SII-SWORD/CoKE huggingface dataset:
Pfam PF01425: Amidase (domain)
This entry represents the amidase signature domain that consists structurally of a core domain that is covered by alpha-helices. In most members, this is found as a standalone domain, while in others, such as Scytalone dehydratase-like protein Arp1, it is found in association with other domains.
Wikipedia: In enzymology, an amidase (EC 3.5.1.4, acylamidase, acylase (misleading), amidohydrolase (ambiguous), deaminase (ambiguous), fatty acylamidase, N-acetylaminohydrolase (ambiguous)) is an enzyme that catalyzes the hydrolysis of an amide. In this way, the two substrates of this enzyme are an amide and H2O, whereas its two products are monocarboxylate and NH3.
Pfam PF01763: Herpesvirus UL6 like (family)
This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome.
Pfam PF08262: Leucophaea maderae tachykinin-related peptide (family)
These peptides are designated Leucophaea maderae tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific.  The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of the Locusta migratoria.  They stimulate visceral muscle contractions of the oviduct and the foregut of Locusta migratoria.
Pfam PF12237: Phosphorylated CTD interacting factor 1 WW domain (family)
This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity.
Pfam PF18722: MazG C-terminal domain (domain)
An alpha+beta fold domain found C-terminal to the MazG superfamily pyrophosphatase domain. The domain has a conserved DxYRxHDxxH motif indicative of catalytic activity. Based on its broader context in DNA modification, it is proposed to function as a nucleotide kinase.
Pfam PF17867: Midasin AAA lid domain (domain)
This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. This lid domain is found in midasin proteins.
Pfam PF12475: Amdovirus non-structural protein 1-3 (family)
This domain family is found in non-structural proteins 1-3 (NS1-3) from Amdoparvovirus, including Aleutian mink disease parvovirus (ADV) and it is approximately 50 amino acids in length. ADV utilises caspase activity to cleave its major non-structural protein (NS1), enable the localization of this protein to the nucleus and facilitate virus replication. The smaller NS2/3 are also encoded during viral infection and are essential for the replication of the virus.
Pfam PF03987: Autophagocytosis associated protein, active-site domain (domain)
Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex.
Wikipedia: In molecular biology, autophagy related 3 (Atg3) is the E2 enzyme for the LC3 lipidation process. It is essential for autophagy. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place.
Pfam PF19450: Family of unknown function (DUF5988) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 68 and 82 amino acids in length. There are two conserved sequence motifs: GGP and YEHF.
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 PF16874: Glycosyl hydrolase family 36 C-terminal domain (domain)
This domain is found at the C-terminus of many family 36 glycoside hydrolases. It has a beta-sandwich structure with a Greek key motif.
Pfam PF12595: Inactive rhomboid proteins 1/2, N-terminal (domain)
This entry includes inactive rhomboid proteins (iRhom1/2), which are catalytically inactive rhomboid protease homologues that play crucial roles within the secretory pathway, including protein degradation, trafficking regulation, and inflammatory signaling. These are metazoan specific pseudoproteases which regulate ADAM17 protease, a sheddase of the epidermal growth factor (EGF) receptor ligands and TNF, acting as trafficking factors that escort ADAM17 from the ER to the later secretory pathway. They are required for the cleavage and release of a variety of membrane-associated proteins. iRhoms share a common structure comprising 7-helix transmembrane-spanning domains (TMDs) which is a conserved rhomboid fold ([pfam:PF01694]), an extended N-terminal cytosolic domain and a luminal loop. These proteins have been linked to the development and progression of several  autoimmune diseases including rheumatoid arthritis, lupus nephritis, as well as as hemophilic arthropathy and also in neurological disorders such a Alzheimer's and Parkinson's diseases, inflammation, cancer and skin diseases. This entry represents an N-terminal helical segment of iRhom 1/2.
Pfam PF23187: UBX7 N-terminal domain (domain)
This domain is found N-terminal in the family of UBX domain-containing proteins such as UBX7, UBX6, UBXN4. This domain shares significant sequence similarity with UAS domain and it is predicted to adopt similar structure with thioredoxin-like topology.
Pfam PF18823: Inorganic Pyrophosphatase (domain)
A type I Inorganic Pyrophosphatase family domain that is found in polyvalent proteins.
Pfam PF18771: APOBEC3 (family)
APOBEC3 deaminases act as restriction factors in the innate response to retroviruses and various retroelements.
Pfam PF20189: Family of unknown function (DUF6552) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Proteobacteria. Proteins in this family are approximately 90 amino acids in length and some members are associated with Ubiquinone biosynthesis methyltransferases.
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 PF15581: Immunity protein 58 (family)
A predicted immunity protein with an alpha+beta fold and YxxxD, WxG, KxxxE motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene.
Pfam PF20918: SPOCS_spoVID-N (domain)
This is the SPOCS (SpoVID-CotE-SipL) domain consisting of a beta-strand-rich sandwich fold with long twisted strands found at the N-terminal of Stage VI sporulation protein D (SpoVID) from Bacillus subtilis.
Pfam PF23196: NOMO sixth transthyretin-like domain (domain)
This domain is found in the family of human Nodal modulators NOMO1, NOMO2, NOMO3 and in other related proteins. The Nodal modulators are components of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the membrane lipid bilayer. They play important role in the protein topogenesis and cells lacking these components show reduced multipass protein stability. The domain represented by this entry has a weak sequence similarity to Transthyretin-like domains and it is predicted to adopt similar structure that consists of seven-stranded beta-sandwich. Nodal modulators are predicted to contain a tandem of twelve Transthyretin-like domains and this domain is the sixth in the tandem.
Pfam PF15331: Cellular tumour antigen p53-inducible 5 (family)
TP53IP5 suppresses cell growth, and its intracellular location and expression change in a cell-cycle-dependent manner.
Pfam PF16546: Homodimerisation domain of SGTA (domain)
SGTA_dimer is a short N-terminal domain at the start of SGTA or small glutamine-rich tetratricopeptide repeat-containing proteins.  It is the homodimerisation domain of the SGTA, a heat-shock protein (HSP) co-chaperone involved in the targeting of tail-anchor membrane proteins to the endoplasmic reticulum. This N-terminal homodimerisation domain mediates the association with a single copy of Get4 or Get5 proteins, providing a link to the rest of the GET pathway.
Pfam PF23081: Kinesin-like protein KIF26A/B, tri-helical (domain)
This domain is found in Kinesin-like protein KIF26A/B from Mus musculus and similar sequences mainly found in vertebrates. KIF26A plays a key role in enteric neuron development while KIF26B is essential for embryonic kidney development. This domain is predicted to form an helical bundle.
Pfam PF09377: SBDS protein, domain II (domain)
Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. SBDS protein is composed of three domains. The N-terminal ([pfam:PF01172]) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II) represented in this entry consists of a three-helical bundle and the C-terminal domain that has a ferredoxin-like fold.
Wikipedia: Ribosome maturation protein SBDS is a protein that in humans is encoded by the SBDS gene. An alternative transcript has been described, but its biological nature has not been determined. This gene has a closely linked pseudogene that is distally located. This gene encodes a member of a highly conserved protein family that exists in all archaea and eukaryotes.
Pfam PF20580: Domain of unknown function (DUF6784) (domain)
This presumed domain is found at the C-terminal of uncharacterised proteins from bacteria. It contains the conserved sequence motifs WW/FPLHPLGY and RxGG.
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 PF22056: ORF239-like (family)
This family represents ORF239 from Pyrobaculum Spherical Virus, which shows an all-alpha configuration.
Pfam PF23182: AtC3H46 PABC domain (domain)
This PABC-like domain is found N-terminal in Zinc finger CCCH domain-containing protein 46 (AtC3H46) from Arabidopsis thaliana and related proteins found mainly in plants. AtC3H46 is know to possess RNA-binding and ribonuclease activities in vitro.
Pfam PF01004: Flavivirus envelope glycoprotein M (family)
Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.
Pfam PF08123: Histone methylation protein DOT1 (domain)
The DOT1 domain regulates gene expression by methylating histone H3. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast.
Pfam PF07993: Male sterility protein (family)
This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila.  A sequence-related jojoba acyl CoA reductase is also included.
Pfam PF22701: Mal s 1 allergenic protein-like (repeat)
This protein family includes Mal s 1 allergenic protein from the yeast Malassezia sympodialis (Mala s 1), which forms a relatively compact cup-like beta-propeller consisting of six blades each with four antiparallel beta-strands.
Pfam PF02632: BioY family (family)
A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin. BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes.
Pfam PF15717: Pericentriolar material 1 C terminus (family)
This entry represents the C-terminal domain of pericentriolar material 1 (PCM1), a protein involved in the assembly of centrosomal proteins and microtubule organisation .
Wikipedia: Pericentriolar material 1, also known as PCM1, is a protein which in humans is encoded by the PCM1 gene.
Pfam PF24271: HVO_2833, C-terminal (domain)
This is the C-terminal domain of the predicted ArsR family transcription regulator HVO_2833 from Haloferax volcanii. Its specific funtion is unknown.
Pfam PF11334: Protein of unknown function (DUF3136) (family)
This family of proteins with unknown function appear to be restricted to 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 PF16510: Phage P22-like portal protein (family)
The portal protein of P22 and similar Podoviridae tail phages is a dodecameric structure consisting of a hip (2), a leg(1) and a barrel(3).  DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Domains 1 and 3 are mostly helical and form the majority of the DNA-translocating channel. Domain 2 adopts an alpha-beta-fold characterised by two sheets of eight beta-strands, which cross each other to form a beta-barrel-like structure.
Pfam PF02285: Cytochrome oxidase c subunit VIII (family)
Cytochrome c oxidase, a 13 sub-unit complex, [ec:1.9.3.1] is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIII.
Pfam PF07108: PipA protein (family)
This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis. The family carries a highly conserved HEXXH sequence motif along with several highly conserved glutamic acid residues which might be indicative of the family being a metallo-peptidase.
Pfam PF11431: Membrane transport protein MerF (family)
The mercury transport membrane protein, MerF has a core helix-loop-helix domain. It has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm.
Wikipedia: The mercury transporter superfamily is a family of transmembrane bacterial transporters of mercury ions. The common origin of all Mer superfamily members has been established. The common elements between family members are included in TMSs 1-2. A representative list of the subfamilies and proteins that belong to those subfamilies is available in the Transporter Classification Database.
Pfam PF03405: Fatty acid desaturase (domain)
Fatty acid desaturases are enzymes that catalyse the insertion of a double bond at the delta position of fatty acids.

There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related.

Family 1 is composed of:


 * Stearoyl-CoA desaturase (SCD) (1.14.19.1) .


Family 2 is composed of:


 * Bacterial fatty acid desaturases.
 * Plant stearoyl-acyl-carrier-protein desaturase (1.14.19.1) , this enzyme catalyses the introduction of a double bond at the delta(9) position of steraoyl-ACP to produce oleoyl-ACP. This enzyme is responsible for the conversion of saturated fatty acids to unsaturated fatty acids in the synthesis of vegetable oils.
 * Cyanobacterial DesA , an enzyme that can introduce a second cis double bond at the delta(12) position of fatty acid bound to membranes glycerolipids. DesA is involved in chilling tolerance; the phase transition temperature of lipids of cellular membranes being dependent on the degree of unsaturation of fatty acids of the membrane lipids.


This entry contains fatty acid desaturases belonging to Family 2, also known as Acyl-ACP (Acyl Carrier Protein) desaturases.
Wikipedia: Fatty acid desaturases are a family of enzymes that convert saturated fatty acids into unsaturated fatty acids and polyunsaturated fatty acids. For the common fatty acids of the C18 variety, desaturases convert stearic acid into oleic acid. Other desaturases convert oleic acid into linoleic acid, which is the precursor to alpha-linolenic acid, gamma-linolenic acid, and eicosatrienoic acid.
Pfam PF17496: Family of unknown function (DUF5431) (family)
This is a family of unknown function found in Enterobacteriaceae.
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 PF24190: Ribonuclease R second OB domain (domain)
This entry represents the second OB domain found in ribonuclease R (RNR) from bacteria. This protein is a conserved ribonuclease likely to be responsible for the degradation of defective messengers and is dispensable in H. pylori. The function of this domain is unknown.
Pfam PF04114: Gaa1-like, GPI transamidase component (family)
GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex.  Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase  that adds glycosylphosphatidylinositols (GPIs) to newly  synthesised proteins.
Pfam PF01138: 3' exoribonuclease family, domain 1 (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 PF15895: CAAX box cerebral protein 1 (family)
CAAX_1 is a family of primate proteins. CAAX refers to the highly characteristic C-terminal residues, a cysteine and two aliphatic residues followed by any residue, a C-terminal tetrapeptide recognition motif called the Ca1a2X box. This motif on substrates is recognised by prenyltransferases that then attach an isoprenoid lipid (a process termed prenylation), one of the many post-translational modifications that occur in cells. The function of the prenylated family is not known.
Pfam PF08265: YL1 nuclear protein C-terminal domain (domain)
This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins.
Pfam PF21584: Poxvirus, 2L, N-terminal domain (domain)
This domain is found at the N-terminal end of 2L protein from Yaba-like disease virus (YLDV) and similar proteins from poxvirus. 2L binds tumour necrosis factor-alpha (TNFalpha) to inhibit host antiviral and immune responses. This entry represents the alpha1- alpha2 superdomain which consists of an antiparallel beta-sheet that is topped by two alpha-helices. It shows similarity with the same domain in classical class I MHC molecules and MHC homologs ([pfam:PF00129]).
Pfam PF05164: Cell division protein ZapA (family)
ZapA is a cell division protein which interacts with FtsZ.  FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle.  The interaction of FtsZ with ZapA drives its polymerisation and promotes FtsZ filament bundling thereby contributing to the spatio-temporal tuning of the Z-ring.
Wikipedia: In molecular biology, the ZapA protein family is a group of related proteins that includes the cell division protein ZapA. The structure of ZapA has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.
Pfam PF13132: Domain of unknown function (DUF3950) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 30 amino acids in length. There is a conserved NFS sequence motif.
Pfam PF17836: PglD N-terminal domain (domain)
This alpha/beta domain is found at the N-terminus of proteins such as PglD. This domain binds a UDP-sugar substrate.
Pfam PF03699: Uncharacterised protein family (UPF0182) (family)
This family contains uncharacterised integral membrane proteins.
Pfam PF24140: Transportin-3/Importin-13 third TPR domain (repeat)
This entry represents the third TPR domain found in Transportin-3 (TNPO3) from animals, as well as orthologues MTR10 and uncharacterised protein YNR7 from yeast and MOS14 from plants. This entry also includes Importin-13 (IPO3) from animals. These proteins are involved in transport of target proteins into the nucleus. TNPO3 mediates the nuclear import of splicing factor serine/arginine (SR) proteins, such as RBM4, SFRS1 and SFRS2, by recognizing phosphorylated SR domains. This domain is part of TPR structure that binds proteins for nuclear transport.
Pfam PF09487: Bacterial type III secretion protein (HrpB2) (family)
This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia.