SII-SWORD/CoKE huggingface dataset:
Pfam PF12781: ATP-binding dynein motor region (domain)
This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk.
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 PF03866: Hydrophobic abundant protein (HAP) (family)
Expression of HAP is thought to be developmentally regulated and possibly involved in spherule cell wall formation.
Pfam PF08794: Factor H binding protein, C-terminal (domain)
Factor H binding protein (also known as GNA1870) is a surface exposed lipoprotein in Neisseria meningitidis that is a potent antigen and a potential candidate for a vaccine against meningococcal disease. The structure of the C-terminal domain consists of an anti-parallel beta barrel overlaid by a short alpha helical region. This domain is highly similar to Transferrin-binding protein B  beta barrel ([pfam:PF01298]).
Pfam PF02492: CobW/HypB/UreG, nucleotide-binding domain (domain)
This domain is found in HypB, a hydrogenase expression / formation protein, and  UreG a urease accessory protein.  Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity  and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K ([swissprot:P31521]), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the  cobW gene product ([swissprot:P29937]), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF10843: Respiratory growth induced protein 1 (family)
This family of fungal proteins includes RGI1, standing  for respiratory growth induced 1. RGI1 is involved in  aerobic energetic metabolism.
Pfam PF14508: Glycosyl-hydrolase 97 N-terminal (domain)
This N-terminal domain of glycosyl-hydrolase-97contributes part of the active site pocket. It is also important for contact with the catalytic and C-terminal domains of the whole.
Wikipedia: In molecular biology, glycoside hydrolase family 97 is a family of glycoside hydrolases.
Pfam PF23512: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AR83] from the parasite Babesia bovis.
Pfam PF22193: MvcA insertion domain (domain)
This entry represents the insertion domain of MvcA, the MavC paralogue A of bacterial effector MavC from Legionella pneumophila. MvcA catalyses the reverse reaction of MavC, removing Ub from Ube2N through hydrolysis which regulates MavC activity. MvcA is similar at sequence and structural levels to MavC, and it exhibits deamidase activity toward ubiquitin. This domain is crucial for substrate recognition.
Pfam PF07850: Renin receptor-like transmembrane spanning segment (family)
The sequences featured in this family are similar to a region of the human renin receptor ([swissprot:Q8NG15]) that bears a putative transmembrane spanning segment.  The renin receptor is involved in intracellular signal  transduction by the activation of the ERK1/ERK2 pathway,  and it also serves to increase the efficiency of angiotensinogen  cleavage by receptor-bound renin, therefore facilitating  angiotensin II generation and action on a cell surface.
Pfam PF07809: RTP801 C-terminal region (family)
The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene. Two members of this family expressed by Drosophila melanogaster, Scylla ([swissprot:Q9NHN4]) and Charybde ([swissprot:Q9NHN5]), are designated by the GenBank as Hox targets.  RTP801 is thought to be involved in various cellular processes.  Its overexpression caused the apoptosis- resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells. Moreover, the protein product of the mouse homolog of RTP801 (dig2 ([swissprot:Q9D3F7])) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment.
Pfam PF04730: Agrobacterium VirD5 protein (family)
The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterised products. This family represents the VirD5 protein.
Pfam PF20030: MoxR domain in the MoxR-vWA-beta-propeller ternary systems (domain)
Core MoxR component domain of the MoxR-vWA-beta-propeller ternary systems, a class of NTP-dependent biological conflict systems.
Pfam PF07358: Protein of unknown function (DUF1482) (family)
This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family 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 PF22811: Transcriptional repressor NrdR-like, N-terminal domain (domain)
This entry represents the N-terminal domain of the Transcriptional repressor NrdR and similar sequences, which is a zinc beta-ribbon domain, followed by an ATP-cone domain ([pfam:PF03477]). These proteins negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. This domain harbors two conserved CxxC motifs that coordinate a zinc ion, and binds to the highly conserved NrdR boxes.
Pfam PF20312: Family of unknown function (DUF6608) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length.
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 PF22711: Short NACHT-associated C-Terminal domain, family 5 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF11152: Cofactor assembly of complex C subunit B, CCB2/CCB4 (family)
Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organisms performing oxygenic photosynthesis. The CCB system consists of four proteins: CCB1-4. CCB2 and CCB4 are paralogues derived from a unique cyanobacterial ancestor. Orthologues are conserved  in higher plants.
Pfam PF20388: Family of unknown function (DUF6683) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 260 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.
Pfam PF14567: SMI1-KNR4 cell-wall (domain)
Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins.
Pfam PF01036: Bacteriorhodopsin-like protein (domain)
The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins.  Some fungal examples are: [swissprot:O74870], [swissprot:P25619], [swissprot:P38079], [swissprot:Q12117].
Wikipedia: Microbial rhodopsins, also known as bacterial rhodopsins, are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point for retinal. Most microbial rhodopsins pump inwards, however "mirror rhodopsins" which function outwards. have been discovered.
Pfam PF14980: TIP39 peptide (family)
This entry represents Tuberoinfundibular peptide of 39 residues (TIP39), which is a potent and selective agonist of the parathyroid hormone 2 receptor (PTH2R) . In human, TIP39 expression was detected by RT-PCR in the brain, trachea, fetal liver, kidney and heart. In the brain, TIP39 is expressed in only three sites, the medial and lateral parts of the subparafascicular area in the caudal thalamus, and the medial paralemnsical nucleus in the lateral pons . The TIP39-PTH2R system is a unique neuropeptide-receptor system that plays a role in limbic, endocrine, viscerosensory, and auditory functions .
Wikipedia: Tuberoinfundibular peptide of 39 residues is a protein that in humans is encoded by the PTH2 gene.
Pfam PF22958: E3 ubiquitin-protein ligase listerin, N-terminal domain (repeat)
This domain is found at the N-terminal end of E3 ubiquitin -protein ligase listerin from Saccharomyces cerevisiae (Ltn1) and similar eukaryotic proteins. Ltn1 is a component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesised nascent chains for proteasomal degradation. This domain is predominantly composed of alpha -helices that are arranged into HEAT repeats, each consisting of two antiparallel alpha-helices that pack against each other in a repeating array.
Pfam PF11697: Protein of unknown function (DUF3293) (family)
This bacterial family of 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 PF17370: Family of unknown function (DUF5392) (family)
This is a family of unknown function found in Bacilli. Family members are predicted to have 2 trans-membrane regions.
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 PF24130: Family of unknown function (DUF7397) (family)
This entry represents a small family of uncharacterised phage proteins. These proteins are around 50-60 residues 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.
Pfam PF14164: YqzH-like protein (family)
The YqzH-like protein family includes the B. subtilis YqzH protein [swissprot:O32014], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF21083: Cell-division protein ZapC, N-terminal (domain)
ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring. This entry represents the N-terminal alpha/beta region which contains a pocket, termed the N-domain pocket, lined with residues important for ZapC function as an FtsZ bundler.
Pfam PF08908: Putative oxygenase MesX (family)
This family represents MesX, the putative oxygenase component of an oxygen-dependent methionine synthase MesD. It is required for MesD for activity.
Pfam PF03600: Citrate transporter (family)
This domain is found in proteins belonging to the CitM transporter, NhaD Na+/H+ antiporter and Na+/sulfate symporter families, such as CitM from Bacillus subtilis , NhaD from Halomonas elongata  and SLT1 from Chlamydomonas reinhardtii .
Pfam PF01759: UNC-6/NTR/C345C module (domain)
Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in. Subsequently, many additional members of the family were identified on the basis of sequence similarity between the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type I pro-collagen C-proteinase enhancer proteins (PCOLCEs), which are homologous with the N-terminal domains of tissue inhibitors of metalloproteinases (TIMPs).  The TIMPs are classified as a separate family in Pfam ([pfam:PF00965]). This expanded domain family has been named as the NTR module.
Pfam PF12501: Phosphate ATP-binding cassette transporter (family)
This domain family is found in bacteria, and is typically between 143 and 173 amino acids in length. The family is found in association with [pfam:PF00528]. There is a single completely conserved residue P that may be functionally important.
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 PF16261: Domain of unknown function (DUF4915) (repeat)
This family consists of uncharacterized proteins around 370 residues in length and is mainly found in various species, such as Shewanella, Rheinheimera, Saccharophagus, Leptolyngbya and so on. It contains serveral TPR repeat-containing proteins. The function of this family is unknown.
Pfam PF09663: Amidohydrolase ring-opening protein (Amido_AtzD_TrzD) (family)
Members of this family are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (CAH) ([ec:3.5.2.15]) (AtzD and TrzD) and barbituric acid hydrolase (BAH). Note that barbiturase does not act as defined for [ec:3.5.2.1] (barbiturate + water = malonate + urea) but rather catalyses the ring opening of barbiturase acid to ureidomalonic acid. Cyanuric acid hydrolases (AtzD) and barbiturases are homologous and found almost exclusively in bacteria. CAH is a homotetramer, the monomer of which possesses a fold that is dubbed the Toblerone fold. Although not obvious from the protein sequence, each CAH monomer possesses 3-fold rotational symmetry, for which the repeated structural motif is structurally similar to that of the YjgF superfamily of proteins (two alpha helices and a four-strand antiparallel beta-sheet), despite having low sequence similarity. This suggests that the Toblerone fold evolved from concatenated YjgF family proteins. The 3-fold symmetry of each CAH monomer extends to the active site, which contains three Arg-Lys-Ser triads, which bind the substrate via an extensive hydrogen bonding network.
Pfam PF20141: Brassinosteroid receptor island domain (domain)
The island domain in BRI1 corresponds to a large insertion in the regular repeat-structure between LRRs 21 and 22. The resulting 70-residue segment forms a small domain that folds back into the interior of the LRR superhelix, where it makes extensive polar and hydrophobic interactions with LRRs 13-25. The domain fold is characterized by an anti-parallel beta-sheet, which is sandwiched between the LRR core and a 3-10 helix and stabilized by a disulphide bridge.  The insertion of a folded domain into the LRR repeat has not been observed in other LRR receptor structures, and is probably an adaptation to the challenge of sensing a small steroid ligand (rather than larger ligands, such as proteins, nucleic acids, or lipids.
Pfam PF06322: Phage NinH protein (family)
This family consists of several phage NinH proteins. The function of this family is unknown.
Pfam PF07661: MORN repeat variant (repeat)
This family represents an apparent variant of the [pfam:PF02493] repeat (personal obs:C Yeats).
Pfam PF08461: Ribonuclease R winged-helix domain (domain)
This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF01603: Protein phosphatase 2A regulatory B subunit (B56 family) (repeat)
Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also [pfam:PF01240]), this family is called the B56 family.
Wikipedia: Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. Phosphorylation enables the activation or The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family.
Pfam PF18620: Domain of unknown function (DUF5627) (domain)
This is a domain of unknown function found in bacteria. It may adopt a beta-barrel structure.
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 PF11968: 25S rRNA (adenine(2142)-N(1))-methyltransferase, Bmt2 (family)
This entry represents Bmt2 and its homogues. In Saccharomyces cerevisiae, Bmt2 is a nucleolar S-adenosylmethionine-dependent rRNA  methyltransferase that is responsible for the N-1-methyl-adenosine base modification of  25S rRNA.It specifically methylates the N1  position of adenine 2142 in 25S rRNA.
Pfam PF25100: Domain of unknown function (DUF7809) (domain)
This domain is found in a group of uncharacterised proteins from animals. It is predicted to adopt a mainly alpha-helical configuration.
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 PF11283: Protein of unknown function (DUF3084) (family)
This bacterial family of 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 PF06623: MHC_I C-terminus (family)
This family represents the C-terminal region of the MHC class I antigen. The family is found in conjunction with [pfam:PF00129] and [pfam:PF00047].
Pfam PF23241: PRP39 C-terminal HAT repeat (repeat)
This entry includes HAT (Half A TPR) repeat proteins including Pre-mRNA-processing factor 39, SART3, PRP42 and similar proteins. PRP39 is a component of the spliceosome that functions prior to stable branch point recognition by the U1 snRNP particle to facilitate or stabilize the U1 snRNP/5'-splice site interaction and has a direct role in spliceosome assembly. PRP42 from yeast is an essential component of the U1 snRNP particle, which recognises and binds the 5'-splice site of pre-mRNA. This entry represents the C-terminal segment of the HAT repeats, which are structurally similar to TPRs.