SII-SWORD/CoKE huggingface dataset:
Pfam PF12258: Microcephalin protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 384 and 835 amino acids in length. Microcephalin is involved in determining the size of the brain in animals. It is a protein, which if expressed homozygously causes the organism to have the condition microcephaly. Organisms expressing the mutated form of this protein in a homozygous manner develop a condition called microcephaly - a drastically reduced brain mass and volume. Microcephalin is predicted to contain three BRCA1 C-terminal domains, the first of which is the probable microcephaly mutation site.
Wikipedia: Microcephalin (MCPH1) is a gene that is expressed during fetal brain development. Certain mutations in MCPH1, when homozygous, cause primary microcephaly—a severely diminished brain. Hence, it has been assumed that variants have a role in brain development. However, in normal individuals no effect on mental ability or behavior has yet been demonstrated in either this or another similarly studied microcephaly gene, ASPM. However, an association has been established between normal variation in brain structure, as measured with MRI but only in females, and common genetic variants within both the MCPH1 gene and another similarly studied microcephaly gene, CDK5RAP2.
Pfam PF05369: Monomethylamine methyltransferase MtmB (family)
Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG. The structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold.
Pfam PF10374: Telomerase activating protein Est1 (repeat)
Est1 is a protein which recruits or activates telomerase at the site of polymerisation. Structurally it resembles a TPR-like repeat.
Pfam PF08701: GNL3L/Grn1 putative GTPase (family)
Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA.  This family contains a potential nuclear localisation signal.
Pfam PF07505: Protein of unknown function (DUF5131) (family)
This is a family of bacterial and phage proteins of unknown function. There are three highly conserved cysteine residues in the disposition, Cx6Cxxc, amongst many highly conserved residues.
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 PF02719: Polysaccharide biosynthesis protein (family)
This is a family of diverse bacterial polysaccharide biosynthesis  proteins including the CapD protein ([swissprot:P39853]), WalL protein ([swissprot:O86159]) mannosyl-transferase ([swissprot:O05349]) and several putative epimerases (e.g. WbiI [swissprot:O69130]).
Pfam PF16602: Linker region of USP19 deubiquitinase (disordered)
This region is generally located between a CS domain [pfam:PF04969] and the enzymatic UCH domain [pfam:PF00582] of USP19 deubiquitinases. This region is predicted to be natively unstructured. Its precise functional role is not known.
Pfam PF16115: Domain of unknown function (DUF4831) (family)
This family consists of several uncharacterized proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF18029: Glyoxalase-like domain (domain)
This entry comprises a diverse set of domains related to the Glyoxalase domain. The exact specificity of these proteins is uncertain.
Pfam PF04162: Gyrovirus capsid protein (VP1) (family)
Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein.
Pfam PF00072: Response regulator receiver domain (domain)
This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Wikipedia: In molecular biology, a response regulator is a protein that mediates a cell's response to changes in its environment as part of a two-component regulatory system. Response regulators are coupled to specific histidine kinases which serve as sensors of environmental changes. Response regulators and histidine kinases are two of the most common gene families in bacteria, where two-component signaling systems are very common; they also appear much more rarely in the genomes of some archaea, yeasts, filamentous fungi, and plants. Two-component systems are not found in metazoans.
Pfam PF13346: ABC-2 family transporter protein (family)
This family is related to the ABC-2 membrane transporter family [pfam:PF01061].
Wikipedia: In molecular biology, ATP-binding domain of ABC transporters  is a water-soluble domain of transmembrane ABC transporters.
Pfam PF14146: Domain of unknown function (DUF4305) (family)
This family includes the B. subtilis YdiK protein [swissprot:O05524], which is functionally uncharacterised.  This is not a homologue of E. coli YdiK, which belongs to [pfam:PF01594].  This family of proteins is found in bacteria. Proteins in this family are approximately 60 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 PF16758: Herpes-like virus membrane glycoprotein UL141 (domain)
UL141 is a family of glycoproteins from herpesvirus species. At it N-terminus it carries an Ig-like beta-sandwich domain, which binds to the cysteine-rich region of TRAIL-R2, a family of tumour necrosis factor receptor proteins. UL141 is both necessary and sufficient to retain TRAIL receptors in the ER, thereby preventing their cell surface expression and it is also necessary and sufficient to inhibit cell surface expression of CD155.
Wikipedia: V-set domains are Ig-like domains resembling the antibody variable domain. V-set domains are found in diverse protein families, including immunoglobulin light and heavy chains; in several T-cell receptors such as CD2, CD4, CD80, and CD86; in myelin membrane adhesion molecules; in junctional adhesion molecules (JAM); in tyrosine-protein kinase receptors; and in the programmed cell death protein 1 (PD1).
Pfam PF01479: S4 domain (domain)
The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA.
Wikipedia: In molecular biology, S4 domain refers to a small RNA-binding protein domain found in a ribosomal protein named uS4. The S4 domain is approximately 60-65 amino acid residues long, occurs in a single copy at various positions in different proteins and was originally found in pseudouridine syntheses, a bacterial ribosome-associated protein.
Pfam PF11514: Protein of unknown function (DUF3219) (family)
This family of proteins with unknown function appears to be restricted to Bacillaceae. Some members in this family of proteins are annotated as YkvR however this cannot be confirmed.
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 PF19713: Family of unknown function (DUF6208) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000976) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the curacin A biosynthetic  gene cluster from Moorea producens 3L. This family appears to  be predominantly found in Cyanobacteria.
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 PF03911: Sec61beta family (family)
This family consists of homologues of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane.
Wikipedia: Sec61, termed SecYEG in prokaryotes, is a membrane protein complex found in all domains of life. As the core component of the translocon, it transports proteins to the endoplasmic reticulum in eukaryotes and out of the cell in prokaryotes. It is a doughnut-shaped pore through the membrane with 3 different subunits (heterotrimeric), SecY (α), SecE (γ), and SecG (β). It has a region called the plug that blocks transport into or out of the ER. This plug is displaced when the hydrophobic region of a nascent polypeptide interacts with another region of Sec61 called the seam, allowing translocation of the polypeptide into the ER lumen.
Pfam PF06468: Spondin_N (domain)
This conserved region is found at the in the N-terminal half of several Spondin proteins. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells ().
Pfam PF23283: Uromodulin-like, D8C domain (domain)
This domain, described as D8C domain (cysteine-rich domain), is found in human Uromodulin (UMOD) and similar animal proteins. UMOD functions in biogenesis and organization of the apical membrane of epithelial cells of the thick ascending limb of Henle's loop and may serve as a receptor for binding and endocytosis of cytokines (IL-1, IL-2) and TNF. This domain adopts a predominantly beta structure.
Pfam PF00691: OmpA family (family)
The Pfam entry also includes MotB and related proteins which are not included in the Prosite family.
Wikipedia: In molecular biology, the OmpA domain is a conserved protein domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins, such as porin-like integral membrane proteins, small lipid-anchored proteins, and MotB proton channels. The N-terminal half of these proteins is variable although some of the proteins in this group have the OmpA-like transmembrane domain at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules. MotB serve two functions in E. coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor.
Pfam PF02928: C5HC2 zinc finger (domain)
Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.
Pfam PF03725: 3' exoribonuclease family, domain 2 (domain)
This family includes 3'-5' exoribonucleases.  Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction.  The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA.  Three of its five protein components, [swissprot:P46948] [swissprot:Q12277] and [swissprot:P25359] contain a copy of this domain. [swissprot:Q10205], a hypothetical protein from S. pombe appears to belong to an uncharacterised subfamily. This subfamily is found in both eukaryotes and archaebacteria.
Pfam PF16722: Pathogenicity island protein gp6 in Staphylococcus (family)
SAPIS-gp6 is a family of proteins produced from the pathogenicity island SAPI1 in pathogenic Staphylococcus aureus. This is a mobile genetic element that carries genes for several superantigen toxins. SAPIS-gp6 is a dimeric protein produced from the pathogenicity island with a helix-loop-helix motif similar to that of bacteriophage scaffolding proteins.  It is thought to determine the size of the capsids of distribution of the SAPI1 genome as it acts as an internal scaffolding protein during capsid size determination.
Pfam PF16740: Spindle and kinetochore-associated protein 2 (domain)
Spindle and kinetochore-associated protein 2 (SKA2) interacts with the N-termini of SKA1 and SKA3 and forms the Ska complex. This is a microtubule binding complex required for chromosome segregation.
Pfam PF05405: Mitochondrial ATP synthase B chain precursor (ATP-synt_B) (family)
The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L).
Pfam PF16212: Phospholipid-translocating P-type ATPase C-terminal (family)
PhoLip_ATPase_C is found at the C-terminus of a number of phospholipid-translocating ATPases.  It is found in higher eukaryotes.
Pfam PF15454: Late endosomal/lysosomal adaptor and MAPK and MTOR activator (family)
LAMTOR is a family of eukaryotic proteins that have otherwise been referred to as Lipid raft adaptor protein p18, Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1, and Protein associated with DRMs and endosomes. It is found to be one of three small proteins constituting the Rag complex or Ragulator that interact with each other, localise to endosomes and lysosomes, and play positive roles in the MAPK pathway. The complex does this by interacting with the Rag GTPases, recruiting them to lysosomes, and bringing about mTORC1 activation.
Pfam PF20714: DpiA-like helix-turn-helix domain (domain)
This entry represents a DNA-binding helix-turn-helix domain found at the C-terminus of the DpiA transcriptional regulator protein.
Pfam PF11914: Domain of unknown function (DUF3432) (repeat)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with [pfam:PF00096]. This domain has two conserved sequence motifs: YPSPV and PSP.
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 PF07490: Translocated intimin receptor (Tir) N-terminus (family)
Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir N-terminal domain  which is involved in Tir stability and Tir secretion.
Pfam PF06825: Heat shock factor binding protein 1 (coiled_coil)
Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response.
Pfam PF10114: Sensory domain found in PocR (domain)
PocR, a ligand binding domain, has a novel variant of the PAS-like Fold. Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol. In (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter)
Pfam PF14655: Rab3 GTPase-activating protein regulatory subunit N-terminus (repeat)
This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily.
Pfam PF20922: Anamorsin, N-terminal (domain)
Anamorsin (also named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1), is the human homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS). Anamorsin is found to be up-regulated in hepatocellular cancer,  is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis. In addition, it mediates the anti-apoptotic effects of various cytokines. This entry represents the N-terminal domain, which has a S-adenosylmethionine methyltransferase-like fold.
Pfam PF05430: S-adenosyl-L-methionine-dependent methyltransferase (family)
This family is a S-adenosyl-L-methionine (SAM)-dependent methyltransferase. It is often found in association with [pfam:PF01266], where it is responsible for catalysing the transfer of a methyl group from S-adenosyl-L-methionine to 5-aminomethyl-2-thiouridine to form 5-methylaminomethyl-2-thiouridine.
Pfam PF08729: HPC2 and ubinuclein domain (domain)
HPC2 (Histone promoter control 2) is required for cell-cycle regulation of histone transcription.  It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex which allows RNA Pol II to elongate through nucleosomes. Hpc2 is one of the proteins  of one of the multi-subunit complexes that mediate replication- independent nucleosome assembly, along with histone chaperone  proteins. the Hip4 sequence from SCH. pombe is an integral component  of this complex that is required for transcriptional silencing at multiple loci. HPC2, ubinuclein/yemanuclein, and the cell cycle  regulator FLJ25778 share a conserved domain that is predicted to  bind histone tails. This domain is also referred to as the  HRD or Hpc2-related domain.
Pfam PF08698: Fcf2 pre-rRNA processing (family)
This is a family of eukaryotic nucleolar proteins that are involved in pre-rRNA processing.
Pfam PF11870: Lactate utilisation protein B, C-terminal (domain)
This domain is functionally uncharacterised. This domain is found at the C-terminal of a family of 4Fe-4S, iron-sulphur cluster binding proteins, including Lactate utilisation protein B (LutB). These proteins have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4Fe-4S iron-sulphur clusters. This domain is found in LutB proteins in association with the LUD domain ([pfam:PF02589]) and usually Fer4_8 ([pfam:PF13183]). The LutABC operon is involved in lactate-utilisation and is essential.
Pfam PF17688: Family of unknown function (DUF5536) (family)
This is a family of unknown function found in mammals.
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 PF02486: Replication initiation factor (family)
Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a  sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family,  including myelin transcription factor 2 ([swissprot:O15150]) and cerebrin-50 ([swissprot:Q16301]).
Pfam PF08954: Trimerisation motif (coiled_coil)
This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It appears to have the function of stabilising the topology of short coiled-coils in proteins.
Pfam PF12586: Protein of unknown function (DUF3760) (family)
This domain family is found in eukaryotes, and is typically between 46 and 64 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 PF16447: Domain of unknown function (DUF5044) (family)
This family consists of several uncharacterized proteins around 220 residues in length and is mainly found in various Clostridiales species. 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 PF24788: AtPDCT1/2 (domain)
This entry represents a domain found in the Phosphatidylcholine diacylglycerol cholinephosphotransferase 1 (PDCT1 or ROD1) and 2 (PDCT2) from Arabidopsis thaliana. PDCT1 catalyses the transfer of the phosphocholine headgroup from phosphatidylcholine (PC) to diacylglycerol, a major reaction for the transfer of 18:1 into phosphatidylcholine for desaturation and also for the reverse transfer of 18:2 and 18:3 into the triacylglycerols synthesis pathway. This domain has a detectable similarity to domains members of the Acid phosphatase/Vanadium-dependent haloperoxidase superfamily and it is predicted to adopt similar structure. This domain is composed of five transmembrane helices.
Pfam PF13040: Fur-regulated basic protein B (family)
This family of proteins is regulated by the ferric uptake regulator protein Fur. This family represses expression of the lutABC operon encoding iron sulfur-containing enzymes necessary for growth on lactate.