDNA ligands.  Pot1 proteins are the proteins responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres.
Pfam PF15632: ATP-grasp in the biosynthetic pathway with Ter operon (domain)
This ATP-grasp family is related to carbamoyl phosphate synthetase. These genes are found in the biosynthetic operon associated with the Ter  stress response operon and are predicted to  be involved in the biosynthesis of a ribo-nucleoside involved in stress response.
Pfam PF03121: Herpesviridae UL52/UL70 DNA primase (family)
Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits.  Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52 [see 2,3]. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 [swissprot:P10236] is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and  glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments  have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable.  This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains (e.g. [swissprot:P17149]), which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV  strains also possess a DNA helicase-primase complex, the other subunits  being protein UL105 (with known similarity to HSV1 UL5) and protein UL102.
Pfam PF16537: Type II secretion system protein B (family)
This is the B protein from some operons of bacterial secretion systems of type II. The exact function of the B protein is not known, though in the case of Vibrio cholerae there is a fusion protein between proteins A and B that includes an AAA domain, a PG_binding domains well as this domain at the C-terminus. Many of the other species have no A or B domain genes in this operon. The type II secretion pathway is conserved in Gram-negative bacteria that are prevalent in bacterial pathogens of plants (Pseudomonas fluorescens, Erwinia or Xanthomonas species), animals (Aeromonas hydrophila) and humans (Klebsiella oxytoca, Pseudomonas aeruginosa, Vibrio cholerae or Legionella pneumophila). Typical type II secretion systems (T2SSs) are encoded by a set of 12 to 16 gsp (general secretion pathway) genes organised into large operons including the conserved 'core' genes denoted C to O and in some bacterial species, as indicated above, extra gsp genes such as gspAB, gspN or gspS. A different nomenclature is used for Pseudomonas T2SSs, so the B gene is referred to as the P protein.
Pfam PF01000: RNA polymerase Rpb3/RpoA insert domain (domain)
Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal
Pfam PF03885: Protein of unknown function (DUF327) (family)
The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues. with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13396: Phospholipase_D-nuclease N-terminal (domain)
This family is often found at the very N-terminus of proteins from the phospholipase_D-nuclease family, PLDc, [pfam:PF00614]. However, a large number of members are full-length within this family.
Pfam PF14313: N-terminal region of Paramyxovirinae phosphoprotein (P) (domain)
The soyouz module moiety is the N-terminal region of the phosphoprotein (P) from the subfamily Paramyxovirinae of the family Paramyxoviridae viruses. The main genera in this subfamily include the Rubulaviruses, avulaviruses, respiroviruses, henipaviruses, and morbilliviruses, all of which are enveloped viruses with a non-segmented, negative, single-stranded RNA genome encapsidated by the nucleoprotein (N) within a helical nucleocapsid.
Pfam PF19149: Family of unknown function (DUF5831) (family)
This family of unknown function is found mostly in prasinoviruses.
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 PF08484: C-methyltransferase C-terminal domain (family)
This domain is found in bacterial C-methyltransferase proteins. This domain is found C-terminal to methyltransferase domains such as [pfam:PF08241] or [pfam:PF08242]. But this domain is not a methyltransferase.
Pfam PF22949: Heme-regulated eIF-2-alpha kinase, helical domain (domain)
This domain is found N-terminal in the homologues of Heme-regulated eIF-2-alpha kinase (HRI2). This enzyme phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (EIF2S1/eIF-2-alpha) in response to various stress conditions. HRI2 is a key activator of the integrated stress response (ISR) required for adaptation to various stress, such as heme deficiency, oxidative stress, osmotic shock and others. This domain is predicted to fold into an alpha-helical structure consisting of three alpha-helices.
Pfam PF16470: Peptidase S8 pro-domain (domain)
This domain is the pro-domain of several peptidases belonging to family S8.
Pfam PF23001: Membrane-bound Site-1 Protease Family N-terminal domain (domain)
The protein family consists of serine proteases involved in regulated intramembrane proteolysis (RIP) of various substrates, playing a crucial role in cellular signaling and regulation. These proteases cleave after hydrophobic or small residues, with a preference for Arg or Lys at the P4 position. They are responsible for the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), cyclic AMP-dependent transcription factors (ATF6 and ATF6B), and other factors like BDNF, GNPTAB, and FAM20C. This activation process is essential for lipid homeostasis, lysosome biogenesis, osteoblast differentiation, and ER stress response. Additionally, they regulate M6P-dependent trafficking of lysosomal enzymes and are involved in collagen trafficking through the activation of CREB3L2/BBF2H7. In plants, they participate in stress response signaling and cell wall remodeling by processing factors like BZIP17 and pectinesterases. Overall, the family plays a key role in various cellular processes, including lipid metabolism, stress response, and developmental pathways.
Pfam PF20707: Bacterial Death-like domain 2 (domain)
This bacterial adaptor domain of the Death-domain fold is involved in protein-protein interactions in biological conflict systems. bDLDs 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 and iSTAND. Further copies of the same bDLD are fused to either effector or signal-transducing domains, or additional Effector-associated domains (EADs). bDLD 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 the bDLD-bDLD coupling approximates the advantages of collinear transcription.
Pfam PF03920: Groucho/TLE N-terminal Q-rich domain (family)
The N-terminal domain of the Grouch/TLE co-repressor proteins are involved in oligomerisation.
Pfam PF00188: Cysteine-rich secretory protein family (domain)
This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins.  Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences. The Ca++-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how [swissprot:Q91055] blocks the Ca++ transporting ryanodine receptors.
Wikipedia: The CAP superfamily is a large superfamily of secreted proteins that are produced by a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes.
Pfam PF07016: Cysteine-rich acidic integral membrane protein precursor (repeat)
This family consists of several 24 residue repeats from the Trypanosoma brucei cysteine-rich, acidic integral membrane protein precursor (CRAM). CRAM is concentrated in the flagellar pocket, an invagination of the cell surface of the trypanosome where endocytosis has been documented.